δ-Protocadherin Function: From Molecular Adhesion Properties to Brain Circuitry
DISSERTATION
Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University
By
Sharon Rose Cooper
Graduate Program in Molecular, Cellular and Developmental Biology
The Ohio State University
2017
Dissertation Committee:
Dr. James Jontes, Advisor
Dr. Marcos Sotomayor, Co-advisor
Dr. Heithem El-Hodiri
Dr. Sharon Amacher
Copyrighted by
Sharon Rose Cooper
2017
Abstract
Selective cell-to-cell adhesion is essential for normal development of the vertebrate brain, contributing to coordinated cell movements, regional partitioning and synapse formation. Members of the cadherin superfamily mediate calcium-dependent cell adhesion, and selective adhesion by various family members is thought to contribute to the development of neural circuitry. Members of the δ-protocadherin subfamily of cadherins are differentially expressed in the vertebrate nervous system and have been implicated in a range of neurodevelopmental disorders: schizophrenia, mental retardation, and epilepsy. However, little is known about how the δ- protocadherins contribute to the development of the nervous system, nor how this development is disrupted in the disease state.
Here I focus on one member of the δ-protocadherin family, protocadherin-19
(pcdh19), since it has the clearest link to a neurodevelopmental disease, being the second most clinically relevant gene in epilepsy. Using pcdh19 transgenic zebrafish, we observed columnar modules of pcdh19-expresing cells in the optic tectum. In the absence of Pcdh19, the columnar organization is disrupted and visually guided behaviors are impaired. Furthermore, similar columns were observed in pcdh1a transgenic zebrafish, located both in the tectum and in other brain regions. This suggests protocadherin defined columns may be a theme of neural development. ii Our X-ray crystal structure of Pcdh19 reveals the adhesion interface for Pcdh19 and infers the molecular consequences of epilepsy causing mutations. We found several epilepsy causing mutations were located at the interface and disrupted adhesion, which further validated the interface and revealed a possible biochemical cause of Pcdh19 dysfunction. Furthermore, sequence alignments of other δ-protocadherins with Pcdh19 suggest that this interface may be relevant to the entire δ-protocadherin subfamily.
We used the information gained about Pcdh19 to design PCDH19-FE mutations in the genome of zebrafish for comparing the circuitry of embryos with wild-type pcdh19, non-adhesive pcdh19 or without pcdh19. The combination of in vitro adhesion studies and in vivo brain imaging analysis provides a more comprehensive understanding of protocadherin-19 function, and suggests a broader role for the δ- protocadherin family in differential adhesion during brain development.
iii
This work is dedicated to my family for their unconditional love and support.
iv Acknowledgments
First, I would like to thank both of my advisors, Dr. James Jontes and Dr. Marcos
Sotomayor, for their mentorship. I appreciate their sincere investment in my research projects and my development as a scientist. I am also thankful to my committee members for their guidance.
Thank you to all the members of the Jontes and Sotomayor labs for their comradery and scientific insights. A special thank you goes to Dr. Michelle Emond, who has taught me many valuable research techniques. I would also like to thank Deepanshu Choudhary and Avinash
Jaiganesh for their advice on differential scanning fluorimetry, and Dr. Raul Araya-Secchi for his assistance with structural biology software.
Additionally, I would like to thank our collaborator, Marc Wolman, for performing behavioral analysis on the pcdh19 mutant zebrafish. I am also grateful for technical assistance and advice from Dr. Min An, Dr. Jared Talbot, Dr. Michael Berberoglu, Dr. Hao Le, and Phan Duy.
I would like to acknowledge the Jeffery J. Seilhamer Cancer foundation for its financial support during my final years of graduate school. Thank you for the honor and privilege of being a Seilhamer fellow.
Last but not least, I would like to thank my family for their constant encouragement, particularly my husband for his understanding and support through the ups-and downs of pursuing my doctorate.
v Vita
2009 ...... Research Intern, University of Arkansas for
Medical Sciences
2010 ...... Research Intern, Princeton University
2010 ...... B.S. Molecular and Cellular Biology,
Cedarville University
2011 to present ...... Graduate Research Associate,
Department of Neuroscience, and
Department of Chemistry and Biochemistry,
The Ohio State University
Publications
1. Cooper, S. R., Emond, M. R., Duy, P. Q., Liebau, B. G., Wolman, M. A., & Jontes, J. D. (2015). Protocadherins control the modular assembly of neuronal columns in the zebrafish optic tectum. The Journal of Cell Biology, 211(4), 807–814. http://doi.org/10.1083/jcb.201507108
2. Cooper, S. R., Jontes, J. D., & Sotomayor, M. (2016). Structural determinants of adhesion by Protocadherin-19 and implications for its role in epilepsy. eLife, 5. http://doi.org/10.7554/eLife.18529
Fields of Study
Major Field: Molecular, Cellular and Developmental Biology vi Table of Contents
Abstract ...... ii
Acknowledgments...... v
Vita ...... vi
List of Tables ...... x
List of Figures ...... xi
Chapter 1: Introduction ...... 1
The Cadherin Superfamily and Adhesion ...... 3
Neural Circuitry, Neurodevelopmental Disease, and the δ-Protocadherins ...... 19
Pcdh19 Female Epilepsy ...... 25
Zebrafish as a Neurodevelopmental Model ...... 30
Multidisciplinary Approach to a Fundamental Question ...... 34
Chapter 2: Protocadherins Control the Modular Assembly of Neuronal Columns in the
Zebrafish Optic Tectum ...... 40
Abstract ...... 40
Introduction ...... 41
Results and Discussion ...... 42
Materials and Methods ...... 48
vii Chapter 3: Structural Determinants of Adhesion by Protocadherin-19 and Implications for its Role in Epilepsy ...... 65
Abstract ...... 65
Introduction ...... 66
Results ...... 69
Discussion and Conclusions ...... 83
Materials and Methods ...... 87
Chapter 4: Creating PCDH19 Female Epilepsy Mutations in the Endogenous Zebrafish pcdh19 Gene by CRISPR Genome Editing ...... 115
Introduction ...... 115
Results ...... 117
Conclusions and Future Directions ...... 119
Materials and Methods ...... 120
Chapter 5: Anatomy of Protocadherin1a Expressing Cells Reveals a Theme of Columnar
Development in the Zebrafish Brain ...... 129
Introduction ...... 129
Results ...... 130
Discussion ...... 134
Material and methods ...... 135
Chapter 6: Conclusion ...... 144
Columnar Development of the Nervous System ...... 144
Adhesion Mechanism of δ-Protocadherins ...... 145 viii Implications for PCDH19 Female Epilepsy ...... 147
References ...... 149
Appendix A: Pcdh19-FE Mutations Found in Literature Search ...... 171
Appendix B: Quantification of Aggregation Assays ...... 176
Appendix C: Sequences Used for Conservation Analysis of Protocadherin-19 ...... 180
Appendix D: Sequences Used for Conservation Analysis between Protocadherin Family
Members ...... 194
ix List of Tables
Table 1.1. δ-protocadherin members association with brain circuitry functions and neurodevelopmental disease...... 39
Table 3.1. X-ray diffraction statistics for drPcdh19EC1-4 and drPcdh19EC3-4...... 114
Table A.1. Pcdh19-FE mutations found in literature search ...... 172
Table B.1. Quantification of aggregation assays – time point 0 minutes (t=0) ...... 176
Table B.2. Quantification of aggregation assays – time point 60 minutes (t=60) ...... 177
Table B.3. Quantification of aggregation assays – time point 1 minute rocking (t=R1) . 178
Table B.4. Quantification of aggregation assays – time point 2 minute rocking (t=R2) . 179
x List of Figures
Figure 1.1. Extracellular cadherin (EC) repeat architecture...... 36
Figure 1.2. The cadherin superfamily...... 37
Figure 1.3. Known adhesion mechanism of the cadherin superfamily...... 38
Figure 2.1. δ-pcdhs define neuronal columns in the zebrafish optic tectum...... 58
Figure 2.2. Pcdh19+ neuronal columns are clonal...... 59
Figure 2.3. Partitioning of the optic tectum by δ-pcdh expression...... 60
Figure 2.4. Loss of pcdh19 disrupts the columnar organization of the optic tectum...... 61
Figure 2.5. Cell autonomous and non-cell autonomous requirement for Pcdh19...... 62
Figure 2.6. Increased proliferation in the optic tectum of pcdh19-/- mutants...... 63
Figure 2.7. pcdh19-/- mutants exhibit impaired visually-guided behaviors...... 64
Figure 2.8. pcdh19-/- mutants show normal motor behavior in phototaxis assay...... 64
Figure 3.1. Electron density maps for the EC3-4 linker...... 96
Figure 3.2 Pcdh19 EC1-4 structure reveals location of PCDH19-FE missense mutations. 97
Figure 3.3. Sequence alignment of zebrafish, mouse, and human Pcdh19 EC repeats. .. 98
Figure 3.4. Predicted structural consequences of PCDH19-FE mutations...... 99
Figure 3.5. Two states for Pcdh19 EC1-4 in solution...... 100
xi Figure 3.6. A crystallographic Pcdh19 antiparallel interface involves fully overlapped
EC1-4 repeats...... 100
Figure 3.7. Alternate crystallographic antiparallel interface involves EC1 to EC5 repeats.
...... 101
Figure 3.8. Pcdh19 dimer interfaces and predicted glycosylation and glycation sites. . 102
Figure 3.9. Modified bead aggregation assays can detect calcium-dependent homophilic
Pcdh19 interactions...... 103
Figure 3.10. Minimal adhesive Pcdh19 fragment includes repeats EC1-4...... 104
Figure 3.11. PCDH19-FE mutations at Pcdh19-I1 antiparallel interface impair Pcdh19- mediated bead aggregation...... 105
Figure 3.12. PCDH19-FE mutations at Pcdh19-I1 impair bead aggregation even in the presence of N-cadherin...... 106
Figure 3.13. PCDH19-FE mutations at Pcdh19-I1 do not abolish the interaction between the extracellular domains of Pcdh19 and N-cadherin...... 106
Figure 3.14. Pcdh19-I1 antiparallel EC1-4 dimer interface involves charged, hydrophilic, and hydrophobic residues...... 107
Figure 3.15. A common binding mechanism with sequence-diverse interfaces for and clustered protocadherins...... 108
Figure 3.16. Sequence alignment of Pcdh19 EC1-4...... 109
Figure 3.17. Sequence alignment of selected protocadherins (next page)...... 110
Figure 3.18. Structural comparison of Pcdh19-I1 EC1-4 dimer to clustered-protocadherin dimers...... 112 xii Figure 3.19. Structural comparison of protocadherin 1 and 2 EC3 repeats...... 113
Figure 4.1. Schematic of the CRISP-Cas9 system (modified from Ramalingam, Annaluru,
& Chandrasegaran, 2013)...... 123
Figure 4.2. PCDH19-FE missense mutation at Pcdh19 adhesion interface...... 124
Figure 4.3. Design of CRISPR induced recombination...... 125
Figure 4.4. Screen of T147 CRISPR injected embryos by restriction digest...... 126
Figure 4.5. Screen of E314 CRISPR injected embryos by high resolution melt analysis
(HRMA)...... 127
Figure 4.6. Screening for highly efficient CRISPR...... 128
Figure 5.1: TgBAC(pcdh1a:Gal4-VP16, USA:lifeact-GFP) recapitulates endogenous pcdh1a expression...... 139
Figure 5.2: pcdh1a expression in the zebrafish midbrain...... 140
Figure 5.3: pcdh1a expression in the zebrafish forebrain...... 141
Figure 5.4: pcdh1a expression in the zebrafish hindbrain...... 142
Figure 5.5. A variety of motor neurons, sensory neurons and interneurons express pcdh1a in the spinal cord...... 143
xiii Chapter 1: Introduction
During early embryonic development, cells must differentially adhere to one another to form the diverse tissues and organs of the body. In concept, the very existence of a multicellular organism necessitates associations between cells, as the absence of all such interactions would make each cell an independent unicellular organism by definition. Additionally, cells of multicellular organisms must sort into distinct tissue layers during embryonic development, which caused early researchers to wonder at the mechanisms of the morphogenic process. The inherent ability of dispersed cells of an organism to reassemble into organized tissue layers was first observed in spongi and later in amphibians, leading to the differential adhesion hypothesis, which proposed that cells have varying strengthens of adhesion causing them to sort according to thermodynamic principles. (Steinberg, 2007; Townes &
Holtfreter, 1955; Wilson, 1907).
Several families of cell adhesion molecules have been discovered that influence the sorting of cells during morphogenesis, including the immunoglobulins (Ig), integrins, and the cadherins (Bock, 1991; McMillen & Holley, 2015; Niessen, Leckband, & Yap,
2011; Shimono, Rikitake, Mandai, Mori, & Takai, 2012). Each of these cell surface proteins physically interacts with molecules on adjacent cells to form stable links, and this process is called cell adhesion. The cadherin superfamily consists of over one 1 hundred calcium-dependent cell adhesion molecule and is divided into multiple subfamilies, including classical cadherins, clustered protocadherins and non-clustered δ- protocadherins. These cadherins have various functions during embryo morphogenesis and some members of the cadherin superfamily are important for the segregation of cell types (Bock, 1991; Niessen, Leckband, & Yap, 2011; Takeichi, 1990). For example, E- cadherin and N-cadherin function in neural tube formation and C-cadherin and paraxial protocadherin (PAPC) play a role in cell sorting during gastrulation (Chen & Gumbiner,
2006; Hatta, Takagi, Fujisawa, & Takeichi, 1987).
Cell-to-cell recognition is particularly critical during neurodevelopment for partitioning brain regions and forming intricate brain circuitry within and between brain regions. Neural circuits require numerous precise connections throughout the brain, with each neuron making hundreds of synaptic connections. Furthermore, disruption of brain wiring processes (e.g. axon guidance and synaptogenesis) are increasingly recognized for their involvement in neuropsychiatric disorders (Guilmatre et al., 2009;
Mitchell, 2011; Nugent, Kolpak, & Engle, 2012). Although only a small percent of psychiatric disorder cases have a known genetic cause, many members of the cadherin superfamily are associated with increased susceptibly for these diseases (Mitchell, 2011;
Redies, Hertel, & Hübner, 2012; Sakurai, 2016). Moreover, one adhesion molecule in particular, Protocadherin-19 (PCDH19), presents a clear causal relationship between genetic mutations in this cadherin gene and epilepsy, with PCDH19 being the second most clinically relevant gene in epilepsy (Depienne & LeGuern, 2012; Dibbens et al.,
2008). 2 Since many neurological disorders are thought to originate from aberrant embryonic development of the brain and have been linked to many cell adhesion molecules, it is critical to understand how these cell adhesion molecules function at the molecular level and how they contribute to brain development. This chapter will review the cadherin superfamily, specifically as it relates to their adhesion properties. In addition, the chapter will address principles of neural circuitry development, along with the role of δ-protocadherins in these processes, and specifically the involvement of
Pcdh19 in epilepsy. Finally, amenable features of zebrafish for the study of neurodevelopment will be presented along with this model’s limitations.
The Cadherin Superfamily and Adhesion
The cadherin superfamily was originally discovered as a group of calcium- dependent cell adhesion molecules (Hyafil, Babinet, and Jacob 1981; Kemler et al. 1977;
Takeichi 1988; Takeichi 2004). Each of the family members is a transmembrane glycoprotein containing extracellular repeat domains that mediate adhesion and a disordered intracellular domain that anchors some cadherins to the cytoskeleton
(Aberle, Schwartz, & Kemler, 1996; Klezovitch & Vasioukhin, 2015). The extracellular cadherin (EC) repeats have a common protein fold consisting of seven antiparallel β- stands forming a β-sandwich (Figure 1.1A,B), but each EC repeat differs in its exact amino acid sequence. Between each tandem EC repeat, three calcium ions bind to calcium-coordinating residues, which are conserved across the entire cadherin
3 superfamily (Figure 1.1C). The coordination of these calcium ions stabilizes the linker region between EC repeats, and protects the protein from degradation by trypsin
(Pokutta, Herrenknecht, Kemler, & Engel, 1994). Furthermore, these conserved calcium- binding motifs are the defining feature of EC repeats; and cadherin superfamily members, by definition, must contain at least two of these EC repeats (Hirano &
Takeichi, 2012; Sotomayor, Gaudet, & Corey, 2014; Takeichi, 1990).
Although all the members of the cadherin superfamily have many similar features, their underlying differences give them their unique functions and adhesive specificities. For example, the number of EC repeats varies immensely, from having only two EC repeats (e.g. calsyntenins) to having more than thirty EC repeats (e.g. fats)
(Hintsch et al., 2002; Mitsui, Nakajima, Ohara, & Nakayama, 2002). Furthermore, the sequence variation within each of these repeats distinguishes the various cadherin binding mechanisms and provides adhesive specificity to particular family members.
Cadherins are able to interact with one another either in the same cell (cis interactions) or between adjacent cells (trans interactions). The trans interactions are responsible for mediating the adhesion, but the cis interactions are thought to modify the strength and specificity of adhesion (Brasch, Harrison, Honig, & Shapiro, 2012; Emond, Biswas,
Blevins, & Jontes, 2011; Schreiner & Weiner, 2010). While the extracellular variation between cadherins appears to alter adhesion specificity, cadherins also have considerable variation in their intracellular motifs which impart diverse signaling capacities. These variations, both intracellular and extracellular, have lead to further subclassification of the cadherin superfamily. However, the classification for some 4 members is less clear, and the best classification system for the family is still being worked out (Hirano & Takeichi, 2012; Hulpiau & van Roy, 2009, 2011; Marcos
Sotomayor et al., 2014). Here I will discuss a few of the larger well-defined groups within the cadherin superfamily: classical cadherins, clustered protocadherins, and non- clustered δ-protocadherins (Figure 1.2). Due to the large size of this superfamily this will not be a comprehensive review of all the subfamilies, but is intended to put the δ- protocadherins in context of the larger superfamily, particularly as it relates to their adhesive function.
Classical cadherins
The classical cadherin subfamily contains the best characterized members of the cadherin superfamily, which are well documented to mediate strong homophilic adhesion at adherens junctions (Meng & Takeichi, 2009; Yonemura, 2011). Members of this subfamily can be distinguished from the rest of the cadherin superfamily by their highly conserved intercellular domain, containing two catenin binding motifs which indirectly link the cadherins to microtubules and the actin cytoskeleton (Akhmanova,
Stehbens, & Yap, 2009; Shahbazi et al., 2013; Masatoshi Takeichi, 2014). In addition, the extracellular domain of classical cadherins contains five EC repeats along with a prodomain, which must be cleaved off for adhesion (Koch et al., 2004; Ozawa & Kemler,
1990). Within EC1, classical cadherins have conserved tryptophan residues that are critical for their adhesion and further subdivide the classical cadherins into two groups:
5 type I containing a single conserved tryptophan (Trp2) and type II containing two conserved tryptophans (Trp2 and Trp4).
All members of the classical cadherin subfamily (both type I and type II) exhibit a similar adhesion mechanism involving the exchange of their N-terminal β-strands
(strand-swap dimer), which occurs via an X-shaped intermediate state (X-dimer) (Brasch,
Harrison, Honig, & Shapiro, 2012; Harrison et al., 2010). By using X-ray crystallography, researchers have been able to view each conformational state with intricate detail. The protomers containing all five EC repeats were oriented in the crystal lattices as though emanating from adjacent cells with EC1 engaging in the strand swap. The strand-swap dimer features the conserved Trp2 residue (or Trp2 and Trp4 in the case of Type II classical cadherins) intercalating deep into a hydrophobic pocket of the adjacent cadherin protomer; this results in the swapping of an entire β-strand of each protomer
(Figure 1.3A) (Boggon et al., 2002; Harrison et al., 2011; Patel et al., 2006; Shapiro et al.,
1995). Mutations of these critical tryptophans result in a complete loss of cellular adhesion and dramatically reduced affinities, which strengthens the case that the interface observed in multiple classical cadherin structures is relevant to in vivo adhesion (Emond, Biswas, Blevins, and Jontes, 2011; Tamura, Shan, Hendrickson,
Colman, and Shapiro, 1998). Although the tryptophan can also insert into a protomer’s own hydrophobic pocket, this self insertion is unfavorable in the calcium-bound condition. Specifically, when calcium binds Glu11 at the linker between EC1 and EC2, the preceding β-stand becomes taut and strained between the hydrophobic core anchored
Trp2 and the calcium bound Glu11. This calcium-induced strain on the monomer favors 6 the swapping of tryptophans, along with the entire β-strand (Vendome et al., 2011;
Vunnam and Pedigo, 2011). In the process of switching from a monomeric form to a dimeric form, the classical cadherins pass through the X-dimer intermediate state, which has been captured in protein crystals with mutations or cloning artifacts that inhibit the final strand-swap (Harrison et al., 2010; Nagar, Overduin, Ikura, & Rini, 1996; Pertz et al.,
1999). These structures show significant interaction of the EC1-EC2 linkers of each protomer crossing each other and the first β-strand in the EC1 of each protomer closely apposed; yet the Trp2 residues are still inserted into their own hydrophobic pocket.
Additional crystal structures depict the transition from the initial X-dimer state to the stand swap state, and suggests that the X-dimer creates an increasingly non-polar physicochemical environment favorable for tryptophan exchange (Kudo, Caaveiro, &
Tsumoto, 2016). Furthermore, when salt-bridges seen in the X-dimer are mutated, the binding rates of classical cadherins are reduced, but retain similar affinity as measured by equilibrium analytical ultracentrifugation. These same mutations abolish adhesion, further demonstrating the relevance of this intermediate X-dimer state (Harrison et al.,
2010).
While the extracellular domain directly forms the adhesive bond between cells, the intracellular domain also has a role in modulating adhesion and relaying signals. The most prominent intracellular interaction partners of cadherins are the catenins. p120- catenin binds to a conserved classical cadherin motif near the cell membrane to regulate localization of the classical cadherins at the cellular surface (Pieters, van Roy, & van Hengel, 2012). Another conserved classical cadherin motif is located at the C- 7 terminus and is responsible for binding β-catenin which indirectly links the cadherins to the actin cytoskeleton (Klezovitch and Vasioukhin, 2015). The mechanical forces experienced by the actin cytoskeleton through these cadherin-catenin links at the adherence junction are critical for proper tissue morphogenesis (Klezovitch &
Vasioukhin, 2015; Yonemura, 2011).
Although the classical cadherins have roles in many cellular and developmental processes (Niessen et al., 2011), here I will focus on their role in embryogenesis to briefly highlight their essential role in the life of multicellular organisms. During gastrulation the presence of dominant negative forms of either E-cadherin or C-cadherin
(type I classical cadherins) disrupts adhesion and causes discontinuities in the epidermis
(Lee and Gumbiner, 1995; Levine, Lee, Kintner, and Gumbiner, 1994). Furthermore, null mutations in several of the classical cadherins have been shown to be embryonically lethal. For example, E-cadherin knockout mice, which fail to form the trophectoderm cell layer, are embryonically lethal (Larue, Ohsugi, Hirchenhain, and Kemler, 1994).
Similarly, zebrafish homozygous for non-adhesive missense mutation in N-cadherin
(Trp2Gly) exhibit defects in somitogenesis, cardiac performance, and neuroepithelial integrity and die early in larval development, (Bagatto, Francl, Liu, and Liu, 2006; Malicki et al., 1996; Malicki, Jo, and Pujic, 2003; Pujic and Malicki, 2001). These drastic phenotypes emphasize the critical role of cadherin-mediated adhesion during tissue development and morphogenesis.
8 Clustered protocadherins
The clustered protocadherin subfamily contains over 50 members, which are located in three distinct clusters on chromosome 5 in the human genome (PCDHα,
PCDHβ, PCDHγ). Each cluster contains multiple genes with independent promoters and a variable first exon, which gets spliced to a common C-terminal for the given cluster. For example, to make PCDHγA1, the A1 promoter initiates transcription of the A1 variable exon, and this variable exon is spliced to C-terminal exons that are common to all genes in the PCDHγ cluster. In all the clusters, each variable exon contains six EC repeats, a transmembrane domain, and a small portion of the cytoplasmic domain. The constant regions of pcdhα and pcdhγ each contain three exons that form the remainder of the cytoplasmic domain. However, the pcdhβ cluster does not contain a constant region, simply being a tandem cluster of single exon genes with high sequence similarity (Hirano et al., 2012; Sugino et al., 2000; Tasic et al., 2002; Wang, Su, & Bradley, 2002; Yagi,
2008). This genomic organization of the clustered protocadherins is their defining feature.
Compared to the classical cadherins, the clustered protocadherins mediate very weak adhesion, and even their weak homophilic adhesion has been debated (Morishita et al., 2006; Mutoh, Hamada, Senzaki, Murata, & Yagi, 2004; Reiss et al., 2006; Sago et al., 1995; Thu et al., 2014a). These clustered protocadherins lack the conserved tryptophan required for classical cadherin adhesion, and initial tests showed only weak aggregation of L-cells (a non-adhesive, cadherin deficient cell line) transfected with
9 various clustered protocadherins (Sago et al., 1995; Sano et al., 1993; Tachibana et al.,
2000). Furthermore, when the extracellular domains of clustered protocadherins were purified on beads, no aggregates were observed for the clustered protocadherin, while classical cadherin control beads aggregated under the same conditions (Morishita et al.,
2006; Mutoh et al., 2004). However, recent cell adhesion assays showed each clustered protocadherin could mediate adhesion with a distinct homophilic specificity, while purified ectodomains still failed to mediate bead aggregation (Schreiner & Weiner,
2010; Thu et al., 2014a). These differences between cellular adhesion and bead aggregation could indicate that the affinity of the interaction is too weak to be detected by some methods, or that additional cofactors or conditions are necessary for the interaction.
In just the last two years, the clustered protocadherin adhesion mechanism has been revealed by X-ray crystallography and confirmed by additional cell adhesion assays. Adhesion assays predicted that EC repeats one through four were responsible for mediating the adhesion (Rubinstein et al., 2015; Thu et al., 2014a), although the first glimpse of the adhesion interface came from a structure of pcdhγA1 EC1-3 (J M
Nicoludis et al., 2015). The pcdhγA1 EC1-3 structure showed the antiparallel interface between EC2 and EC3 and suggested that EC1 would interact with EC4. Later structures containing more EC repeats confirmed these predictions and revealed the entire EC1-4 adhesion interface (Figure 1.3C) (Goodman, Rubinstein, Thu, and Bahna, et al. 2016;
Goodman, Rubinstein, Thu, and Mannepalli, et al. 2016; Nicoludis et al. 2016). Each of the clustered protocadherins interfaces solved by X-ray crystallography show similar 10 secondary structure elements located at the interface. However, the identity of amino acid side chains varies to provide their adhesive specificity. To validate the interfaces observed in the crystal structures, mutations were designed at interfacing surface residues to disrupt the interface. When these mutated constructs were subjected to cellular adhesion assays, aggregation was ablated (Goodman, Rubinstein, Thu, and
Bahna, et al., 2016). In addition to the trans binding interfaces, cell adhesion assays and analytical ultracentrifugation data suggest that clustered protocadherins form cis oligomers, that together form a trans adhesion complex. Although no cis interaction has been observed in crystal structures of the clustered protocadherins, truncation series and mutagenesis has implicated EC6 (with possible contributions from EC5) in mediating cis oligomerization. Also, the cis interaction can occur promiscuously among members of all three clusters, unlike the trans interaction which appears to be strictly homophilic
(Goodman, Rubinstein, Thu, and Bahna, et al., 2016; Goodman, Rubinstein, Thu, and
Mannepalli, et al., 2016; Schreiner & Weiner, 2010; Thu et al., 2014). The interfaces observed for the clustered protocadherins depict a vastly different mechanism of adhesion compared to the classical cadherins, and small variations in the binding interface of each member of the clustered protocadherin family provide specificity for their homophilic adhesion.
Researchers have proposed that the diversity of the clustered protocadherins and the specificity of their adhesion uniquely positions this group to function in neuron self avoidance. Self avoidance is a process where the dendritic branches from a single neuron repel each other, while still being able to interact with neighboring cell dendrites 11 (Grueber & Sagasti, 2010). This requires a mechanism for neurons to distinguish between self and non-self, and the clustered protocadherins have been suggested to facilitate this discrimination in the vertebrate nervous system. In mammals, the clustered protocadherins are mostly expressed in the nervous system and are present at synapses. Each individual neuron expresses a random combination of the clustered protocadherin genes present in the genome, which has the potential to provide each neuron a unique molecular identity (Yagi, 2012). Although these clustered protocadherins could provide every neuron a unique identity, self and non-self discrimination functions have only been observed for clustered protocadherins in a couple neuron types. The most direct support comes from a couple studies of Pcdhγs in cell types with planar dendritic arbors, where deletion of the Pcdhγ gene cluster resulted in a loss of self avoidance (Gibson et al., 2014; Kostadinov & Sanes, 2015;
Lefebvre, Kostadinov, Chen, Maniatis, & Sanes, 2012). The expression of a single Pcdhy gene (PcdhyA1 or PcdhyC3) in retinal starburst amacrine cells restored self-avoidance yet inhibited normal contact with neighboring cells. Similar results were also found in planar cerebral Purkinje cells, but not in neuron types with non-planar, bushy dendritic arbors; instead neurons with bushy arbors exhibited smaller arbor size in Pcdhγ knockouts (Garrett, Schreiner, Lobas, & Weiner, 2012; Suo, Lu, Ying, Capecchi, & Wu,
2012). It is possible that the other clusters of protocadherins (or other genes) are able to compensate for loss of Pcdhγs differential in various types of neuron, or the function of clustered protocadherins may vary depending on the type of neuron. Of note, even in the planar cells exhibiting Pcdhγ dependent self avoidance, the mechanism of repulsion 12 by these cell adhesion molecules is unclear and likely requires an unidentified signaling partner (Hayashi & Takeichi, 2015; Mah & Weiner, 2016; Weiner & Jontes, 2013).
δ-protocadherins
The δ-protocadherins (δ-pcdhs) are non-classical, non-clustered protocadherins that were distinguished from the rest of the cadherin superfamily by conserved cytoplasmic motifs (Wolverton & Lalande, 2001). Members of this subfamily have six or seven EC repeats, and are scattered among several chromosomes (human chromosomes 4, 5, 13, X and Y), unlike the clustered protocadherins. Within the cytoplasmic domain, a couple conserved motifs are present in all δ-pcdhs (CM1 and
CM2), while the presence of a third conserved motif (CM3) distinguishes the subgroup of δ1-pcdhs (human genes: PCDH1, PCDH7, PCDH9, PCDH11X, and PCDH11Y), from the
δ2-pcdhs (human genes: PCDH8, PCDH10, PCDH17, PCDH18, PCDH19) which lack CM3
(Hayashi & Takeichi, 2015; Redies, Vanhalst, & van Roy, 2005). Unlike the classical cadherins, the cytoplasmic domain of δ-pcdhs does not contain any known catenin binding motifs to link them to the actin cytoskeleton, but many δ-pcdhs (Pcdh9 and all
δ2-pcdhs) do have a WIRS motif (WAVE interacting receptor sequence) that binds the
WAVE complex and in turn could regulate actin (Chen et al., 2014; Hayashi et al., 2014).
A couple of additional human genes PCDH12 and PCDH20 are sometimes included with the δ-pcdhs due to similarities in their extracellular domains, despite lacking the CM1,
CM2, and CM3 motifs. These two genes are neither δ1-pcdhs nor δ2-pcdhs, but some
13 researchers give PCDH20 a separate designation of δ0, and PCDH12 does contain the
WIRS motif (Hulpiau & van Roy, 2009; Jontes, 2016).
All the δ-pcdhs are expressed extensively in the nervous system, with additional member dependent expression in some other tissues. Within the nervous system each
δ-pcdh has differential regional expression, which along with their association with neurodevelopmental disorders (discussed in a later section), has led many to speculate that the δ-pcdhs could contribute to a molecular code in the regionalization and circuitry of the developing brain. Although each member has variation in their specific expression patterns and adhesive functions, here I will present Pcdh1 and Pcdh19 as case studies of δ1-pcdhs and δ2-pcdhs respectively, since these (particularly Pcdh19) will be the focus of later chapters.
Pcdh1: a δ1-protocadherin case study
Pcdh1 (also called pc42 and AXPC) was the first δ-protocadherin indentified, which was cloned from rat brain cDNA (Sano et al., 1993). Expression within the brain is widespread, with the highest expression observed in the hippocampus and olfactory bulb (Blevins, Emond, Biswas, & Jontes, 2011; S-Y Kim, Chung, Sun, & Kim, 2007; Redies,
Heyder, Kohoutek, Staes, & Van Roy, 2008). Beyond expression in the brain, in situ hybridization shows Pcdh1 expression in the spinal cord, blood vessels, placenta, and epithelial cells of many organs including lung (Koning et al., 2012; Redies et al., 2008).
Up regulation of Pcdh1 has been correlated with angiogenesis in tissues following
14 ischemia, and knockdown of Pcdh1 in chicken results in subtle mislocalization of neural crest cells (Bononi, Cole, Tewson, Schumacher, & Bradley, 2008; Hayward et al., 2011;
Krishna-K & Redies, 2009). Although it has been hypothesized that pcdh1 (along with all the other δ1 and δ2-pcdhs) plays a role in neural circuitry, direct evidence is lacking, and the strongest evidence of this subfamily’s role comes from other δ-pcdhs being implicated in neurodevelopmental disorders (discussed in a later section).
Recently, a role for PCDH1 in asthma susceptibility has become prominent in the limited literature on PCDH1 function. Bronchial hyperresponsiveness, a hallmark of asthma, was initially associated with PCDH1 by genetic linkage analysis (Koppelman et al., 2009). They later showed mouse Pcdh1 transcripts localizes to airway epithelial cells and transcript levels decrease with cigarette smoke exposure (Koning et al., 2014). Even though Pcdh1 is expressed in tissue relevant to asthma, additional studies on the genetics linkage of PCDH1 to particular asthma symptoms in human patients are conflicting (Mortensen, Kreiner-Moller, Hakonarson, Bonnelykke, & Bisgaard, 2014;
Toncheva et al., 2012). Nonetheless, recent in vitro studies showed interaction between
PCDH1 and another known asthma susceptibility gene (SMAD3), and down regulation of pcdh1 reduced the barrier function of culture bronchial epithelial cells (Faura Tellez et al., 2015, 2016; Kozu et al., 2015). Therefore, altered expression or function of Pcdh1 could impact airway epithelial function, but it is unclear the impact of PCDH1 allele variations in any particular patient.
The adhesion mechanism for Pcdh1 is still unknown; in fact, it has been debated whether Pcdh1 and other δ-pcdhs are even bonafide cell adhesion molecules. As with 15 the clustered protocadherins, different cell types and conditions result in either no adhesion or weak adhesion, which could indicate cell-type specific roles or the necessity of cofactors for their adhesion (Blevins et al., 2011; Kuroda, Inui, Sugimoto, Hayata, &
Asashima, 2002; Obata et al., 1995; Sano et al., 1993). Although no X-ray structures of the δ1-pcdhs have been solved, recent evidence from a Pcdh19 structure suggests
Pcdh1 may interact homophilically using a similar interface as Pcdh19 (details presented in chapter 3). However, with Pcdh1 ꟷ along with the rest of the δ1-pcdhs ꟷ having seven EC repeat, it is unclear whether they will use the same mechanism as Pcdh19 containing only six EC repeats (Cooper, Jontes, & Sotomayor, 2016).
Pcdh19: a δ2-protocadherin case study
Pcdh19 was first identified in 2001 and is expressed primarily in the central nervous system (Wolverton & Lalande, 2001). Within the brain, the strongest expression was seen within the thalamus, hippocampus, cerebral cortex, and optic tectum. Besides the brain, pcdh19 expression has also been reported in portions of the retina, spinal cord, kidney, stomach and pancreas (Cooper et al., 2015; Gaitan & Bouchard, 2006; S-Y
Kim et al., 2007; Q. Liu, Chen, Kubota, Pan, & Murakami, 2010). Pcdh19 knockouts in both zebrafish and mouse are homozygous viable and exhibit very mild phenotypes.
While no gross morphological defects were observed, the knockout zebrafish had defects in visual circuitry, and the mice had defects in neuron motility (Cooper et al.,
2015; Pederick et al., 2016). On the other hand morpholino knockdown of pcdh19 had a
16 more drastic phenotype, hampering cell convergence during zebrafish neurulation and resulting in defects in forebrain and midbrain morphogenesis. These differences in severity could be explained by compensation mechanisms activated in the genetic absence of pcdh19 (Kok et al., 2015), or varied levels of knockdown in cells may create more havoc than complete absence of the protein. Most importantly, in human patients, PCDH19 missense mutations cause a specific form of epilepsy limited to females (Pcdh19 female epilepsy, Pcdh19-FE). This suggests that PCDH19 has a significant role in neural circuitry, which will be further discussed in later sections and chapters.
As with the majority of the δ-protocadherins, Pcdh19 has weak adhesion that may be context dependent. The ability of Pcdh19 to mediate weak adhesion has been observed both in cellular aggregation assays with full length protein, and in bead aggregation assays with the purified extracellular domain (Cooper et al., 2016; Tai,
Kubota, Shiono, Tokutsu, & Suzuki, 2010). In addition, Pcdh19 mediated adhesion can be strengthened by cis interactions with Ncad, and this stronger adhesion does not require
Ncad’s conserved tryptophan (Emond et al., 2011). Recently, the adhesion interface for
Pcdh19 alone was solved by X-ray crystallography, and this interface appears to be relevant even in the presence of Ncad. The Pcdh19 interface involves EC repeats one to four (Figure 1.3C), similar to the clustered protocadherins, and further details will be described in chapter 3.
17 Additional cadherin family members
There are many additional cadherins not discussed above, but here I will just briefly mention the few with known adhesion mechanisms. First, crystal structures of some desmosomal cadherins (desmocollins and desmogleins) showed an adhesion mechanism similar to the classical cadherins, as the tryptophan exchange occurs in each of these subfamilies (Harrison et al., 2016) (Figure 1.3A). Although only homophilic complexes of desmosomal cadherins have been crystallized thus far, heterophilic interactions between desmocollins and desmoglein have been observed in many biochemical assays (e.g. bead aggregation assays, acoustic force microscopy, and surface plasmon resonance) (Harrison et al., 2016; Lowndes et al., 2014; Syed et al.,
2002). When these desmosomal cadherins do not function properly defects occur in tissues that undergo high mechanical stress, including heart muscles and skin (Al-Jassar,
Bikker, Overduin, & Chidgey, 2013; Stahley & Kowalczyk, 2015).
Second, a heterophilic adhesion complex between Cdh23 and Pcdh15 occurs between hair cell stereocilia in the inner ear, which is essential for hearing. Crystal structures show the interaction involves the first two EC repeats of each cadherin interacting by an “extended handshake” mechanism (Marcos Sotomayor, Weihofen,
Gaudet, & Corey, 2012) (Figure 1.3B). Furthermore, a mutation in Pcdh15 (I108N) at the
Pcdh15-Cdh23 interface disrupts the organization of the inner ear hair cell stereocilia and ultimately results in deafness (Geng et al., 2013).
18 The cadherin superfamily is a diverse group with many different organismal functions and several adhesive mechanisms. Although the adhesive mechanisms of some have been worked out in extensive detail, the mechanisms of others are largely unknown, or their capacity to mediate adhesion is still unclear. While many cadherins contribute to brain development, the δ-protocadherins in particular are highly expressed in the brain and implicated in several neurodevelopmental disorders discussed below.
Neural Circuitry, Neurodevelopmental Disease, and the δ-Protocadherins
The brain contains numerous neurons which connect to one another forming neural circuits. During development, the primordial brain is divided into various regions: first broadly into forebrain, midbrain, and hindbrain, and then more specific subdivisions are generated (e.g. cerebral cortex, hippocampus, and cerebellum). In turn, neurons from each brain region must synapse with other neurons, both within the same region and between distal regions. These interconnected neurons form functional units called neuronal circuits, which allows for interregional communication and integration of input signals. In the end, over 80 billion neurons must be specified and make appropriate synapses to form a normal human brain. Furthermore, miswiring of brain circuitry is believed to underlie many neurodevelopmental disorders (Azevedo et al., 2009; Kahr,
Vandepoele, & van Roy, 2013; Mitchell, 2011). This leads to a central question in
19 neurodevelopment: How do neurons discern between appropriate and inappropriate synapses to form the brains intricate neural circuitry?
Principles and examples of neural circuits
Numerous factors likely contribute to the reliable establishment of brain circuitry, including chemoaffinity gradients, correlated neural activity, and molecular recognition codes. Various protein gradients are known to function in many stages of brain development, as well as during many other embryonic patterning processes.
Chemoaffinity gradients were initially proposed by Sperry to explain the wiring of the retinotectal circuit, in which the nasal to temporal origin of the retinal ganglion cell correlated with its axonal target location in tectum, posterior to anterior respectively
(Sperry, 1963). Later, proteins expressed in gradients were identified in the retina and tectum. These proteins were a family of ligand and receptor pairs, with ephrin gradients
(the ligand) located in the tectum and eph receptor gradients located in the retinal ganglion cells. When an ephrin binds to its eph receptor, growth cone repulsion occurs, such that retinal ganglion cells with lower levels of the eph receptor are able to penetrate further (more posterior) into the tectal tissue (Flanagan & Vanderhaeghen,
1998; Kita, Scott, & Goodhill, 2015; McLaughlin & O’Leary, 2005). Although the chemoaffinity gradients are well recognized to play a role in neural development and circuitry, it is unlikely that they could explain all the intricate circuitry of the brain.
20 Correlation in the action potentials of neurons is not only a byproduct of circuits, but also influences the development of neural circuits. This principle was initially proposed by Donald Hebb in his cell assembly theory, which is commonly summarized with the phase “cells that fire together wire together” (Hebb, 1949; Shatz, 1992). This principle can be seen in the importance of spontaneous rhythmic activity during axon pathfinding and motor axon refinement (Hanson, Milner, & Landmesser, 2008; Moody &
Bosma, 2005). When motor axons first innervate muscle their axonal processes are exuberant, leading to a single muscle cell being innervated by multiple motor axons.
After pruning directed by spontaneous activity, each muscle cell will be left with one winning motor axon innervation (Chung & Barres, 2009). Similar phenomena have been observed in other CNS circuits with spontaneous activity pruning axons in visual and cerebral circuits (Apuschkin, Ougaard, & Rekling, 2013).
As another principle of neural circuitry, some researchers have proposed a matching molecular code between neurons to be responsible for specifying synaptic partners like postal zip codes (Yogev & Shen, 2014). Initially, the olfactory system was thought to be the prime example of this mechanism. Here, the olfactory sensory neurons (OSNs) within the nasal epithelium each express a single olfactory receptor
(OR), out of ~1000 possible ORs, and only OSNs that express the same receptor innervate a common glomerulus in the olfactory bulb. At first researchers thought that the ORs themselves provided the topographic instructions for innervating the glomeruli
(Mombaerts, 2006), but additional studies showed this simple explanation to be naïve
(Imai, Sakano, & Vosshall, 2010). Even if these ORs were responsible for the 21 topographical map in the olfactory bulb, this type of mechanism would be too genomically costly to be used prolifically in brain wiring, with olfactory receptors being
1% of the mouse genome (Mombaerts, 1999). However, variants of this molecular code theory may be involved in circuitry throughout the brain, and combinatorial codes could effectively reduce the number of necessary genes. For example, a small number of spatially and temporally regulated proteins could specify discrete neural circuit modules. Even so, multiple mechanisms are likely involved in any given circuit of the brain beyond even what could be included above (Hassan & Hiesinger, 2015; Yogev &
Shen, 2014).
Involvement of δ-protocadherins in neurodevelopment
The δ-protocadherins (δ-pcdhs) have been proposed to contribute to brain circuitry and may function by a molecular code-like mechanism to partition brain regions and direct interactions between neurons. As discussed earlier, each member of the δ-pcdh family has a distinct expression pattern, both overall in the brain and within specific brain regions (Cooper et al., 2016; Krishna-K, Hertel, & Redies, 2011), and members have been shown to sort cells by their homophilic interactions (Emond et al.,
2011; Tai et al., 2010). In addition, several δ-pcdhs are involved in circuitry related functions and have been linked to various neurodevelopmental disorders, including autism, epilepsy, and schizophrenia (Table 1.1) (Kahr et al., 2013; K J Mitchell, 2011;
Redies et al., 2012). Because of these attributes, researchers widely presume that the δ-
22 protocadherins are involved in neural circuitry, possibly specifying synaptic partners
(Hirano & Takeichi, 2012; Sakurai, 2016).
Almost all the δ-pcdhs have been implicated in some form of circuitry related function, including axon guidance, dendritic outgrowth, and synapse dynamics (Table
1.1) (Hayashi & Takeichi, 2015; Jontes, 2016; Kahr et al., 2013). Specifically, Pcdh11x negatively regulates dendritic branching by promoting PI3K/AKT signaling (Wu et al.,
2015). Whereas, Pcdh18b promotes axon branching presumably through its interaction with Nap1, which regulates actin dynamics (Biswas et al., 2014). Pcdh17 knockout mice also exhibit axon defects, with amygdala axons exhibiting abnormal axon-axon interactions and reduced extension (Hayashi et al., 2014). Similar axon extension defects are observed in Pcdh10 knockout mice in the thalamocortical projections, and additional axon guidance defects are observed in olfactory sensory neurons when pcdh10 expression is altered (Uemura, Nakao, Suzuki, Takeichi, & Hirano, 2007; Williams et al.,
2011). Defects in synapses also occur both in pcdh10 knockdowns and in pcdh8 knockout neurons, but these defects occur by different mechanisms. Pcdh10 functions in activity dependent synapse elimination by targeting ubiquitinated PSD95 to the proteasome (Tsai et al., 2012), but Pcdh8 interacts with Ncad and mediates endocytosis of the complex through a TAO2β kinase signaling cascade (Yasuda et al., 2007). In addition to all of these δ-pcdh member specific defects in various brain regions, the entire family has been suggested to partition the zebrafish optic tectum into functional modules. Several of the δ-pcdhs were expressed in discrete columns, and the columnar
23 organization was lost in pcdh19 knockout zebrafish (discussed fully in chapter 2) (Cooper et al., 2015).
In addition to the observed functions of the δ-pcdhs in model organisms, mutations in many of these cadherins have been indentified in human patients with various neurodevelopmental disorders. For example, among the genes associated with autism spectrum disorder are four δ-pcdhs: PCDH8, PCDH9, PCDH10, PCDH19. In a screen of structural gene variants in autism (insertions, deletions, translocations, etc.),
PCDH9 was indentified in two unrelated families. Both probands had insertions in a
PCDH9 intron (insertion size, ~189kb or ~172kb), without disrupting other genes
(Marshall et al., 2008). In a separate study, a 321kb deletion was found near the PCDH10 gene in an autism patient, which may affect its expression (untested) (Morrow et al.,
2008). A PCDH8 missense mutation (A404V) was identified in a single patient during a whole genome sequencing study of female autism patients (Butler, Rafi, Hossain,
Stephan, & Manzardo, 2015). A dyslexia study has implicated a δ-pcdh (PCDH11X)
(Veerappa, Saldanha, Padakannaya, & Ramachandra, 2013), and three δ-pcdhs (PCDH9,
PCDH12, and PCDH17) have been associated with schizophrenia (Gregorio et al., 2009;
Pedrosa et al., 2010; Dean et al. 2007). Of all the δ-pcdhs, PCDH19 the has clearest link to neurodevelopmental disease, affecting over 170 families with 97% penetrance
(Dibbens et al., 2008; Duszyc, Terczynska, & Hoffman-Zacharska, 2015; van Harssel et al., 2013; Walters, Wells-Kilpatrick, & Pandeleos, 2014).
24 Pcdh19 Female Epilepsy
Discovery and characterization of Pcdh19 female epilepsy
A hereditary form of epilepsy limited to females was originally discovered in
1971 in an American family of Hungarian descent (Juberg & Hellman, 1971), and the disease was termed epilepsy and mental retardation limited to females (EFMR) (Ryan et al., 1997). However, mutations in protocadherin-19 (PCDH19) were not recognized as the genetic cause until 2008 (Dibbens et al., 2008; Scheffer et al., 2008). Since then, the disease has been renamed PCDH19 Female Epilepsy (PCDH19-FE, the name used here)
(Walters et al., 2014), and numerous additional PCDH19 missense and nonsense mutations (>120 mutations in >250 patients) have been identified, making PCDH19 the second most clinically relevant gene in epilepsy (Depienne & LeGuern, 2012; Duszyc,
Terczynska, & Hoffman-Zacharska, 2015).
With the increasing number of identified patients with epilepsy caused by
PCDH19 mutations, this specific form of epilepsy was able to be more thoroughly characterized. Patients typically begin having seizures in early childhood (4 months to 5 years old), and the seizures often subside with age, with many patients being seizure free around the age of puberty (average age of 12 years old) (Depienne et al., 2011;
Jamal, Basran, Newton, Wang, & Milunsky, 2010; van Harssel et al., 2013). While some seizures are localized to a specific brain region (focal seizure), many encompass both brain hemispheres (generalized seizure). In addition, the clinical seizure types experienced by these patients are very diverse including tonic, atonic, tonic-clonic,
25 status epilepticus, and absence seizures, with many of the initial seizures being provoked by fever (febrile seizures) (van Harssel et al., 2013). After the onset of seizures, many of the patients suffer from developmental delay and intellectual disability, which is reflected in the initial name for the disease, EFMR. However, since about a quarter of Pcdh19-FE patients have a normal IQ, some prefer to use the newer name (Cooper et al., 2016; Walters et al., 2014).
The genetic pedigree of PCDH19-FE is particularly interesting in that the seizure patients are almost exclusively female. Although carrier males may have more rigid personalities, they do not have seizure activity (Scheffer et al., 2008). With PCDH19 being located on the X-chromosome, one would expect a greater proportion of males to have the disease, as occurs in many X-linked recessive disorders. In X-linked recessive disorders the heterozygous females are spared while hemizygous males or homozygous females have the disease characteristics, leading to a majority of males with the disease.
In X-linked dominant, hemizygous males, homozygous females, and heterozygous females are all affected, but the heterozygous females exhibit a less severe phenotype.
Alternatively in X-linked dominant disorders, only females have the disease due to male lethality. However, for Pcdh19-FE the heterozygous females have seizures, while the hemizygous carrier males are spared (no homozygous females have been documented).
This unusual disease inheritance pattern has elicited speculation by researchers on the cellular mechanism involved. One possibility is a compensatory gene expressed on the
Y-chromosome, such as PCDH11Y, compensating for the loss of PCDH19 in males. A second possibility is a differential function of PCDH19 in male and females (Dibbens et 26 al., 2008; Tan et al., 2015). However, currently the most prominent explanation is the cellular interference hypothesis.
X-inactivation and cellular interference
The term cellular interference refers to a disease mechanism where the mosaic heterozygote has more severe symptoms than individuals lacking any functional gene
(homozygous mutant), due to the cellular mosaic state interfering with transmembrane protein-protein interactions. The term was initially coined by Wieacker and colleges to explain the unusual inheritance of craniofrontonasal syndrome, and was later applied to
PCDH19-FE which has a similar inheritance pattern (Depienne et al., 2009; Dibbens et al., 2008; Wieacker & Wieland, 2005). In both diseases the casual genes are located on the X-chromosome, with random X-chromosome inactivation causing mosaic gene expression.
Every cell of a female person contains two X-chromosomes, and in order to maintain similar gene dosage as males, one of the X-chromosomes will be inactivated by
DNA methylation. This X-chromosome inactivation (XCI) occurs twice in the developing embryo, with a short period of X-chromosome reactivation (XCR) occurring in between.
The first XCI exclusively silences the paternal X-chromosome, and then XCR occurs just in the embryonic fated cells, while the extraembryonic cells will maintain the paternal X- inactivation. With all the embryonic cells expressing both X-chromosomes, another period of X-inactivation occurs. This time the XCI occurs randomly in each cell, either
27 inactivating the paternal or maternal X-chromosome. In the mouse model, this random
XCI occurs between E4.5 and E6.5 as the pluripotent cells are on the verge of differentiating into the three germ cell layers (endoderm, mesoderm, ectoderm) (Payer,
2016). Shortly thereafter in mouse development (E7) neural induction occurs, regions of the central nervous system are specified, and neurulation begins (E8) (A. J. Levine &
Brivanlou, 2007). Once each cell independently inactivates one of its X-chromosomes, either maternal or paternal, all the progeny of that cell will maintain that same choice.
This results in the clonal mosaic expression of the maternal or paternal alleles of the X- chromosome throughout the embryo. Specifically, the neurons in the brain will also be mosaic, since an assortment of cells is induced to become neuroectoderm after XCI occurs. Within the context of a disease gene, such as PCDH19, some of the neurons of
PCDH9-FE patients will express the wild-type PCDH19, while some other neurons of the patient will only express mutant PCDH19.
Now the question still remains how does the mosaic expression of PCDH19 in the nervous system adversely affect neural development and cause epilepsy with its unusual pattern of inheritance? Since PCDH19 is a cell adhesion molecule, researchers have proposed that the mosaic mixture of mutant-PCDH19 neurons and wildtype-
PCDH19 neurons may interfere with proper cell adhesion and synapse formation; whereas, if all cells contain the mutant PCDH19 (as in the hemizygous male) the cells are able to adhere better than in the mosaic case (Depienne & LeGuern, 2012; Depienne et al., 2009; Dibbens et al., 2008). It may be that when all cells have mutant PCDH19, other compensatory mechanisms are activated. In addition, differential affinity of cells with 28 and without the PCDH19 may cause these subpopulations to aberrantly sort from one another disrupting neural circuits, since even cells with varied levels of cadherin expression have been shown to sort in vitro (Steinberg, 2007; Steinberg & Takeichi,
1994). In summary, if the cadherin protein family is providing a combinatorial adhesion code, completely lacking one member (such as PCDH19) may have a smaller impact on neural circuitry than having a member with random differential allele expression in neurons throughout the brain.
Currently the most convincing evidence for the cellular interference hypothesis is the following finding: the few males affected by PCDH19-FE are also mosaic (Depienne et al., 2009; Terracciano et al., 2016; Thiffault et al., 2016). The mosaic expression in male patients occurs when a de novo somatic mutation occurs during embryonic development resulting in some cells having a mutant gene and others the wild-type gene. This creates an analogous situation to the heterozygote females, in that both are mosaics and both have epilepsy. This strengthens the case that the mosaicism of the
PCDH19 alleles is the major problem for proper neural development, as the cellular interference hypothesis predicts.
In addition, the cellular interference theory may help explain the wide variety in the severity of PCDH19-FE symptoms described earlier. Moreover, a few heterozygote females in the PCDH19-FE pedigrees have been identified as carriers for the disease, while being completely asymptomatic (Depienne et al., 2011; Dibbens et al., 2011;
Dimova, Kirov, Todorova, Todorov, & Mitev, 2012; Terracciano et al., 2012). Some speculate that skewing of the X-inactivation and allelic expression may explain this 29 phenomenon of ~97% penetrance, such that if the majority of the neural tissue has the same parental X-chromosome inactivated, the cells will be able to associate normally to form brain circuitry (Dibbens et al., 2008; Duszyc et al., 2015). Similarly, it may be more critical for certain subsets of neurons or certain regions of the brain to have homogeneous expression of the same PCDH19 allele. However this explanation is difficult to test, since the skew of allelic expression can be different in various tissues
(Terracciano et al., 2012). Furthermore, the incomplete penetrance of the disease could also be explained by variation in the genetic background with variation in compensatory factors, yet this would not explain the reported variation between monozygotic twin girls with PCDH19-FE (Higurashi et al., 2012). In fact a combination of the genetic background, the degree of X-chromosome inactivation skewing, and the random location distribution of each allele’s expression likely contribute to the severity of the disease.
Zebrafish as a Neurodevelopmental Model
The zebrafish model provides an excellent system for studying the foundational mechanisms of neurodevelopment. When George Streisinger aspired to understand the genetics of neurodevelopment, he chose to pioneer a new model organism, a small tropical fish named Danio rerio (zebrafish) (Grunwald & Eisen, 2002). One main advantage of zebrafish is its transparent ex utero development, allowing for the non- invasive observation of brain development in real time. Moreover, by using fluorescent
30 transgenes, subsets of neurons can be tracked during brain development. In order to recapitulate endogenous expression, bacterial artificial chromosomes (BACs) have been utilized, containing large segments of genomic DNA that allow transgenes to be regulated in the context of normal cis elements. Additional advantageous features of zebrafish are their large clutch sizes and rapid embryonic development which has been beneficial for numerous forward genetic screens (Gerlai, 2012; Jontes & Emond, 2012;
Wyatt, Bartoszek, & Yaksi, 2015). Furthermore, in recent years, development of several genome engineering approaches made reverse genetic possible for zebrafish researchers. Of particular interest, the TALEN and CRISPR technologies allow researchers to design protein or RNA guides to knockout genes of interest or to facilitate homologous recombination that introduces point mutations (Cermak et al., 2011;
Hwang et al., 2013). By combining knockout and transgenic technologies, subtle defects present only in a subset of cells that express the gene of interest can be observed. This is particularly important when studying genes involved in neurodevelopmental disease, as one may expect overall morphogenesis to be normal and subtle defects may be hidden amid a milieu of normal neurons.
As with all model organisms, one must recognize the differences between the zebrafish and human brain: zebrafish are not mini humans. Although many neurodevelopmental principles are common, the anatomic features of the brain clearly differ. One significant difference in the zebrafish brain is the absence of a laminar cerebral cortex, which is limited to mammals. However, many analogous neural processes are believed to occur in the nuclear masses in the telencephalic pallium in 31 zebrafish (Ito & Yamamoto, 2009; Mueller, Dong, Berberoglu, & Guo, 2011; Vargas,
Lopez, & Portavella, 2009). For example, the spatial learning, which occurs in the mammalian hippocampus, has been attributed to the lateral portion of the telencephalic pallium, and avoidance learning (mammalian amygdala) occurs in the medial pallium (Portavella, Torres, Salas, & Papini, 2004; Rodriguez et al., 2002).
Likewise, in the visual system of zebrafish and mammals, the retinal ganglion cells
(RGCs) exit the eye though the optic nerve and innervate several brain regions. In zebrafish, the RGCs have ten distinct arborization fields (AF1-AF10) for which only some have been functionally characterized, appearing to correspond with parallel mammalian structures (Burrill & Easter, 1994). One such structure, the zebrafish optic tectum (also known as AF10) corresponds to the mammalian superior colliculus. Both of these laminar structures are located within the midbrain and receive topographical innervations from the eye. For zebrafish, the optic tectum performs the majority of visual processing, receiving terminal inputs from over 97% of RGCs; whereas in mammals a significant portion of RGCs also terminate in the lateral geniculate nucleus
(LGN), which integrates visual information and relays it to the visual cortex. Although all the zebrafish RGC projections have been mapped, little is known about the function of the non-tectal arborization fields (AF1-AF9) nor how they may correspond to mammalian brain regions (Robles, Laurell, & Baier, 2014). While the zebrafish brain is not simply a mini version of a human brain, their brain has many comparable regions and the smaller size is advantageous for brain reconstructive imaging. Therefore, zebrafish provides a good platform to discover neurodevelopmental principles, but 32 specific extrapolations to the human species should be done cautiously as with any predictive model (Maximino et al., 2015).
Some atypical genomic features should also be considered when using zebrafish as a neurodevelopmental model. First, zebrafish often have two genes serving as homologues to a single human gene. Some of these could have partially redundant functions, which should be considered during functional analysis of these genes. Such genes are typically denoted with “a” or “b” appended to the gene name (e.g. pcdh1a and pcdh1b) (Westerfield, 2007). Of note, human PCDH19 (which will be discussed extensively in chapters 2-4) only has a single homologue in the zebrafish genome, pcdh19. Another divergent feature of the zebrafish genome is the lack of sex chromosomes (Sola & Gornung, 2001). Thus, zebrafish homologues of X-linked human genes no longer have mosaic cellular expression of each allele; instead, both alleles of the gene are expressed in all cells. In cases such as PCDH19, the mosaic nature of the mutant and wild-type alleles plays a significant role in the disease mechanism (Depienne et al., 2009; Terracciano et al., 2016; Thiffault et al., 2016). Thus, one would not expect the heterozygote female zebrafish (pcdh19+/-) to phenocopy the female human condition. In order to recapitulate the mosaic state in zebrafish, two different methods can be used: cell transplants, or CRISPR injections at multi-cell stage. Both of these methods allow the researcher to influence the proportion of cells expressing mutant or
WT protein. Furthermore, this ability to alter the skew of mosaic expression in zebrafish allows researchers to test how skew may impact phenotype severity.
33 Multidisciplinary Approach to a Fundamental Question
One of the fundamental questions in developmental neuroscience is how the immensely complex developing nervous system gets wired into precise stereotyped neural circuits. In order to understand the contribution of δ-protocadherins in this process, I took a multidisciplinary approach and present data from behavioral assays in zebrafish all the way down to the atomic detail of protein structures. We focused primarily on pcdh19, as it has the clearest connection to neurodevelopmental disease, and assessed its function in vivo with transgenic and knockout technologies in zebrafish
(Chapter 2). GFP-tagged pcdh19 transgenic exhibited striking columnar expression in the optic tectum, which was disrupted in the pcdh19 knockouts. Further exploration of other δ-pcdhs led to a modular δ-pcdh-dependent model of optic tectum development, which may also apply to other brain regions (Chapter 2 and 5). In tandem, X-ray crystallography revealed the adhesive mechanism of Pcdh19 in atomic detail, and sequence alignments suggest that other δ-pcdhs may adhere by a similar mechanism
(Chapter 3). Furthermore, the amino acid variations between different members of the
δ-pcdh family could underlie a molecular code. In addition, the X-ray crystal structure of
Pcdh19 provided a framework for mapping PCDH19-FE mutations and verifies mutations located at the adhesion interface disrupt adhesion in vitro. Moving forward I am utilizing the CRISPR technology to create non-adhesive PCDH19-FE missense mutations in the genome of zebrafish; then, I will compare phenotypes of these missense mutant zebrafish with pcdh19 knockout and wild-type zebrafish (Chapter 4). This
34 multidisciplinary approach supports a role for δ-protocadherins in partitioning the nervous system by a code like mechanism, and provides insight into mutations causing
PCDH19 Female Epilepsy.
35 Figure 1.1. Extracellular cadherin (EC) repeat architecture. (A) Topology diagram of two tandem EC repeats which defines the cadherin superfamily (adapted from Cooper, Jontes, Sotomayor 2016). Each EC repeat contains seven β strands (labeled A through G), which form hydrogen bonds with the adjacent strands. In addition, α-helixes and 310-helixes are observed in some cadherins between β-strands, which are seen here between β-strands B-C and between C-D. In a canonical EC linker region, three calcium ions are bound (labeled 1 through 3). (B) A 3-dimentional rendering of tandem EC repeats with the three canonical calcium ions shown as green spheres and calcium-coordinating side chains or backbone carboxyls shown in stick. (C) Enlargement of calcium binding linker region shown in B.
36 Figure 1.2. The cadherin superfamily. Domain architecture of the main subfamilies of cadherins along with some additional members to represent the diversity of the cadherin superfamily. The first and last extracellular cadherin (EC) repeats are numbered, and the legend in the upper left defines the various extracellular and intercellular features of the cadherin superfamily members. Adapted from Hirano and Takeichi 2012).
37 Figure 1.3. Known adhesion mechanism of the cadherin superfamily. Three main classes of adhesion mechanisms have been discovered for the cadherin family, and various handshakes can be used to represent each (on the left) (A) A “pinky swear” represents the tryptophan exchange which occurs in classical and desmosomal cadherins. A surface representation of Ncad (PDB: 3Q2W) is shown on the right as an example of the “pinky swear” mechanism (Brasch et al., 2012; Harrison et al., 2011). The zoom box highlights the tryptophan exchange, showing one protomer in stick so the embedded tryptophan from the alternate protomer (surface representation) can be visualized. (B) An “extended handshake” represents the heterophilic mechanism of adhesion between Pcdh15 and Cdh23. On the right, a surface representation shows overlap of EC1 and EC2 of both proteins (PDB: 4APX) (M Sotomayor, Weihofen, Gaudet, & Corey, 2012). EC repeats not present in the crystal structure are represented as ovals with a jagged line for additional intervening repeats. (C) A “forearm handshake” represents the homophilic adhesion mechanism of clustered (α, β, γ) and non-clustered (δ) protocadherins. On the right, a surface representation shows EC1-4 of each protomer forming a large interaction interface (PDB: 5IU9) (Cooper et al., 2016). EC repeats not present in the crystal structure are represented as ovals. Handshake line art was kindly provided by Brandon Neel.
38 Group Name Alternative Circuitry related Neurodevelopmental References names functions disorders PCDH1 AXPC, pc42 PCDH7 NF-Pcdh, Axon growth and Epilepsy, Rett syndrome Lal et al. 2015; Miyake NFPC, BH- guidance et al. 2011; Piper et al. pc, BHPCDH 2008 PCDH9 Neurite localization Autism, schizophrenia Izuta et al. 2015; Marshall et al. 2008; δ1 Gregorio et al. 2009; Pedrosa et al. 2010 PCDH11X Pcdh5 Dendritic growth, Dyslexia, language delay Carrasquillo et al. 2009; neuron proliferation Veerappa et al. 2014; Speevak et al. 2011 PCDH11Y PcdhY, Language delay Speevak et al., 2011 Pcdh22 PCDH8 PAPC, Synapse elimination Autism Yasuda et al. 2007; arcadlin Butler et al. 2015 PCDH10 OL-Pcdh Synapse elimination, Autism Tsai et al. 2012; axon guidance, axon Williams et al. 2011; tract formation Uemura et al. 2007; Morrow et al. 2008 PCDH17 Pcdh68 Axon fasciculation, Bipolar disorder, Hayashi et al. 2014; δ2 axon growth, and schizophrenia Hoshina et al. 2013; synaptic vesicles Chang et al. 2017; Dean et al. 2007 PCDH18 Pcdh68L Axon arbor growth Intellectual disability Kasnauskiene et al. 2012; Biswas et al. 2014 PCDH19 Neural association Epilepsy, intellectual Cooper et al. 2015; and proliferation disability, autism Dibbens et al. 2008 PCDH12 Schizophrenia, Gregorio et al. 2009; microcephaly Pedrosa et al. 2010; δ like Aran et al. 2016 PCDH20 Pcdh13
Table 1.1. δ-protocadherin members association with brain circuitry functions and neurodevelopmental disease.
39 Chapter 2: Protocadherins Control the Modular Assembly of Neuronal Columns in the
Zebrafish Optic Tectum[1]
Abstract
Cell-cell recognition guides the assembly of the vertebrate brain during development. The δ-protocadherins comprise a family of neural adhesion molecules that are differentially expressed and have been implicated in a range of neurodevelopmental disorders. Here we show that the expression of δ-protocadherins partitions the zebrafish optic tectum into radial columns of neurons. Using in vivo 2- photon imaging of BAC transgenic zebrafish, we show that pcdh19 is expressed in discrete columns of neurons, and that these columnar modules are derived from proliferative pcdh19+ neuroepithelial precursors. Elimination of pcdh19 results both in a disruption of columnar organization, as well as defects in visually guided behaviors.
These results reveal a fundamental mechanism for organizing the developing nervous system; subdivision of the early neuroepithelium into precursors with distinct molecular identities guides the autonomous development of parallel neuronal units, organizing neural circuit formation and behavior.
______[1]This chapter was previously published in The Journal of Cell Biology, 211(4), 807–814. The author contributed to the generation of all zebrafish transgenic and knockout lines, in situ hybridization, cryosectioning, immunohistochemistry, confocal and two-photon imaging.in collaboration with Dr. James Jones and Dr. Michelle Emond. Dr. Marc Wolman performed the behavioral analysis. Phan Duy performed experiments related to EdU labeling and phosphohistone staining. Cell body modeling was performed by Bandon Liebau. 40 Introduction
The vertebrate nervous system becomes progressively regionalized during development (Kiecker & Lumsden, 2005). These compartments may be large morphological subdivisions such as the cerebellum, functional specializations such as visual cortex, or local regions such as laminae or nuclei. This partitioning of the nervous system into distinct domains enables each region to undergo a distinct developmental program. Despite the importance to nervous system development, the molecular and cellular mechanisms governing this modular assembly are not well understood.
The optic tectum is the largest subdivision in the zebrafish brain, and it processes retinal inputs to mediate vision (Portugues & Engert, 2009). Morphological studies in frog (Lazar, 1973) and fish (Meek & Schellart, 1978; Vanegas, Laufer, & Amat, 1974) have identified multiple types of tectal neurons and have also revealed a conserved laminated structure. However, neither the cellular architecture of the optic tectum nor the mechanisms governing tectum development are known (Recher et al., 2013). The δ- protocadherins (δ-pcdhs) comprise a family of homophilic cell adhesion molecules
(Vanhalst, Kools, Staes, van Roy, & Redies, 2005; Wolverton & Lalande, 2001), and prior work has shown that δ-pcdhs are strongly expressed in the zebrafish optic tectum
(Biswas & Jontes, 2009; Blevins et al., 2011; Emond, Biswas, & Jontes, 2009; Q. Liu et al.,
2010; Q. Liu, Chen, Pan, & Murakami, 2009). Although the detailed function of these molecules is unclear, members of this family can participate in axon guidance (Leung et al., 2013), arborization (Biswas et al., 2014), and fasciculation (Hayashi et al., 2014). The
41 δ-pcdhs are essential for neural development, as several have been implicated in neurodevelopmental disorders (Hirano & Takeichi, 2012; Redies et al., 2012). In particular, mutations in human PCDH19 result in a female-limited form of infant-onset epilepsy (Depienne et al., 2009; Dibbens et al., 2008), making PCDH19 the second most clinically relevant gene in epilepsy (Christel Depienne & LeGuern, 2012). However, it is not known how loss of pcdh19 alters neural development or leads to epileptogenesis.
Here we show that δ-pcdhs are expressed in radial columns of neurons in the developing zebrafish optic tectum, and neurons within a column arise from a common progenitor cell. Elimination of pcdh19 degrades the columnar organization of the tectum, due to reduced cell cohesion and increased cell proliferation. Moreover, pcdh19 mutants also exhibit defects in visually guided behaviors. These data reveal a previously unknown columnar architecture of the optic tectum, suggesting that the tectum has an organization more similar to mammalian cortex than previously realized. In addition, the defects in visual processing suggest that the columnar organization is important for neural function. Thus, our results provide an initial link between δ-pcdhs, the development of neural architecture and neural function.
Results and Discussion
To better understand the expression of δ-pcdhs within the tectum, we imaged horizontal sections of zebrafish larvae at 4 days post-fertilization (dpf), which were labeled with riboprobes against pcdh19, pcdh9 and pcdh10b (Figure 2.1B-D). Strikingly,
42 larvae exhibited stripes of expression in the tectum, revealing that neurons expressing a particular δ-pcdh are organized as radial columns. These columns are not apparent in either wholemount larvae or in transverse sections. To investigate this in more detail, we identified a BAC clone harboring the complete pcdh19 gene and generated a BAC transgenic line, TgBAC(pcdh19:Gal4-VP16,UAS:Lifeact-GFP)os49. The doubly-modified
BAC clone uses the regulatory elements of pcdh19 to express Gal4-VP16, which activates expression of Lifeact-GFP (Riedl et al., 2008) and labels F-actin in pcdh19- expressing cells. At 30 hours post-fertilization (hpf), the pcdh19 reporter generates a striped pattern in the midbrain neuroepithelium that will give rise to the optic tectum
(Figure 2.1E). Consistent with the in situ hybridization data, cells that express pcdh19 in
3-4 dpf larvae are organized as radial columns (Figure 2.1F). Individual columns consist of clusters of neurons tightly associated with the radial fibers of one or more radial glia- like cells (Figure 2.1G,H). These cells are likely radial glia, as they express common glial markers, including Glutamine Synthase (Figure. 2.1I-L) and Her4.1 (Figure 2.1M-O).
The columnar organization of pcdh19-expressing neurons is reminiscent of the proliferative radial units observed in the developing mammalian cortex (Mountcastle,
1997; Rakic, 1988). To address the question of whether the neurons within a pcdh19+ column are siblings (Noctor, Flint, Weissman, Dammerman, & Kriegstein, 2001), we used two methods to mosaically label cells in the optic tectum. First, we transplanted 20-40 cells from transgenic (TgBAC(pcdh19:Gal4-VP16,UAS:Lifeact-GFP)os49) blastula stage embryos into unlabeled host embryos (Figure 2.2A). These cells disperse during gastrulation and contribute to different parts of the embryo; those cells fated to express 43 pcdh19 will be labeled with Lifeact-GFP. Labeled tectal cells were predominantly organized in columns, even in the absence of other tectal expression, suggesting that these cells were derived from a common progenitor (Figure 2.2B,C). Additionally, we injected BAC DNA into embryos to transiently express Lifeact-GFP in pcdh19+ cells
(Figure 2.2D). Transient expression of fluorescent reporters was largely restricted to radial columns (Figure 2.2E,F), again suggesting that the neurons within these columns arise from an initial pcdh19+ precursor. To further investigate the origins of tectal columns, we imaged individual TgBAC(pcdh19:Gal4-VP16,UAS:Lifeact-GFP)os49 embryos on consecutive days (Figure 2.2G-I). In fortuitous cases, isolated columns identified at 3-
4 dpf (Figure 2.2H,I) could be unambiguously traced back to labeled neuroepithelial cells
(Figure 2.2G). Our observations demonstrate that pcdh19 is expressed in radial columns within the optic tectum and that these columns assemble from the proliferation of one or a small number of pcdh19+ precursors.
To show whether other δ-pcdhs define similar developmental units, as suggested by in situ hybridization (Figure 2.1B-D), we injected BAC clones of zebrafish pcdh18b and pcdh1a, modified as was done for pcdh19. In each case, we observed columns of labeled cells (Figure 2.3A,B), supporting the idea that the zebrafish optic tectum could be partitioned into distinct radial domains, based on the expression of δ-pcdhs (Figure
2.3C). To test this, we performed double fluorescent in situ hybridization with riboprobes directed against pcdh7a and pcdh19 (Figure 2.3D-I). While some overlap of labeling can be observed (Figure 2.3F,I), the columnar distribution of pcdh7a and pcdh19
44 largely appears to be mutually exclusive, arguing that the expression of each δ-pcdh labels distinct sets of columns.
To investigate the role of pcdh19 in the formation of tectal columns, we used transcriptional activator-like effector nucleases (Bedell et al., 2012; Cermak et al., 2011;
Dahlem et al., 2012) (TALENs) to generate germline lesions in zebrafish pcdh19 (Figure
2.4A). Homozygous mutants completely lack Pcdh19 (Figure 2.4B), but do not exhibit gross defects in neural organization (unpublished data). To investigate the effects of pcdh19 loss in detail, we injected BAC(pcdh19:Gal4-VP16,UAS:Lifeact-GFP) into 1-cell stage wild type and mutant embryos (Figure 2.4C,D). At 4 dpf, 58% of labeled wild type larvae exhibited columns (Figure 2.4C,E; n=21/36 larvae). In contrast, only 31% of mutant larvae exhibited evidence of columnar organization (Figure 2.4D,E; n=10/32 larvae, P=0.028, Fisher's exact test). Labeled neurons in mutants were more dispersed and arborized over a larger area within the synaptic neuropil (Figure 2.4D). To further assess the effects of Pcdh19 loss, we crossed the pcdh19-/- mutants into the
TgBAC(pcdh19:Gal4,UAS:Lifeact-GFP) os49 line. Elimination of pcdh19 severely disrupted columnar organization in TgBAC(pcdh19:Gal4,UAS:Lifeact-GFP)os49 larvae (Figure 2.4F-H;
WT: 82%, n=39/47, pcdh19-/-: 41%, n=16/38; P=0.0001, Fisher's exact test). In addition, cell transplantation experiments indicated that Pcdh19 is required in both host and donor cells for normal column development and for normal neurite outgrowth and arborization (Figure 2.5). While groups of pcdh19+ cells appear less tightly clustered in pcdh19-/- mutants (Figure 2.4D), the loss of apparent columnar organization could also be due to an increased number of labeled cells. 45 To determine whether there is an increase of cells expressing Lifeact-GFP in mutants, we identified and counted all labeled cells in image stacks collected from the optic tecta of six wild type and five mutant larvae (Figure 2.6A-C). We found that there was a ~2-fold increase in the number of labeled cells in the mutants (wild type: 181 ± 29, n=6; pcdh19-/-: 328 ± 56, n=5; P=0.036), suggesting an increase of proliferation within this cell population. To directly assess levels of proliferation within the optic tectum, we sectioned and labeled 2 dpf embryos with antibodies against phospho-Histone H3
(Figure 2.6D-F). There was an increase in phospho-Histone labeled nuclei in pcdh19-/- mutants compared to wild type (pcdh19-/-: 20.3±3.5 (n=4); wild type 9.3±2.4 (n=3);
P=0.04, Student's t-test). Similarly, we injected EdU into 2 dpf embryos then fixed them at 4 dpf (Figure 2.6G-I). Again, we found evidence for increased proliferation in pcdh19-
/- mutants (pcdh19-/-: 84.5.3±9.8 (n=4); wild type 63.8±7.6 (n=4); P=0.032, Student's t- test). Our data indicate that the loss of pcdh19 degrades the columnar organization of pcdh19+ neurons through both an increase in neuron production and a reduction in cell cohesion.
Distinct tectal regions are known to differentially process visual input; therefore, disruption of tectal columnar organization may alter visually guided behaviors. To determine whether pcdh19 loss of function affects visual processing, we tested 6 dpf larvae for positive phototaxis, a behavior in which larvae stereotypically turn and swim towards a target light. Compared to wild type larvae, fewer pcdh19-/- larvae reached the target light area and the pcdh19-/- larvae that did show positive phototaxis required more time to reach the target (Figure 2.7A,B) (Burgess, Schoch, & Granato, 2010). 46 Kinematic analyses of turning and swimming behaviors with millisecond resolution indicated that the reduced phototaxis was not caused by motor impairment (Figure 2.8).
To determine whether the reduced phototaxis in pcdh19-/- larvae was due to a visual processing defect, we asked whether pcdh19-/- larvae initiated turns and swims that were biased toward the target light. As expected, wild type larvae showed a strong bias to swim or turn towards the target light based on their orientation (Burgess et al.,
2010); however, pcdh19-/- larvae showed no directional bias, indicating that a visual impairment underlies the phototaxis defect (Figure 2.7C,D). Consistent with these results, we also find that pcdh19-/- larvae show a reduced likelihood of initiating the O- bend maneuver (Figure 2.7E), a stereotyped visuomotor behavior to a sudden extinguishment of light (Burgess & Granato, 2007). Again, once initiated, the performance of O-bend maneuvers was indistinguishable between wild type and pcdh19-/- larvae (Figure 2.7F-H), suggesting the behavior initiation defect is due to a visual, not motor impairment. In contrast, the acoustic startle response was normal in the pcdh19-/- mutants (unpublished data). Thus, visual processing is impaired in pcdh19-
/- larvae, potentially due to disrupted tectal neuronal columns.
Retroviral lineage tracing has suggested the radial development of the optic tectum in chick (Gray & Sanes, 1991, 1992) and in Medaka (Nguyen et al., 1999). Here we show that this radial development results in neuronal columns that may be analogous to the microcolumns found in mammalian cortex (Peters & Sethares, 1996;
Peters & Walsh, 1972). However, it remains to be shown if the columns defined by δ- pcdh expression correspond to functional microcircuits. While our results suggest the 47 existence of a molecular code in which differential expression of δ-pcdhs could partition the optic tectum into columnar modules with distinct identities, further work is required to determine whether this expression is mutually exclusive (one δ-pcdh per column) or combinatorial. In addition, we show that pcdh19+ columns derive from the proliferation of neural progenitors expressing pcdh19. Thus, continued expression of a δ-pcdh could provide continuity between early patterning and differentiation with the final stages of synaptogenesis and circuit assembly. Further investigation is required to dissect the involvement of δ-pcdhs at different stages of column and neuronal development, as pcdh19 mutants exhibit defects in a range of processes that include cell proliferation, fasciculation of primary processes and neurite arborization. Loss of pcdh19 impairs visually-guided behaviors, revealing specific functional defects. It will be instructive to determine whether other δ-pcdhs exhibit comparable defects, and how this family of molecules collaborates to guide both circuit assembly and the development of neural function.
Materials and Methods
Fish maintenance
Adult zebrafish (Danio rerio) and embryos of the Tübingen longfin and AB strains were maintained at ~28.5C and staged according to Westerfield (1995). Embryos were raised in E3 embryo medium (Monte. Westerfield, 1995) with 0.003% phenylthiourea
(Sigma-Aldrich) to inhibit pigment formation.
48
Whole mount in situ hybridization
Riboprobes directed against -protocadherins were amplified by PCR, as described previously (Biswas et al., 2014; Biswas & Jontes, 2009; Emond et al., 2009). A
T7 RNA Polymerase binding site was included in each of the reverse primers, and these
PCR products were used as templates for in vitro transcription (Promega). Antisense riboprobes were labeled with digoxygenin-dUTP (Roche). Whole mount in situ hybridizations were carried out using standard methods (Monte. Westerfield, 1995).
Briefly, embryos were fixed at 4C overnight in 4% paraformaldehyde in PBS, dehydrated in a methanol series and stored in 100% methanol overnight at -20C. They were rehydrated in decreasing concentrations of methanol and embryos 24 hpf and older were permeabilized using Proteinase K (10µg/ml, Roche). Embryos were refixed in
4% paraformaldehyde prior to hybridization. Digoxygenin-dUTP-labeled riboprobe was added to the hybridization buffer at a final concentration of 200 ng/ml and hybridization was carried out at 65C overnight. Alkaline phosphatase-conjugated anti-digoxygenin
Fab fragments (Roche) were used at 1:5000 dilution. NBT/BCIP (Roche) was used for the coloration reaction. Labeled embryos were equilibrated in 30% sucrose in PBS overnight. They were then embedded in OCT (Ted Pella), sectioned on a cryostat at 14
m, and placed on gelatin-coated glass slides. Images were captured on a Zeiss AxioStar.
For double fluorescent in situ hybridization, 3 and 4 dpf fish were fixed and hybridized with riboprobes against pcdh7a (labeled with digoxygenin-dUTP) and pcdh19
49 (labeled with fluorescein-dUTP). The digoxygenin-labeled probe was detected using anti-digoxygenin Fab-POD (Roche), and developed using the tetramethylrhodamine substrate from the TSA Plus kit (Perkin-Elmer). Subsequently, the fluorescein probe was detected with an anti-fluorescein primary antibody (Roche) and a goat anti-mouse-HRP secondary antibody (Invitrogen), and developed using the fluorescein substrate from the TSA Plus kit.
The PCR primers used to generate DNA template for riboprobe synthesis are as follows:
pcdh19-F: 5'-ATGCATTCCAAGGACATGGATTTCG-3' pcdh19-T7R: 5'-GTAATACGACTCACTATAGGGCGAGACTGGTCCGATTTGTTCCTGTGC-3' pcdh10b-F: 5'-ATGTTTGTGTTTTTGCTCCTGCTG-3' pcdh10b-T7R: 5'-GTAATACGACTCACTATAGGGCGAACGCGTCTTTGGCCTTGGCCGTGC-3' pcdh9-F: 5'-GCAACATTAGTTGCTTGTTTCTGG-3' pcdh9-T7R: 5'-CGTAATACGACTCACTATAGGGCGCATCACAGTACCGTTGGTTGG-3' pcdh7a-F: 5'-ATGGCAGAAAACGCCCCACCTGGC-3' pcdh7a-T7R: 5'-CGTAATACGACTCACTATAGGGCGGTCCCGAACGAGGATTCGTCC-3' her4.1-F: 5'-ATGACTCCTACAATCACTGG-3' her4.1-T7R: 5'-GTAATACGACTCACTATAGGGCGAATTAAGTCTACCAGGGTCTCC-3'
Cryosectioning and immunocytochemistry
Zebrafish larvae were fixed for 1 hour in 4% paraformaldehyde in PBS, then equilibrated in 30% sucrose in PBS overnight. They were then embedded in OCT (Ted
50 Pella, Inc., Redding, CA, USA), sectioned on a cryostat at 16-20 m, and placed on gelatin-coated glass slides. Sections were permeabilized and blocked in PBS, 0.5% Triton
X-100, 1% DMSO, and 10% normal goat serum. For immunocytochemistry sections were labeled with chicken anti-GFP (1:1000; Abcam), rabbit anti-glutamine synthase (1:100;
Genetex) and rabbit anti-phosphohistone H3 (1:200; Cell Signaling). Rhodamine- and fluorescein-conjugated secondary antibodies were used at 1:500 (Jackson
ImmunoResearch). Images were obtained using a Leica TCS-SL confocal microscope
(Leica Microsystsms) and either a Leica 20x/NA0.7 HC Plan Apo multi-immersion
(phosphohistone-H3 or EdU) or a 40x HCX Plan Apo oil NA0.75-1.25 (glutamine synthase).
To label larvae with EdU, 1 nL of 25 g/mL EdU (Life Technologies) was injected into the yolk of wild type and mutant embryos at 2 dpf. All fish were then fixed at 4 dpf with 4% paraformaldehyde at 4C overnight. Embryos were transferred into 30% sucrose in PBS at room temperature for 3 hours, then mounted in OCT and frozen on dry ice. Fish were sectioned on a cryostat at a thickness of 25 m. Staining was performed using the Click-IT EdU Alexa Flour 555 Imaging kit (Life Technologies) according to the manufacturer's protocol.
BAC recombineering and transgenesis
The BAC clone CH211-156N5 was obtained from BACPAC Resources, Children's
Hospital Oakland, (http://bacpac.chori.org). CH211-156N5 includes 21kb upstream of
51 the start codon and 15kb downstream of the stop codon. Purified BAC DNA was introduced into EL250 cells (E. C. Lee et al., 2001) obtained from N. Copeland, NIH, http://ncifrederick.cancer.gov). To facilitate transgenesis, we first introduced an inverted Tol2 cassette (iTol2) into the backbone (Suster, Abe, Schouw, & Kawakami,
2011). We then inserted a Gal4-VP16-FRT-Kanamycin-FRT cassette into exon 1 of the pcdh19 gene. The kanamycin marker was excised by arabinose induction of Flpe recombinase. Finally, a 5xUAS:Lifeact-GFP cassette was introduced into exon 2, which is
~45kb downstream of exon 1. This same procedure was carried out for BAC clones harboring genes for pcdh1a (DKEY-225G6; www.sourcebioscience.com) and pcdh18b
(CH211-154P8; https://bacpac.chori.org). The CHORI-211 library (CH211) was built in the pTARBAC2.1 vector, while the DanioKey library (DKEY) was built in the pIndigoBac-536 vector. Each of the BAC clones contained a complete protocadherin gene.
To generate germline BAC transgenic zebrafish, we co-injected 1-cell stage embryos with 1 nL of 100 ng/µL purified BAC DNA and 100 ng/µL mRNA encoding the
Tol2 transposase. At 2 dpf, embryos were screened for Lifeact-GFP expression and fluorescent embryos were grown to adulthood. To establish stable lines, founders were outcrossed with wild type zebrafish and fluorescent embryos were pooled and grown to adulthood. For transient expression, injections were performed as described, but embryos were kept in 0.01% PTU and imaged at 3-4 dpf.
52 TALEN construction and production of germline lesions
We used the online tool ZiFit (Sander et al., 2010) (https://zifit.partners.org) to search for a TALEN target site in exon 1 of zebrafish pcdh19. We identified an appropriate target site downstream of the signal peptide,
TTTCGTACAAATGTTTGtgtgctttctcttgTGCTGGACTGGAGTCGA (uppercase indicates TAL left and right binding sites). The TALEN arrays (left: NG-NG-HD-NN-NG-NI-HD-NI-NI-NI-
NG-NN-NG-NG-NG-NN and right: HD-NN-NI-HD-NG-HD-NI-NN-NG-HD-HD-NI-NN-HD-NI) were assembled in RCIscript-GoldyTALEN (Bedell et al., 2012) using the TAL Effector Kit
1.0 (Cermak et al., 2011) obtained from Addgene (www.addgene.org). Plasmid encoding assembled TALENs was linearized with SacI, and used as template for mRNA synthesis with a T3 mMessage Machine kit (Ambion). To generate germline lesions in zebrafish pcdh19, we injected 1 cell stage embryos with 50 pg mRNA encoding the left and right nucleases. Injected embryos were grown to adulthood and screened for germline lesions. For screening, adult F0 fish were outcrossed with wild types, and genomic DNA was prepared from eight embryos of each cross. High resolution melt analysis (HRMA) was used to identify putative founders (Dahlem et al., 2012). PCR products exhibiting aberrant melting curves were cloned and sequenced. F0 adults exhibiting frameshift mutations were outcrossed and the F1 embryos were grown to adulthood. To screen the adult F1 fish, genomic DNA was prepared from caudal fin clips screened by HRMA.
We obtained three mutants: 1bp deletion (-1), 10bp deletion (-10), and 13bp deletion
(-13). These heterozygote F1 founders were outcrossed again and the F2 offspring
53 were raised and screened to establish mutant lines, pcdh19os50, pcdh19os51 and pcdh19os52. To obtain homozygous pcdh19 mutants, which are viable and fertile, heterozygotes for each allele were incrossed and embryos were grown to adulthood and screened by HRMA.
To establish mutant/transgenic lines, each of the three homozygous mutant lines was crossed with TgBAC(pcdh19:Gal4VP16; UAS:Lifeact). Fluorescent embryos were selected and grown to adulthood. These transgenic-pcdh19+/- fish were incrossed and the offspring were raised to adulthood and screened for homozygous mutants.
Western blotting
Protein lysates were prepared by homogenizing 40 deyolked embryos at 3 dpf in lysis buffer (20 mM Tris, pH 7.5, 150 mM NaCl, 0.5% Triton X-100, 1 mM PMSF, and
Complete protease inhibitor cocktail [Roche]). Lysates were microcentrifuged at 4°C for
10 min and identical volumes were loaded onto NuPAGE 10% Bis-Tris SDS-PAGE gels
(Life Technologies) for each condition. Proteins were subjected to electrophoresis, and then transferred (Bio-Rad Laboratories) to PVDF (GE Healthcare), blocked with 5% nonfat milk in TBST (10 mM Tris-HCL pH 7.6, 100 mM NaCl, 0.1% Tween-20), and incubated overnight with primary antibody (1:1,000 anti-Pcdh19, custom polyclonal made by Covance; 1:5,000 mouse monoclonal anti--actin, Santa Cruz Biotechnology).
HRP-conjugated secondary antibodies (Jackson ImmunoResearch Laboratories, Inc.) were used at 1:5,000, and the chemiluminescent signal was amplified using Western
54 Lightning Ultra (PerkinElmer). Blots were imaged on a molecular imaging system
(Omega 12iC; UltraLum, Inc.). Custom polyclonal antibodies against zebrafish Pcdh19 were generated in rabbit, directed against the Pcdh19 intracellular domain (amino acids
702-1083).
Two-photon imaging
Two-photon imaging of live embryos and larvae was performed at room temperature on a custom-built microscope controlled by ScanImage (Pologruto,
Sabatini, & Svoboda, 2003). Excitation was provided by a Chameleon-XR Ti:Sapphire laser (Coherent, Inc.) tuned to 890nm. Fluorescence was detected using a Multiphoton
Detection Unit mounted on a SliceScope (Scientifica). We used water immersion objectives from Olympus, either 60x/NA1.0 (LUMPLFLN60X/W) or 20x/NA1.0
(XLUMPLFLN20XW). For imaging larvae were embedded in 1% low melting-point agarose, covered with embryo medium (5 mM NaCl, 0.17 mM KCl, 0.33 mM CaCl2, 0.33 mM MgCl2) and imaged at room temperature.
For the imaging of transgenic/mutant larvae, TgBAC/pcdh19+/- fish were crossed and embryos were kept in individual wells of a 24-well plate. After imaging, fish were genotyped by HRMA to identify homozygous mutants. As homozygous mutants are viable and fertile, some of the experiments were performed on incrossed
TgBAC/pcdh19-/- adults.
55 Image analysis
All image analysis was performed in Fiji (Schindelin et al., 2012). For cell identification and modeling, the TrakEM2 (Cardona et al., 2012) plugin in Fiji was used.
Image stacks of ~100 optical sections were collected from the transgenically labeled tecta of wild type or pcdh19-/- larvae. Each detected cell body was modeled as a sphere and primary projections were traced from cell bodies to the synaptic neuropil when possible. Multipanel images were assembled in Adobe Photoshop (Adobe), and figures were made in Adobe Illustrator (Adobe).
Cell transplantation
Transplantations were performed as described previously (Biswas et al., 2014).
Host and donor embryos were dechorionated with pronase, then arranged in an agar injection tray. At 3-3.5 hpf, 20-40 cells from transgenic donor embryos (either wild type or pcdh19-/-) were transplanted into unlabeled host embryos (either wild type or pcdh19-/-). Embryos were maintained in embryo medium supplemented with penicillin/streptomycin. At 24 hpf, embryos were screened for health, normal morphology and fluorescence. At 3-4 dpf, larvae exhibiting fluorescence in the brain were imaged on a two-photon microscope as described above.
Visual behavior analysis
Behavioral experiments were performed at 6 dpf and analyzed with the FLOTE 56 software package as previously described (Burgess & Granato, 2007; Burgess et al.,
2010). Video was captured at 1000 frames per second with an IDT MotionPro Y4 camera. 20 larvae of identical genotype were grouped in a 6 cm wide Petri dish with 9 mL of E3 embryo media and pre-adapted to the uniform light intensity for 3 hours prior to testing. 3 dishes of each genotype were tested for positive phototaxis and a response to a sudden removal of pre-adapted light (termed a “dark flash”). The phototaxis assay was performed as described previously to elicit positive phototaxis (Burgess et al.,
2010). Larvae were given 30 seconds to reach the target light and only larvae initially positioned on the opposite side of the dish from the target light were included in our analyses. To determine directionality of turns and swims (Figure 2.7C,D), the 30 seconds of video was partitioned into 30 one-second events. For each event, larvae oriented within 30 degrees of the target light were considered “facing” the target and used for swim direction analyses (Figure 2.7C). Larvae oriented between 75-104 degrees away from the target light were used for turn direction analyses (Figure 2.7D). The visual dark flash assay was performed and analyzed as previously described (Burgess & Granato,
2007). Briefly, larvae are adapted to uniform light, then exposed to 10 1s periods of darkness separated by 30s of light. Larvae are expected to perform an O-bend, which has stereotyped kinematic parameters.
57 Figure 2.1. δ-pcdhs define neuronal columns in the zebrafish optic tectum. (A) A schematic of the optic tectum of a larval zebrafish. Neurons are organized around a synaptic neuropil that includes both the axons and dendrites of tectal neurons, as well as the axonal arbors of retinal ganglion cells. Abbreviations: Cb, cerebellum; Hb, hindbrain, OT, optic tectum; PML, peripheral midbrain layer; syn, synaptic neuropil; V, ventricle.(B) A horizontal section through the optic tectum of a 4 dpf larva that was labeled with a riboprobe against pcdh19. Labeling for pcdh19 is concentrated into radial stripes (arrows). The posterior boundary of the tectum is shown by red outlines. Scale bar = 50 μm (B-D). (C,D) Horizontal sections of optic tecta labeled with riboprobes against pcdh9 (C) and pcdh10b (D) showing radial stripes comparable to those observed for pcdh19. (E) A single optical section from a 2-photon image stack of a 30 hpf BAC transgenic embryo expressing the F-actin marker, Lifeact-GFP, under the control of pcdh19 regulatory elements. The midbrain neuroepithelium expresses Lifeact-GFP in distinct stripes (arrows). Scale bar = 50 μm. (F) A maximum intensity projection of 5 optical sections (1 μm spacing) of a 4 dpf BAC transgenic larva. Lifeact-GFP is expressed in discrete columns of neurons, as was observed by in situ hybridization for endogenous pcdh19. (G) A maximum intensity projection of 5 optical sections (1 μm spacing) of a 3 dpf BAC transgenic larva. Labeled neurons are clustered around a central radial glia (magenta arrow) and most of the primary neurites fasciculate as they project to the synaptic neuropil (blue arrow). Va, vasculature; PML, posterior midbrain layer. (H) A single optical section through a column in a 3 dpf larva. Columns of pcdh19+ neurons are typically associated with one or more pcdh19+ radial glia (magenta arrows). Fasciculation of neuronal processes is highlighted by blue arrows. Neurons arborize in the area immediately adjacent to the column. Scale bar = 20 μm for F,G,H. (I-L) Horizontal sections through the optic tectum of a 4 dpf BAC transgenic larva, labeled with antibodies against Glutamine synthase (Glul) to reveal radial glia (I, K) or GFP (J). Boxed area in (I) is highlighted in (J-L). (L) Glul staining reveals that a subset of radial glia are also pcdh19+ (arrow). Scale bars = 30 m (I), 15 m (J-L). (M-O) A single optical section through the dorsal optic tectum of a 3 dpf larva labeled by double fluorescent in situ hybridization with riboprobes against pcdh19 (M) or the neural progenitor marker her4.1 (N). White lines show the posterior boundary of the tectum. An overlay of the signals reveals co-localization along the medial and posterior margins of the tectum (O). Scale bar = 50 m. 58 Figure 2.2. Pcdh19+ neuronal columns are clonal. (A) Schematic outlining our approach to mosaically label zebrafish larva by using blastula stage cell transplantation. Cells were transplanted from BAC transgenic donor embryos into unlabeled wild type host embryos. (B) A 2-photon image stack of a 4 dpf host embryo with a single pcdh19+ column present in the bottom hemi-tectum. (C) A higher magnification image of the labeled cells shown in B. Labeled neurons are organized as a column and their neurites arborize within an adjacent, restricted region. (D) Schematic outlining approach to mosaically label zebrafish larva by injecting a recombinant BAC. BAC DNA is injected at the 1-cell stage along with mRNA for the Tol2 transposase. (E) A 2-photon image stack of a 4 dpf larva that had been injected with recombinant pcdh19 BAC DNA. The only labeled cells in the bottom hemi-tectum are present in a column reminiscent of those found in the BAC transgenic larvae. (F) A higher magnification view of the column shown in E. (G-I) Image sequence from a BAC transgenic zebrafish collected on consecutive days. (G) Single optical section collected through the dorsal optic tectum of a 2 dpf embryo, showing one or two strongly labeled neuroepithelial cells. Yellow lines define the boundaries of of the neuroepithelium. NE, neuroepithelial cell; Ven, ventricle. At 3 dpf (H) and 4 dpf (I), columns of neurons are visible at the same position within the tectum. Yellow lines mark the ventricular surface of the tectum. Scale bar = 80 m (B,E), 40 µm (C,F,G-I).
59 Figure 2.3. Partitioning of the optic tectum by δ-pcdh expression. (A,B) Injection of recombinant BAC clones for other δ-pcdhs, such as pcdh18b (A) and pcdh1a (B) also labels columns, suggesting that these protocadherins also define neuronal columns that are derived from δ-pcdh-specific progenitor cells. Scale bar = 20 m. (C) A model of organization of the zebrafish optic tectum. Each color represents the expression of a distinct δ-pcdh. (D-I) Double fluorescent in situ hybridization with riboprobes against pcdh7a (D,G) and pcdh19 (E,H). Examples are from two, different embryos. Columnar stripes of expression are apparent for both probes (arrows). Overlays (F,I) show that the expression of pcdh7a and pcdh19 are largely non-overlapping. Scale bar = 50 m.
60 Figure 2.4. Loss of pcdh19 disrupts the columnar organization of the optic tectum. (A) Germline lesioning of the pcdh19 gene using TALENs. Exon 1 encodes the entire extracellular domain of Pcdh19, as well as the transmembrane domain and a short segment of the intracellular domain. We designed a TALEN pair against a target site just downstream of the signal peptide encoding sequence within exon 1. We isolated mutants with germline frameshift indel mutations that result in premature stop codons early within EC1. (B) Western blotting with a polyclonal antibody directed against the Pcdh19 intracellular domain confirms the loss of Pcdh19 in the mutants. (C-E) Individual clusters of neurons were labeled by BAC DNA injection in wild type (C) or pcdh19-/- (D) larvae at 4 dpf. Distinct columns were observed in 58% (n=21/36) of wild type larvae with expression in the tectum, while columns were observed in only 31% (n=10/32) of pcdh19-/- larvae (E). (P=0.028, Fisher’s exact test.) (F-H) The pcdh19 mutants were crossed with the BAC transgenics. The transgenic:pcdh19-/- mutants exhibited a loss of columnar organization (41%, n=16/38) compared to transgenic:pcdh19+/+ larvae (82%, n=39/47, P=0.0001, Fisher's exact test). Scale bar = 50 m.
61 Figure 2.5. Cell autonomous and non-cell autonomous requirement for Pcdh19. (A-C) Blastula stage cell transplantation experiments were performed in which donor cells (20-40) were taken from TgBAC(pcdh19:Gal4-VP16; UAS: Lifeact-GFP) embryos and introduced into unlabeled wild type hosts (A). (B) A maximum intensity projection (5 optical sections) of an optic tectum of a 4 dpf host larva, exhibiting extensive labeling of radial glia and columns of labeled neurons. (C) A maximum intensity projection (10 optical sections) of an optic tectum of a 4 dpf host larva showing a labeled column of neurons and their adjacent arborization field. Scale bar = 75 m (B,E,H), 20 m (C,F,I). (D-F) Blastula stage cell transplantation experiments were performed in which donor cells (20-40) were taken from TgBAC(pcdh19:Gal4-VP16; UAS: Lifeact-GFP) embryos and introduced into unlabeled pcdh19-/- hosts (D). (E) A maximum intensity projection (5 optical sections) of an optic tectum of a 4 dpf pcdh19-/- host larva. Each block of labeled cells is larger and more disorganized. (F) A maximum intensity projection (10 optical sections) of an optic tectum of a 4 dpf pcdh19-/- host larva. Transplanted cells exhibit aberrant patterns of arborization, with processes tending to clump, as well as extend out of the synaptic neuropil (yellow arrows). (G-I) Blastula stage cell transplantation experiments were performed in which donor cells (20-40) were taken from mutant pcdh19-/-; TgBAC(pcdh19:Gal4-VP16; UAS: Lifeact-GFP) embryos and introduced into unlabeled wild type hosts (G). (H) A maximum intensity projection (5 optical sections) of an optic tectum of a 4 dpf pcdh19-/- host larva. Each block of labeled cells is larger and more disorganized. (I) A maximum intensity projection (10 optical sections) of an optic tectum of a 4 dpf wild type host larva. In addition to an increased number of labeled cells occupying a larger volume, transplanted cells exhibit exuberant arborization.
62 Figure 2.6. Increased proliferation in the optic tectum of pcdh19-/- mutants. (A-C) 2-photon image stacks were collected in wild type (A) or pcdh19-/- larvae (B). The 3D positions of transgenically labeled cell bodies were modeled as spheres. (C) The number of labeled cells was counted, confirming the visual impression of increased numbers of labeled cells in the pcdh19-/- mutants. (wild type: 181 ± 29, n=6; pcdh19-/-: 328 ± 56, n=5; P=0.036, Student's t-test). Scale bar = 20 m (A), 25 m (B). (D-F) To determine whether rates of cell proliferation in the tectum are changed in the mutants, we performed phospho-Histone H3 (pH3) immuocytochemistry at 2 dpf in both wild type (D) and pcdh19-/- larvae (E). (F) The number of pH3 labeled cells in the tectum was counted, revealing a significant increase in proliferation in the pcdh19-/- mutants. (wild type: 9.3 ± 2.4, n=3; pcdh19-/-: 20.3 ± 3.5, n=4; P=0.04, Student's t-test) (G-I) To confirm our observations with pH3 labeling, we labeled wild type (G) or pcdh19-/- larvae (H) with EdU at 2 dpf and fixed the larvae at 4 dpf (I) The number of EdU labeled cells in the tectum were counted, confirming a significant increase in proliferation in the pcdh19-/- mutants. (wild type: 63.8 ± 7.6, n=4; pcdh19-/-: 84.5 ± 9.8, n=4; P=0.032, Student's t-test) Scale bar = 50 m.
63 Figure 2.7. pcdh19-/- mutants exhibit impaired visually-guided behaviors. (A) Mean percentage of larvae that reach target light within 30 seconds during phototaxis. (B) Mean time to reach target area by larvae showing phototaxis. (C-D) Insets represent larvae’s orientation to target light (insets) at each second prior to reaching the target. Mean percentage of swims (C) and turns (D) biased towards target. N shown at bottom of bars indicates larvae (A, B) or # of events based on orientation (C,D). (E) Mean initiation of O-bend response to dark flash stimulus. N= 3 groups of 15 larvae/group. (F-H) Mean turning angle (F), duration (G), and distance moved (H) per O-bend maneuver. N shown at bottom of bars indicates # of O-bend maneuvers per genotype. Error bars denote SEM. *P<0.001 ANOVA vs. WT.
Figure 2.8. pcdh19-/- mutants show normal motor behavior in phototaxis assay. (A,B) Mean swim half-cycles (tail undulations, [A] and distance moved [B] per swim bout). (C,D) Mean head turning angle (C) and distance moved (D) per turning maneuver. N shown at bottom of bars indicates # of swimming and turning bouts. Error bars denote SEM.
64 Chapter 3: Structural Determinants of Adhesion by Protocadherin-19 and Implications
for its Role in Epilepsy[1]
Abstract
Non-clustered -protocadherins are homophilic cell adhesion molecules essential for the development of the vertebrate nervous system, as several are closely linked to neurodevelopmental disorders. Mutations in protocadherin-19 (PCDH19) result in a female-limited, infant-onset form of epilepsy (PCDH19-FE). Over 100 mutations in
PCDH19 have been identified in patients with PCDH19-FE, about half of which are missense mutations in the adhesive extracellular domain. Neither the mechanism of homophilic adhesion by PCDH19, nor the biochemical effects of missense mutations are understood. Here we present a crystallographic structure of the minimal adhesive fragment of the zebrafish Pcdh19 extracellular domain. This structure reveals the adhesive interface for Pcdh19, which is broadly relevant to both non-clustered and clustered protocadherin subfamilies. In addition, we show that several PCDH19-FE missense mutations localize to the adhesive interface and abolish Pcdh19 adhesion in in vitro assays, thus revealing the biochemical basis of their pathogenic effects during brain development.
______[1]This chapter was previously published in eLife 2016;5:e18529. The author performed all experiments in this chapter with guidance from Dr. James Jontes and Dr. Marcos Sotomayor. 65 Introduction
Nervous system function is critically dependent on the underlying neural architecture, including patterns of neuronal connectivity. Cell-cell recognition by cell surface receptors is central to establishing these functional neural circuits during development (Kiecker & Lumsden, 2005; Steinberg, 2007; Zipursky & Sanes, 2010). The cadherin superfamily is a large and diverse family of homophilic cell adhesion molecules that are strongly expressed in the developing nervous system (Hirano and Takeichi
2012; Suzuki 1996; Frank and Kemler 2002; Shapiro, Love, and Colman 2007; Gumbiner
2005; Chen and Maniatis 2013). The differential expression of classical cadherins and protocadherins, the largest groups within the cadherin superfamily, suggests that they play important roles in the development of neural circuitry (Hirano & Takeichi, 2012;
Weiner & Jontes, 2013), an idea supported by their involvement in a range of neurodevelopmental disorders (Redies, Hertel, and Hübner 2012; Hirabayashi and Yagi
2014). In particular, the non-clustered -protocadherins have been linked to autism spectrum disorders, intellectual disability, congenital microcephaly and epilepsy.
Protocadherin-19 (PCDH19) is a member of the non-clustered 2-protocadherin subfamily (Emond et al., 2009; Gaitan & Bouchard, 2006; Liu et al., 2010; Vanhalst et al.,
2005; Wolverton & Lalande, 2001) that is located on the X-chromosome. Mutations in
PCDH19 cause an X-linked, female-limited form of infant-onset epilepsy (PCDH19
Female Epilepsy, PCDH19-FE; OMIM 300088) that is associated with intellectual disability, as well as compulsive or aggressive behavior and autistic features (Dibbens et
66 al. 2008; Scheffer et al. 2008; Depienne and LeGuern 2012; van Harssel et al. 2013;
Leonardi et al. 2014; Thiffault et al. 2016; Terracciano et al. 2016; Walters, Wells-
Kilpatrick, and Pandeleos 2014). To date, well over 100 distinct mutations in PCDH19 have been identified in epilepsy patients, making it the second most clinically relevant gene in epilepsy. Approximately half of these mutations are missense mutations distributed throughout the extracellular domain of the PCDH19 protein. Despite the clear importance of PCDH19 and other non-clustered -protocadherins to neural development, their specific roles are only beginning to be revealed. For example, Pcdh7,
Pcdh17 and Pcdh18b are involved in axon outgrowth or arborization (Biswas et al.,
2014; Hayashi et al., 2014; Piper et al., 2008), while several -protocadherins, including
Pcdh19, regulate cell motility during early development (Aamar & Dawid, 2008; Biswas,
Emond, & Jontes, 2010; Emond et al., 2009; Yamamoto et al., 1998). In zebrafish, pcdh19, regulates the formation of neuronal columns in the optic tectum, and loss of pcdh19 degrades visually-guided behaviors (Cooper et al., 2015). However, it is not known how mutations in PCDH19 lead to PCDH19-FE.
Cadherins typically mediate adhesion using their extracellular domains, which are made of two or more consecutive extracellular cadherin (EC) repeats (Brasch,
Harrison, Honig, & Shapiro, 2012; Takeichi, 1990) . The adhesion mechanism used by classical cadherins is well known and involves a tip-to-tip interaction that is stabilized by the reciprocal exchange of tryptophan residues at the N-terminal EC1 repeat most distant from the membrane (Overduin et al. 1995; Shapiro et al. 1995; Nagar et al. 1996;
Boggon et al. 2002; Patel et al. 2006; Zhang et al. 2009; Sivasankar et al. 2009; Harrison 67 et al. 2010; Ciatto et al. 2010; Leckband and Sivasankar 2012). However, PCDH19 along with the rest of the non-classical cadherins lack these critical tryptophan residues and must mediate adhesion by an alternative mechanism (Biswas et al., 2010; Emond et al.,
2011; Marcos Sotomayor et al., 2014). In the case of the non-classical protocadherin-15 and cadherin-23 proteins, an adhesive interface is formed by overlapping, antiparallel interactions of their EC1 and EC2 tips (Elledge et al., 2010; Geng et al., 2013; Marcos
Sotomayor, Weihofen, Gaudet, & Corey, 2010; Marcos Sotomayor et al., 2012). For clustered protocadherins, recent binding assays and structures suggest that adhesion is mediated by an antiparallel interaction of fully overlapping EC1 to EC4 domains
(Goodman, Rubinstein, Thu, and Bahna, et al., 2016; Nicoludis et al., 2015; Rubinstein et al., 2015). Yet how non-clustered - protocadherins and PCDH19 form adhesive bonds and how these bonds are altered by disease-causing mutations is unknown.
Here we present crystals structures of the highly homologous zebrafish
Protocadherin-19 (Pcdh19) encompassing repeats EC1-4 and EC3-4. The structures allow us to map >70% of the disease-causing missense mutations and provide a structural framework to interpret their functional impact. In addition, the structures suggest two possible homophilic adhesive interfaces, and complementary binding assays validate one of them, which is affected by multiple PCDH19-FE mutations. This interface involves fully overlapping EC1 to EC4 domains and likely represents a general interaction mechanism for the non-clustered -protocadherins.
68 Results
To understand the mechanism of Pcdh19 function and to determine the structural role of PCDH19-FE mutations, the Danio rerio Pcdh19 EC1-4 and the EC3-4 fragments (70% identity, 83% similarity to Homo sapiens EC1-4) were produced in E. coli, refolded from inclusion bodies, and used for crystallization and structural determination (see Methods). The solved structure for Pcdh19 EC3-4 (2.51 Å, Table 3.1,
Figure 3.1A) includes four molecules in the asymmetric unit, each starting from Pro 213 and continuing to Asp 422 (numbering corresponds to the processed Danio rerio protein, see Methods). Root-mean-square-deviation (RMSD) among these four molecules is <2.4 Å. One of the Pcdh19 EC3-4 molecules was used to solve the Pcdh19
EC1-4 structure (3.59 Å, Table 3.1, Figure 3.1B), which contains two molecules in the asymmetric unit, each starting from Val 1 to Asp 422 (RMSD of 1.4 Å). The EC3-4 repeats from both structures superpose well (RMSD 2.1 Å), and good quality electron density maps allowed us to unambiguously position side chains for most residues (Methods and
Figure 3.1). Given the similarities among our structures and chains, we will describe features as seen in the more complete chain B of Pcdh19 EC1-4, unless otherwise explicitly stated.
The architecture of all Pcdh19 EC repeats matches that observed for other cadherins (Shapiro et al. 1995; Overduin et al. 1995), with the typical Greek-key motif comprised of seven strands (A-G) forming a sandwich fold (Figure 3.2A). The EC1 repeat has a disulfide bond at the E-F loop, typical of clustered protocadherins, as well
69 as one of two -helices (at the B-C loop) also found in structures of clustered protocadherins (Goodman, Rubinstein, Thu, and Bahna, et al., 2016; Morishita et al.,
2006; Nicoludis et al., 2015; Rubinstein et al., 2015) (Figure 3.2A,B). The three linker regions of Pcdh19 (EC1-2, EC2-3, EC3-4) have canonical cadherin calcium-binding sites
(Nagar et al., 1996) (Figure 3.2E-G). Overall, our structures show canonical features and provide a unique framework to analyze >70% of the PCDH19-FE mutations.
PCDH19-FE mutations analyzed in the context of the Pcdh19 EC1-4 structure
There are 51 PCDH19-FE mutations (out of 70) that can be mapped to 43 locations in the Pcdh19 EC1-4 structure (Figure 3.2B and Figure 3.3). These mutations can be classified in three groups. The first group (18 mutations at 14 locations) corresponds to residues whose side chains are pointing toward the hydrophobic core of an EC repeat (Figure 3.2B,C). The second group involves residues whose side chains are at the surface of the protein (10 mutations at 10 sites; Figure 3.2B,D). The last group includes residues at calcium-binding motifs, with 19 locations affected by 23 different mutations (Figure 3.2B,E-G). Mutations in each group are predicted to have different effects on the protein’s structure (Figure 3.4).
PCDH19-FE mutations altering residues in the first group may often cause protein misfolding or structural instability. For instance, mutations L81R and I115K
(corresponding to L58 and I92 in the crystal structure) would result in impossible conformations in which a positively charged residue side chain is pointing toward the
70 hydrophobic core of EC1 (Figure 3.2C). Thus, these mutants are unlikely to fold properly.
Mutation L25P (L4) will interfere with hydrogen bonding and secondary structure formation, while V72G (V50) is subtler, as it replaces a rather large hydrophobic residue with a different and smaller side chain that may only affect the packing of the EC1 hydrophobic core. The mutation A153T (A130) in EC2, in which a small hydrophobic residue is replaced by a larger hydrophilic threonine, may result in structural instability as well. A similar analysis can be done for all 18 mutations in this group (Figure 3.4).
Protein misfolding and structural instability caused by these mutations are likely to inhibit PCDH19 adhesive function, either directly, allosterically, or by altering the strength of cell-cell adhesion due to a reduced number of functional molecules on the cell surface.
The effect of ten PCDH19-FE mutations on residues with side chains at the protein surface (second group) is less clear. Two of them (S276P and L433P) may affect packing and folding, as these mutations to proline are predicted to prevent formation of hydrogen bonds important for strand formation and loop structure. Six of them are involved in putative homophilic interfaces, and their effect on binding is discussed below. The V191L mutation site is not directly involved in homophilic binding, but it is near residues that are, and may allosterically alter binding. Alternatively, this mutation may alter interactions with N-cadherin (Emond et al., 2011) or other PCDH19 molecular partners yet to be determined. The last mutation, D417H, is not involved in any known interface, but this epilepsy patient has a pair of mutations in PCDH19 (D417H and
71 D596Y). It is unclear whether both mutations contribute to the epileptic syndrome
(Appendix A) (Higurashi et al., 2015; Hoshina et al., 2015).
The third group of mutations involves residues that are at one of the canonical calcium-binding motifs between EC repeats (XEXBASE and DRE from the first EC repeat,
DXNDN from the linker, and DXD and XDXTOP from the second repeat). Two of these
PCDH19-FE mutations involve charge reversal for a calcium-coordinating residue (E31K at XEX & E307K at DYE), and may result in impaired folding and impaired calcium binding. Twelve PCDH19-FE mutations in this group replace a charged, calcium- coordinating residue by a neutral residue (D90V at DRE, D121N at DXNDN, D157N at
DXD, E199Q at DRE, D230N at DXNDN, E249G at XEX, D264H at DXD, D341G at DXNDN,
D375Y at DXD, D377N & D377H at DXD, and E414Q at DRE). Some of these mutations only affect charge, but not size of the side chain (D to N and E to Q), and may decrease affinity for calcium. Others involve more drastic side-chain size changes (D to Y or G) and will not only impair calcium binding, but might also induce protein instability. In addition, three mutations alter the size, but not the charge of a coordinating residue
(E249D at XEX, D341E at DXNDN, and D377E DXD), indicating that even subtle perturbations at the calcium-binding linkers might result in impaired function. Three more PCDH19-FE mutations involve substituting a coordinating asparagine residue by a serine (N232S & N340S at DXNDN, and N234S at DXNDN), with one of these mutations present in over twenty unrelated individuals (N340S). Similarly, the mutation NP342-
343KT at DXNDN involves a coordinating asparagine residue, but it is mutated to lysine and accompanied by a proline to threonine mutation. In addition, one mutation involves 72 the non-calcium binding residue of the DRE motif (R198L), which may disrupt calcium binding. The last PCDH19-FE mutation in this group involves duplication of three residues (SEA139-141dup at XEX), one of which is directly coordinating calcium. This duplication might change the architecture of the loop and alter calcium binding as well.
Overall, mutations at PCDH19 calcium-binding motifs are varied, with some predicted to have drastic effects on protein folding and calcium binding, and others predicted to have minor effect yet still causing protein malfunction.
There are 19 PCDH19-FE missense mutations not found within EC1-4 (Figure 3.3),
14 of which are at conserved calcium-binding motifs (N557K, D594H, D596G,H,V,Y) or at other structurally conserved sites for cadherin repeats (P451L, G486R, G513R, L543P,
P561R, G601D, V642M, L652P). Two mutations involve insertion or deletion of residues
(N449_H450insN and S489del), and will likely disrupt strand folding. However, the effect of the remaining three is unclear (R550P in strand G of EC5, P567L in strand A of EC6, and D618N likely at the end of strand D); perhaps they are involved in cis interactions with PCDH19 or other cadherins.
To gain insights into the molecular mechanism of the most common PCDH19-FE mutation, N340S (N317S, Appendix A), we introduced this mutation into the Pcdh19
EC3-4 construct and compared its thermal stability with the wild-type (WT) Pcdh19 fragment (Figure 3.2H). The Pcdh19 EC3-4 N317S fragment refolded well as assessed by size exclusion chromatography (SEC), but its melting temperature is considerably lower
(40.7 0.6 C vs. 52.4 0.3 C), even in the presence of 2 mM CaCl2. Another PCDH19-
FE mutation of a surface residue (E313K, equivalent to E290K) did not show a dramatic 73 shift in melting temperature (50.4 0.1 C). These SEC and thermal stability results indicate that the EC3-4 fragment carrying the N317S mutation is folded, and may bind calcium, yet it is not as stable as the wild-type fragment.
Antiparallel interfaces in crystal contacts of the Pcdh19 EC1-4 structure
Crystal structures have previously revealed the adhesive interfaces for classical cadherins, clustered protocadherins, and the protocadherin-15 and cadherin-23 complex (Boggon et al., 2002; Ciatto et al., 2010; Goodman, Rubinstein, Thu, and Bahna, et al., 2016; Nagar et al., 1996; Nicoludis et al., 2015; Patel et al., 2006; Sotomayor et al.,
2012). Although the Pcdh19 EC3-4 structure does not reveal any relevant interface, the
Pcdh19 EC1-4 structure does. The purified Pcdh19 EC1-4 fragment elutes in two well- defined peaks in size exclusion chromatography experiments (SEC), with these peaks most likely representing monomeric and dimeric states in solution (Figure 3.5). Pcdh19
EC1-4 crystals were grown from the putative dimer SEC peak elution, and two plausible adhesive interfaces are observed in our Pcdh19 EC1-4 structure. The first one, which we will refer to as Pcdh19-I1, arises from contacts between the two Pcdh19 EC1-4 molecules in the asymmetric unit, and involves a fully-overlapped antiparallel dimer in which EC1 from one molecule interacts with EC4 from the other (EC1:EC4), EC2 with EC3
(EC2:EC3), EC3 with EC2 (EC3:EC2), and EC4 with EC1 (EC4:EC1; Figure 3.6A,B). Within the same protein crystal structure, the second antiparallel interface (Pcdh19-I2) involves the opposite side of Pcdh19 with observed EC2:EC4, EC3:EC3, and EC4:EC2 interactions,
74 as well as potential (not observed) EC1:EC5 and EC5:EC1 contacts (Figure 3.7A). Several lines of evidence favor the first interface Pcdh19-I1 as the most likely to mediate biological function.
Analysis of the Pcdh19-I1 antiparallel interface with the Protein Interfaces,
Surfaces and Assemblies (PISA) server (Krissinel & Henrick, 2007) and with the NOXclass classifier (Zhu, Domingues, Sommer, & Lengauer, 2006) revealed a large interface
(~1650 Å2), that is unlikely to be a crystal packing artifact (89.21% biological, 81% obligate). In contrast, the possible antiparallel Pcdh19-I2 interface is predicted by
NOXclass to be non physiological, as its smaller interface area (~930 Å2) and the nature of its contacts matches those of crystal packing interactions (42.97% biological, 20.21% obligate). Yet, both interface areas are larger than 856 Å2, an empirical cut-off that can distinguish biological interfaces from crystal contacts with 85% accuracy (Ponstingl,
Henrick, & Thornton, 2000), and our analysis of the Pcdh19-I2 interface lacks contributions from possible EC1-EC5 contacts, which might be significant. Moreover, shape correlation (Lawrence & Colman, 1993) for Pcdh19-I1 is lower than for the
Pcdh19-I2 interface (Sc-I1 = 0.44 vs. Sc-I2 = 0.61), as there is a large gap between the main
EC2-EC3:EC3-EC2 contacts and the EC1-EC4:EC4-EC1 interactions zones (Figure 3.6A).
To further differentiate between the possible Pcdh19-I1 and Pcdh19-I2 interfaces, we evaluated whether any of the six PCDH19-FE mutations altering surface residues at crystal contacts, but not necessarily protein structure, could interfere with binding. Five of these mutations (S139L, T146R, P149S, E313K, and T404I; all at conserved sites) change residues involved in the Pcdh19-I1 interface (S116, T123, P126, 75 E290, T381 respectively in Figure 3.6B-E), where we define residues at a given interface as those with a buried surface area that is at least 20% of their accessible surface area according to PISA. In all cases we predict altered EC1-4 homophilic binding, as the size and nature of the residue is changed by each mutation (hydrophobic vs. hydrophilic; charged vs. non-charged). The remaining mutation (H203P) involves a non-conserved residue at the Pcdh19-I2 interface, which could impair its formation (R180 in Figure
3.7A). However, the patient with the H203P mutation also carries another PCDH19-FE mutation (F206C) at a location mutated in other epilepsy patients (Marini et al. 2012;
Depienne et al. 2011); thus it is unclear if H203P is contributing to epilepsy. In contrast, all five PCDH19-FE mutations at the Pcdh19-I1 interface are likely causal, which suggests that Pcdh19-I1 is relevant in vivo.
We also analyzed predicted glycosylation sites that might interfere with binding and thereby reveal non-physiological interfaces, as observed for VE-cadherin (Brasch et al., 2011). There are 14 glycosylation sites within EC1-4, and none of them involve residues at the Pcdh19-I1 interface (Figure 3.8A). An O-linked glycosylation site is predicted to be at the Pcdh19-I2 interface (T232), and an additional O-linked glycosylation site is predicted for the human PCDH19 protein at S204 (the equivalent
N202 in Pcdh19 is predicted to be non-glycosylated), also at the Pcdh19-I2 interface
(Figure 3.8B). Glycation sites, for which sugar molecules might be added randomly and to long-lived proteins, are predicted at both interfaces (K156 and K308 in Pcdh19-I1 and
K204 in Pcdh19-I2), but may not interfere directly with either, since glycation depends on environmental conditions and it has never been reported for cadherins (Salahuddin, 76 Rabbani, & Khan, 2014; Simm et al., 2015). Thus the lack of glycosylation sites at the
Pcdh19-I1 interface renders it as the most likely to be functional.
While not conclusive, all the analyses presented above favor the Pcdh19-I1 antiparallel dimer over the Pcdh19-I2 interface in terms of physiological relevance. The larger surface area of the Pcdh19-I1 dimer, the nature of the residues involved, the number of PCDH19-FE mutations at this interface, and the lack of predicted glycosylation sites, all suggest that the Pcdh19-I1 interface may occur and be functional in vivo.
Binding assays probing Pcdh19 interfaces
To conclusively test which binding interface mediates Pcdh19 adhesion, and whether PCDH19-FE mutations at the protein surface can interfere with one of the two possible Pcdh19 interfaces described above, we used modified bead aggregations assays, mutagenesis, and size exclusion chromatography experiments. Previous cell- based assays showed weak homophilic adhesion for the chicken Pcdh19 (Tai et al.,
2010). In addition, previous assays in which the full-length Pcdh19 extracellular cadherin domain fused to Fc (Pcdh19ECFc) was incubated with protein A beads showed calcium- dependent aggregation only when it was co-purified with N-cadherin (Biswas et al.,
2010; Emond et al., 2011). To study Pcdh19 homophilic interactions, we modified the previous protocol (Emond & Jontes, 2014) and added a final step in which beads were rocked (Sano et al., 1993) in a controlled fashion for up to two minutes (see Methods).
77 The modified protocol allowed us to identify clear bead aggregates mediated by
Pcdh19ECFc alone (Figure 3.9).
To identify the minimal adhesive unit of Pcdh19 we used our modified protocol with truncated versions of Pcdh19 containing different numbers of EC repeats:
Pcdh19ECFc (EC1-6), Pcdh19EC1-5Fc, Pcdh19EC1-4Fc, Pcdh19EC1-3Fc, Pcdh19EC1-2Fc, and Pcdh19EC2-6Fc (Figure 3.10). Bead aggregation was observed only when using
Pcdh19ECFc, Pcdh19EC1-5Fc, and Pcdh19EC1-4Fc, thus suggesting that Pcdh19EC1-4 is the minimal adhesive unit and highlighting the biological relevance of the antiparallel
Pcdh19-I1 interface, which involves EC1-4 only.
Next, we introduced two PCDH19-FE mutations (T146R and E313K located at the
Pcdh19-I1 interface, Figure 3.6B) in the full-length Pcdh19 extracellular domain and tested bead aggregation with these protein constructs (Figure 3.11). Bead aggregates were not detected when the Pcdh19ECFc carried these mutations under the conditions tested (Figure 3.11B-C,E-H). In contrast, the mutation R364E, predicted to impair the
Pcdh19-I2 interface, did not eliminate bead aggregation (Figure 3.7B-D). Moreover, the presence of a N-cadherin (Ncad) fragment known to enhance Pcdh19-mediated adhesion (Emond et al., 2011) did not qualitatively change the effect of the T146R and
E313K mutations. Bead aggregates were greatly diminished for T146R and abolished for
E313K in the presence of NcadEC W2A/R14E His, a non-adhesive Ncad mutant previously used to study Pcdh19-mediated homophilic adhesion (Emond et al., 2011;
Harrison et al., 2010) (Figure 3.12B-C,E-F). In addition, these mutations did not abolish the interaction between Pcdh19ECFc and NcadEC W2A/R14E His (Figure 3.13). It is 78 possible that the T146R and 313K mutations affect interactions with N-cadherin in a subtle way (directly or allosterically), yet our experimental results suggest that these mutations directly impair Pcdh19 homophilic adhesion.
We also introduced the T146R and E313K mutations at the Pcdh19-I1 interface into the bacterially expressed Pcdh19 EC1-4 protein fragment, and used analytical size exclusion chromatography to determine whether the mutant fragments were eluting as putative dimers or monomers in solution. Both mutations resulted in a shift of the elution peak that indicated a smaller, monomeric state (Figure 3.11I). Taken together, our crystallographic structure analyses and binding assays including PCDH19-FE mutations strongly support a model in which fully overlapped EC1-4 domains (Pcdh19-I1 interface) form the functional adhesive unit of Pcdh19 (Figure 3.11J).
Model for PCDH19 adhesive interaction and implications for other protocadherins
The antiparallel Pcdh19-I1 dimer interface validated above reveals a homophilic
“forearm handshake” binding mechanism for PCDH19, involving overlap of 4 ECs from each protomer wrapping around each other. This is different from the mechanism used by classical cadherins, only involving EC1 (Brasch et al., 2012) or the heterophilic
“extended handshake” used by protocadherin-15 and cadherin-23, involving overlap of only EC1-2 of each protein (Marcos Sotomayor et al., 2012). The forearm handshake is similar to the binding mechanism recently reported for clustered protocadherins
79 (Goodman, Rubinstein, Thu, and Bahna, et al., 2016; Nicoludis et al., 2015; Rubinstein et al., 2015) and might be used by other non-clustered protocadherins.
The Pcdh19-I1 interface involves extended and mostly symmetric, in-register contacts between repeats EC2: EC3 that account for ~58% of the interfacial area, as well as smaller, separate EC1:EC4 contacts (~350 Å2 2) that are slightly off-register. The
EC1:EC4 contacts arise as both repeats bend to meet after the C-terminal end of EC3 and the N-terminal end of EC2 separate from each other. In this arrangement, the EC2-3 linkers from each protomer are right next to each other, while the EC3-EC4 linker in one protomer is separated from the EC1-2 linker of the binding partner by a large opening.
The interface is generally amphiphilic, with ~49% of the interfacial area involving hydrophobic residues, ~28% hydrophilic, and ~23% charged residues (Figure 3.14).
Interestingly, the contact formed by EC1:EC4 is more hydrophobic (58%; 22%; 20%) than the one formed by EC2:EC3 (41%; 33%; 26%), yet salt-bridge pairs across protomers are present in both: R40-E328 and E81-R39 enhance the EC1 to EC4 contacts (Figure 3.6C) and R158-E290 links EC2 to EC3 (Figure 3.6D). While the R40-E328 pair seems to be zebrafish specific, the other two salt-bridges are highly conserved across sequenced species, along with most of the residues involved in the Pcdh19 EC1-4 interface (Figure
3.15A and Figure 3.16). The same set of residues is highly variable across different members of the 1, 2, and the clustered protocadherins (Figure 3.15B and Figure 3.17), suggesting that binding mechanisms might differ across subfamilies or that residue variability might confer specificity within a common binding mechanism.
80 A comparison of our Pcdh19-I1 interface to recently reported models and structures of clustered protocadherin interfaces (Goodman, Rubinstein, Thu, and Bahna, et al., 2016; Nicoludis et al., 2015) reveals multiple similarities among them. The most complete models of and -protocadherins show similar, fully overlapped antiparallel
EC1-4 dimers (Figure 3.18A-D), with the same extended EC2:EC3 antiparallel connection accompanied with smaller EC1:EC4 contacts and salt-bridges across protomers.
Structural alignments show that the relative arrangements of protomers within the antiparallel dimers for Pcdh19, Mm Pcdh4 (5DZW), and Mm Pcdh7 (5DZV) are the most similar to each other with slight shifting in some EC repeats (Figure 3.18A,B). The
Mm Pcdh6 (5DZX) and Mm Pcdh8 (5DZY) structures show similar dimeric interfaces, but the relative arrangement of protomers within the dimer is slightly shifted for all EC repeats (Figure 3.18C,D). Similarly, the Mm PcdhA1 EC1-3 interface (4ZI9) matches and aligns well with the Pcdh19 EC1-4 dimer (Figure 3.18E). Mapping of all interaction sites to the Pcdh19 EC1-4 topology diagram (Figure 3.15C) reveals a pattern for common interacting domains in odd and even EC repeats across these structures, which include the F-G hairpin and strand A for repeats EC1 and EC3, as well as the A-B and D-E hairpins for EC2 and EC4. While there are differences in some of the interacting domains, dimeric arrangements, and contact details, including diversity of interfacial residues, clustered protocadherins seem to use the same binding mechanism that
Pcdh19 uses to mediate adhesion.
81 A conserved RGD sequence motif within Pcdh19 EC2 (residues 158 to 160) at its
D-E loop is similar to an integrin-binding RGD site within EC1 (C-D loop) in the - protocadherins (Mutoh et al., 2004; Ruoslahti, 1996). The EC1 RGD motif is exposed in the Mm Pcdh4 and Mm Pcdh7 homo-dimers while the EC2 RGD motif of Pcdh19 (also present in Pcdh17 (Kim et al. 2011)) is buried at the EC2:EC3 contacts in the Pcdh19-I1 interface. This suggests that homophilic binding could regulate the availability of this potential, untested, integrin-binding site.
Pcdh19 belongs to the 2-protocadherin subfamily, and given the sequence similarity among subfamily members, it is likely that all use the same dimer interface to mediate adhesion. This is less obvious for the 1 subfamily, with members that have seven EC repeats and that display some critical differences at interaction sites, such as the presence of a positively charged residue (R or K) at position 290, where most 2 members have a negatively charged glutamate that interacts with an arginine at position 158 (Figure 3.6D, Figure 3.17, and Figure 3.19). The PCDH19-FE E313K mutation at this site (E290) prevents binding (Figure 3.11C,H-I and Figure 3.12), suggesting that
1-protocadherins, which effectively carry the same mutation, should use a different interface to mediate adhesion. Yet, residues at position 157 and 158 in 1- protocadherins are also charge swapped, with aspartates and glutamates that would restore this critical salt-bridge interaction at the EC2:EC3 interface, and at the same time prevent heterophilic interactions with 2-protocadherins (Figure 3.17, and Figure 3.19).
82 Thus, it is likely that all non-clustered -protocadherins use fully overlapped EC1-4 antiparallel interfaces, like the one observed for Pcdh19, to mediate adhesion.
Discussion and Conclusions
The non-clustered -protocadherins are increasingly linked with human neurodevelopmental disorders, emphasizing both their importance to brain development and their relevance to human health (Redies, Vanhalst, and van Roy 2005;
Redies, Hertel, and Hübner 2012; Hirabayashi and Yagi 2014). In particular, mutations in
PCDH19 cause a female-limited form of infant-onset epilepsy (Dibbens et al. 2008;
Scheffer et al. 2008; Depienne and LeGuern 2012; van Harssel et al. 2013; Leonardi et al.
2014; Thiffault et al. 2016; Terracciano et al. 2016). Therefore, it is imperative to understand the developmental roles of PCDH19 and other non-clustered - protocadherins, the structural basis of homophilic adhesion by these molecules, and the functional impact of pathogenic missense mutations. The structural and biochemical data presented here provide a first view on the molecular mechanism of Pcdh19 adhesion, which is likely used by all non-clustered and clustered protocadherins.
Moreover, our Pcdh19 EC1-4 structural model shows >70% of the missense mutations identified in PCDH19-FE patients, and reveals the biochemical basis for the deleterious effects for many of these mutations.
The Pcdh19 EC1-4 structure reveals an antiparallel dimer that is consistent with a trans adhesive interface, a conclusion supported by multiple lines of evidence. Notably,
83 several missense mutations identified in PCDH19-FE patients localize to this interface.
Two of these missense mutations (T146R and E313K) impair dimerization, as assessed by analytical gel filtration, and adhesion as assessed in bead aggregation assays, with and without N-cadherin. Sequence analysis suggests that the antiparallel adhesive mechanism presented here is broadly relevant to other, related -protocadherins.
Recent work with clustered protocadherins, implicated in self-avoidance and self/non- self recognition (Kostadinov & Sanes, 2015; Lefebvre et al., 2012; Yagi, 2012), have revealed a similar antiparallel adhesive interface for these clustered protocadherins
(Goodman, Rubinstein, Thu, and Bahna, et al., 2016; Nicoludis et al., 2015; Rubinstein et al., 2015). Thus, the Pcdh19-I1 adhesive interface observed in our Pcdh19 EC1-4 structure likely represents the mechanism used by both non-clustered -protocadherins and clustered protocadherins, which, together, represent the largest group within the cadherin superfamily.
Our structural data for Pcdh19, as well as recent work with the clustered protocadherins raises an interesting conundrum. The adhesive interface for protocadherins is extensive and involves interactions extending throughout EC1-4. This contrasts sharply with the adhesive interface of classical cadherins, which is restricted to
EC1 and involves the reciprocal swap of A-strands that is stabilized by burying Trp2 in a hydrophobic pocket (Brasch et al., 2012). However, the KD for dimerization of - and - protocadherins is in the micromolar range (similar to classical cadherins), bead aggregation and cell-based assays have consistently shown weak adhesion by both non- clustered and clustered protocadherins, and protocadherins are widely recognized as 84 being only weakly adhesive (Rubinstein et al., 2015; Sano et al., 1993; Schreiner &
Weiner, 2010; Thu et al., 2014). This disparity suggests that other mechanisms could modulate protocadherin adhesion in vivo. For instance cis-oligomerization could compete with trans adhesive interactions, or interactions with other proteins, including
N-cadherin, could sequester protocadherins or mask their adhesive interface. Further studies will be required to better understand protocadherin adhesion, how it may be altered in the presence of N-cadherin, and how it is regulated in vivo.
In addition to mutations that disrupt adhesion, our data reveal the potential effects of two other classes of mutations. In the first class, many mutations are predicted to directly impair folding and stability, which could lead to reduced levels of protein on the surface, due to impaired trafficking or enhanced protein degradation. In the second, PCDH19-FE mutations affecting calcium-binding sites are likely to cause shifts in calcium affinity as well as protein instability. Similar mutations in cadherin-23 and protocadherin-15 have been shown to decrease protein affinity for calcium, with KD shifts that are relevant in the context of the low calcium concentration to which these proteins are exposed (Marcos Sotomayor et al., 2010). Yet PCDH19 is expected to be in interstitial space with high calcium concentration, so it is more likely that the relevant effect of PCDH19-FE mutations at calcium-binding sites is compromised stability (even at saturating calcium concentrations), as shown here for the N340S mutation. Finally, analysis of one PCDH19-FE mutation within EC1-4, and three within EC5-6, reveal no obvious predicted consequences at the structural level, as they are exposed residues that should not affect calcium-binding, protein stability or adhesion. These mutations 85 may impact a variety of protein-protein interactions. Although the physiological relevance is unclear, both non-clustered and clustered protocadherins can form cis- homo- or cis-hetero-oligomers (Chen et al. 2007; Schreiner and Weiner 2010), and mutations affecting the formation of cis-oligomers could adversely impact protocadherin function. Similarly, protocadherins participate in a variety of protein complexes beyond homophilic trans adhesion: Pcdh19 has been shown to associate in cis with N-cadherin (Emond et al., 2011); protocadherins associate with the Wnt co- receptor, Ryk (Berndt et al., 2011); PAPC interacts with Frizzled-7 and FLRT3 (Chen et al.
2009; Kraft et al. 2012); and Pcdh17 and Pcdh19 have highly conserved RGD sequences, suggesting that they may interact with integrins (Kim et al., 2011; Mutoh et al., 2004;
Ruoslahti, 1996). Thus, further experimental characterization of key mutants in vitro and in vivo will continue to reveal correlations between structural defects, cellular-level defects, and different aspects of PCDH19-FE.
The non-clustered protocadherins are increasingly recognized as a family of molecules that play important roles during neural development. In addition to the role of PCDH19 in epilepsy, mutation of PCDH12 was found to underlie a syndrome of microcephaly that is associated with epilepsy and developmental disability (Aran et al.,
2016). Moreover, both PCDH9 and PCDH10 have been associated with autism spectrum disorders (Marshall et al., 2008; Morrow et al., 2008). Ongoing work will likely uncover further links between members of this family and neurodevelopmental disorders. Our
Pcdh19 EC1-4 model is the first to show the structural basis of adhesion by the non- clustered -protocadherins, and reveals that some of the missense mutations identified 86 in PCDH19-FE occur at the adhesive interface and act by abolishing adhesion. This represents an initial stage in understanding the mechanisms of non-clustered - protocadherin homophilic adhesion and provides insight into the biochemical basis of protocadherin-based neurodevelopmental disease.
Materials and Methods
Cloning and mutagenesis
Zebrafish Pcdh19 repeats EC1-4 and EC3-4 were subcloned into NdeI and XhoI sites of the pET21a vector for bacterial expression. Constructs for mammalian expression were created from previously reported constructs (Pcdh19, Pcdh19EC, Ncad, and NcadECW2A/R14E) and cloned into CMV:N1-Fc and CMV:N1-His backbones, respectively (Biswas et al., 2010; Emond et al., 2011). Truncated versions of Pcdh19
(Pcdh19EC1-5, Pcdh19EC1-4, Pcdh19EC1-3, Pcdh19EC1-2, Pcdh19EC2-6) were created by PCR subcloning of a Kozak sequence (GCCACC), the signal peptide, and appropriate
EC domains into CMV:N1-Fc. Mutations were created in both the bacterial and mammalian expression constructs by site-directed mutagenesis. All constructs were sequence verified.
Expression and purification of Pcdh19 fragments for structural determination
Each construct was expressed in BL21CodonPlus(DE3)-RIPL cells (Stratagene), cultured in TB (EC1-4) or LB (EC3-4), induced at OD600 = 0.6 with 100 µM (EC1-4) or 200 87 µM (EC3-4) IPTG and grown at 30 °C (EC1-4) or 25 °C (EC3-4) for ~16 hr. Cells were lysed by sonication in denaturing buffer (20 mM TrisHCl [pH7.5], 6 M guanidine hydrochloride, 10 mM CaCl2 and 20 mM imidazole). The cleared lysates were loaded onto Ni-Sepharose (GE Healthcare), and eluted with denaturing buffer supplemented with 500 mM imidazole. Pcdh19 EC3-4 was refolded by overnight dialysis against 20 mM
TrisHCl [pH 7.5], 150 mM NaCl, 400 mM arginine, 2 mM CaCl2, 2 mM DTT using MWCO
2000 membranes. Pcdh19 EC1-4 was refolded by iterative dilution of the denaturing buffer with refolding buffer (100 mM TrisHCl [pH 8.5], 10 mM CaCl2) (Dechavanne et al.,
2011). Refolded protein was further purified on a Superdex200 column (GE Healthcare) in 20 mM TrisHCl [pH 8.0], 150 mM NaCl, 2 mM CaCl2 and 1 mM DTT.
Crystallization, data collection and structure determination
Crystals were grown by vapor diffusion at 4 °C by mixing equal volumes of protein (Pcdh19 EC3-4 = 14.4 mg/ml and Pcdh19 EC1-4 = 7.7 mg/ml) and reservoir solution (Pcdh19 EC3-4 contained 100 mM calcium acetate, 100 mM sodium cacodylate
[pH 6.1], 25% MPD; Pcdh19 EC1-4 contained 200 mM sodium chloride, 100 mM TrisHCl
[pH 8.1], 8% PEG 20,000). Crystals were cryoprotected in reservoir solution (Pcdh19 EC3-
4) or with 25% glycerol added (Pcdh19 EC1-4), and then cryo-cooled in liquid N2. X-ray diffraction data was collected as indicated in Table 3.1 and processed with HKL2000 or
HKL3000 (Minor, Cymborowski, Otwinowski, & Chruszcz, 2006). The Pcdh19 EC3-4 structure was determined by molecular replacement using separate homology models
88 for each repeat (4AQE_A for EC3 and 1L3W for EC4) as an initial search model using
MrBUMP (Keegan & Winn, 2007) and PHASER (McCoy et al., 2007). Model building was done with COOT (Emsley, Lohkamp, Scott, & Cowtan, 2010) and restrained TLS refinement was performed with REFMAC5 (Murshudov et al., 2011). Likewise, the
Pcdh19 EC1-4 structure was determined through molecular replacement using Pcdh19
EC3-4 as the initial search model in PHASER. Data collection and refinement statistics are provided in Table 3.1. The final model for Pcdh19 EC3-4 is missing residues 243-246 in chain A, and residues 244-248 in chain B (chains C and D are complete). The Pcdh19
EC1-4 model is missing residues 32-36 in chain A, residue V1 in chain B, and side chains for residues K17, K75, K419 in chain A and for residues K5, R71, and E95 in chain B. All molecular images were generated with VMD (Humphrey, Dalke, & Schulten, 1996).
Differential scanning fluorimetry
The wild-type (WT) and mutant Pcdh19 EC3-4 fragments were purified as described above and used for differential scanning fluorimetry (DSF) (Lavinder, Hari,
Sullivan, & Magliery, 2009; Niesen, Berglund, & Vedadi, 2007). Experiments were repeated three to nine times using protein at 0.3 mg/ml for WT (n = 9), N317S (n = 9), and E290K (n = 3) in buffer (20 mM TrisHCl [pH 8.0], 150 mM NaCl, 2 mM CaCl2 and 1 mM DTT) mixed with SYPRO Orange dye (final concentration 5x; Invitrogen). Fluorescent measurements were performed in a BioRad CFX96 RT-PCR instrument while samples
89 were heated from 10 °C to 95 °C in 0.2 °C steps. Melting temperatures were estimated when the normalized fluorescence reached 0.5.
Analytical size exclusion chromatography
Refolded proteins (Pcdh19 EC1-4 WT, E313K, and T146R) were separated from unfolded aggregate protein on a Superdex200 16/60 column (GE Healthcare) with 20 mM TrisHCl [pH 8.0], 150 mM NaCl, 2 mM CaCl2 and 1 mM DTT at 4 °C. The fraction corresponding to greatest absorbance was run subsequently on a Superdex200
PC3.2/3.0 column with the same buffer at 4 °C. An AKTAmicro system provided a controlled flow rate of 50 µl/min with the sample being injected from a 100 µl loop.
Bead aggregation assays
Bead aggregation assays were modified from those described previously (Emond et al., 2011; Emond & Jontes, 2014; Sivasankar, Zhang, Nelson, & Chu, 2009) to detect the weak homophilic adhesion of Pcdh19EC. The Pcdh19ECFc fusion constructs were transfected alone or with NcadEC W2A/R14E His into HEK293 cells using calcium- phosphate transfection (Barry et al., 2014; Jiang & Chen, 2006; Kwon & Firestein, 2013).
Briefly, solution A (10 g of plasmid DNA and 250 mM CaCl2) was added drop-wise to solution B (2x HBS) while mildly vortexing, and the final transfection solution was added drop-wise to two 100 mm dishes of cultured HEK293 cells. The next day, cells were rinsed twice with 1xPBS and serum-free media. Cells were allowed to grow in the 90 serum-free media for 2-3 days before collecting the media containing the secreted Fc fusions. The media was concentrated using ultracel (Millipore) and incubated with 1.5 µl of protein G Dynabeads (Invitrogen) while rotating at 4 °C for 1-3 hrs. The beads were washed in binding buffer (50 mM TrisHCl [pH 7.5], 100 mM NaCl, 10 mM KCl, and 0.2%
BSA) and split into two tubes with either 2 mM EDTA or 2 mM CaCl2. Beads were allowed to aggregate in a glass depression slide in a humidified chamber for 60 min without motion, followed by two 1 min intervals of rocking (5 oscillations/min, 7° from horizontal). Images were collected upon adding EDTA or CaCl2, after 60 min incubation, and after each rocking interval using a microscope (AxioStar; Carl Zeiss) with a 10x objective. Bead aggregates were quantified using ImageJ software as described previously (Emond et al., 2011; Emond & Jontes, 2014). Briefly, the images were thresholded, the area of the detected aggregate particles was measured in units of pixels, and the average size was calculated. Assays were repeated three times from separate protein preps and their mean aggregate size (± SEM) at each time point was plotted. Assays were excluded from analysis only if western blots failed to show protein expression.
Western blots were performed on a portion of media containing the Fc fusion proteins before incubation with the beads to confirm expression and secretion of the protein. The media was mixed with sample loading dye, boiled for 5 min and loaded onto 10% Bis-Tris NuPAGE gels (Invitrogen) for electrophoresis. Proteins were transferred to PVDF membrane (GE healthcare) and blocked with 5% nonfat milk in TBS with 0.1% tween before incubating overnight with anti-human IgG or anti-His (1:200 91 Jackson ImmunoResearch Laboratories, Inc.; 1:1000 NeuroMab). After several washes, the blot was incubated with anti-goat or anti-mouse HRP-conjugated secondary (1:5000,
Santa Cruz Biotechnology; 1:5000 Jackson ImmunoResearch Laboratories Inc.) for chemiluminescent detection with Western Lightning substrate (Perkin Elmer).
Pull-down assays
HEK293 cells were transfected with Pcdh19ECFc (wild-type or mutant) and
NcadEC W2A/R14E His constructs using calcium-phosphate transfection as described above. Briefly, solution A (8 µg of plasmid DNA, and 250 mM CaCl2) was added drop- wise to solution B (2x HBS) while mildly vortexing, and the final transfection solution was added drop-wise to 60 mm dishes of cultured HEK293 cells. 24 hrs after transfection, cells were washed twice with 1x PBS and once with serum free media, then cells were allowed to grow in the serum free media for 2-3 days. Media containing the secreted protein was collected and incubated overnight with 10 µl protein G dynabeads
(Invitrogen) at 4 °C. Beads were washed once in wash buffer (20 mM TrisHcl [pH7.5],
150 mM NaCl, 0.5% triton X-100), then re-suspended in loading buffer. In addition, loading buffer was added to a small amount of reserved input media for each sample.
Samples were loaded onto 10% Bis-Tris NuPAGE gels (Invitrogen) for electrophoreses.
Proteins were transferred to PVDF membrane (GE healthcare) and blocked with 5% nonfat milk in TBS with 0.1% tween before incubating overnight with anti-human IgG or anti-his (1:200 Jackson ImmunoResearch Laboratories, Inc.; 1:1000 NeuroMab). After
92 several washes in TBS with 0.1% tween, the blot was incubated with anti-goat or anti- mouse HRP-conjugated secondary (1:5000, Santa Cruz Biotechnology; 1:5000 Jackson
ImmunoResearch Laboratories Inc.), washed, and developed with chemiluminescent detection with Western Lightning substrate (Perkin Elmer).
Sequence analysis and residue numbering
For analysis of Pcdh19 residue conservation across species, 102 sequences were obtained from the NCBI protein database and processed manually to include only the extracellular domain through the end of EC4, using the canonical calcium-binding motifs and SignalP4.1 (Petersen, Brunak, von Heijne, & Nielsen, 2011) as guides. These Pcdh19 sequences (Appendix C) were then aligned using Clustal Omega (Sievers & Higgins,
2014) and the alignment file was put into ConSurf (Ashkenazy et al., 2016) to calculate relative conservation of each residue and categorize the degree of conservation into nine color bins. Similarly, conservation between selected and clustered protocadherins was calculated in ConSurf. All human -protocadherin sequences and sequences for deposited structures of clustered protocadherins were selected and aligned to the sequences from our structure (5IU9) for input into Consurf (Appendix D). Residue numbering throughout the text and in the structure corresponds to the processed protein, except when referencing human disease mutations for which the number follows standard numbering for the human protein, including the signal peptide (see also Appendix A).
93
PCDH19-FE mutation list
The PCDH19 Female Epilepsy (PCDH19-FE) disease has been cataloged in the
Online Mendelian Inheritance in Man (OMIM 300088) and has previously been referred to by several different names including: Juberg-Hellman syndrome, epilepsy and mental retardation limited to females (EFMR), and Early Infantile Epileptic Encephalopathy-9
(EIEE9). A thorough list of the currently known PCDH19-FE mutations is presented in
Appendix A.
Prediction of glycosylation and glycation sites
Potential Pcdh19 glycosylation sites were predicted for both the human
(NP_001171809.1) and zebrafish (ACQ72596.1) sequences using the following servers:
NetNGlyc 1.0 (N-glycosylation, GlcNAc-β-Asn), NetOGlyc 4.0 (O-glycosylation, GalNAC-α-
Ser/Thr) (Hansen et al., 1998; Steentoft et al., 2013), and NetCGylc 1.0 (C-glycosylation,
Man-α-Trp) (Julenius, 2007). In addition, we mapped conserved O-mannosylation sites found in the related -protocadherins (Vester-Christensen et al., 2013), and mapped the glycosylation sites found in published clustered protocadherin structures from mammalian cells (Rubinstein et al., 2015). Potential Protocadherin-19 glycation sites were predicted using the NetGlycate 1.0 server for both the human and zebrafish sequences (Johansen, Kiemer, & Brunak, 2006).
94 Accession numbers
Coordinates for PCDH19 EC1-4 and EC3-4 have been deposited in the Protein
Data Bank with entry codes 5IU9 and 5CO1, respectively.
95
Figure 3.1. Electron density maps for the EC3-4 linker. (A) Stereo view of the 2Fo-Fc electron density map (purple mesh) from the Pcdh19 EC3-4 structure (2.51 Å) contoured at 2.5 σ. (B) Electron density map from the Pcdh19 EC1-4 structure (3.59 Å) contoured at 1.8 σ.
96 Figure 3.2 Pcdh19 EC1-4 structure reveals location of PCDH19-FE missense mutations. (A) Topology diagram of Pcdh19 EC1-4. A typical cadherin fold is observed for each EC repeat with seven strands labeled A to G. Calcium and sodium ions are shown as green and yellow circles, respectively. (B) Molecular surface representation and ribbon diagram of Pcdh19 EC1-4 shown in two orientations. Forty-three sites mutated in PCDH19- FE are highlighted in dark red on the protein surface (when applicable), shown in stick representation on the ribbon diagram, and listed. Mutations are indicated in parenthesis using the human gene numbering, with three non- conserved sites listed in italic gray. Residues whose side chains point to the protein core are underlined. Sites at inter- repeat, calcium-binding linker regions are listed on the right panel. The N317 site, involved in >20 PCDH19-FE cases (N340S), is in red. Cysteine amino-acids are in lime; none are exposed. Paired mutations in single PCDH19-FE patients are indicated with a star (*). See also Appendix A. (C) Detail of EC1 highlighting mutation sites (yellow sticks) in which residue side chains are pointing to the protein core. Neighboring hydrophobic core residues are shown in cyan. (D) Detail of EC3 highlighting a mutation site in which the residue side chain is exposed and pointing away from the protein surface. (E-G) Detail of calcium-binding inter-repeat linkers EC1-2 (E), EC2-3 (F), and EC3-4 (G). Calcium ions are shown in green and calcium-coordinating side chains in stick. Mutation sites are labeled and shown in yellow. (H) Melting temperature for the Pcdh19 EC3-4 wild type (WT) fragment, the N317S (equivalent to human N340S) and E290K (E313K) mutants determined using differential scanning fluorimetry. A clear decrease in thermostability is observed for the N317S mutant fragment in 2 mM CaCl2, but not for the E290K mutant. Curves represent the average for each construct with vertical bars representing standard error of the mean.
97
98
Figure 3.3. Sequence alignment of zebrafish, mouse, and human Pcdh19 EC repeats. All 6 EC repeats for each species are aligned to each other (EC1 to EC6). Conserved calcium-binding motifs are labeled. Residues that are mutated in PCDH19-FE are highlighted with red boxes. Residues involved in PCDH19-FE and located at the Pcdh19 EC1-4 antiparallel interface are highlighted with red and yellow boxes.
Figure 3.4. Predicted structural consequences of PCDH19-FE mutations. Schematics illustrate how missense mutations can alter protein behavior (adapted from (Marcos Sotomayor et al., 2010)). Mutations of residues at the linker region may affect flexibility (A), calcium-binding affinity (B), or impair folding/stability (C). Mutations outside the linker may also impair folding, as well as cis or trans binding. PCH19-FE mutations seen within the Pcdh19 EC1-4 structure are listed and grouped according to predicted structural effects (from visual inspection and sequence analyses) as discussed in the text. Paired mutations in single PCDH19-FE patients are indicated with a star (*). See also Appendix A. 99
Figure 3.5. Two states for Pcdh19 EC1-4 in solution. Elution profile from a size exclusion chromatography experiment showing two clear, separate peaks of distinct hydrodynamic size. Crystallization of the Pcdh19 EC1-4 fragment was carried out with fractions collected from the peak representing the largest species (68.4 ml).
Figure 3.6. A crystallographic Pcdh19 antiparallel interface involves fully overlapped EC1-4 repeats. (A) Molecular surface representation of two Pcdh19 EC1-4 molecules interacting in the crystallographic asymmetric unit. In this dimeric arrangement, an interaction interface is formed by fully overlapped and antiparallel EC1-4 protomers (Pcdh19-I1). Red, dashed boxes indicate three interaction sites highlighted in panels (C-E). (B) Side views of the Pcdh19 dimer and the interaction surface exposed with interfacing residues listed and shown in cyan. Sites mutated in PCDH19-FE located at the interface are shown in dark red. Sites with residue side chains pointing to the protein core are labeled in gray text. Three inter-molecular salt bridges are indicated (*: R40-E328; **: E81-R349; ^: R158-E290). (C-E) Detail of antiparallel interface (red dashed boxes in A). Interfacing residues are in cyan and yellow (PCDH-FE). Left panel is in the same orientation as A, middle and right panels are rotated around the dimer’s longest axis. Labels for one of the protomers are in italics. 100
Figure 3.7. Alternate crystallographic antiparallel interface involves EC1 to EC5 repeats. (A) Molecular surface representation of two Pcdh19 EC1-4 molecules forming an antiparallel dimer that would involve fully overlapped EC1-5 repeats (Pcdh19-I2 interface). Side views and interaction surface exposed with interfacing residues listed and shown in cyan. Sites mutated in PCDH19-FE located at the interface are shown in dark red. Sites with residue side chains pointing to the protein core are labeled in gray text. Labels for one of the protomers are in italics. Two residues involved in a Pcdh19-I2 interface salt-bridge are indicated with a plus sign (+). Buried surface area in this interface is 310 Å2 per interacting EC, compared to 413 Å2 per interacting EC for the Pcdh19-I1 interface (Figure 3.6). (B-C) Protein G beads coated with full-length extracellular wild-type (WT) Pcdh19ECFc (B) or an engineered mutation (C) imaged after incubation for 1 hr followed by rocking for 2 min in the presence of calcium. Bar – 100 µm. (D) Mean aggregate sizes for WT and R364E in the presence of calcium after 1 hr of incubation followed by rocking for 1 min (R1) and 2 min (R2). Error bars are standard error of the mean (n = 3 for each construct, Appendix B). Aggregation of Pcdh19-I2 interface mutant R364E is within the variation of WT samples (see also Figure 3.10H).
101
Figure 3.8. Pcdh19 dimer interfaces and predicted glycosylation and glycation sites. (A) Molecular surface representation of the Pcdh19-I1 interface (left) with interaction surface exposed (right) and with all predicted glycosylation (green) and glycation (light cyan) sites listed. Interfacing residues are shown in cyan. Sites mutated in PCDH19-FE and at the interface are shown in dark red. None of the predicted glycosylation sites involve interfacial residues, but two glycation sites do (K156 and K308). To the best of our knowledge, glycation has never been reported for cadherins. (B) Molecular surface of the alternate Pcdh19-I2 interface shown as in (A). Glycosylation (T232) and glycation (K204) sites are predicted for interfacial residues. O-linked glycosylation is also predicted for human PCDH19 S204, equivalent to N202 in Pcdh19. Non-conserved sites are in gray text. 102
Figure 3.9. Modified bead aggregation assays can detect calcium-dependent homophilic Pcdh19 interactions. (A) Protein G beads coated with full-length extracellular Pcdh19ECFc or NcadECFc imaged after incubation for 1 hr followed by rocking for 2 min in buffer with calcium. Representative images for parallel experiments in the absence of calcium are shown in panels labeled EDTA. Bar – 100 m. (B) Western blot shows efficient production and secretion of Pcdh19ECFc (also shown in Figure 3.11G WT lane) and NcadECFc, the latter present with and without cleavage of its prodomain. (C) Aggregate size for Pcdh19ECFc and NcadECFc in the presence and absence of calcium after 1 hr of incubation followed by rocking for 1 min (R1) and for 2 min (R2; see also Figure 3.10H). (D) Detail of plot in (C). Aggregate size for Pcdh19ECFc in the presence of calcium (Ca2+, green) is larger than in the absence of it (black) after rocking. See also Appendix B.
103
Figure 3.10. Minimal adhesive Pcdh19 fragment includes repeats EC1-4. (A-F) Protein G beads coated with full-length (A) and truncated versions (B-F) of the Pcdh19 extracellular domain imaged after incubation for 1 hr followed by rocking for 2 min in the presence of calcium. Bar – 100 m. (G) Western blot shows efficient production and secretion of full-length and truncated Pcdh19 extracellular domains. (H) Aggregate size for full-length and truncated versions of the Pcdh19 extracellular domain after 1 hr of incubation followed by rocking for 1 min (R1) and for 2 min (R2). Error bars are standard error of the mean (n = 3 for all aggregation assays and constructs). Inset: zoom-in showing pixel size from 15 to 85 (y axis). Bead aggregation was observed for constructs including EC1-6Fc, EC1-5Fc, and EC1-4Fc. Data for EC1-6 is also plotted in Figure 3.7D (WT), Figure 3.9C (Pcdh19ECFc (Ca2+)), and Figure 4H (WT (Ca2+)) for comparison to additional constructs. See also Appendix B.
104
Figure 3.11. PCDH19-FE mutations at Pcdh19-I1 antiparallel interface impair Pcdh19-mediated bead aggregation. (A-F) Protein G beads coated with full-length extracellular wild-type (WT) Pcdh19ECFc (A) and two PCDH19-FE mutants (B,C) imaged after incubation for 1 hr followed by rocking for 2 min in the presence of calcium. Representative images for parallel experiments in the absence of calcium are shown in panels D to F (EDTA). All full- length extracellular domains were produced in HEK293 cells. Bar – 100 m. (G) Western blot shows efficient production and secretion of both WT and mutant proteins used for bead aggregation assays. Parallel black lines indicate a two-lane gap between samples. (H) Aggregate size for WT and PCDH-FE mutants in the presence (Ca2+) and absence (EDTA) of calcium after 1 hr of incubation followed by rocking for 1 min (R1) and for 2 min (R2). Error bars are standard error of the mean (n = 3 for all aggregation assays and constructs, Appendix B). Aggregation is only observed for Pcdh19 WT in the presence of calcium and after rocking (see also Figure 3.10H). (I) Analytical size exclusion chromatogram traces for WT (green) and mutant (orange and red) Pcdh19 EC1-4 fragments produced in E. coli. A shift in peak elution volumes indicates impaired homophilic interaction for mutants. (J) Schematics of proposed homophilic “forearm handshake” for the Pcdh19 adhesion complex validated through binding assays with protein carrying PCDH19-FE mutations.
105
Figure 3.12. PCDH19-FE mutations at Pcdh19-I1 impair bead aggregation even in the presence of N-cadherin. (A-D) Protein G beads allowed to bind protein from cellular media containing NcadEC W2A/R14E His by itself (D), with Pcdh19ECFc (A), or with a PCDH19-FE mutants (B-C) imaged after incubation for 1 hr followed by rocking for 2 min. To test trans interactions mediated by Pcdh19, we used the NcadEC W2A/R14E mutant, which abolishes Ncad-based homophilic adhesion (Emond et al., 2011; Harrison et al., 2010). (E) Western blots show the presence of both Pcdh19ECFc (wild-type and mutant forms) and NcadEC W2A/R14E His in the cellular media used for aggregation assays. (F) Aggregate sizes for NcadEC W2A/R14E His by itself, with Pcdh19ECFc WT, or Pcdh19ECFc mutants after 1 hr incubation followed by rocking for 1 min (R1) and for 2 min (R2). Error bars are standard error of the mean (n = 3 for all aggregation assays). Construct labels with a star (*) are shortened in graph legend.
Figure 3.13. PCDH19-FE mutations at Pcdh19-I1 do not abolish the interaction between the extracellular domains of Pcdh19 and N-cadherin. Co-immunoprecipitation of Pcdh19ECFc (WT or with PCDH19-FE mutations at Pcdh19-I1) pulls down NcadEC W2A/R14E His. Therefore, the PCDH19-FE mutations at the Pcdh19-I1 interface do not abolish the interaction between Pcdh19 and Ncad extracellular domains. 106
Figure 3.14. Pcdh19-I1 antiparallel EC1-4 dimer interface involves charged, hydrophilic, and hydrophobic residues. Molecular surface representation of the Pcdh19-I1 antiparallel dimer with interfacial residues exposed and labeled. Surface is colored according to residue type (apolar: white; polar: green; negatively charged: red; positively charged and histidines: blue). Interfacing residues are labeled as in Figure 3.6B.
107
Figure 3.15. A common binding mechanism with sequence-diverse interfaces for and clustered protocadherins. (A) Molecular surface representation of the closed (left) and exposed (right) Pcdh19-I1 antiparallel dimer. Interfacing residues are colored according to sequence conservation among 102 species (Figure 3.16 and Appendix C). Most of them are highly conserved. Labels as in Figure 3.6B. (B) Antiparallel Pcdh19 EC1-4 dimer shown as in (A), with interfacing residues colored by sequence conservation among selected members of the non-clustered 1 and 2 protocadherins, as well as selected , , and clustered protocadherins (Figure 3.17 and Appendix D). (C) Location of interfacing residues for Pcdh19, Mm pcdhC3, Mm pcdh4 & 7, Mm pcdhA1, and Mm pcdh6 & 8, mapped onto the Pcdh19 topology diagram. Shared structural motifs involved in binding include: The F-G loop along with the beginning of strands A, G and C in EC1; the A-B loop, most of strand B, the D-E loop, and the beginning of strand E in EC2; the EC2-3 linker; the C-D loop, parts of strands F & G and the F-G loop in EC3; the loop within strand A, strand B, and the D-E loop in EC4. Red/orange circles indicate sites mutated in PCDH19-FE. Common contact zones in EC1 & EC3, as well as EC2 & EC4, are highlighted with a brown background.
108
109
Figure 3.16. Sequence alignment of Pcdh19 EC1-4. Alignment of Human, Zebrafish, Mouse, Rat, Chicken, and Monkey sequences for Pcdh19 EC1-4. Residues are colored according to conservation based on ConSurf (Ashkenazy et al., 2016) and an alignment of sequences from 102 species (Appendix C; gray indicates insufficient data due to inadequate diversity). Conserved calcium- binding motifs are shown on top of the alignment and labeled. Residues at the Pcdh19 EC1-4 interface are labeled with an orange dot on top of the alignment. Human residues mutated in PCDH19-FE are in bold white or dark red font.
Figure 3.17. Sequence alignment of selected protocadherins (next page). Alignment of selected sequences for 1 and 2 protocadherins, as well as selected clustered , , and protocadherins of known structure (Appendix D). Residues are colored according to conservation based on ConSurf as in Figure 3.16. Conserved Ca2+-binding motifs are shown on top of the alignment. Residues at the Pcdh19 EC1-4 interface are labeled with an orange dot. Predicted glycosylation and glycation sites are labeled with green and light cyan dots, respectively. Pairs of salt-bridges observed at the Pcdh19 EC1-4 interface are indicated in bold red above the alignment. Human residues mutated in PCDH19-FE are in bold white or dark red font. Residues involved in any of the clustered protocadherin interfaces are labeled with a light blue dot below the alignment, and shown in italic bold. Secondary structure of Pcdh19 EC1-4 is shown in gray below the alignment. Long residue insertions were omitted for clarity in the sequences of pcdh7 EC2 (QEP157~209RSS), pcdh8 EC4 (AAP334~361GTP), pcdh10 EC2 (GGG192~210QRT), and pcdh17 EC4 (VLG377~391SVP). Abbreviations: Dr, Danio rerio; Hs, Homo sapiens; Mm, Mus musculus.
110
111
Figure 3.17. Sequence alignment of selected protocadherins (figure legend on previous page).
Figure 3.18. Structural comparison of Pcdh19-I1 EC1-4 dimer to clustered-protocadherin dimers. (A) Two views of structurally aligned monomers (gray, EC1-EC4) and their partners for Pcdh19 (cyan) and pcdh4 (blue, 5DZW (Goodman, Rubinstein, Thu, Bahna, et al., 2016)). Arrows point to regions of significant structural differences. (B) Two views of Pcdh19 and pcdh7 (5DZV (Goodman, Rubinstein, Thu, Bahna, et al., 2016)) shown as in (A). Right panel shows schematics highlighting differences in dimer arrangement. (C-F) Structural alignments as in (A- B) for pcdh6 (C, 5DZY (Goodman, Rubinstein, Thu, Bahna, et al., 2016)), pcdh8 (D, 5DZX (Goodman, Rubinstein, Thu, Bahna, et al., 2016)), pcdhA1 (E, 4ZI9 (John M Nicoludis et al., 2015)), and pcdhC3 (F, 4ZI8 (John M Nicoludis et al., 2015)). 112
Figure 3.19. Structural comparison of protocadherin 1 and 2 EC3 repeats. (A) Ribbon representation of EC3 repeats from Pcdh19 (2, cyan), pcdh7 (1, dark cyan, PDB 2YST), and pcdh9 (1, ice blue, PDB 2EE0) structurally aligned to each other. (B) Molecular representation of the Pcdh19 EC3 (left) and EC2 (right) repeats within the Pcdh19-I1 EC1-4 dimer. Interfacing residues are exposed and shown in cyan, with E290 shown in dark red to indicate its involvement in PCDH19-FE. Location of R158, which interacts with E290, is shown in EC2. Surface is also shown colored according to residue type (apolar: white; polar: green; negatively charged: red; positively charged and histidines: blue). N and C-termini are indicated. (C&D) Molecular surface representations for Pcdh7 EC3 and Pcdh9 EC3, as in (B), with predicted interfacing residues shown in dark cyan and ice blue, respectively. Charges of the E290-R158 pair are predicted to be swapped in Pcdh7 (salt-bridge R-D) and Pcdh9 (salt-bridge K-E; Figure 3.17).
113
Parameters DrPcdh19EC1-4 DrPcdh19EC3-4 Data collection Space group P21 C2 Unit cell a, b, c (Å) 66.390, 59.776, 165.925 149.355, 86.631,132.583 Unit cell , , (°) 90, 94.39, 90 90, 122.13, 90 Molecules per asymmetric unit 2 4 Beam source MicoMax-003 APS 24-ID-C Wavelength (Å) 1.54187 0.97920 Resolution (Å) 50.00-3.59 (3.66-3.59) 50.00-2.51 (2.55-2.51) Unique reflections 15416 47847 Completeness (%) 94.8 (86.0) 98.0 (88.1) Redundancy 2.7 (2.4) 4.4 (3.2) I / (I) 4.90 (2.10) 16.59 (2.21) Rmerge 0.182 (0.386) 0.072 (0.591) Rmeas 0.224 (0.480) 0.081 (0.690) Rpim 0.129 (0.281) 0.037 (0.348) CC1/2 0.833 (0.774) 0.964 (0.792) CC* 0.966 (0.934) 0.991 (0.940) Refinement Resolution range (Å) 50.00-3.59 (3.68 – 3.59) 50.00-2.51 (2.58-2.51) Rwork (%) 24.6 (41.3) 18.8 (38.3) Rfree (%) 30.5 (45.2) 23.9 (41.6) Protein Residues 839 827 Ligands/ions 20 16 Water molecules 15 49 Bond length rmsd (Å) 0.0094 0.0112 Bond angles rmsd(°) 1.4661 1.3915 Average B-factor of protein 90.75 77.93 Average B-factor of ligand/ion 57.01 55.32 Average B-factor of water 45.40 60.92 Ramachandran Plot Region (PROCHECK) Most favored (%) 78.6 85.6 Additionally allowed (%) 20.4 13.5 Generously allowed (%) 1.1 1.0 Disallowed (%) 0.0 0.0 PDB ID code 5IU9 5CO1
Table 3.1. X-ray diffraction statistics for drPcdh19EC1-4 and drPcdh19EC3-4.
114
Chapter 4: Creating PCDH19 Female Epilepsy Mutations in the Endogenous Zebrafish
pcdh19 Gene by CRISPR Genome Editing[1]
Introduction
Early neurodevelopment lays the foundation for a properly functioning brain in adulthood. When neuronal adhesion and specification are disrupted, many neurodevelopmental diseases can result such as schizophrenia, autism, and epilepsy
(Mitchell, 2011; Redies et al., 2012; Sakurai, 2016). Mutations in protocadherin-19
(PCDH19), an adhesion molecule of the cadherin superfamily, are known to cause a specific form of epilepsy limited to females (PCDH19 Female Epilepsy, PCDH19-FE)
(Christel Depienne & LeGuern, 2012; Dibbens et al., 2008; Walters et al., 2014).
Furthermore, PCDH19 has quickly risen to be the second most clinically relevant gene in epilepsy, yet little is known about the disease mechanism, although the mosaic expression of the mutant protein appears to be key (Depienne et al., 2009; Dibbens et al., 2008; Duszyc, Terczynska, & Hoffman-Zacharska, 2015; Terracciano et al., 2016;
Thiffault et al., 2016).
Pcdh19 knockout zebrafish and mice exhibit very subtle defects, which is consistent with the absence of gross brain morphology abnormalities in female epilepsy
______[1] This chapter is not published. The author designed and performed all experiments in this chapter except for injection of the E313K CRISPR, which was kindly performed by Min Ahn. 115
patients and hemizygous male carriers (Cooper et al., 2015; Pederick et al., 2016;
Scheffer et al., 2008). In zebrafish, Pcdh19 functions in conferring cellular identity on columns of cohesive cells in the optic tectum, and lack of Pcdh19 function in one cell can negatively impact the neighboring cells (non-cell-autonomous function) (Cooper et al.,
2015). However, to my knowledge, no one has studied the effects of the missense mutations in vivo or the effects of varying numbers of cells expressing the mutant or wild-type protein (also known as skewed X-chromosome allele expression). With the increased genetic tools for zebrafish, CRISPR-Cas9 technology now allows for genetic engineering of missense mutation into the genome of zebrafish (Figure 4.1). A simple method for CRISPR-Cas9 promoting recombination with DNA oligos has been pioneered by Hwang and colleagues. In addition they expanded the possible target sites for
CRISPRs by relaxing the 5` GG constraint (Hwang et al., 2013). This is critical for finding amenable CRISPRS near the desired codon for genomic engineering of missense mutations.
Here we use the recent CRISPR/Cas9 technological advancements to create
Pcdh19 missense mutations in the zebrafish genome. Based on the recent crystal structure of Pcdh19, we have chosen PCDH19-FE mutations that were shown to disrupt adhesion (T146R and E313K) (Cooper et al., 2016). By introducing these missense mutations into the zebrafish genome, we can begin teasing apart Pcdh19 function by comparing phenotypes of WT embryos, pcdh19 nulls (pcdh19-/-), and mutants that express non-adhesive Pcdh19 (Pcdh19T147R/T147R and Pcdh19E314K/E314K). Furthermore,
116
these phenotypes can be compared to zebrafish mosaic mutants with varying ratios of wild-type and mutant cells created by cell transplants at blastula stage.
Results
To understand the adhesive role of Pcdh19 in vivo, we designed CRISPRs and
DNA oligos to create non-adhesive PCDH19-FE mutations in the zebrafish genome. Our recent crystal structures of the Pcdh19 revealed five disease mutations at the adhesion interface that do not coordinate calcium (S139L, T146R, P149S, E313K, and T404I) and confirmed the lack of adhesive capabilities for two of these (T146R and E313K) (Figure
4.2). Furthermore, E313K was demonstrated to have similar protein stability as WT protein, and T146R stability is expected to be similar as well (Cooper et al., 2016).
Therefore, T147R and E314K, the equivalent residues in zebrafish, were selected for genome engineering (Figure 4.2C and Appendix A).
CRISPR sites located near the codons of interest (T147 and E314) with high specificity were selected, and recombination oligos were designed. The CRISPR guide
RNA selected for engineering the T147R missense mutation directs Cas9 to cut 5bp upstream of the threonine codon, likely disrupting the Acc651 restriction site, (Figure
4.3A) and encourages homologous recombination to repair the lesion. The oligo template for recombination exchanges the threonine codon for an arginine codon, and also creates a restriction enzyme site (HincII) for simple and economical screening of recombination efficiency. Similarly for engineering E314K, the CRISPR cuts the genomic
117
DNA 16bp upstream of the glutamate codon (Figure 4.3B), and recombination with the oligo template mutates the glutamate to a lysine while creating a SacI restriction enzyme site.
The day following injection of Cas9 mRNA, guide RNA, and DNA oligo into single- celled embryos, DNA was prepared from a small subset of the injected embryos to test recombination efficiency, while remaining embryos were grown to adulthood. For testing T147R genome engineering efficiency, digestion of DNA amplicons with Acc651 and HincII revealed low efficiency of CRISPR genomic lesions (1/9) and no signs of homologous recombination with the template oligo (0/12) (Figure 4.4A). These low rates of Cas9 cutting and lack of recombination in the tested embryos indicated a low probability of success in obtaining the desired mutations in the germline. Nevertheless, upon reaching sexual maturity, adults were incrossed to test for germline transmission of the missense mutation (Figure 4.4B). However, all results were negative for homologous recombination, while HincII enzyme fidelity was demonstrated under the same conditions (Figure 4.4C).
In light of the results of the T147R genome engineering attempt, the E314K
CRISPR efficiency was tested before attempting homologous recombination. Cas9 mRNA and guide RNA for the E314K site was injected into single-cell embryos, and DNA was prepared from whole embryos the following day. Since no restriction sites are expected to be disrupted by the CRISPR lesion, high resolution melt analysis (HRMA) was performed to test E314K CRISPR efficiency. Two out of sixteen embryos displayed a
118
varied melt curve compared to WT controls, indicating CRISPR induced DNA lesions are only occurring in ~12.5% of injected embryos (Figure 4.5).
Conclusions and Future Directions
Thus far, we have tested CRISPRs for the zebrafish equivalent residues of T146R and E313K (T147R and E314K is zebrafish). However, the tested CRISPRs had low DNA cleavage efficiency with less than 15% of embryos having DNA lesions at the site of interest. Without efficient DNA cleavage, homologous recombination is improbable.
Thus we were unsurprised when tests showed no signs of homologous recombination in any embryos. My results demonstrate the importance of a high efficiency CRISPR, when attempting CRISPR induced recombination.
Therefore, additional CRISPRs should be screened for higher cleavage efficiency
(>50%), before proceeding with additional recombination attempts. Fifteen guide RNAs
(eleven T147 guides and four E314 guides) remain to be tested for cutting efficiency
(Figure 4.6). Each of these can be screened by HRMA one day after injection to determine the cutting efficiency, as with the E314 CRISPR. Upon indentifying a few high efficiency CRISPRs, homologous recombination oligos will be co-injected with each and embryos will be screened for homologous recombination by restriction digest.
Once a successful zebrafish line has been developed with a PCDH19-FE missense mutation disrupting Pcdh19 mediated cell adhesion, their aberrant neuronal phenotype can be studied and compared to WT and Pcdh19 knockout lines. By injecting the
119
missense mutants with the previously developed BAC (pcdh19:Gal4-VP16;UAS:Lifeact- green), the cell dynamics can be evaluated, and columnar adhesion in the optic tectum can be compared with previous results in the Pcdh19 knockout (Cooper et al., 2015).
Furthermore, interactions between cells expressing WT or mutant Pcdh19 can be analyzed in mosaics by using a two color system. If the Pcdh19 missense mutant line is crossed into a red transgenic, (pcdh19:Gal4-VP16;UAS:Lifeact-red), then transplanted into wild-type green transgenics (pcdh19:Gal4-VP16;UAS:Lifeact-green), this will reveal dynamics between cells expressing different forms of the Pcdh19. Since Pcdh19 mosaicism appears to play an important role in human epilepsy, these cellular interactions will provide valuable insight into possible disease mechanism.
Materials and Methods
Fish maintenance
All zebrafish experiments and maintenance were performed in accordance with the Ohio State Institution Animal Care and Use Committee protocols. All experiments were performed in a hybrid zebrafish strain of AB* and Tübingen longfin and grown at
~28.5°C.
120
CRISPR target site identification and cloning
Potential CRISPR sites were identified and guide RNA site specificity was scored using the MIT CRISPR Design tool (http://crispr.mit.edu/) (Hsu et al., 2013). Chosen
Guide RNAs were cloned into a BsaI digested pDR274 vector using the following hybridized oligos (naming corresponds to Figure 4.6):
T146#2-oligo1: 5’ TAGGGAAATCTGGTACCGGGAG 3’
T146#2-oligo2: 5’ AAACCTCCCGGTACCAGATTTC 3’
E313#2-oligo1: 5’ TAGGTGAATGTGCAGTTCCTCG 3’
E313#2-oligo2: 5’ AAACCGAGGAACTGCACATTCA 3’
A detailed protocol can be found in Talbot & Amacher, 2014.
RNA production and zebrafish embryo microinjection
Guide RNA was transcribed from linearized CRISPRs in the pDR274 vector using the MAXIscript T7 kit (ThermoFisher), and Cas9 mRNA was transcribed from a linearized
Cas9 expression vector using the mMessage mMachine kit (ThermoFisher). Guide RNA
(12.5ng/nl) and Cas9 mRNA (200ng/µl) were co-injected, with or without the corresponding DNA oligo (40ng/µl) for homologous recombination, into one-cell stage embryos. Genomic DNA was extracted from a subset of injected embryos (8-16 embryos) along with WT controls for efficiency testing, while remaining injected embryos were grown to adulthood.
121
Genotyping by high resolution melt analysis (HRMA) and restriction digest
Genomic DNA extracted from embryos (or pools of embryos in the case screening for germline transmission from adult incrosses) is PCR amplified by Standard
Taq Polymerase (New England BioLabs) for restriction digest screening or by Precision
Melt Supermix (BioRad) in HRMA screening. In the case of HRMA, PCR amplification and melt analysis are performed in the CFX Connect system (Bio Rad) according to manufacturer’s instructions for detection of lesion-induced SNPs (single nucleotide polymorphisms). For restriction digest screening, digestion with HincII or Acc651 is performed in PCR buffer at 37° following normal DNA amplification of a ~500bp segment. Digestion products are run through a 2% agarous gel with 0.5ug/ml ethidium bromide and pictured using the Bio-rad Gel Doc XR imaging system.
122
Figure 4.1. Schematic of the CRISP-Cas9 system (modified from Ramalingam, Annaluru, & Chandrasegaran, 2013). (A) Depiction of CRISPR cutting at a target site. Guide RNA binds to the reverse strand of the target site matching it 5’ 20bp sequence. The target must contain a PAM site (NGG) immediately downstream of the matching 20bp sequence. With the guide RNA bound to the target site, a Cas9 protein is recruited and typically cuts 3bp upstream of the PAM site. (B) Flow chart of repair mechanisms following CRISPR induced DNA cleavage. CRISPR mediated double strand breaks can be repaired by two main mechanisms: non-homologous enjoining (NHEJ), which can result in random insertion or deletion of nucleotides at the lesioned site, and homologous recombination (HR), which uses another copy of homologous DNA as a template for repair. HR can use either the paired chromosome as a template or an exogenous donor DNA template.
123
Figure 4.2. PCDH19-FE missense mutation at Pcdh19 adhesion interface. (A) The entire Pcdh19 adhesion interface seen in the zebrafish Pcdh19EC1-4 structure (PDB code: 5IU9) (Cooper et al., 2016). Interface residues are shown in cyan or a greener shade in alternate protomer. Disease mutations at the interface are shown in yellow, and non-interface residues that coordinate calcium are in gray along with the ribbon representation of the remaining structure. Green spheres represent chelated calcium ions, and red dashed boxes represent the location of interface details shown in B-D. (B-D) Details of the adhesion interface (red dashed boxes in A) highlighting residues at the interface equivalent to the following human disease mutations: T404I (T405 in B), E313K, P149S, T146R (E314, P150, T147 in C), S139L, SEA139-141duplication, N232S (S140, SEN140-142, N233 in D). 124
Figure 4.3. Design of CRISPR induced recombination. (A,B) The double stranded DNA sequence surrounding the target site is shown at the top with the amino acid translation above. Light purple highlights the CRISPR target sequence, except for codon targeted for recombination in yellow, and dark purple highlights the adjacent PAM site (NGG). Regions with identity to the oligo’s homologous recombination arms are highlighted in green. The arrow head points to the predicted cut site. Crosses in the middle panel represent homologous recombination occurring with the oligo. The bottom panel shows the final production of homologous recombination. Red text represents changes in the sequence occurring with homologous recombination, which is designed to create the missense mutation, inhibit CRISPR binding to the recombination product, and create a restriction site for easy genotyping, HincII in T147R (A) and SacI in E314K (B).
125
Figure 4.4. Screen of T147 CRISPR injected embryos by restriction digest. (A) 2% agarose gel of genomic DNA extracted from embryos injected with T147 CRISPR and from uninjected controls that was digested with HincII and Acc651. CRISPR lesions disrupting the Acc651 site (adjacent to the canonical CRISPR cut site) will result in a 500bp band; whereas WT DNA should be cut into 380bp and 120bp fragments (note: the 120bp band is hidden by the dye front. Small portions of uncut DNA can be seen even in WT lanes; however, one lane exhibits a strong band at 500bp indicating successful disruption of the Acc651 site in the embryo genome. Digestion by HincII would create bands at ~380bp and ~120bp. However, the undigested 500bp band indicates no appreciable recombination in any of the injected embryos (see also Figure 4.3A). (B) Embryos injected along with those tested in A were grown to adulthood and incrossed to screen for germline transmission, as small numbers of cells with recombination may not be detectable in A. Here representatives pools (each lane is a pool of 2 embryos) of embryos from two incrossed clutches. The 500bp band in all indicates no homologous recombination. (C) To ensure HincII enzyme fidelity and efficiency, an alternate genomic location known to contain the HincII restriction site was amplified and digested under the same conditions as A and B. HincII exhibits high fidelity and efficiency as the expected band at 254bp/277bp is clearly seen, and no remaining uncut transcript is observed at 531bps (lane +). Uncut PCR product (-) is run as a reference.
126
Figure 4.5. Screen of E314 CRISPR injected embryos by high resolution melt analysis (HRMA). (A-C) Graphs from melt analysis of genomic amplicons of E314 CRISPR injected and uninjected control embryos. Each graph shows the difference in normalized fluorescence (difference in relative fluorescence units, RFU) between injected embryos and the uninjected wild-type controls. Results for all embryos are shown in A, only uninjected controls in B, and only E314 CRISPR injected embryos in C.
127
Figure 4.6. Screening for highly efficient CRISPR. (A, B) Location of all CRISPRs at the T147 (A) and E314 (B) target sites with their canonical cut site represented with an arrow head. Those above the DNA represent CRISPR with sequences matching the sense strand and those below match the antisense strand. (C) List of all CRISPR target sequences with statistics for each CRISPR cut site shown in A and B. Location # represents numbering from 5’ to 3’ as depicted in A and B. Caret (^) represents the canonical cut site for each CRISPR, which is used to calculate the distance from the target codon. The MIT quality score depicts the specificity of the CRISPR for the target of interest over any other possible site in the zebrafish genome. Finally the percent of lesions comes from the experiments shown in Figure4.4A and Figure4.5C.
128
Chapter 5: Anatomy of Protocadherin1a Expressing Cells Reveals a Theme of Columnar
Development in the Zebrafish Brain[1]
Introduction
The vertebrate nervous system, which begins as a simple tube of neuroepithelial cells, develops into a precisely interconnected brain and spinal cord. In the process of neurodevelopment, the neuroepithelium is partitioned into basic brain regions, which are initially connected by a simple scaffold of axon tracts (Cavodeassi & Houart, 2012;
Easter et al., 1994). As brain development continues, more specific subdivisions are defined, and the complexity of neural networks increases. Morphogens, transcription factors, and cell adhesion molecules have all been implicated in this progressive regionalization, with expression boundaries or gradients corresponding to cell fate
(Cavodeassi & Houart, 2012; Kiecker & Lumsden, 2005)
Protocadherin-1a (pcdh1a) is a member of the δ-protocadherin subfamily of cadherins, which are calcium-dependent cell adhesion molecules, and is one of two zebrafish homologues (pcdh1a and pcdh1b) of the human PCDH1 gene (Blevins et al.,
2011; Redies et al., 2005). Each member of the δ-protocadherin subfamily has a distinct expression pattern within the developing and adult nervous system (Blevins et al. 2011; ______[1]This chapter is not published. The author contributed to all aspects of this chapter with the assistance of Dr. James Jontes for the two-photon imaging and the assistance of Dr. Shelly Emond for the development of the transgene construct.
129
Krishna-K et al., 2011; Vanhalst et al., 2005). Although little is known about the role of
Pcdh1 in neural development, a cell sorting function has been observed in both frogs and chicken (Bononi et al., 2008; Kuroda et al., 2002). Recently, we showed that δ- protocadherins (including pcdh1a) define columnar modules within the zebrafish visual processing center, the optic tectum (Cooper et al., 2015). The differential expression of the δ-protocadherins throughout the nervous system suggests similar roles for these proteins in other brain regions.
Here we investigate the anatomical organization of pcdh1a expressing cells throughout the zebrafish central nervous system, using bacterial artificial chromosome
(BAC) transgenic technology. This allowed us to indentify regions of pcdh1a expression along with specific cell types. In the process of cataloguing pcdh1a expression, we observed a theme of pcdh1a expression in presumptive radial glia cells and columnar organization akin to those observed previously in the optic tectum (Cooper et al., 2015).
These results suggest the role of protocadherins in modular development may apply broadly across many brain regions.
Results
Developing a pcdh1a transgenic zebrafish line
In order to study the detailed morphology of pcdh1a expressing cells throughout the nervous system we developed a transgenic zebrafish line with a fluorescent reporter construct: BAC(pcdh1a:Gal4-VP16, UAS:Lifeact-GFP). This BAC uses the pcdh1a
130
regulatory elements to drives expression of Gal4 and, in turn, Lifeact-GFP (Riedl et al.,
2008), which labels F-actin in pcdh1a-expressing cells. Zebrafish embryos injected with the BAC were screened for germline transmission, and the expression in the founder progeny were compared with in situ hybridization patterns in previous pcdh1a studies
(Blevins et al., 2011; S-Y Kim et al., 2007; Redies et al., 2008). As expected, transgene expression is primarily observed in the forebrain telencephalon at 2 dpf, followed by more extensive expression in the brain and retina by 4 dpf (Figure 5.1B-C). To further validate the transgenic line, we perform two-color in situ hybridization against the Gal4-
VP16 transgene and the endogenous pcdh1a. Here, individual spots of hybridization for each probe within the same cell often do not occur in the same subcellular location, resulting in a more speckled appearance within regions of common expression.
Although background fluorescence and the varied subcellular location complicate the analysis, the transgene expression appears to match the endogenous pcdh1a expression pattern (Figure 5.1D).
Columnar Pcdh1a-expression patterns revealed in zebrafish brain
To explore Pcdh1a expression in more detail, we viewed each region of the central nervous system at high resolution with a two-photon microscope (Figure 5.2F,
5.3H, 5.4F, 5.5H). Within the midbrain, the optic tectum is prominently labeled (Figure
5.2A-B), along with tectal commissures (Figure5.1A) and the ventral tegmental commissure (Figure 5.2C). Columns of pcdh1a-expressing cells are observed in the optic
131
tectum, similar to those observed in our previous study (Figure 5.2A,D-E) (Cooper et al.,
2015). Depending on the orientation of a column relative to the plane of optical section, these columns can missed among the milieu of surrounding cells (Figure 5.2A).
However, some clear examples of columns are highlighted in Figure 5.2B-C, in which columns contain clusters of cells often associated with a radial glia cell (identified by their prototypical end feet).
Continuing to other brain regions, we documented both locations of pcdh1a expression along with apparent columnar developmental units. Many of the prominent forebrain commissures are labeled providing convenient landmarks when indentifying subdivisions of the brain: anterior commissure (figure 5.3D), post-optic commissure
(figure 5.3D), ventral tegmental commissure (figure 5.2C), commissure of the posterior tuberculum (figure 5.3C), and habenular commissure (figure 5.3A). The strongest transgene expression is observed in the pallium and olfactory bulb located dorsally from the anterior commissure which connects their hemispheres (figure 5.3A-D). Within these regions, the cells are so tightly packed that columnar organization is difficult to determine, but some cells with radial glia like morphology were observed in the pallium
(figure 5.3G). Therefore it is unclear whether these radial glia could be part of columnar units that are obscured by the tight packing of labeled cells. However, within the thalamus and pretectum, a columnar group of cells visibly associates with the presumptive glia (figures 5.3F and figure 5.3E respectively). Of note, the olfactory epithelium also expresses pcdh1a (figure 5.3B,D); although it is not technically part of
132
the central nervous system, (Wulliman, Rupp, & Reichert, 2012), it does provide input stimuli to the olfactory bulb.
Within the hindbrain, we observed pcdh1a-expressing cells in the cerebellum, in the medulla oblongata, and in two hindbrain ganglion cell clusters. The trigeminal ganglion cluster mediates touch sensitivity and projects its axons caudally into the lateral longitudinal fasciculus (figure 5.4C) (Metcalfe, Myers, Trevarrow, Bass, & Kimmel,
1990). Secondly, statoacoustic ganglion clusters extend their dendrites into the ear’s sensory patches, while the axons project within the VIIIth nerve along the medial side of otic vesicle (the developing ear) (Raible & Kruse, 2000; Whitfield, Riley, Chiang, &
Phillips, 2002). Although no columnar units are apparent in the hindbrain from the dorsally view, the lateral view revealed columnar cell clusters around presumptive radial glia progenitors in the medulla oblongata. Combining observations from the forebrain, midbrain and hindbrain, all three major brain regions exhibit some columnar modules, although areas such as the pallium are very unclear due to dense cell packing.
Pcdh1a is expressed in a variety of spinal cord neurons
A variety of neurons in the zebrafish spinal cord express pcdh1a, but no cells were observed with radial glia morphology. Moreover, columnar modules were not observed in the spinal cord from dorsal (figure 5.5A-G) or lateral (data not shown) viewpoints. However, the axon and dendrite projections of the pcdh1a-expressing cells allowed for the identification of various sensory neuron, motor neuron and interneuron
133
types (Bernhardt, Chitnis, Lindamer, & Kuwada, 1990; Hale, Ritter, & Fetcho, 2001;
Myers, Eisen, & Westerfield, 1986). The most frequently observed cells in the spinal cord were Rohon-beard sensory neurons (figure 5.5A-C,F-H), which innervate the skin of the trunk for tactile responses, as the trigeminal ganglion cluster does in head (Metcalfe et al., 1990). Another sensory neuron type in the spinal cord, dorsal root ganglion cells, also frequently expressed the pcdh1a transgene (figure 5.5B). Several rostral and middle primary motor neurons (RoP and MiP respectively) are marked by the transgene, but no caudal primary motor neurons (CaP) were observed during data collection (figure
5.5A,D,H). In the few cases where secondary neurons expressed pcdh1a, adjacent primary neurons were also labeled making axon projection of the secondary neuron ambiguous (figure 5.5D). Thus the secondary neurons could not be more specifically classified by axonal trajectory (Menelaou & McLean, 2012). Interneurons CoSa and CiD
(figure 5.5C) were seen repeatedly, while only a couple CoBL, UCoD, and VeMe interneurons (figure 5.5E-G respectively) were observed. The variety of neurons observed in the spinal cord is summarized in figure5.5H.
Discussion
For over three decades, cadherin family members have been proposed to facilitate partitioning of the brain, due to their distinctive patterns of expression in the brain and their cellular adhesion functions (Redies, Neudert, and Lin 2011; Kiecker and
Lumsden 2005; Inoue et al. 2001). However, the molecular mechanisms used in
134
partitioning the brain are still unclear. Our previous study on protocadherins in the optic tectum revealed clonal columns defined by δ-protocadherin expression (Cooper 2015).
Here we observed similar columns of pcdh1a-expressing cells in several regions of the forebrain, the optic tectum of the midbrain, and the medulla oblongata of the hindbrain, but not in the spinal cord. The clonality of the columns observed in this work is inferred from similarity to the tectal columns reported previously, but must still be confirmed. Lineage tracing studies could provide valuable insight into this clonal development, particularly in regions with dense populations of pcdh1a-labeled cells
(Kretzschmar & Watt, 2012). Also, the transgenic line could be combined with knockout technologies to determine if pcdh1a is required for proper columnar development and possibly discover additional pcdh1a functions. Overall, this study supports a role for protocadherins in partitioning the nervous system, and suggests the model of columnar modules defined by δ-protocadherins in the tectum may apply to additional brain regions.
Material and methods
BAC recombineering
A BAC clone harboring pcdh1a (DKEY-225G6) was obtained from Source
Biosciences. This BAC contains the complete gene along with ~9 kb upstream of the start codon and ~176 Kb downstream of the stop codon. The BAC DNA was introduced into EL250 cells for sequential addition of transgene components by homologous
135
recombination (E. C. Lee et al., 2001). First, an inverted iTol2-Ampicillin cassette was introduced into the backbone of the BAC to increase transgenesis efficiency (Suster et al., 2011). Second we inserted a Gal4-FRT-Kanamycin-FRT cassette at the pcdh1a start site in exon 2 (ENSDART00000091004.5; figure 5.1A), followed by excision of the kanamycin marker by arabinose induction of flpe recombinase. Last, a 5xUAS:Lifeact-
GFP-Kanamycin cassette was inserted into exon 3 to create the final transgene construct
BAC(pcdh1a:Gal4-VP16, USA:lifeact-GFP). The EL250 cells were provided by N. Copeland
(National Institute of Health, Bethesda, MD), and M. Suster provided the iTol2 regents
(Uni Research AS High Technology Center, Bergen, Norway).
Zebrafish transgenesis and animal care
One-cell stage embryos were injected with 1nl of 50ng/µl BAC DNA and 100ng/µl
Tol2 transposase mRNA. Embryos were screened for fluoresce at 2dpf and fluorescent embryo were grown to adulthood. To establish a stable line, a founder with germline transmission of the transgene was identified and outcrossed with wild-type zebrafish.
The transgenic line was developed in a Tübingen longfin and AB hybrid strain of zebrafish (Danio rerio). Adult zebrafish and embryos were maintained at ~28.5° C in accordance with the Ohio State Institution Animal Care and Use Committee protocols.
Imaged embryos were raised in E3 embryo media with 0.003% phenylthiourea to inhibit pigmentation and staged according to Westerfield, 1995.
136
Two-color Fluorescent in situ hybridization (FISH)
DNA templates for Riboprobes were generated by PCR with the following primers including a T7 RNA polymerase site in each reverse primer:
Pcdh1aF, 5’-GCTGAC TGGTGCGGTTGGTGGC-3’
Pcdh1a-T7R, 5’-CGTAATACGACTCACTATAGGGCGGTGGGTCAC AAGACCAATTCC-3’
Gal4F, 5’-GCCTCCTGAAAGATGAAGCTA-3’
Gal4-T7R, 5’-CGTAATACGACTCACTATAGGCCGCTACATATCCAGAGCGCCGTA -3’
Antisense riboprobes were transcribed in vitro (Promega) using digoxygenin-dUTP
(Roche) or fluorescein-dUTP for the pcdh1a and Gal4 probes respectively. Two-color whole mount in situs were performed as previously described. Briefly, embryos were fixed overnight at 4°C in 4% paraformaldehyde, dehydrated in 100% MeOH, and store at
-20°C. Embryos were rehydrated with a methanol series of decreasing methanol concentration and were permeabilized with proteinase K (10µg/ml; Roche). Embryos were refixed in 4% paraformaldehyde, then hybridized with pcdh1a (1ng/µl) and Gal4 probes (1ng/µl) at 65°C overnight. The digoxygenin-labled pcdh1a probe detected with antidigoxygenin Fab-HRP (Roche) followed by development in tetramethylrhodamine substrate (Perkin-Elmer TSA Plus kit). Subsequently, the fluorescein-labeled probe was developed with an anti-fluorescein primary antibody (Roche), a goat anti-mouse HRP secondary antibody (Invitrogen), and fluorescein substrate (Perkin-Elmer TSA Plus kit).
137
Two-photon imaging and image processing
Two-photon imaging of live zebrafish larvae was performed at previously described in Cooper et al. 2015 on a custom built microscope controlled by ScanImage
(Pologruto et al., 2003). Briefly, larvea were embedded in 1% low melting point agarose and imaged with water immersion objectives from Olympus: 60x/NA1.0
(LUMPLFLN60X/W) or 20x/NA1.0 (XLUMPLFLN20XW). Images were processed in imageJ software (https://imagej.nih.gov/ij/) to create maximum intensity projections and color- coded z-stack projections, using the time-lapse color coder plugin.
138
Figure 5.1: TgBAC(pcdh1a:Gal4-VP16, USA:lifeact-GFP) recapitulates endogenous pcdh1a expression. (A) Schematic of BAC(pcdh1a:Gal4-VP16, USA:lifeact-GFP), which was modified from BAC clone DKEY-225G6 (see methods). Black filling of boxes represents coding regions of pcdh1a, gray filling represents the 5’ and 3’ untranslated regions, and white or green filling represents inserted transgene components. Abbreviations: Amp, ampicillin; Kan, kanamycin; LA, Lifeact-GFP. (B-C) Low magnification widefield images of transgenic line. Lateral (B) and dorsal (C) images were obtained at 2 days post fertilization (dpf), 3 dpf, and 4 dpf with (top panel) and without (bottom panel) limited transmitted light for viewing of reference structures. Dorsal is at the top in B, and rostral is to the left in B and C. Scale bar is 1 mm in B and C. (D) Two-color fluorescent in situ hybridization of transgenic embryos at 4 dpf. Gal4 probe represented in Green (left), pcdh1a probe represented in magenta (middle), and merge shown in right panel. Rostral is to the left. Scale bar, 200µm.
139
Figure 5.2: pcdh1a expression in the zebrafish midbrain. (A-C) Two-photo maximum intensity z-stacks at varying depths in the midbrain from a dorsal view: most dorsal (A), medial (B) ventral (C). (A’-C’) Color scale represents the depth of each optical section contributing to the corresponding maximum intensity projection in A-C. Dashed line in C marks the boundary between forebrain and midbrain (D-E) Higher–magnification views of the columnar organization in the optic tecti from additional zebrafish larvae. A caudal portion of a right tectum is shown in D, and the rostral portion of a left tectum is shown in E; see also location in panel F. Arrow heads point to radial glia with a column of associated neurons. The two arrow heads pointing upward in E are radial glia associated with columns in the contralateral tectum. (F) Schematic of zebrafish brain showing the location of each image in A-E. Rostal is toward the left in all images. Scale Bar 150µm (A-C), 60µm (D-E). Abbreviations: AC, anterior commissure; C, caudal; Ce, cerebellum; CPT, commissure of the caudal tuberculum; D, dorsal; FB, forebrain; HaC, habenular commissure; HB, hindbrain; HiC, hindbrain commissure; LLF, lateral logitudinal fasiculus; MB, midbrain; MLF, medial logitudinal fasiculus; MO, medulla oblongata; OB, olfactory bulb; OC, optic chiasm; OE, olfactory epithelium; OT, optic tectum; Pa, Pallium; PC, posterior commissure; POC, post-optic commissure; Pr, pretectum; R, rostral; SAC, statoacoustic ganglion; Sp, subpallium; TC, tectal commissure; Th, thalamus; TG, trigeminal ganglion; V, ventral; VTC, ventral tegmental commissure.
140
Figure 5.3: pcdh1a expression in the zebrafish forebrain. (A-D) Two-photo maximum intensity z-stacks at varying depths in the forebrain from a dorsal view: most dorsal (A), dorsomedial (B), ventromedial (C), and most ventral (D). Dashed line in A marks the boundary between forebrain and midbrain. (A’-D’) Color scale represents the depth of each optical section contributing to the corresponding maximum intensity projection in A-D. (E-G) Higher–magnification views of the columnar organization around radial glia (arrow heads) in pretectum (E) and thalamus (F); radial glia without clear columns are seen in the pallium (G). (H) Schematic of zebrafish brain showing the location of each image in A-G. Rostral is toward the left in all images. Scale bar 150µm (A-D), 60µm (E-G). Abbreviations: See list in figure 5.2.
141
Figure 5.4: pcdh1a expression in the zebrafish hindbrain. (A-C) Two-photo maximum intensity z-stacks at varying depths in the hindbrain from a dorsal view: most dorsal (A), medial (B), and most ventral (C). (A’-C’) Color scale represents the depth of each optical section contributing to the corresponding maximum intensity projection in A-C. (D) Two-photo maximum intensity z-stack from a lateral view allows visualization of columns in the medulla oblongata. (E) Higher magnification view of additional columns in the medulla oblongata of the same larva shown in D. Arrow heads mark columns in D and E. Scale Bar: 150µm (A-D), 60µm (E). Abbreviations: See list in figure 5.2
142
Figure 5.5. A variety of motor neurons, sensory neurons and interneurons express pcdh1a in the spinal cord. (A-C) Examples of neurons frequently seen in the pcdh1a transgenic zebrafish. Asterisk (*) marks Rohan-Beard neurons. Arrows mark the axon projection of MiP in A and of CoSa in C. Arrow heads mark the bipolar projections of the DRG in B and the axon projection of CiD in C. Skin cells and a blood vessel with pcdh1a expression are bracketed in C and B respectively. Scale Bar: 50µm in A and C-G; 39µm in B. (A’-C’) Color scale represents the depth of each optical section contributing to the corresponding maximum intensity projection in A-C. (D-G) Examples of neurons occasionally seen in the pcdh1a transgenic zebrafish. (D’-G’) Color represents the depth of each optical section contributing the maximum intensity projection in D-G. See color-depth scale in A’. (H) Schematic summarizing the neurons indentified in the spinal cord, adapted from Bernhardt et al. 1990. Abbreviations: CaP, caudal primary motor neuron; CiD, circumferential descending interneuron; CoBL, commissural bifurcating longitudinal interneuron; CoSa, commissural secondary ascending interneuron; DRG, dorsal root ganglion; MiP, middle primary motor neuron; RoP, rostral primary motor neuron; S, secondary motor neuron; UCoD, unipolar commissural descending; VeMe, ventral medial; Asterisk (*), Rohan-Beard neurons.
143
Chapter 6: Conclusion
δ-protocadherins have been implicated in numerous neurodevelopmental disorders including autism, epilepsy, and schizophrenia (Jontes, 2016; Kahr et al., 2013;
Redies et al., 2012). However, the molecular mechanisms by which they direct neurodevelopmental processes is still unclear. Here, we explored δ-protocadherin function, both from a molecular perspective, by determining their mechanism of adhesion, and from a developmental perspective, by tracking δ-protocadherin expressing cells in vivo during zebrafish brain development.
Columnar Development of the Nervous System
While examining protocadherin expression patterns, we noticed radial columns of expression in the optic tectum of the zebrafish brain. Further study in a protocadherin-19 transgenic line TgBAC(pcdh19:Gal4-VP16,UAS:Lifeact-GFP)os49 revealed columnar developmental units built by pcdh19+ progenitor cells in the neuroepithelium. Moreover, the absence of pcdh19 disrupted the columnar organization in the tectum and perturbed visually-guided behaviors (Cooper et al.,
2015). This suggests the columnar organization may be important for the development and function of visual circuitry.
144
Similarly, while surveying the expression of a transgenic line for another protocadherin, pcdh1a, we saw columnar organization in the thalamus, pretectum and medulla oblongata (in addition to the optic tectum), suggesting that protocadherins may have a role in subdividing columnar units throughout the brain (chapter 5). Additional studies are needed to further examine the developmental properties of these columns.
For example, it is unclear whether these protocadherin-defined columns continue until the adult stage, or if it is only a transient pattern used for directing early brain development. In addition, each columnar unit could be defined by a single δ- protocadherin or by a combination of δ-protocadherins being expressed. It would be insightful to combine protocadherin transgenic lines with different color outputs, so the relationship between each of the protocadherin expression domains can be evaluated at the cellular level.
Adhesion Mechanism of δ-Protocadherins
Although the cadherin family is well known for their adhesive function, it is unclear whether all members of the family can directly mediate adhesion (X. Chen &
Gumbiner, 2006a; Hirofumi Morishita & Yagi, 2007; Weiner & Jontes, 2013). For the δ- protocadherin subfamily, different methods have yielded varying results regarding their adhesive capabilities. Bead aggregation assays for Pcdh19, Pcdh1b, Pcdh7b, and Pcdh9 showed no evidence of homophilic adhesion, but cell-based aggregation assays demonstrated weak homophilic adhesion for Pcdh19, Pcdh1, and Pcdh10 (also called
145
OL-protocadherin) (Biswas et al., 2010; Blevins et al., 2011; Emond et al., 2011; S Hirano,
Yan, & Suzuki, 1999; Sano et al., 1993). It is possible that certain assays may be more sensitive in detecting adhesion or that necessary cofactors are only present in the cellular context. For Pcdh19, we were only able to detect substantial bead aggregation with a modified assay, including gentle rocking and longer incubation times (Cooper
2016), which suggests weaker adhesion may be overlooked in some methods. However, this does not diminish the possibility of cofactors influencing adhesive capabilities.
Moreover, interactions of δ-protocadherins with the classical cadherins has been shown to strengthen the adhesive ability of some protocadherins, but this adhesion does not depend on the classical cadherin’s tryptophan. For example, Pcdh19 can form a cis adhesion complex with Ncad which has increased strength compared to Pcdh19 alone
(Emond et al., 2011).
Through X-ray crystallography, we discovered the Pcdh19 adhesive interface, and validated it by showing mutations at the putative interface disrupt adhesion by
Pcdh19. Furthermore, these same mutations disrupt adhesion by the Pcdh19-Ncad complex, indicating that Pcdh19 uses a similar (if not the same) interface even in the presence of Ncad (Cooper et al., 2016). Yet, it is still unclear how Ncad is promoting stronger adhesion of the complex compare to Pcdh19 alone.
Based on alignments between Pcdh19 and the other δ-protocadherins, we proposed all the δ-protocadherins may use similar modes of adhesion, with residue variations providing adhesive specificity to each member of the subfamily (Cooper et al.,
2016). The varied specificities could lead to cell sorting during regionalization and 146
contribute to the columnar organization we observed in the zebrafish brain (Cavodeassi
& Houart, 2012; Cooper et al., 2015; Redies et al., 2011).
Implications for PCDH19 Female Epilepsy
The intriguing pedigrees of PCDH19 Female Epilepsy (PCDH19-FE) and genetic analysis of PCDH-FE patients implicates mosaicism as a critical factor in the disease mechanism (Depienne et al. 2009; Dibbens et al. 2008; Terracciano et al. 2016).
Furthermore, the cellular interference hypothesis suggests that improper interactions of cells expressing mutant PCDH19 with cells expressing wild-type PCDH19 result in aberrant neural development (Depienne and LeGuern 2012). Our finding that the zebrafish brain develops with clonal columnar units implies that the PCDH19 allele expressed in human columnar progenitors will be passed down to each of the cells of the column, since the random X-chromosome inactivation is established much earlier
(Cooper et al., 2015; Payer, 2016). Consequently, each columnar developmental unit would express either wild-type PCDH19 (PCDH19WT) or mutant PCDH19 (PCDH19MUT).
Therefore, aberrant interactions between pcdh19MUT cell and pcdh19WT cells would have to occur either before radial clonal units develop, or between adjacent columns, or between distantly connecting brain regions.
With the structure of Pcdh19 EC1-4 (extracellular cadherin repeats 1-4), we were able to map >70% of missense Pcdh19-FE mutations (Cooper 2016). This provided a framework for inferring the impact of each mutation on biochemical properties of the
147
protein, and revealed mutations that disrupt adhesion without significantly impacting the stability of the protein. The mutations at the adhesion interface are particularly interesting for exploring the cellular interference hypothesis. By implementing the genome engineering design in chapter 4 and making a mosaic model with different colors marking pcdh19MUT cells and Pcdh19WT cell, we can learn how the mutant and wild-type cells interact at various stages of development.
The research laid out in this dissertation informs current theories on embryonic brain development, protocadherin adhesion mechanisms, and molecular mechanism of neurodevelopmental disease. With a greater understanding of the molecular mechanisms involved, we hope better treatments will become available for both
PCDH19 Female Epilepsy and the many other neurodevelopmental diseases.
148
References
Aamar, E., & Dawid, I. B. (2008). Protocadherin-18a has a role in cell adhesion, behavior and migration in zebrafish development. Developmental Biology, 318(2), 335–46. http://doi.org/10.1016/j.ydbio.2008.03.040
Aberle, H., Schwartz, H., & Kemler, R. (1996). Cadherin-catenin complex: protein interactions and their implications for cadherin function. Journal of Cellular Biochemistry, 61(4), 514–523. http://doi.org/10.1002/(SICI)1097- 4644(19960616)61:4<514::AID-JCB4>3.0.CO;2-R
Akhmanova, A., Stehbens, S. J., & Yap, A. S. (2009). Touch, grasp, deliver and control: functional cross-talk between microtubules and cell adhesions. Traffic (Copenhagen, Denmark), 10(3), 268–274. http://doi.org/10.1111/j.1600-0854.2008.00869.x
Al-Jassar, C., Bikker, H., Overduin, M., & Chidgey, M. (2013). Mechanistic basis of desmosome-targeted diseases. Journal of Molecular Biology, 425(21), 4006–4022. http://doi.org/10.1016/j.jmb.2013.07.035
Antelmi, E., Mastrangelo, M., Bisulli, F., Spaccini, L., Stipa, C., Mostacci, B., … Tinuper, P. (2012). Semiological study of ictal affective behaviour in epilepsy and mental retardation limited to females (EFMR). Epileptic Disorders : International Epilepsy Journal with Videotape, 14(3), 304–309. http://doi.org/10.1684/epd.2012.0526
Apuschkin, M., Ougaard, M., & Rekling, J. C. (2013). Spontaneous calcium waves in granule cells in cerebellar slice cultures. Neuroscience Letters, 553, 78–83. http://doi.org/10.1016/j.neulet.2013.08.022
Aran, A., Rosenfeld, N., Jaron, R., Renbaum, P., Zuckerman, S., Fridman, H., … Levy-Lahad, E. (2016). Loss of function of PCDH12 underlies recessive microcephaly mimicking intrauterine infection. Neurology, 86(21), 2016–24. http://doi.org/10.1212/WNL.0000000000002704
Ashkenazy, H., Abadi, S., Martz, E., Chay, O., Mayrose, I., Pupko, T., & Ben-Tal, N. (2016). ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules. Nucleic Acids Research. http://doi.org/10.1093/nar/gkw408
Azevedo, F. A. C., Carvalho, L. R. B., Grinberg, L. T., Farfel, J. M., Ferretti, R. E. L., Leite, R. E. P., … Herculano-Houzel, S. (2009). Equal numbers of neuronal and nonneuronal cells make the human brain an isometrically scaled-up primate brain. The Journal of Comparative Neurology, 513(5), 532–541. http://doi.org/10.1002/cne.21974
Bagatto, B., Francl, J., Liu, B., & Liu, Q. (2006). Cadherin2 (N-cadherin) plays an essential role in zebrafish cardiovascular development. BMC Developmental Biology, 6, 23. http://doi.org/10.1186/1471-213X-6-23
Barry, J., Gu, Y., Jukkola, P., O’Neill, B., Gu, H., Mohler, P. J., … Gu, C. (2014). Ankyrin-G directly binds to kinesin-1 to transport voltage-gated Na+ channels into axons. Developmental Cell, 28(2), 117–31. http://doi.org/10.1016/j.devcel.2013.11.023
Bedell, V., Campbell, J., Poshusta, T., Starker, C., Krug, R. 2nd, Tan, W., … Wang, Y. (2012). In vivo genome editing using a high-efficiency TALEN system. Nature, 491(7422), 114–118.
Berndt, J. D., Aoyagi, A., Yang, P., Anastas, J. N., Tang, L., & Moon, R. T. (2011). Mindbomb 1, an E3 ubiquitin ligase, forms a complex with RYK to activate Wnt/β-catenin signaling. The Journal of Cell Biology, 194(5), 737–50. http://doi.org/10.1083/jcb.201107021 149
Bernhardt, R. R., Chitnis, A. B., Lindamer, L., & Kuwada, J. Y. (1990). Identification of spinal neurons in the embryonic and larval zebrafish. The Journal of Comparative Neurology, 302(3), 603–616. http://doi.org/10.1002/cne.903020315
Biswas, S., Emond, M. R., Duy, P. Q., Hao, L. T., Beattie, C. E., & Jontes, J. D. (2014). Protocadherin-18b interacts with Nap1 to control motor axon growth and arborization in zebrafish. Molecular Biology of the Cell, 25(5), 633–42. http://doi.org/10.1091/mbc.E13-08-0475
Biswas, S., Emond, M. R., & Jontes, J. D. (2010). Protocadherin-19 and N-cadherin interact to control cell movements during anterior neurulation. The Journal of Cell Biology, 191(5), 1029–41. http://doi.org/10.1083/jcb.201007008
Biswas, S., & Jontes, J. D. (2009). Cloning and characterization of zebrafish protocadherin-17. Development Genes and Evolution, 219(5), 265–271. http://doi.org/10.1007/s00427-009-0288-6
Blevins, C. J., Emond, M. R., Biswas, S., & Jontes, J. D. (2011). Differential expression, alternative splicing, and adhesive properties of the zebrafish δ1-protocadherins. Neuroscience, 199, 523–34. http://doi.org/10.1016/j.neuroscience.2011.09.061
Bock, E. (1991). Cell-cell adhesion molecules. Biochemical Society Transactions, 19(4), 1076–1080.
Boggon, T. J., Murray, J., Chappuis-Flament, S., Wong, E., Gumbiner, B. M., & Shapiro, L. (2002). C-cadherin ectodomain structure and implications for cell adhesion mechanisms. Science (New York, N.Y.), 296(5571), 1308–13. http://doi.org/10.1126/science.1071559
Bononi, J., Cole, A., Tewson, P., Schumacher, A., & Bradley, R. (2008). Chicken protocadherin-1 functions to localize neural crest cells to the dorsal root ganglia during PNS formation. Mechanisms of Development, 125(11–12), 1033–1047. http://doi.org/10.1016/j.mod.2008.07.007
Brasch, J., Harrison, O. J., Ahlsen, G., Carnally, S. M., Henderson, R. M., Honig, B., & Shapiro, L. (2011). Structure and binding mechanism of vascular endothelial cadherin: a divergent classical cadherin. Journal of Molecular Biology, 408(1), 57–73. http://doi.org/10.1016/j.jmb.2011.01.031
Brasch, J., Harrison, O. J., Honig, B., & Shapiro, L. (2012). Thinking outside the cell: how cadherins drive adhesion. Trends in Cell Biology, 22(6), 299–310. http://doi.org/10.1016/j.tcb.2012.03.004; 10.1016/j.tcb.2012.03.004
Brasch, J., Harrison, O. J., Honig, B., & Shapiro, L. (2012). Thinking outside the cell: how cadherins drive adhesion. Trends in Cell Biology, 22(6), 299–310. http://doi.org/10.1016/j.tcb.2012.03.004
Burgess, H. A., & Granato, M. (2007). Modulation of locomotor activity in larval zebrafish during light adaptation. The Journal of Experimental Biology, 210(Pt 14), 2526–2539. http://doi.org/10.1242/jeb.003939
Burgess, H. A., Schoch, H., & Granato, M. (2010). Distinct retinal pathways drive spatial orientation behaviors in zebrafish navigation. Current Biology : CB, 20(4), 381–386. http://doi.org/10.1016/j.cub.2010.01.022
Burrill, J. D., & Easter, S. S. J. (1994). Development of the retinofugal projections in the embryonic and larval zebrafish (Brachydanio rerio). The Journal of Comparative Neurology, 346(4), 583–600. http://doi.org/10.1002/cne.903460410
Butler, M. G., Rafi, S. K., Hossain, W., Stephan, D. A., & Manzardo, A. M. (2015). Whole exome sequencing in females with autism implicates novel and candidate genes. International Journal of Molecular Sciences, 16(1), 1312– 1335. http://doi.org/10.3390/ijms16011312
Camacho, A., Simon, R., Sanz, R., Vinuela, A., Martinez-Salio, A., & Mateos, F. (2012). Cognitive and behavioral profile in females with epilepsy with PDCH19 mutation: two novel mutations and review of the literature. Epilepsy & Behavior : E&B, 24(1), 134–137. http://doi.org/10.1016/j.yebeh.2012.02.023 [doi] 150
Cappelletti, S., Specchio, N., Moavero, R., Terracciano, A., Trivisano, M., Pontrelli, G., … Cusmai, R. (2015). Cognitive development in females with PCDH19 gene-related epilepsy. Epilepsy & Behavior : E&B, 42, 36–40. http://doi.org/10.1016/j.yebeh.2014.10.019
Cardona, A., Saalfeld, S., Schindelin, J., Arganda-Carreras, I., Preibisch, S., Longair, M., … Douglas, R. J. (2012). TrakEM2 software for neural circuit reconstruction. PloS One, 7(6), e38011. http://doi.org/10.1371/journal.pone.0038011
Carrasquillo, M. M., Zou, F., Pankratz, V. S., Wilcox, S. L., Ma, L., Walker, L. P., … Younkin, S. G. (2009). Genetic variation in PCDH11X is associated with susceptibility to late-onset Alzheimer’s disease. Nature Genetics, 41(2), 192–198. http://doi.org/10.1038/ng.305
Cavodeassi, F., & Houart, C. (2012). Brain regionalization: of signaling centers and boundaries. Developmental Neurobiology, 72(3), 218–233. http://doi.org/10.1002/dneu.20938
Cermak, T., Doyle, E. L., Christian, M., Wang, L., Zhang, Y., Schmidt, C., … Voytas, D. F. (2011). Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic Acids Research, 39(12), e82. http://doi.org/10.1093/nar/gkr218
Chang, H., Hoshina, N., Zhang, C., Ma, Y., Cao, H., Wang, Y., … Li, M. (2017). The protocadherin 17 gene affects cognition, personality, amygdala structure and function, synapse development and risk of major mood disorders. Molecular Psychiatry. http://doi.org/10.1038/mp.2016.231
Chen, B., Brinkmann, K., Chen, Z., Pak, C. W., Liao, Y., Shi, S., … Rosen, M. K. (2014). The WAVE regulatory complex links diverse receptors to the actin cytoskeleton. Cell, 156(1–2), 195–207. http://doi.org/10.1016/j.cell.2013.11.048
Chen, X., & Gumbiner, B. M. (2006a). Crosstalk between different adhesion molecules. Current Opinion in Cell Biology, 18(5), 572–578. http://doi.org/10.1016/j.ceb.2006.07.002
Chen, X., & Gumbiner, B. M. (2006b). Paraxial protocadherin mediates cell sorting and tissue morphogenesis by regulating C-cadherin adhesion activity. The Journal of Cell Biology, 174(2), 301–313. http://doi.org/10.1083/jcb.200602062
Chen, X., Koh, E., Yoder, M., & Gumbiner, B. M. (2009). A protocadherin-cadherin-FLRT3 complex controls cell adhesion and morphogenesis. PloS One, 4(12), e8411. http://doi.org/10.1371/journal.pone.0008411
Chen, X., Molino, C., Liu, L., & Gumbiner, B. M. (2007). Structural elements necessary for oligomerization, trafficking, and cell sorting function of paraxial protocadherin. The Journal of Biological Chemistry, 282(44), 32128–37. http://doi.org/10.1074/jbc.M705337200
Chen, W. V, & Maniatis, T. (2013). Clustered protocadherins. Development (Cambridge, England), 140(16), 3297–302. http://doi.org/10.1242/dev.090621
Chung, W.-S., & Barres, B. A. (2009). Selective Remodeling: Refining Neural Connectivity at the Neuromuscular Junction. PLOS Biology, 7(8), e1000185. Retrieved from http://dx.doi.org/10.1371%252Fjournal.pbio.1000185
Ciatto, C., Bahna, F., Zampieri, N., VanSteenhouse, H. C., Katsamba, P. S., Ahlsen, G., … Shapiro, L. (2010). T-cadherin structures reveal a novel adhesive binding mechanism. Nature Structural & Molecular Biology, 17(3), 339–47. http://doi.org/10.1038/nsmb.1781
Cooper, S. R., Emond, M. R., Duy, P. Q., Liebau, B. G., Wolman, M. A., & Jontes, J. D. (2015). Protocadherins control the modular assembly of neuronal columns in the zebrafish optic tectum. The Journal of Cell Biology, 211(4), 807–814. http://doi.org/10.1083/jcb.201507108
151
Cooper, S. R., Jontes, J. D., & Sotomayor, M. (2016). Structural determinants of adhesion by Protocadherin-19 and implications for its role in epilepsy. eLife, 5. http://doi.org/10.7554/eLife.18529
Dahlem, T. J., Hoshijima, K., Jurynec, M. J., Gunther, D., Starker, C. G., Locke, A. S., … Grunwald, D. J. (2012). Simple methods for generating and detecting locus-specific mutations induced with TALENs in the zebrafish genome. PLoS Genetics, 8(8), e1002861. http://doi.org/10.1371/journal.pgen.1002861
Dean, B., Keriakous, D., Scarr, E., & Thomas, E. A. (2007). Gene expression profiling in Brodmann’s area 46 from subjects with schizophrenia. The Australian and New Zealand Journal of Psychiatry, 41(4), 308–320. http://doi.org/10.1080/00048670701213245
Dechavanne, V., Barrillat, N., Borlat, F., Hermant, A., Magnenat, L., Paquet, M., … Chevalet, L. (2011). A high- throughput protein refolding screen in 96-well format combined with design of experiments to optimize the refolding conditions. Protein Expression and Purification, 75(2), 192–203. http://doi.org/10.1016/j.pep.2010.09.008
Depienne, C., Bouteiller, D., Keren, B., Cheuret, E., Poirier, K., Trouillard, O., … Leguern, E. (2009). Sporadic infantile epileptic encephalopathy caused by mutations in PCDH19 resembles Dravet syndrome but mainly affects females. PLoS Genetics, 5(2), e1000381. http://doi.org/10.1371/journal.pgen.1000381 [doi]
Depienne, C., & LeGuern, E. (2012). PCDH19-related infantile epileptic encephalopathy: an unusual X-linked inheritance disorder. Human Mutation, 33(4), 627–34. http://doi.org/10.1002/humu.22029
Depienne, C., Trouillard, O., Bouteiller, D., Gourfinkel-An, I., Poirier, K., Rivier, F., … LeGuern, E. (2011). Mutations and deletions in PCDH19 account for various familial or isolated epilepsies in females. Human Mutation, 32(1), E1959-75. http://doi.org/10.1002/humu.21373 [doi]
Dibbens, L. M., Kneen, R., Bayly, M. A., Heron, S. E., Arsov, T., Damiano, J. A., … Scheffer, I. E. (2011). Recurrence risk of epilepsy and mental retardation in females due to parental mosaicism of PCDH19 mutations. Neurology, 76(17), 1514–1519. http://doi.org/10.1212/WNL.0b013e318217e7b6 [doi]
Dibbens, L. M., Tarpey, P. S., Hynes, K., Bayly, M. A., Scheffer, I. E., Smith, R., … Gécz, J. (2008). X-linked protocadherin 19 mutations cause female-limited epilepsy and cognitive impairment. Nature Genetics, 40(6), 776–81. http://doi.org/10.1038/ng.149
Dimova, P. S., Kirov, A., Todorova, A., Todorov, T., & Mitev, V. (2012). A novel PCDH19 mutation inherited from an unaffected mother. Pediatric Neurology, 46(6), 397–400. http://doi.org/10.1016/j.pediatrneurol.2012.03.004
Duszyc, K., Terczynska, I., & Hoffman-Zacharska, D. (2015). Epilepsy and mental retardation restricted to females: X- linked epileptic infantile encephalopathy of unusual inheritance. Journal of Applied Genetics, 56(1), 49–56. http://doi.org/10.1007/s13353-014-0243-8
Easter, S. S. J., Burrill, J., Marcus, R. C., Ross, L. S., Taylor, J. S., & Wilson, S. W. (1994). Initial tract formation in the vertebrate brain. Progress in Brain Research, 102, 79–93. http://doi.org/10.1016/S0079-6123(08)60533-6
Elledge, H. M., Kazmierczak, P., Clark, P., Joseph, J. S., Kolatkar, A., Kuhn, P., & Müller, U. (2010). Structure of the N terminus of cadherin 23 reveals a new adhesion mechanism for a subset of cadherin superfamily members. Proceedings of the National Academy of Sciences of the United States of America, 107(23), 10708–10712. http://doi.org/10.1073/pnas.1006284107
Emond, M. R., Biswas, S., Blevins, C. J., & Jontes, J. D. (2011). A complex of Protocadherin-19 and N-cadherin mediates a novel mechanism of cell adhesion. The Journal of Cell Biology, 195(7), 1115–1121. http://doi.org/10.1083/jcb.201108115; 10.1083/jcb.201108115
Emond, M. R., Biswas, S., & Jontes, J. D. (2009). Protocadherin-19 is essential for early steps in brain morphogenesis. Developmental Biology, 334(1), 72–83. http://doi.org/10.1016/j.ydbio.2009.07.008 152
Emond, M. R., & Jontes, J. D. (2014). Bead Aggregation Assays for the Characterization of Putative Cell Adhesion Molecules, (92), e51762. http://doi.org/doi:10.3791/51762
Emsley, P., Lohkamp, B., Scott, W. G., & Cowtan, K. (2010). Features and development of Coot. Acta Crystallographica. Section D, Biological Crystallography, 66(Pt 4), 486–501. http://doi.org/10.1107/S0907444910007493
Faura Tellez, G., Vandepoele, K., Brouwer, U., Koning, H., Elderman, R. M., Hackett, T.-L., … Nawijn, M. C. (2015). Protocadherin-1 binds to SMAD3 and suppresses TGF-beta1-induced gene transcription. American Journal of Physiology. Lung Cellular and Molecular Physiology, 309(7), L725-35. http://doi.org/10.1152/ajplung.00346.2014
Faura Tellez, G., Willemse, B. W. M., Brouwer, U., Nijboer-Brinksma, S., Vandepoele, K., Noordhoek, J. A., … Koppelman, G. H. (2016). Protocadherin-1 Localization and Cell-Adhesion Function in Airway Epithelial Cells in Asthma. PloS One, 11(10), e0163967. http://doi.org/10.1371/journal.pone.0163967
Flanagan, J. G., & Vanderhaeghen, P. (1998). The ephrins and Eph receptors in neural development. Annual Review of Neuroscience, 21, 309–345. http://doi.org/10.1146/annurev.neuro.21.1.309
Frank, M., & Kemler, R. (2002). Protocadherins. Current Opinion in Cell Biology, 14(5), 557–62.
Gagliardi, M., Annesi, G., Sesta, M., Tarantino, P., Conti, P., Labate, A., … Gambardella, A. (2015). PCDH19 mutations in female patients from Southern Italy. Seizure, 24, 118–120. http://doi.org/10.1016/j.seizure.2014.08.010
Gaily, E., Anttonen, A.-K., Valanne, L., Liukkonen, E., Traskelin, A.-L., Polvi, A., … Lehesjoki, A.-E. (2013). Dravet syndrome: new potential genetic modifiers, imaging abnormalities, and ictal findings. Epilepsia, 54(9), 1577– 1585. http://doi.org/10.1111/epi.12256
Gaitan, Y., & Bouchard, M. (2006). Expression of the delta-protocadherin gene Pcdh19 in the developing mouse embryo. Gene Expression Patterns : GEP, 6(8), 893–9. http://doi.org/10.1016/j.modgep.2006.03.001
Garrett, A. M., Schreiner, D., Lobas, M. A., & Weiner, J. A. (2012). gamma-protocadherins control cortical dendrite arborization by regulating the activity of a FAK/PKC/MARCKS signaling pathway. Neuron, 74(2), 269–276. http://doi.org/10.1016/j.neuron.2012.01.028
Geng, R., Sotomayor, M., Kinder, K. J., Gopal, S. R., Gerka-Stuyt, J., Chen, D. H.-C., … Alagramam, K. N. (2013). Noddy, a mouse harboring a missense mutation in protocadherin-15, reveals the impact of disrupting a critical interaction site between tip-link cadherins in inner ear hair cells. The Journal of Neuroscience : The Official Journal of the Society for Neuroscience, 33(10), 4395–404. http://doi.org/10.1523/JNEUROSCI.4514-12.2013
Gerlai, R. (2012). Using zebrafish to unravel the genetics of complex brain disorders. Current Topics in Behavioral Neurosciences, 12, 3–24. http://doi.org/10.1007/7854_2011_180
Gibson, D. A., Tymanskyj, S., Yuan, R. C., Leung, H. C., Lefebvre, J. L., Sanes, J. R., … Ma, L. (2014). Dendrite self- avoidance requires cell-autonomous slit/robo signaling in cerebellar purkinje cells. Neuron, 81(5), 1040–1056. http://doi.org/10.1016/j.neuron.2014.01.009
Goodman, K. M., Rubinstein, R., Thu, C. A., Bahna, F., Mannepalli, S., Ahlsén, G., … Shapiro, L. (2016). Structural Basis of Diverse Homophilic Recognition by Clustered α- and β-Protocadherins. Neuron. http://doi.org/10.1016/j.neuron.2016.04.004
Goodman, K. M., Rubinstein, R., Thu, C. A., Mannepalli, S., Bahna, F., Ahlsen, G., … Shapiro, L. (2016). gamma- Protocadherin structural diversity and functional implications. eLife, 5. http://doi.org/10.7554/eLife.20930
Gray, G. E., & Sanes, J. R. (1991). Migratory paths and phenotypic choices of clonally related cells in the avian optic tectum. Neuron, 6(2), 211–225.
153
Gray, G. E., & Sanes, J. R. (1992). Lineage of radial glia in the chicken optic tectum. Development (Cambridge, England), 114(1), 271–283.
Gregorio, S. P., Sallet, P. C., Do, K.-A., Lin, E., Gattaz, W. F., & Dias-Neto, E. (2009). Polymorphisms in genes involved in neurodevelopment may be associated with altered brain morphology in schizophrenia: preliminary evidence. Psychiatry Research, 165(1–2), 1–9. http://doi.org/10.1016/j.psychres.2007.08.011
Grueber, W. B., & Sagasti, A. (2010). Self-avoidance and tiling: Mechanisms of dendrite and axon spacing. Cold Spring Harbor Perspectives in Biology, 2(9), a001750. http://doi.org/10.1101/cshperspect.a001750
Grunwald, D. J., & Eisen, J. S. (2002). Headwaters of the zebrafish -- emergence of a new model vertebrate. Nature Reviews. Genetics, 3(9), 717–724. http://doi.org/10.1038/nrg892
Guilmatre, A., Dubourg, C., Mosca, A.-L., Legallic, S., Goldenberg, A., Drouin-Garraud, V., … Campion, D. (2009). Recurrent rearrangements in synaptic and neurodevelopmental genes and shared biologic pathways in schizophrenia, autism, and mental retardation. Archives of General Psychiatry, 66(9), 947–956. http://doi.org/10.1001/archgenpsychiatry.2009.80
Gumbiner, B. M. (2005). Regulation of cadherin-mediated adhesion in morphogenesis. Nature Reviews. Molecular Cell Biology, 6(8), 622–34. http://doi.org/10.1038/nrm1699
Hale, M. E., Ritter, D. A., & Fetcho, J. R. (2001). A confocal study of spinal interneurons in living larval zebrafish. The Journal of Comparative Neurology, 437(1), 1–16.
Hansen, J. E., Lund, O., Tolstrup, N., Gooley, A. A., Williams, K. L., & Brunak, S. (1998). NetOglyc: prediction of mucin type O-glycosylation sites based on sequence context and surface accessibility. Glycoconjugate Journal, 15(2), 115–30.
Hanson, Mg., Milner, L. D., & Landmesser, L. T. (2008, January). Spontaneous rhythmic activity in early chick spinal cord influences distinct motor axon pathfinding decisions. Brain Research Reviews. http://doi.org/10.1016/j.brainresrev.2007.06.021
Harrison, O. J., Bahna, F., Katsamba, P. S., Jin, X., Brasch, J., Vendome, J., … Shapiro, L. (2010). Two-step adhesive binding by classical cadherins. Nature Structural & Molecular Biology, 17(3), 348–357. http://doi.org/10.1038/nsmb.1784; 10.1038/nsmb.1784
Harrison, O. J., Bahna, F., Katsamba, P. S., Jin, X., Brasch, J., Vendome, J., … Shapiro, L. (2010). Two-step adhesive binding by classical cadherins. Nature Structural & Molecular Biology, 17(3), 348–57. http://doi.org/10.1038/nsmb.1784
Harrison, O. J., Brasch, J., Lasso, G., Katsamba, P. S., Ahlsen, G., Honig, B., & Shapiro, L. (2016). Structural basis of adhesive binding by desmocollins and desmogleins. Proceedings of the National Academy of Sciences of the United States of America, 113(26), 7160–7165. http://doi.org/10.1073/pnas.1606272113
Harrison, O. J., Jin, X., Hong, S., Bahna, F., Ahlsen, G., Brasch, J., … Honig, B. (2011). The extracellular architecture of adherens junctions revealed by crystal structures of type I cadherins. Structure (London, England : 1993), 19(2), 244–256. http://doi.org/10.1016/j.str.2010.11.016; 10.1016/j.str.2010.11.016
Hassan, B. A., & Hiesinger, P. R. (2015, October). Beyond Molecular Codes: Simple Rules to Wire Complex Brains. Cell. http://doi.org/10.1016/j.cell.2015.09.031
Hatta, K., Takagi, S., Fujisawa, H., & Takeichi, M. (1987). Spatial and temporal expression pattern of N-cadherin cell adhesion molecules correlated with morphogenetic processes of chicken embryos. Developmental Biology, 120(1), 215–227.
154
Hayashi, S., Inoue, Y., Kiyonari, H., Abe, T., Misaki, K., Moriguchi, H., … Takeichi, M. (2014). Protocadherin-17 mediates collective axon extension by recruiting actin regulator complexes to interaxonal contacts. Developmental Cell, 30(6), 673–87. http://doi.org/10.1016/j.devcel.2014.07.015
Hayashi, S., & Takeichi, M. (2015). Emerging roles of protocadherins: from self-avoidance to enhancement of motility. Journal of Cell Science, 128(8), 1455–1464. http://doi.org/10.1242/jcs.166306
Hayward, N. M. E. A., Yanev, P., Haapasalo, A., Miettinen, R., Hiltunen, M., Grohn, O., & Jolkkonen, J. (2011). Chronic hyperperfusion and angiogenesis follow subacute hypoperfusion in the thalamus of rats with focal cerebral ischemia. Journal of Cerebral Blood Flow and Metabolism : Official Journal of the International Society of Cerebral Blood Flow and Metabolism, 31(4), 1119–1132. http://doi.org/10.1038/jcbfm.2010.202
Hebb, D. O. (1949). The organization of behavior : a neuropsychological theory. New York: Wiley.
Higurashi, N., Nakamura, M., Sugai, M., Ohfu, M., Sakauchi, M., Sugawara, Y., … Hirose, S. (2013). PCDH19-related female-limited epilepsy: further details regarding early clinical features and therapeutic efficacy. Epilepsy Research, 106(1–2), 191–199. http://doi.org/10.1016/j.eplepsyres.2013.04.005
Higurashi, N., Shi, X., Yasumoto, S., Oguni, H., Sakauchi, M., Itomi, K., … Hirose, S. (2012). PCDH19 mutation in Japanese females with epilepsy. Epilepsy Research, 99(1–2), 28–37. http://doi.org/10.1016/j.eplepsyres.2011.10.014 [doi]
Higurashi, N., Takahashi, Y., Kashimada, A., Sugawara, Y., Sakuma, H., Tomonoh, Y., … Hirose, S. (2015). Immediate suppression of seizure clusters by corticosteroids in PCDH19 female epilepsy. Seizure, 27, 1–5. http://doi.org/10.1016/j.seizure.2015.02.006
Hildebrand, M. S., Myers, C. T., Carvill, G. L., Regan, B. M., Damiano, J. A., Mullen, S. A., … Mefford, H. C. (2016). A targeted resequencing gene panel for focal epilepsy. Neurology, 86(17), 1605–1612. http://doi.org/10.1212/WNL.0000000000002608
Hintsch, G., Zurlinden, A., Meskenaite, V., Steuble, M., Fink-Widmer, K., Kinter, J., & Sonderegger, P. (2002). The calsyntenins--a family of postsynaptic membrane proteins with distinct neuronal expression patterns. Molecular and Cellular Neurosciences, 21(3), 393–409.
Hirabayashi, T., & Yagi, T. (2014). Protocadherins in neurological diseases. Advances in Neurobiology, 8, 293–314.
Hirano, K., Kaneko, R., Izawa, T., Kawaguchi, M., Kitsukawa, T., & Yagi, T. (2012). Single-neuron diversity generated by Protocadherin-β cluster in mouse central and peripheral nervous systems . Frontiers in Molecular Neuroscience . Retrieved from http://journal.frontiersin.org/article/10.3389/fnmol.2012.00090
Hirano, S., & Takeichi, M. (2012). Cadherins in brain morphogenesis and wiring. Physiological Reviews, 92(2), 597– 634. http://doi.org/10.1152/physrev.00014.2011
Hirano, S., Yan, Q., & Suzuki, S. T. (1999). Expression of a novel protocadherin, OL-protocadherin, in a subset of functional systems of the developing mouse brain. The Journal of Neuroscience : The Official Journal of the Society for Neuroscience, 19(3), 995–1005.
Hoshina, M., Higurashi, N., Abe, Y., Mishima, H., Hosoya, M., Nakayama, T., & Hirose, S. (2015). [A patient with an early diagnosis of PCDH19-related epilepsy]. No to hattatsu. Brain and development, 47(4), 305–309.
Hoshina, N., Tanimura, A., Yamasaki, M., Inoue, T., Fukabori, R., Kuroda, T., … Yamamoto, T. (2013). Protocadherin 17 regulates presynaptic assembly in topographic corticobasal Ganglia circuits. Neuron, 78(5), 839–854. http://doi.org/10.1016/j.neuron.2013.03.031
155
Hsu, P. D., Scott, D. A., Weinstein, J. A., Ran, F. A., Konermann, S., Agarwala, V., … Zhang, F. (2013). DNA targeting specificity of RNA-guided Cas9 nucleases. Nature Biotechnology, 31(9), 827–832. http://doi.org/10.1038/nbt.2647
Hulpiau, P., & van Roy, F. (2009). Molecular evolution of the cadherin superfamily. The International Journal of Biochemistry & Cell Biology, 41(2), 349–369. http://doi.org/10.1016/j.biocel.2008.09.027
Hulpiau, P., & van Roy, F. (2011). New insights into the evolution of metazoan cadherins. Molecular Biology and Evolution, 28(1), 647–57. http://doi.org/10.1093/molbev/msq233
Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–38. http://doi.org/10.1016/0263-7855(96)00018-5
Hwang, W. Y., Fu, Y., Reyon, D., Maeder, M. L., Kaini, P., Sander, J. D., … Yeh, J. R. (2013). Heritable and precise zebrafish genome editing using a CRISPR-Cas system. PloS One, 8(7), e68708. http://doi.org/10.1371/journal.pone.0068708 [doi]
Hyafil, F., Babinet, C., & Jacob, F. (1981). Cell-cell interactions in early embryogenesis: a molecular approach to the role of calcium. Cell, 26(3 Pt 1), 447–454.
Hynes, K., Tarpey, P., Dibbens, L. M., Bayly, M. A., Berkovic, S. F., Smith, R., … Scheffer, I. E. (2010). Epilepsy and mental retardation limited to females with PCDH19 mutations can present de novo or in single generation families. Journal of Medical Genetics, 47(3), 211–216. http://doi.org/10.1136/jmg.2009.068817
Imai, T., Sakano, H., & Vosshall, L. B. (2010). Topographic mapping--the olfactory system. Cold Spring Harbor Perspectives in Biology, 2(8), a001776. http://doi.org/10.1101/cshperspect.a001776
Inoue, T., Tanaka, T., Takeichi, M., Chisaka, O., Nakamura, S., & Osumi, N. (2001). Role of cadherins in maintaining the compartment boundary between the cortex and striatum during development. Development (Cambridge, England), 128(4), 561–569.
Ito, H., & Yamamoto, N. (2009). Non-laminar cerebral cortex in teleost fishes? Biology Letters, 5(1), 117–121. http://doi.org/10.1098/rsbl.2008.0397
Izuta, Y., Taira, T., Asayama, A., Machigashira, M., Kinoshita, T., Fujiwara, M., & Suzuki, S. T. (2015). Protocadherin-9 involvement in retinal development in Xenopus laevis. Journal of Biochemistry, 157(4), 235–249. http://doi.org/10.1093/jb/mvu070
Jamal, S. M., Basran, R. K., Newton, S., Wang, Z., & Milunsky, J. M. (2010). Novel de novo PCDH19 mutations in three unrelated females with epilepsy female restricted mental retardation syndrome. American Journal of Medical Genetics. Part A, 152A(10), 2475–2481. http://doi.org/10.1002/ajmg.a.33611
Jiang, M., & Chen, G. (2006). High Ca2+-phosphate transfection efficiency in low-density neuronal cultures. Nature Protocols, 1(2), 695–700. http://doi.org/10.1038/nprot.2006.86
Johansen, M. B., Kiemer, L., & Brunak, S. (2006). Analysis and prediction of mammalian protein glycation. Glycobiology, 16(9), 844–53. http://doi.org/10.1093/glycob/cwl009
Jontes, J. D. (2016). The Nonclustered Protocadherins. In S. T. Suzuki & S. Hirano (Eds.), The Cadherin Superfamily: Key Regulators of Animal Development and Physiology (pp. 223–249). Tokyo: Springer Japan. http://doi.org/10.1007/978-4-431-56033-3_9
Jontes, J. D., & Emond, M. R. (2012). Fluorescence imaging of transgenic zebrafish embryos. Cold Spring Harbor Protocols, 2012(5). http://doi.org/10.1101/pdb.prot069245
156
Juberg, R. C., & Hellman, C. D. (1971). A new familial form of convulsive disorder and mental retardation limited to females. The Journal of Pediatrics, 79(5), 726–732. http://doi.org/http://dx.doi.org/10.1016/S0022- 3476(71)80382-7
Julenius, K. (2007). NetCGlyc 1.0: prediction of mammalian C-mannosylation sites. Glycobiology, 17(8), 868–76. http://doi.org/10.1093/glycob/cwm050
Kahr, I., Vandepoele, K., & van Roy, F. (2013). Delta-protocadherins in health and disease. Progress in Molecular Biology and Translational Science, 116, 169–192. http://doi.org/10.1016/B978-0-12-394311-8.00008-X
Kasnauskiene, J., Ciuladaite, Z., Preiksaitiene, E., Matuleviciene, A., Alexandrou, A., Koumbaris, G., … Kucinskas, V. (2012). A single gene deletion on 4q28.3: PCDH18--a new candidate gene for intellectual disability? European Journal of Medical Genetics, 55(4), 274–277. http://doi.org/10.1016/j.ejmg.2012.02.010; 10.1016/j.ejmg.2012.02.010
Keegan, R. M., & Winn, M. D. (2007). Automated search-model discovery and preparation for structure solution by molecular replacement. Acta Crystallographica. Section D, Biological Crystallography, 63(Pt 4), 447–57. http://doi.org/10.1107/S0907444907002661
Kemler, R., Babinet, C., Eisen, H., & Jacob, F. (1977). Surface antigen in early differentiation. Proceedings of the National Academy of Sciences of the United States of America, 74(10), 4449–4452.
Kiecker, C., & Lumsden, A. (2005). Compartments and their boundaries in vertebrate brain development. Nature Reviews. Neuroscience, 6(7), 553–64. http://doi.org/10.1038/nrn1702
Kim, S.-Y., Chung, H. S., Sun, W., & Kim, H. (2007). Spatiotemporal expression pattern of non-clustered protocadherin family members in the developing rat brain. Neuroscience, 147(4), 996–1021. http://doi.org/10.1016/j.neuroscience.2007.03.052
Kim, S.-Y., Yasuda, S., Tanaka, H., Yamagata, K., & Kim, H. (2011). Non-clustered protocadherin. Cell Adhesion & Migration, 5(2), 97–105.
Kita, E. M., Scott, E. K., & Goodhill, G. J. (2015). Topographic wiring of the retinotectal connection in zebrafish. Developmental Neurobiology, 75(6), 542–556. http://doi.org/10.1002/dneu.22256
Klezovitch, O., & Vasioukhin, V. (2015). Cadherin signaling: keeping cells in touch. F1000Research, 4(F1000 Faculty Rev), 550. http://doi.org/10.12688/f1000research.6445.1
Koch, A. W., Farooq, A., Shan, W., Zeng, L., Colman, D. R., & Zhou, M.-M. (2004). Structure of the neural (N-) cadherin prodomain reveals a cadherin extracellular domain-like fold without adhesive characteristics. Structure (London, England : 1993), 12(5), 793–805. http://doi.org/10.1016/j.str.2004.02.034
Kok, F. O., Shin, M., Ni, C.-W., Gupta, A., Grosse, A. S., van Impel, A., … Lawson, N. D. (2015). Reverse genetic screening reveals poor correlation between morpholino-induced and mutant phenotypes in zebrafish. Developmental Cell, 32(1), 97–108. http://doi.org/10.1016/j.devcel.2014.11.018
Koning, H., Sayers, I., Stewart, C. E., de Jong, D., Ten Hacken, N. H. T., Postma, D. S., … Koppelman, G. H. (2012). Characterization of protocadherin-1 expression in primary bronchial epithelial cells: association with epithelial cell differentiation. FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology, 26(1), 439–448. http://doi.org/10.1096/fj.11-185207
Koning, H., van Oosterhout, A. J. M., Brouwer, U., den Boef, L. E., Gras, R., Reinders-Luinge, M., … Nawijn, M. C. (2014). Mouse protocadherin-1 gene expression is regulated by cigarette smoke exposure in vivo. PloS One, 9(7), e98197. http://doi.org/10.1371/journal.pone.0098197
157
Koppelman, G. H., Meyers, D. A., Howard, T. D., Zheng, S. L., Hawkins, G. A., Ampleford, E. J., … Postma, D. S. (2009). Identification of PCDH1 as a novel susceptibility gene for bronchial hyperresponsiveness. American Journal of Respiratory and Critical Care Medicine, 180(10), 929–935. http://doi.org/10.1164/rccm.200810-1621OC
Kostadinov, D., & Sanes, J. R. (2015). Protocadherin-dependent dendritic self-avoidance regulates neural connectivity and circuit function. eLife, 4. http://doi.org/10.7554/eLife.08964
Kozu, Y., Gon, Y., Maruoka, S., Kazumichi, K., Sekiyama, A., Kishi, H., … Hashimoto, S. (2015). Protocadherin-1 is a glucocorticoid-responsive critical regulator of airway epithelial barrier function. BMC Pulmonary Medicine, 15, 80. http://doi.org/10.1186/s12890-015-0078-z
Kraft, B., Berger, C. D., Wallkamm, V., Steinbeisser, H., & Wedlich, D. (2012). Wnt-11 and Fz7 reduce cell adhesion in convergent extension by sequestration of PAPC and C-cadherin. The Journal of Cell Biology, 198(4), 695–709. http://doi.org/10.1083/jcb.201110076
Kretzschmar, K., & Watt, F. M. (2012). Lineage tracing. Cell, 148(1–2), 33–45. http://doi.org/10.1016/j.cell.2012.01.002
Krishna-K, K., Hertel, N., & Redies, C. (2011). Cadherin expression in the somatosensory cortex: evidence for a combinatorial molecular code at the single-cell level. Neuroscience, 175, 37–48. http://doi.org/10.1016/j.neuroscience.2010.11.056
Krishna-K, & Redies, C. (2009). Expression of cadherin superfamily genes in brain vascular development. Journal of Cerebral Blood Flow and Metabolism : Official Journal of the International Society of Cerebral Blood Flow and Metabolism, 29(2), 224–229.
Krissinel, E., & Henrick, K. (2007). Inference of macromolecular assemblies from crystalline state. Journal of Molecular Biology, 372(3), 774–97. http://doi.org/10.1016/j.jmb.2007.05.022
Kudo, S., Caaveiro, J. M. M., & Tsumoto, K. (2016). Adhesive Dimerization of Human P-Cadherin Catalyzed by a Chaperone-like Mechanism. Structure (London, England : 1993), 24(9), 1523–1536. http://doi.org/10.1016/j.str.2016.07.002
Kuroda, H., Inui, M., Sugimoto, K., Hayata, T., & Asashima, M. (2002). Axial protocadherin is a mediator of prenotochord cell sorting in Xenopus. Developmental Biology, 244(2), 267–277. http://doi.org/10.1006/dbio.2002.0589
Kwon, M., & Firestein, B. L. (2013). DNA transfection: calcium phosphate method. Methods in Molecular Biology (Clifton, N.J.), 1018, 107–10. http://doi.org/10.1007/978-1-62703-444-9_10
Kwong, A. K., Fung, C. W., Chan, S. Y., & Wong, V. C. (2012). Identification of SCN1A and PCDH19 mutations in Chinese children with Dravet syndrome. PloS One, 7(7), e41802. http://doi.org/10.1371/journal.pone.0041802 [doi]
Lal, D., Ruppert, A.-K., Trucks, H., Schulz, H., de Kovel, C. G., Kasteleijn-Nolst Trenite, D., … Sander, T. (2015). Burden analysis of rare microdeletions suggests a strong impact of neurodevelopmental genes in genetic generalised epilepsies. PLoS Genetics, 11(5), e1005226. http://doi.org/10.1371/journal.pgen.1005226
Larue, L., Ohsugi, M., Hirchenhain, J., & Kemler, R. (1994, August). E-cadherin null mutant embryos fail to form a trophectoderm epithelium. Proceedings of the National Academy of Sciences of the United States of America.
Lavinder, J. J., Hari, S. B., Sullivan, B. J., & Magliery, T. J. (2009). High-throughput thermal scanning: a general, rapid dye-binding thermal shift screen for protein engineering. Journal of the American Chemical Society, 131(11), 3794–3795. http://doi.org/10.1021/ja8049063
Lawrence, M. C., & Colman, P. M. (1993). Shape complementarity at protein/protein interfaces. Journal of Molecular Biology, 234(4), 946–50. http://doi.org/10.1006/jmbi.1993.1648 158
Lazar, G. (1973). The development of the optic tectum in Xenopus laevis: a Golgi study. Journal of Anatomy, 116(Pt 3), 347–355.
Leckband, D., & Sivasankar, S. (2012). Cadherin recognition and adhesion. Current Opinion in Cell Biology, 24(5), 620– 7. http://doi.org/10.1016/j.ceb.2012.05.014
Lee, C.-H., & Gumbiner, B. M. (1995). Disruption of Gastrulation Movements in Xenopus by a Dominant-Negative Mutant for C-cadheri. Developmental Biology, 171(2), 363–373. http://doi.org/10.1006/DBIO.1995.1288
Lee, E. C., Yu, D., Martinez de Velasco, J., Tessarollo, L., Swing, D. A., Court, D. L., … Copeland, N. G. (2001). A highly efficient Escherichia coli-based chromosome engineering system adapted for recombinogenic targeting and subcloning of BAC DNA. Genomics, 73(1), 56–65. http://doi.org/10.1006/geno.2000.6451
Lefebvre, J. L., Kostadinov, D., Chen, W. V, Maniatis, T., & Sanes, J. R. (2012). Protocadherins mediate dendritic self- avoidance in the mammalian nervous system. Nature, 488(7412), 517–21. http://doi.org/10.1038/nature11305
Leonardi, E., Sartori, S., Vecchi, M., Bettella, E., Polli, R., Palma, L. D., … Murgia, A. (2014). Identification of four novel PCDH19 Mutations and prediction of their functional impact. Annals of Human Genetics, 78(6), 389–398. http://doi.org/10.1111/ahg.12082 [doi]
Leung, L. C., Urbancic, V., Baudet, M.-L., Dwivedy, A., Bayley, T. G., Lee, A. C., … Holt, C. E. (2013). Coupling of NF- protocadherin signaling to axon guidance by cue-induced translation. Nature Neuroscience, 16(2), 166–173. http://doi.org/10.1038/nn.3290
Levine, A. J., & Brivanlou, A. H. (2007). Proposal of a model of mammalian neural induction. Developmental Biology, 308(2), 247–256. http://doi.org/10.1016/j.ydbio.2007.05.036
Levine, E., Lee, C. H., Kintner, C., & Gumbiner, B. M. (1994). Selective disruption of E-cadherin function in early Xenopus embryos by a dominant negative mutant. Development, 120(4), 901 LP-909. Retrieved from http://dev.biologists.org/content/120/4/901.abstract
Liu, A. J., Zhang, Y. H., Xu, X. J., Yang, X. L., Yang, Z. X., Wu, Y., … Wu, X. R. (2016). [Genotype and phenotype of female Dravet syndrome with PCDH19 mutations]. Zhonghua er ke za zhi = Chinese journal of pediatrics, 54(5), 327– 331.
Liu, Q., Chen, Y., Kubota, F., Pan, J. J., & Murakami, T. (2010). Expression of protocadherin-19 in the nervous system of the embryonic zebrafish. The International Journal of Developmental Biology, 54(5), 905–911. http://doi.org/10.1387/ijdb.092882ql
Liu, Q., Chen, Y., Pan, J. J., & Murakami, T. (2009). Expression of protocadherin-9 and protocadherin-17 in the nervous system of the embryonic zebrafish. Gene Expression Patterns : GEP, 9(7), 490–6. http://doi.org/10.1016/j.gep.2009.07.006
Lowndes, M., Rakshit, S., Shafraz, O., Borghi, N., Harmon, R. M., Green, K. J., … Nelson, W. J. (2014). Different roles of cadherins in the assembly and structural integrity of the desmosome complex. Journal of Cell Science, 127(10), 2339 LP-2350. Retrieved from http://jcs.biologists.org/content/127/10/2339.abstract
Mah, K. M., & Weiner, J. A. (2016). Clustered Protocadherins. In S. T. Suzuki & S. Hirano (Eds.), The Cadherin Superfamily: Key Regulators of Animal Development and Physiology (pp. 195–221). Tokyo: Springer Japan. http://doi.org/10.1007/978-4-431-56033-3_8
Malicki, J., Jo, H., & Pujic, Z. (2003). Zebrafish N-cadherin, encoded by the glass onion locus, plays an essential role in retinal patterning. Developmental Biology, 259(1), 95–108.
Malicki, J., Neuhauss, S. C., Schier, A. F., Solnica-Krezel, L., Stemple, D. L., Stainier, D. Y., … Driever, W. (1996). Mutations affecting development of the zebrafish retina. Development (Cambridge, England), 123, 263–273. 159
Marini, C., Darra, F., Specchio, N., Mei, D., Terracciano, A., Parmeggiani, L., … Guerrini, R. (2012). Focal seizures with affective symptoms are a major feature of PCDH19 gene-related epilepsy. Epilepsia, 53(12), 2111–2119. http://doi.org/10.1111/j.1528-1167.2012.03649.x [doi]
Marini, C., Mei, D., Parmeggiani, L., Norci, V., Calado, E., Ferrari, A., … Guerrini, R. (2010). Protocadherin 19 mutations in girls with infantile-onset epilepsy. Neurology, 75(7), 646–653. http://doi.org/10.1212/WNL.0b013e3181ed9e67 [doi]
Marshall, C. R., Noor, A., Vincent, J. B., Lionel, A. C., Feuk, L., Skaug, J., … Scherer, S. W. (2008). Structural variation of chromosomes in autism spectrum disorder. American Journal of Human Genetics, 82(2), 477–88. http://doi.org/10.1016/j.ajhg.2007.12.009
Maximino, C., Silva, R. X. do C., da Silva, S. de N. S., Rodrigues, L. do S. D. S., Barbosa, H., de Carvalho, T. S., … Herculano, A. M. (2015). Non-mammalian models in behavioral neuroscience: consequences for biological psychiatry. Frontiers in Behavioral Neuroscience, 9, 233. http://doi.org/10.3389/fnbeh.2015.00233
McCoy, A. J., Grosse-Kunstleve, R. W., Adams, P. D., Winn, M. D., Storoni, L. C., & Read, R. J. (2007). Phaser crystallographic software. Journal of Applied Crystallography, 40(4), 658–674. http://doi.org/10.1107/S0021889807021206
McLaughlin, T., & O’Leary, D. D. M. (2005). Molecular gradients and development of retinotopic maps. Annual Review of Neuroscience, 28, 327–355. http://doi.org/10.1146/annurev.neuro.28.061604.135714
McMillen, P., & Holley, S. A. (2015). Integration of cell-cell and cell-ECM adhesion in vertebrate morphogenesis. Current Opinion in Cell Biology, 36, 48–53. http://doi.org/10.1016/j.ceb.2015.07.002
Meek, J., & Schellart, N. (1978). A Golgi study of goldfish optic tectum. The Journal of Comparative Neurology, 182(1), 89–122.
Menelaou, E., & McLean, D. L. (2012). A gradient in endogenous rhythmicity and oscillatory drive matches recruitment order in an axial motor pool. The Journal of Neuroscience : The Official Journal of the Society for Neuroscience, 32(32), 10925–10939. http://doi.org/10.1523/JNEUROSCI.1809-12.2012
Meng, W., & Takeichi, M. (2009). Adherens junction: molecular architecture and regulation. Cold Spring Harbor Perspectives in Biology, 1(6), a002899. http://doi.org/10.1101/cshperspect.a002899
Metcalfe, W. K., Myers, P. Z., Trevarrow, B., Bass, M. B., & Kimmel, C. B. (1990). Primary neurons that express the L2/HNK-1 carbohydrate during early development in the zebrafish. Development (Cambridge, England), 110(2), 491–504.
Minor, W., Cymborowski, M., Otwinowski, Z., & Chruszcz, M. (2006). HKL-3000: the integration of data reduction and structure solution--from diffraction images to an initial model in minutes. Acta Crystallographica. Section D, Biological Crystallography, 62(Pt 8), 859–66. http://doi.org/10.1107/S0907444906019949
Mitchell, K. J. (2011). The genetics of neurodevelopmental disease. Current Opinion in Neurobiology, 21(1), 197–203. http://doi.org/10.1016/j.conb.2010.08.009; 10.1016/j.conb.2010.08.009
Mitchell, K. J. (2011). The miswired brain: making connections from neurodevelopment to psychopathology. BMC Biology, 9, 23. http://doi.org/10.1186/1741-7007-9-23
Mitsui, K., Nakajima, D., Ohara, O., & Nakayama, M. (2002). Mammalian fat3: a large protein that contains multiple cadherin and EGF-like motifs. Biochemical and Biophysical Research Communications, 290(4), 1260–1266. http://doi.org/10.1006/bbrc.2002.6338
160
Miyake, K., Hirasawa, T., Soutome, M., Itoh, M., Goto, Y., Endoh, K., … Kubota, T. (2011). The protocadherins, PCDHB1 and PCDH7, are regulated by MeCP2 in neuronal cells and brain tissues: implication for pathogenesis of Rett syndrome. BMC Neuroscience, 12, 81. http://doi.org/10.1186/1471-2202-12-81
Mombaerts, P. (1999). Seven-Transmembrane Proteins as Odorant and Chemosensory Receptors. Science, 286(5440), 707 LP-711. Retrieved from http://science.sciencemag.org/content/286/5440/707.abstract
Mombaerts, P. (2006). Axonal wiring in the mouse olfactory system. Annual Review of Cell and Developmental Biology, 22, 713–737. http://doi.org/10.1146/annurev.cellbio.21.012804.093915
Moody, W. J., & Bosma, M. M. (2005). Ion Channel Development, Spontaneous Activity, and Activity-Dependent Development in Nerve and Muscle Cells. Physiological Reviews, 85(3), 883 LP-941. Retrieved from http://physrev.physiology.org/content/85/3/883.abstract
Morishita, H., Umitsu, M., Murata, Y., Shibata, N., Udaka, K., Higuchi, Y., … Ikegami, T. (2006). Structure of the Cadherin-related Neuronal Receptor/Protocadherin- First Extracellular Cadherin Domain Reveals Diversity across Cadherin Families. Journal of Biological Chemistry, 281(44), 33650–33663. http://doi.org/10.1074/jbc.M603298200
Morishita, H., & Yagi, T. (2007). Protocadherin family: diversity, structure, and function. Current Opinion in Cell Biology, 19(5), 584–592. http://doi.org/10.1016/j.ceb.2007.09.006
Morrow, E. M., Yoo, S.-Y., Flavell, S. W., Kim, T.-K., Lin, Y., Hill, R. S., … Walsh, C. A. (2008). Identifying autism loci and genes by tracing recent shared ancestry. Science (New York, N.Y.), 321(5886), 218–23. http://doi.org/10.1126/science.1157657
Mortensen, L. J., Kreiner-Moller, E., Hakonarson, H., Bonnelykke, K., & Bisgaard, H. (2014). The PCDH1 gene and asthma in early childhood. The European Respiratory Journal, 43(3), 792–800. http://doi.org/10.1183/09031936.00021613
Mountcastle, V. B. (1997). The columnar organization of the neocortex. Brain : A Journal of Neurology, 120 ( Pt 4), 701–722.
Mueller, T., Dong, Z., Berberoglu, M. A., & Guo, S. (2011, March). The Dorsal Pallium in Zebrafish, Danio rerio (Cyprinidae, Teleostei). Brain Research. http://doi.org/10.1016/j.brainres.2010.12.089
Murshudov, G. N., Skubák, P., Lebedev, A. a., Pannu, N. S., Steiner, R. a., Nicholls, R. a., … Vagin, A. a. (2011). REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallographica Section D: Biological Crystallography, 67(4), 355–367. http://doi.org/10.1107/S0907444911001314
Mutoh, T., Hamada, S., Senzaki, K., Murata, Y., & Yagi, T. (2004). Cadherin-related neuronal receptor 1 (CNR1) has cell adhesion activity with beta1 integrin mediated through the RGD site of CNR1. Experimental Cell Research, 294(2), 494–508. http://doi.org/10.1016/j.yexcr.2003.11.019
Myers, P. Z., Eisen, J. S., & Westerfield, M. (1986). Development and axonal outgrowth of identified motoneurons in the zebrafish. The Journal of Neuroscience : The Official Journal of the Society for Neuroscience, 6(8), 2278– 2289.
Nagar, B., Overduin, M., Ikura, M., & Rini, J. M. (1996). Structural basis of calcium-induced E-cadherin rigidification and dimerization. Nature, 380(6572), 360–4. http://doi.org/10.1038/380360a0
Nguyen, V., Deschet, K., Henrich, T., Godet, E., Joly, J. S., Wittbrodt, J., … Bourrat, F. (1999). Morphogenesis of the optic tectum in the medaka (Oryzias latipes): a morphological and molecular study, with special emphasis on cell proliferation. The Journal of Comparative Neurology, 413(3), 385–404.
161
Nicoludis, J. M., Lau, S.-Y., Schärfe, C. P. I., Marks, D. S., Weihofen, W. A., & Gaudet, R. (2015). Structure and Sequence Analyses of Clustered Protocadherins Reveal Antiparallel Interactions that Mediate Homophilic Specificity. Structure (London, England : 1993), 23(11), 2087–98. http://doi.org/10.1016/j.str.2015.09.005
Nicoludis, J. M., Lau, S. Y., Scharfe, C. P., Marks, D. S., Weihofen, W. A., & Gaudet, R. (2015). Structure and Sequence Analyses of Clustered Protocadherins Reveal Antiparallel Interactions that Mediate Homophilic Specificity. Structure (London, England : 1993), 23(11), 2087–2098. http://doi.org/10.1016/j.str.2015.09.005 [doi]
Nicoludis, J. M., Vogt, B. E., Green, A. G., Scharfe, C. P., Marks, D. S., & Gaudet, R. (2016). Antiparallel protocadherin homodimers use distinct affinity- and specificity-mediating regions in cadherin repeats 1-4. eLife, 5. http://doi.org/10.7554/eLife.18449
Niesen, F. H., Berglund, H., & Vedadi, M. (2007). The use of differential scanning fluorimetry to detect ligand interactions that promote protein stability. Nature Protocols, 2(9), 2212–21. http://doi.org/10.1038/nprot.2007.321
Niessen, C. M., Leckband, D., & Yap, A. S. (2011, April). Tissue organization by cadherin adhesion molecules: dynamic molecular and cellular mechanisms of morphogenetic regulation. Physiological Reviews. http://doi.org/10.1152/physrev.00004.2010
Noctor, S. C., Flint, A. C., Weissman, T. A., Dammerman, R. S., & Kriegstein, A. R. (2001). Neurons derived from radial glial cells establish radial units in neocortex. Nature, 409(6821), 714–720. http://doi.org/10.1038/35055553
Nugent, A. A., Kolpak, A. L., & Engle, E. C. (2012). Human disorders of axon guidance. Current Opinion in Neurobiology, 22(5), 837–843. http://doi.org/10.1016/j.conb.2012.02.006
Obata, S., Sago, H., Mori, N., Rochelle, J. M., Seldin, M. F., Davidson, M., … Suzuki, S. T. (1995). Protocadherin Pcdh2 shows properties similar to, but distinct from, those of classical cadherins. Journal of Cell Science, 108 ( Pt 12), 3765–3773.
Overduin, M., Harvey, T. S., Bagby, S., Tong, K. I., Yau, P., Takeichi, M., & Ikura, M. (1995). Solution structure of the epithelial cadherin domain responsible for selective cell adhesion. Science (New York, N.Y.), 267(5196), 386–9.
Ozawa, M., & Kemler, R. (1990). Correct proteolytic cleavage is required for the cell adhesive function of uvomorulin. The Journal of Cell Biology, 111(4), 1645–1650.
Patel, S. D., Ciatto, C., Chen, C. P., Bahna, F., Rajebhosale, M., Arkus, N., … Shapiro, L. (2006). Type II Cadherin Ectodomain Structures: Implications for Classical Cadherin Specificity. Cell, 124(6), 1255–1268. http://doi.org/10.1016/j.cell.2005.12.046
Payer, B. (2016). Developmental regulation of X-chromosome inactivation. Seminars in Cell & Developmental Biology, 56, 88–99. http://doi.org/10.1016/j.semcdb.2016.04.014
Pederick, D. T., Homan, C. C., Jaehne, E. J., Piltz, S. G., Haines, B. P., Baune, B. T., … Thomas, P. Q. (2016). Pcdh19 Loss- of-Function Increases Neuronal Migration In Vitro but is Dispensable for Brain Development in Mice. Scientific Reports, 6, 26765. http://doi.org/10.1038/srep26765
Pedrosa, E., Shah, A., Tenore, C., Capogna, M., Villa, C., Guo, X., … Lachman, H. M. (2010). beta-catenin promoter ChIP-chip reveals potential schizophrenia and bipolar disorder gene network. Journal of Neurogenetics, 24(4), 182–193. http://doi.org/10.3109/01677063.2010.495182
Pertz, O., Bozic, D., Koch, A. W., Fauser, C., Brancaccio, A., & Engel, J. (1999). A new crystal structure, Ca2+ dependence and mutational analysis reveal molecular details of E-cadherin homoassociation. The EMBO Journal, 18(7), 1738–1747. http://doi.org/10.1093/emboj/18.7.1738
162
Peters, A., & Sethares, C. (1996). Myelinated axons and the pyramidal cell modules in monkey primary visual cortex. The Journal of Comparative Neurology, 365(2), 232–255. http://doi.org/10.1002/(SICI)1096- 9861(19960205)365:2<232::AID-CNE3>3.0.CO;2-6
Peters, A., & Walsh, T. M. (1972). A study of the organization of apical dendrites in the somatic sensory cortex of the rat. The Journal of Comparative Neurology, 144(3), 253–268. http://doi.org/10.1002/cne.901440302
Petersen, T. N., Brunak, S., von Heijne, G., & Nielsen, H. (2011). SignalP 4.0: discriminating signal peptides from transmembrane regions. Nature Methods, 8(10), 785–6. http://doi.org/10.1038/nmeth.1701
Pieters, T., van Roy, F., & van Hengel, J. (2012). Functions of p120ctn isoforms in cell-cell adhesion and intracellular signaling. Frontiers in Bioscience (Landmark Edition), 17, 1669–1694.
Piper, M., Dwivedy, A., Leung, L., Bradley, R. S., & Holt, C. E. (2008). NF-protocadherin and TAF1 regulate retinal axon initiation and elongation in vivo. The Journal of Neuroscience : The Official Journal of the Society for Neuroscience, 28(1), 100–5. http://doi.org/10.1523/JNEUROSCI.4490-07.2008
Pokutta, S., Herrenknecht, K., Kemler, R., & Engel, J. (1994). Conformational changes of the recombinant extracellular domain of E-cadherin upon calcium binding. European Journal of Biochemistry, 223(3), 1019–1026.
Pologruto, T. A., Sabatini, B. L., & Svoboda, K. (2003). ScanImage: flexible software for operating laser scanning microscopes. Biomedical Engineering Online, 2, 13. http://doi.org/10.1186/1475-925X-2-13
Ponstingl, H., Henrick, K., & Thornton, J. M. (2000). Discriminating between homodimeric and monomeric proteins in the crystalline state. Proteins, 41(1), 47–57.
Portavella, M., Torres, B., Salas, C., & Papini, M. R. (2004). Lesions of the medial pallium, but not of the lateral pallium, disrupt spaced-trial avoidance learning in goldfish (Carassius auratus). Neuroscience Letters, 362(2), 75–78. http://doi.org/10.1016/j.neulet.2004.01.083
Portugues, R., & Engert, F. (2009). The neural basis of visual behaviors in the larval zebrafish. Current Opinion in Neurobiology, 19(6), 644–647. http://doi.org/10.1016/j.conb.2009.10.007
Pujic, Z., & Malicki, J. (2001). Mutation of the zebrafish glass onion locus causes early cell-nonautonomous loss of neuroepithelial integrity followed by severe neuronal patterning defects in the retina. Developmental Biology, 234(2), 454–469. http://doi.org/10.1006/dbio.2001.0251
Raible, D. W., & Kruse, G. J. (2000). Organization of the lateral line system in embryonic zebrafish. The Journal of Comparative Neurology, 421(2), 189–198.
Rakic, P. (1988). Specification of cerebral cortical areas. Science (New York, N.Y.), 241(4862), 170–176.
Ramalingam, S., Annaluru, N., & Chandrasegaran, S. (2013). A CRISPR way to engineer the human genome. Genome Biology, 14(2), 107. http://doi.org/10.1186/gb-2013-14-2-107
Recher, G., Jouralet, J., Brombin, A., Heuze, A., Mugniery, E., Hermel, J.-M., … Joly, J.-S. (2013). Zebrafish midbrain slow-amplifying progenitors exhibit high levels of transcripts for nucleotide and ribosome biogenesis. Development (Cambridge, England), 140(24), 4860–4869. http://doi.org/10.1242/dev.099010
Redies, C., Hertel, N., & Hübner, C. A. (2012). Cadherins and neuropsychiatric disorders. Brain Research, 1470, 130– 44. http://doi.org/10.1016/j.brainres.2012.06.020
Redies, C., Heyder, J., Kohoutek, T., Staes, K., & Van Roy, F. (2008). Expression of protocadherin-1 (Pcdh1) during mouse development. Developmental Dynamics : An Official Publication of the American Association of Anatomists, 237(9), 2496–2505. http://doi.org/10.1002/dvdy.21650
163
Redies, C., Neudert, F., & Lin, J. (2011). Cadherins in cerebellar development: translation of embryonic patterning into mature functional compartmentalization. Cerebellum (London, England), 10(3), 393–408. http://doi.org/10.1007/s12311-010-0207-4
Redies, C., Vanhalst, K., & van Roy, F. (2005). delta-Protocadherins: unique structures and functions. Cellular and Molecular Life Sciences : CMLS, 62(23), 2840–52. http://doi.org/10.1007/s00018-005-5320-z
Reiss, K., Maretzky, T., Haas, I. G., Schulte, M., Ludwig, A., Frank, M., & Saftig, P. (2006). Regulated ADAM10- dependent ectodomain shedding of gamma-protocadherin C3 modulates cell-cell adhesion. The Journal of Biological Chemistry, 281(31), 21735–21744. http://doi.org/10.1074/jbc.M602663200
Riedl, J., Crevenna, A. H., Kessenbrock, K., Yu, J. H., Neukirchen, D., Bista, M., … Wedlich-Soldner, R. (2008). Lifeact: a versatile marker to visualize F-actin. Nature Methods, 5(7), 605–607. http://doi.org/10.1038/nmeth.1220
Robles, E., Laurell, E., & Baier, H. (2014). The retinal projectome reveals brain-area-specific visual representations generated by ganglion cell diversity. Current Biology : CB, 24(18), 2085–2096. http://doi.org/10.1016/j.cub.2014.07.080
Rodriguez, F., Lopez, J. C., Vargas, J. P., Gomez, Y., Broglio, C., & Salas, C. (2002). Conservation of spatial memory function in the pallial forebrain of reptiles and ray-finned fishes. The Journal of Neuroscience : The Official Journal of the Society for Neuroscience, 22(7), 2894–2903. http://doi.org/20026211
Rubinstein, R., Thu, C. A., Goodman, K. M., Wolcott, H. N., Bahna, F., Mannepalli, S., … Honig, B. (2015). Molecular Logic of Neuronal Self-Recognition through Protocadherin Domain Interactions. Cell, 163(3), 629–42. http://doi.org/10.1016/j.cell.2015.09.026
Ruoslahti, E. (1996). RGD and other recognition sequences for integrins. Annual Review of Cell and Developmental Biology, 12, 697–715. http://doi.org/10.1146/annurev.cellbio.12.1.697
Ryan, S. G., Chance, P. F., Zou, C. H., Spinner, N. B., Golden, J. A., & Smietana, S. (1997). Epilepsy and mental retardation limited to females: an X-linked dominant disorder with male sparing. Nature Genetics, 17(1), 92– 95. http://doi.org/10.1038/ng0997-92
Sago, H., Kitagawa, M., Obata, S., Mori, N., Taketani, S., Rochelle, J. M., … Suzuki, S. T. (1995). Cloning, expression, and chromosomal localization of a novel cadherin-related protein, protocadherin-3. Genomics, 29(3), 631–640. http://doi.org/10.1006/geno.1995.9956
Sakurai, T. (2016). The role of cell adhesion molecules in brain wiring and neuropsychiatric disorders. Molecular and Cellular Neurosciences. http://doi.org/10.1016/j.mcn.2016.08.005
Salahuddin, P., Rabbani, G., & Khan, R. H. (2014). The role of advanced glycation end products in various types of neurodegenerative disease: a therapeutic approach. Cellular & Molecular Biology Letters, 19(3), 407–37. http://doi.org/10.2478/s11658-014-0205-5
Samanta, D. (2016). Epilepsy with PCDH19 mutation masquerading as benign partial epilepsy in infancy. Neurology India. India. http://doi.org/10.4103/0028-3886.177628
Sander, J. D., Maeder, M. L., Reyon, D., Voytas, D. F., Joung, J. K., & Dobbs, D. (2010). ZiFiT (Zinc Finger Targeter): an updated zinc finger engineering tool. Nucleic Acids Research, 38(Web Server issue), W462-8. http://doi.org/10.1093/nar/gkq319
Sano, K., Tanihara, H., Heimark, R. L., Obata, S., Davidson, M., St John, T., … Suzuki, S. (1993). Protocadherins: a large family of cadherin-related molecules in central nervous system. The EMBO Journal, 12(6), 2249–56.
164
Scheffer, I. E., Turner, S. J., Dibbens, L. M., Bayly, M. A., Friend, K., Hodgson, B., … Berkovic, S. F. (2008). Epilepsy and mental retardation limited to females: an under-recognized disorder. Brain : A Journal of Neurology, 131(Pt 4), 918–27. http://doi.org/10.1093/brain/awm338
Schindelin, J., Arganda-Carreras, I., Frise, E., Kaynig, V., Longair, M., Pietzsch, T., … Cardona, A. (2012). Fiji: an open- source platform for biological-image analysis. Nature Methods, 9(7), 676–682. http://doi.org/10.1038/nmeth.2019
Schreiner, D., & Weiner, J. A. (2010). Combinatorial homophilic interaction between gamma-protocadherin multimers greatly expands the molecular diversity of cell adhesion. Proceedings of the National Academy of Sciences of the United States of America, 107(33), 14893–8. http://doi.org/10.1073/pnas.1004526107
Shahbazi, M. N., Megias, D., Epifano, C., Akhmanova, A., Gundersen, G. G., Fuchs, E., & Perez-Moreno, M. (2013). CLASP2 interacts with p120-catenin and governs microtubule dynamics at adherens junctions. The Journal of Cell Biology, 203(6), 1043–1061.
Shapiro, L., Fannon, A. M., Kwong, P. D., Thompson, A., Lehmann, M. S., Grubel, G., … Hendrickson, W. A. (1995). Structural basis of cell-cell adhesion by cadherins. Nature, 374(6520), 327–337. http://doi.org/10.1038/374327a0
Shapiro, L., Love, J., & Colman, D. R. (2007). Adhesion molecules in the nervous system: structural insights into function and diversity. Annual Review of Neuroscience, 30, 451–74. http://doi.org/10.1146/annurev.neuro.29.051605.113034
Shatz, C. (1992). The developing brain. Scientific American, 267(3), 60–67.
Shimono, Y., Rikitake, Y., Mandai, K., Mori, M., & Takai, Y. (2012). Immunoglobulin superfamily receptors and adherens junctions. Sub-Cellular Biochemistry, 60, 137–170. http://doi.org/10.1007/978-94-007-4186-7_7
Sievers, F., & Higgins, D. G. (2014). Clustal Omega, accurate alignment of very large numbers of sequences. Methods in Molecular Biology (Clifton, N.J.), 1079, 105–16. http://doi.org/10.1007/978-1-62703-646-7_6
Simm, A., Müller, B., Nass, N., Hofmann, B., Bushnaq, H., Silber, R.-E., & Bartling, B. (2015). Protein glycation - Between tissue aging and protection. Experimental Gerontology, 68, 71–5. http://doi.org/10.1016/j.exger.2014.12.013
Sivasankar, S., Zhang, Y., Nelson, W. J., & Chu, S. (2009). Characterizing the initial encounter complex in cadherin adhesion. Structure (London, England : 1993), 17(8), 1075–81. http://doi.org/10.1016/j.str.2009.06.012
Sola, L., & Gornung, E. (2001). Classical and molecular cytogenetics of the zebrafish, Danio rerio (Cyprinidae, Cypriniformes): an overview. Genetica, 111(1–3), 397–412.
Sotomayor, M., Gaudet, R., & Corey, D. P. (2014). Sorting out a promiscuous superfamily: towards cadherin connectomics. Trends in Cell Biology, 1–13. http://doi.org/10.1016/j.tcb.2014.03.007
Sotomayor, M., Weihofen, W. A., Gaudet, R., & Corey, D. P. (2010). Structural Determinants of Cadherin-23 Function in Hearing and Deafness. Neuron, 66(1), 85–100. http://doi.org/10.1016/j.neuron.2010.03.028
Sotomayor, M., Weihofen, W. A., Gaudet, R., & Corey, D. P. (2012). Structure of a force-conveying cadherin bond essential for inner-ear mechanotransduction. Nature, 492(7427), 128–132. http://doi.org/10.1038/nature11590 [doi]
Sotomayor, M., Weihofen, W. a, Gaudet, R., & Corey, D. P. (2012). Structure of a force-conveying cadherin bond essential for inner-ear mechanotransduction. Nature, 492(7427), 128–32. http://doi.org/10.1038/nature11590
165
Specchio, N., Fusco, L., & Vigevano, F. (2011). Acute-onset epilepsy triggered by fever mimicking FIRES (febrile infection-related epilepsy syndrome): the role of protocadherin 19 (PCDH19) gene mutation. Epilepsia, 52(11), e172-5. http://doi.org/10.1111/j.1528-1167.2011.03193.x
Specchio, N., Marini, C., Terracciano, A., Mei, D., Trivisano, M., Sicca, F., … Vigevano, F. (2011). Spectrum of phenotypes in female patients with epilepsy due to protocadherin 19 mutations. Epilepsia, 52(7), 1251–1257. http://doi.org/10.1111/j.1528-1167.2011.03063.x [doi]
Speevak, M. D., & Farrell, S. A. (2011). Non-syndromic language delay in a child with disruption in the Protocadherin11X/Y gene pair. American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics : The Official Publication of the International Society of Psychiatric Genetics, 156B(4), 484–489. http://doi.org/10.1002/ajmg.b.31186
Sperry, R. W. (1963). CHEMOAFFINITY IN THE ORDERLY GROWTH OF NERVE FIBER PATTERNS AND CONNECTIONS. Proceedings of the National Academy of Sciences of the United States of America, 50, 703–710.
Stahley, S. N., & Kowalczyk, A. P. (2015). Desmosomes in acquired disease. Cell and Tissue Research, 360(3), 439–456. http://doi.org/10.1007/s00441-015-2155-2
Steentoft, C., Vakhrushev, S. Y., Joshi, H. J., Kong, Y., Vester-Christensen, M. B., Schjoldager, K. T.-B. G., … Clausen, H. (2013). Precision mapping of the human O-GalNAc glycoproteome through SimpleCell technology. The EMBO Journal, 32(10), 1478–88. http://doi.org/10.1038/emboj.2013.79
Steinberg, M. S. (2007). Differential adhesion in morphogenesis: a modern view. Current Opinion in Genetics & Development, 17(4), 281–6. http://doi.org/10.1016/j.gde.2007.05.002
Steinberg, M. S., & Takeichi, M. (1994). Experimental specification of cell sorting, tissue spreading, and specific spatial patterning by quantitative differences in cadherin expression. Proceedings of the National Academy of Sciences of the United States of America, 91(1), 206–209.
Sugino, H., Hamada, S., Yasuda, R., Tuji, A., Matsuda, Y., Fujita, M., & Yagi, T. (2000). Genomic organization of the family of CNR cadherin genes in mice and humans. Genomics, 63(1), 75–87. http://doi.org/10.1006/geno.1999.6066
Suo, L., Lu, H., Ying, G., Capecchi, M. R., & Wu, Q. (2012). Protocadherin clusters and cell adhesion kinase regulate dendrite complexity through Rho GTPase. Journal of Molecular Cell Biology, 4(6), 362–376. http://doi.org/10.1093/jmcb/mjs034
Suster, M. L., Abe, G., Schouw, A., & Kawakami, K. (2011). Transposon-mediated BAC transgenesis in zebrafish. Nature Protocols, 6(12), 1998–2021. http://doi.org/10.1038/nprot.2011.416
Suzuki, S. T. (1996). Protocadherins and diversity of the cadherin superfamily. Journal of Cell Science, 109 ( Pt 1, 2609– 11.
Syed, S.-H., Trinnaman, B., Martin, S., Major, S., Hutchinson, J., & Magee, A. I. (2002). Molecular interactions between desmosomal cadherins. The Biochemical Journal, 362(Pt 2), 317–327.
Tachibana, K., Nakanishi, H., Mandai, K., Ozaki, K., Ikeda, W., Yamamoto, Y., … Takai, Y. (2000). Two cell adhesion molecules, nectin and cadherin, interact through their cytoplasmic domain-associated proteins. The Journal of Cell Biology, 150(5), 1161–1176.
Tai, K., Kubota, M., Shiono, K., Tokutsu, H., & Suzuki, S. T. (2010). Adhesion properties and retinofugal expression of chicken protocadherin-19. Brain Research, 1344, 13–24. http://doi.org/10.1016/j.brainres.2010.04.065
Takeichi, M. (1988). The cadherins: cell-cell adhesion molecules controlling animal morphogenesis. Development (Cambridge, England), 102(4), 639–655. 166
Takeichi, M. (1990). Cadherins: a molecular family important in selective cell-cell adhesion. Annual Review of Biochemistry, 59, 237–52. http://doi.org/10.1146/annurev.bi.59.070190.001321
Takeichi, M. (2004). Discovery and characterization of the cadherin family of cell adhesion molecules. An interview with Masatoshi Takeichi. The International Journal of Developmental Biology. Spain. http://doi.org/10.1387/ijdb.041801ds
Takeichi, M. (2014). Dynamic contacts: rearranging adherens junctions to drive epithelial remodelling. Nature Reviews. Molecular Cell Biology, 15(6), 397–410. http://doi.org/10.1038/nrm3802
Talbot, J. C., & Amacher, S. L. (2014). A streamlined CRISPR pipeline to reliably generate zebrafish frameshifting alleles. Zebrafish, 11(6), 583–585. http://doi.org/10.1089/zeb.2014.1047
Tamura, K., Shan, W. S., Hendrickson, W. A., Colman, D. R., & Shapiro, L. (1998). Structure-function analysis of cell adhesion by neural (N-) cadherin. Neuron, 20(6), 1153–1163.
Tan, C., Shard, C., Ranieri, E., Hynes, K., Pham, D. H., Leach, D., … Gecz, J. (2015). Mutations of protocadherin 19 in female epilepsy (PCDH19-FE) lead to allopregnanolone deficiency. Human Molecular Genetics, 24(18), 5250– 5259. http://doi.org/10.1093/hmg/ddv245
Tasic, B., Nabholz, C. E., Baldwin, K. K., Kim, Y., Rueckert, E. H., Ribich, S. A., … Maniatis, T. (2002). Promoter choice determines splice site selection in protocadherin alpha and gamma pre-mRNA splicing. Molecular Cell, 10(1), 21–33.
Terracciano, A., Specchio, N., Darra, F., Sferra, A., Bernardina, B. D., Vigevano, F., & Bertini, E. (2012). Somatic mosaicism of PCDH19 mutation in a family with low-penetrance EFMR. Neurogenetics, 13(4), 341–345. http://doi.org/10.1007/s10048-012-0342-9 [doi]
Terracciano, A., Trivisano, M., Cusmai, R., De Palma, L., Fusco, L., Compagnucci, C., … Specchio, N. (2016). PCDH19- related epilepsy in two mosaic male patients. Epilepsia, 57(3), e51-5. http://doi.org/10.1111/epi.13295
Thiffault, I., Farrow, E., Smith, L., Lowry, J., Zellmer, L., Black, B., … Saunders, C. (2016). PCDH19-related epileptic encephalopathy in a male mosaic for a truncating variant. American Journal of Medical Genetics. Part A. http://doi.org/10.1002/ajmg.a.37617
Thu, C. A., Chen, W. V, Rubinstein, R., Chevee, M., Wolcott, H. N., Felsovalyi, K. O., … Maniatis, T. (2014a). Single-cell identity generated by combinatorial homophilic interactions between alpha, beta, and gamma protocadherins. Cell, 158(5), 1045–1059. http://doi.org/10.1016/j.cell.2014.07.012
Thu, C. A., Chen, W. V, Rubinstein, R., Chevee, M., Wolcott, H. N., Felsovalyi, K. O., … Maniatis, T. (2014b). Single-cell identity generated by combinatorial homophilic interactions between α, β, and γ protocadherins. Cell, 158(5), 1045–59. http://doi.org/10.1016/j.cell.2014.07.012
Toncheva, A. A., Suttner, K., Michel, S., Klopp, N., Illig, T., Balschun, T., … Kabesch, M. (2012). Genetic variants in Protocadherin-1, bronchial hyper-responsiveness, and asthma subphenotypes in German children. Pediatric Allergy and Immunology : Official Publication of the European Society of Pediatric Allergy and Immunology, 23(7), 636–641. http://doi.org/10.1111/j.1399-3038.2012.01334.x
Townes, P. L., & Holtfreter, J. (1955). Directed movements and selective adhesion of embryonic amphibian cells. J. Exp. Zool. Journal of Experimental Zoology, 128(1), 53–120.
Trump, N., McTague, A., Brittain, H., Papandreou, A., Meyer, E., Ngoh, A., … Scott, R. H. (2016). Improving diagnosis and broadening the phenotypes in early-onset seizure and severe developmental delay disorders through gene panel analysis. Journal of Medical Genetics, 53(5), 310–317. http://doi.org/10.1136/jmedgenet-2015-103263
167
Tsai, N.-P., Wilkerson, J. R., Guo, W., Maksimova, M. A., DeMartino, G. N., Cowan, C. W., & Huber, K. M. (2012). Multiple autism-linked genes mediate synapse elimination via proteasomal degradation of a synaptic scaffold PSD-95. Cell, 151(7), 1581–1594. http://doi.org/10.1016/j.cell.2012.11.040
Uemura, M., Nakao, S., Suzuki, S. T., Takeichi, M., & Hirano, S. (2007). OL-Protocadherin is essential for growth of striatal axons and thalamocortical projections. Nature Neuroscience, 10(9), 1151–1159. http://doi.org/10.1038/nn1960 van Harssel, J. J., Weckhuysen, S., van Kempen, M. J., Hardies, K., Verbeek, N. E., de Kovel, C. G., … Brilstra, E. H. (2013). Clinical and genetic aspects of PCDH19-related epilepsy syndromes and the possible role of PCDH19 mutations in males with autism spectrum disorders. Neurogenetics, 14(1), 23–34. http://doi.org/10.1007/s10048-013-0353-1 [doi]
Vanegas, H., Laufer, M., & Amat, J. (1974). The optic tectum of a perciform teleost. I. General configuration and cytoarchitecture. The Journal of Comparative Neurology, 154(1), 43–60. http://doi.org/10.1002/cne.901540104
Vanhalst, K., Kools, P., Staes, K., van Roy, F., & Redies, C. (2005). delta-Protocadherins: a gene family expressed differentially in the mouse brain. Cellular and Molecular Life Sciences : CMLS, 62(11), 1247–59. http://doi.org/10.1007/s00018-005-5021-7
Vargas, J. P., Lopez, J. C., & Portavella, M. (2009). What are the functions of fish brain pallium? Brain Research Bulletin, 79(6), 436–440. http://doi.org/10.1016/j.brainresbull.2009.05.008
Veerappa, A. M., Saldanha, M., Padakannaya, P., & Ramachandra, N. B. (2013). Genome-wide copy number scan identifies disruption of PCDH11X in developmental dyslexia. American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics : The Official Publication of the International Society of Psychiatric Genetics, 162B(8), 889–897. http://doi.org/10.1002/ajmg.b.32199
Veerappa, A. M., Saldanha, M., Padakannaya, P., & Ramachandra, N. B. (2014). Family based genome-wide copy number scan identifies complex rearrangements at 17q21.31 in dyslexics. American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics : The Official Publication of the International Society of Psychiatric Genetics, 165B(7), 572–580. http://doi.org/10.1002/ajmg.b.32260
Vendome, J., Posy, S., Jin, X., Bahna, F., Ahlsen, G., Shapiro, L., & Honig, B. (2011). Molecular design principles underlying beta-strand swapping in the adhesive dimerization of cadherins. Nature Structural & Molecular Biology, 18(6), 693–700. http://doi.org/10.1038/nsmb.2051
Vester-Christensen, M. B., Halim, A., Joshi, H. J., Steentoft, C., Bennett, E. P., Levery, S. B., … Clausen, H. (2013). Mining the O-mannose glycoproteome reveals cadherins as major O-mannosylated glycoproteins. Proceedings of the National Academy of Sciences of the United States of America, 110(52), 21018–23. http://doi.org/10.1073/pnas.1313446110
Vunnam, N., & Pedigo, S. (2011). Calcium-induced strain in the monomer promotes dimerization in neural cadherin. Biochemistry, 50(39), 8437–8444. http://doi.org/10.1021/bi200902s; 10.1021/bi200902s
Walters, J., Wells-Kilpatrick, K., & Pandeleos, T. (2014). My epilepsy story--PCDH19 alliance. Epilepsia, 55(7), 968–969. http://doi.org/10.1111/epi.12555
Wang, X., Su, H., & Bradley, A. (2002). Molecular mechanisms governing Pcdh-gamma gene expression: evidence for a multiple promoter and cis-alternative splicing model. Genes & Development, 16(15), 1890–1905. http://doi.org/10.1101/gad.1004802
Weiner, J. A., & Jontes, J. D. (2013). Protocadherins, not prototypical: a complex tale of their interactions, expression, and functions. Frontiers in Molecular Neuroscience, 6, 4. http://doi.org/10.3389/fnmol.2013.00004
168
Westerfield, M. (1995). The zebrafish book : a guide for the laboratory use of zebrafish (Danio rerio). [Eugene, OR]: M. Westerfield.
Westerfield, M. (2007). The zebrafish book (5th ed.). University of Oregon Press.
Whitfield, T. T., Riley, B. B., Chiang, M., & Phillips, B. (2002). Development of the zebrafish inner ear. Developmental Dynamics, 223(4), 427–458. http://doi.org/10.1002/DVDY.10073
Wieacker, P., & Wieland, I. (2005). Clinical and genetic aspects of craniofrontonasal syndrome: towards resolving a genetic paradox. Molecular Genetics and Metabolism, 86(1–2), 110–116. http://doi.org/10.1016/j.ymgme.2005.07.017
Williams, E. O., Sickles, H. M., Dooley, A. L., Palumbos, S., Bisogni, A. J., & Lin, D. M. (2011). Delta Protocadherin 10 is Regulated by Activity in the Mouse Main Olfactory System. Frontiers in Neural Circuits, 5, 9. http://doi.org/10.3389/fncir.2011.00009
Wilson, H. V. (1907). A NEW METHOD BY WHICH SPONGES MAY BE ARTIFICIALLY REARED. Science (New York, N.Y.), 25(649), 912–915. http://doi.org/10.1126/science.25.649.912
Wolverton, T., & Lalande, M. (2001). Identification and characterization of three members of a novel subclass of protocadherins. Genomics, 76(1–3), 66–72. http://doi.org/10.1006/geno.2001.6592
Wu, C., Niu, L., Yan, Z., Wang, C., Liu, N., Dai, Y., … Xu, R. (2015). Pcdh11x Negatively Regulates Dendritic Branching. Journal of Molecular Neuroscience : MN, 56(4), 822–828. http://doi.org/10.1007/s12031-015-0515-8
Wulliman, M. F., Rupp, B., & Reichert, H. (2012). Neuroanatomy of the zebrafish brain: a topological atlas. Birkhäuser.
Wyatt, C., Bartoszek, E. M., & Yaksi, E. (2015). Methods for studying the zebrafish brain: past, present and future. The European Journal of Neuroscience, 42(2), 1746–1763. http://doi.org/10.1111/ejn.12932
Xue, J., Li, H., Zhang, Y., & Yang, Z. (2016). Clinical and genetic analysis of two Chinese infants with Mabry syndrome. Brain & Development. http://doi.org/10.1016/j.braindev.2016.04.008
Yagi, T. (2008). Clustered protocadherin family. Development, Growth & Differentiation, 50 Suppl 1, S131-40. http://doi.org/10.1111/j.1440-169X.2008.00991.x
Yagi, T. (2012). Molecular codes for neuronal individuality and cell assembly in the brain. Frontiers in Molecular Neuroscience, 5, 45. http://doi.org/10.3389/fnmol.2012.00045
Yamamoto, A., Amacher, S. L., Kim, S. H., Geissert, D., Kimmel, C. B., & De Robertis, E. M. (1998). Zebrafish paraxial protocadherin is a downstream target of spadetail involved in morphogenesis of gastrula mesoderm. Development (Cambridge, England), 125(17), 3389–97.
Yasuda, S., Tanaka, H., Sugiura, H., Okamura, K., Sakaguchi, T., Tran, U., … Yamagata, K. (2007). Activity-induced protocadherin arcadlin regulates dendritic spine number by triggering N-cadherin endocytosis via TAO2beta and p38 MAP kinases. Neuron, 56(3), 456–471. http://doi.org/10.1016/j.neuron.2007.08.020
Yogev, S., & Shen, K. (2014). Cellular and molecular mechanisms of synaptic specificity. Annual Review of Cell and Developmental Biology, 30, 417–437.
Yonemura, S. (2011). Cadherin-actin interactions at adherens junctions. Current Opinion in Cell Biology, 23(5), 515– 522. http://doi.org/10.1016/j.ceb.2011.07.001
Zhang, Y., Sivasankar, S., Nelson, W. J., & Chu, S. (2009). Resolving cadherin interactions and binding cooperativity at the single-molecule level. Proceedings of the National Academy of Sciences of the United States of America, 106(1), 109–14. http://doi.org/10.1073/pnas.0811350106 169
Zhu, H., Domingues, F. S., Sommer, I., & Lengauer, T. (2006). NOXclass: prediction of protein-protein interaction types. BMC Bioinformatics, 7, 27. http://doi.org/10.1186/1471-2105-7-27
Zipursky, S. L., & Sanes, J. R. (2010). Chemoaffinity revisited: dscams, protocadherins, and neural circuit assembly. Cell, 143(3), 343–53. http://doi.org/10.1016/j.cell.2010.10.009
170
Appendix A: Pcdh19-FE Mutations Found in Literature Search
171
Numbering in Human Pcdh19 PCDH19-FE structures Human PCDH19-FE mutations Zebrafish (Processed mutations excluded Zebrafish numbering zebrafish References clinically evaluating the included (see note) residue ACQ72596.1 protein) patients Notes L25P conserved 28 4 Dibbens et al. 2008 E31K conserved 34 10 van Harssel et al. 2013 V72G conserved 74 50 Higurashi et al. 2012 L81R conserved 82 58 Depienne et al. 2011; Marini et al. 2012 D90V conserved 91 67 Higurashi et al. 2013 I115K conserved 116 92 Samanta 2016 D121N conserved 122 98 Depienne et al. 2009 S139L conserved 140 116 Higurashi et al. 2013 139-141SEAdup SEN 140-142 116-118 Depienne et al. 2011 T146R conserved 147 123 Depienne et al. 2011 172 P149S conserved 150 126 Leonardi et al. 2014
A153T conserved 154 130 Depienne and LeGuern 2012 D157N conserved 158 134 Higurashi et al. 2013 V163G I 164 140 Liu et al. 2016 L190R conserved 191 167 Depienne and LeGuern 2012 V191L conserved 192 168 Higurashi et al. 2012 R198L conserved 199 175 Higurashi et al., 2013, 2015 E199Q conserved 200 176 Depienne et al. 2009 H203P, F206C R 204 180 Patient has two mutations (H203P, F206C) in PCDH19. It is unclear whether both mutations F206C, H203P conserved 207 183 Marini et al., 2010, 2012 contribute to epilepsy. F206Y conserved 207 183 Depienne et al. 2011 D230N conserved 231 207 Trump et al., 2016 Depienne & LeGuern, 2012; Gaily et al., N232S conserved 233 209 2013; Liu et al., 2016; Marini et al., 2012 N234S conserved 235 211 Depienne and LeGuern 2012 Continued Table A.1. Pcdh19-FE mutations found in literature search
Table A.1 continued
Human Human PCDH19-FE PCDH19-FE Zebrafish Numbering in mutations mutations Zebrafish numbering Pcdh19 References clinically evaluating the included excluded residue ACQ72596.1 structures patients Notes Cappelletti et al., 2015; Marini et al., 2012; P236S conserved 237 213 Specchio et al., 2011 P236L conserved 237 213 Trump et al., 2016 E249D conserved 250 226 Depienne et al. 2011 E249G conserved 250 226 Camacho et al., 2012 A262D conserved 263 239 Depienne and LeGuern 2012 D264H conserved 265 241 Marini et al., 2012 Y275N conserved 276 252 van Harssel et al. 2013 Y275S conserved 276 252 van Harssel et al. 2013 S276P conserved 277 253 Hynes et al., 2010 E307K conserved 308 284 Leonardi et al. 2014 E313K conserved 314 290 Leonardi et al. 2014
173 Depienne et al., 2009; Dibbens et al., 2011; Higurashi et al., 2012; Higurashi et al., 2015, 2013; Kwong, Fung, Chan, & Wong, 2012; Liu et al., 2016; Marini et al., 2010, 2012; Specchio et al., 2011; Terracciano et al., 2012; Terracciano et al., 2016; van N340S conserved 341 317 Harssel et al., 2013 D341E conserved 342 318 Depienne et al. 2011 D341G conserved 342 318 van Harssel et al. 2013 Listed as a frameshift mutation in the paper, but the two nucleotide substitutions listed N342_P343delinKT NA 343-344 319-320 Depienne and LeGuern 2012 lead to a two a.a. substitution. P344R conserved 345 321 Depienne and LeGuern 2012 P344L conserved 345 321 van Harssel et al. 2013 D375Y conserved 376 352 van Harssel et al. 2013 Continued
Table A.1 continued Human Human PCDH19-FE PCDH19-FE Zebrafish Numbering in mutations mutations Zebrafish numbering Pcdh19 References clinically evaluating the included excluded residue ACQ72596.1 structures patients Notes Marini et al., 2010, 2012; Specchio, Fusco, D377H conserved 378 354 & Vigevano, 2011 D377E conserved 378 354 Depienne and LeGuern 2012 D377N conserved 378 354 Kwong, Fung, Chan, & Wong, 2012 P393L conserved 394 370 Cappelletti et al., 2015 T404I conserved 405 381 Marini et al., 2010, 2012 E414Q conserved 415 391 Marini et al., 2010 Patient has two mutations (D417H, D596Y) in PCDH19. It is unclear whether both mutations D417H, D596Y conserved 418 394 Higurashi et al., 2015; Hoshina et al., 2015 contribute to epilepsy. L433P conserved 434 410 Marini et al., 2012; Specchio et al., 2011 V441E conserved 442 418 Dibbens et al. 2008
174 N449_H450insN insertion 450_451 Not applicable Liu et al. 2016 P451L conserved 452 Not applicable Terracciano et al., 2016 G486R conserved 487 Not applicable Terracciano et al., 2016 Family epilepsy inheritance is atypical of PCDH19-FE. Extended family could be affected by a different epilepsy condition since neither of her parents carries the S489del conserved 490 Not applicable Antelmi et al., 2012; Marini et al., 2012 mutation. G513R conserved 513 Not applicable Marini et al., 2012; Specchio et al., 2011 L543P conserved 543 Not applicable Depienne et al. 2009 R550P conserved 550 Not applicable Gagliardi et al., 2015 N557K conserved 557 Not applicable Dibbens et al. 2008 P561R conserved 561 Not applicable Depienne et al. 2011 Cappelletti et al., 2015; Depienne & Mother of the patient carries the mutation, P567L conserved 567 Not applicable LeGuern, 2012; Marini et al., 2012 but is asymptomatic. D594H conserved 594 Not applicable van Harssel et al. 2013 Continued
Table A.1 continued Human Human PCDH19-FE PCDH19-FE Zebrafish Numbering in mutations mutations Zebrafish numbering Pcdh19 References clinically evaluating the included excluded residue ACQ72596.1 structures patients Notes D596G conserved 596 Not applicable Higurashi et al., 2015 D596H conserved 596 Not applicable Marini et al., 2012 Patient has two mutations (D417H, D596Y) in PCDH19. It is unclear whether both mutations D596Y, D417H conserved 596 Not applicable Higurashi et al., 2015; Hoshina et al., 2015 contribute to epilepsy. D596V conserved 596 Not applicable Higurashi et al. 2013 G601D conserved 601 Not applicable van Harssel et al. 2013 Mother of the patient carries the mutation, D618N conserved 618 Not applicable Depienne et al. 2011 but is asymptomatic. This residue was excluded because the patient did not have the epilepsy characteristics
175 prototypical of PCDH19-FE. The age of onset E639A Q 639 Not applicable Hildebrand et al., 2016 was 25 years old with no febrile seizures.
V642M conserved 642 Not applicable Depienne and LeGuern 2012 L652P conserved 652 Not applicable Camacho et al., 2012 This residue was excluded since the patient was diagnosed with Mabry Syndrome. The patient also has a mutation in PIGV known to cause Mabry Syndrome. Human transcript D976N conserved 974 Not applicable Xue, Li, Zhang, & Yang, 2016 used: NM_020766.2. This residue was excluded because the patient did not have the epilepsy characteristics prototypical of PCDH19-FE. Age of onset was 11 years old with no febrile seizures. Human A992T conserved 945 Not applicable Hildebrand et al., 2016 transcript used: NM_001184880.1. This residue was excluded because the patient did not have the epilepsy characteristics prototypical of PCDH19-FE. Age of onset was 19 years old with no febrile seizures. Human R1053Q conserved 1004 Not applicable Hildebrand et al., 2016 transcript used: NM_001184880.1.
Appendix B: Quantification of Aggregation Assays Mean from Mean of Mean from Mean of SEM SD SEM SD Sample each N means each N means (SD/√n) (EDTA) (EDTA) (Calcium) (EDTA) (EDTA) (Calcium) (Calcium) (Calcium) 96 166 NcadECFc 59 75.22 19.01 10.98 64 109.8 51.7 29.8 70 100 31 39 Pcdh19EC1-6Fc 30 31.10 0.61 0.35 34 34.3 4.4 2.5 32 30 28 34 Pcdh19EC1-5Fc 28 27.23 0.83 0.48 30 30.9 3.2 1.8 26 28 30 29 Pcdh19EC1-4Fc 27 27.54 2.21 1.28 27 28.0 1.2 0.7 26 28 26 26 Pcdh19EC1-3Fc 29 26.62 2.06 1.19 27 25.9 0.6 0.3 25 25 27 25 Pcdh19EC1-2Fc 28 26.50 1.94 1.12 28 25.4 2.3 1.3 25 23 25 25 Pcdh19EC2-6Fc 28 25.54 1.99 1.15 26 24.8 1.6 0.9 24 23 34 40 Pcdh19EC T146R Fc 33 33.33 0.58 0.33 39 37.0 4.4 2.5 33 32 29 29 Pcdh19EC E313K Fc 28 28.67 0.58 0.33 28 28.7 0.6 0.3 29 29 37 53 Pcdh19EC R364E Fc 35 34.15 2.91 1.68 41 44.0 7.6 4.4 31 39 38 49 Pcdh19ECFc 37 36.69 1.27 0.74 50 48.7 0.9 0.5 NcadEC W2A/R14E His 35 48 44 58 Pcdh19EC T146R Fc 49 45.47 2.72 1.57 50 51.6 5.4 3.1 NcadEC W2A/R14E His 44 47 31 34 Pcdh19EC E313K Fc 32 32.17 1.00 0.58 36 34.4 1.5 0.8 NcadEC W2A/R14E His 33 33 34 31 NcadEC W2A/R14E His 33 33.34 0.47 0.27 29 31.0 1.8 1.0 33 33 Table B.1. Quantification of aggregation assays – time point 0 minutes (t=0)
176
Mean from Mean of Mean from Mean of SEM SD SEM SD Sample each N means each N means (SD/√n) (EDTA) (EDTA) (Calcium) (EDTA) (EDTA) (Calcium) (Calcium) (Calcium) 90 2831 NcadECFc 52 69.24 18.95 10.94 173 1562.7 1333.4 769.8 66 1684 32 48 Pcdh19EC1-6Fc 33 32.28 1.10 0.64 79 54.6 22.2 12.8 31 37 31 38 Pcdh19EC1-5Fc 30 29.79 1.44 0.83 35 35.1 3.2 1.8 28 32 30 43 Pcdh19EC1-4Fc 28 28.85 0.96 0.55 35 38.8 4.2 2.4 29 38 28 30 Pcdh19EC1-3Fc 31 29.44 1.70 0.98 29 29.5 0.3 0.1 29 30 29 29 Pcdh19EC1-2Fc 29 28.25 0.78 0.45 30 28.8 1.4 0.8 27 28 27 26 Pcdh19EC2-6Fc 27 27.27 0.66 0.38 28 27.7 1.6 0.9 28 29 35 37 Pcdh19EC T146R Fc 34 34.33 0.58 0.33 37 36.3 1.2 0.7 34 35 32 33 Pcdh19EC E313K Fc 32 31.67 0.58 0.33 32 32.7 0.6 0.3 31 33 47 80 Pcdh19EC R364E Fc 62 46.80 15.47 8.93 65 68.4 10.4 6.0 31 60 46 175 Pcdh19ECFc 55 51.06 4.41 2.55 128 248.0 168.8 97.5 NcadEC W2A/R14E His 52 441 44 70 Pcdh19EC T146R Fc 48 47.30 2.64 1.53 52 59.5 9.3 5.4 NcadEC W2A/R14E His 50 56 35 39 Pcdh19EC E313K Fc 48 42.95 6.78 3.91 50 44.4 5.8 3.3 NcadEC W2A/R14E His 46 44 37 37 NcadEC W2A/R14E His 56 45.73 9.94 5.74 52 44.8 7.4 4.3 44 45 Table B.2. Quantification of aggregation assays – time point 60 minutes (t=60)
177
Mean from Mean of Mean from Mean of SEM SD SEM SD Sample each N means each N means (SD/√n) (EDTA) (EDTA) (Calcium) (EDTA) (EDTA) (Calcium) (Calcium) (Calcium) 98 11737 NcadECFc 54 76.09 22.05 12.73 558 8420.2 6836.9 3947.3 77 12966 32 59 Pcdh19EC1-6Fc 33 32.05 1.12 0.64 283 127.4 135.5 78.2 31 40 32 51 Pcdh19EC1-5Fc 29 30.08 2.01 1.16 37 40.2 9.6 5.5 28 33 31 66 Pcdh19EC1-4Fc 29 29.70 1.50 0.86 39 48.8 15.3 8.8 29 41 28 30 Pcdh19EC1-3Fc 31 29.31 1.33 0.77 28 29.1 1.0 0.6 29 29 28 30 Pcdh19EC1-2Fc 29 28.41 0.65 0.38 29 28.9 1.3 0.7 28 27 28 28 Pcdh19EC2-6Fc 27 27.68 0.56 0.33 27 28.7 1.5 0.9 28 30 35 40 Pcdh19EC T146R Fc 34 34.33 0.58 0.33 34 36.3 3.2 1.9 34 35 31 34 Pcdh19EC E313K Fc 32 31.33 0.58 0.33 33 33.3 0.6 0.3 31 33 48 129 Pcdh19EC R364E Fc 65 48.12 16.73 9.66 73 108.4 30.9 17.8 32 123 47 2220 Pcdh19ECFc 57 52.91 5.52 3.19 897 1356.3 748.8 432.3 NcadEC W2A/R14E His 55 951 44 115 Pcdh19EC T146R Fc 48 46.85 2.32 1.34 56 78.1 32.4 18.7 NcadEC W2A/R14E His 49 63 36 39 Pcdh19EC E313K Fc 46 43.42 6.47 3.74 51 45.3 6.1 3.5 NcadEC W2A/R14E His 48 46 37 38 NcadEC W2A/R14E His 59 46.84 11.30 6.53 54 45.5 8.4 4.8 44 44 Table B.3. Quantification of aggregation assays – time point 1 minute rocking (t=R1)
178
Mean from Mean of Mean from Mean of SEM SD SEM SD Sample each N means each N means (SD/√n) (EDTA) (EDTA) (Calcium) (EDTA) (EDTA) (Calcium) (Calcium) (Calcium) 119 30249 NcadECFc 65 111.14 42.84 24.74 1635 17364.1 14517.3 8381.6 149 20208 33 86 Pcdh19EC1-6Fc 34 32.58 1.24 0.71 466 204.7 226.5 130.7 31 62 31 81 Pcdh19EC1-5Fc 31 30.09 1.65 0.95 50 58.1 20.3 11.7 28 43 32 152 Pcdh19EC1-4Fc 29 29.56 1.96 1.13 42 80.0 62.4 36.0 28 45 28 29 Pcdh19EC1-3Fc 31 29.40 1.77 1.02 29 28.7 1.0 0.6 29 28 30 31 Pcdh19EC1-2Fc 29 28.79 1.08 0.62 29 29.2 2.1 1.2 28 27 29 29 Pcdh19EC2-6Fc 29 29.35 0.47 0.27 29 29.8 1.7 1.0 30 32 35 45 Pcdh19EC T146R Fc 34 34.67 0.58 0.33 38 39.0 5.6 3.2 35 34 31 35 Pcdh19EC E313K Fc 32 31.67 0.58 0.33 33 34.0 1.0 0.6 32 34 48 195 Pcdh19EC R364E Fc 64 47.57 16.50 9.53 86 238.4 177.7 102.6 31 434 45 3454 Pcdh19ECFc 55 51.46 5.36 3.09 7885 4544.0 2950.6 1703.5 NcadEC W2A/R14E His 54 2294 45 197 Pcdh19EC T146R Fc 47 47.88 3.81 2.20 57 104.9 79.7 46.0 NcadEC W2A/R14E His 52 61 36 39 Pcdh19EC E313K Fc 47 43.48 6.21 3.58 51 45.1 5.7 3.3 NcadEC W2A/R14E His 48 45 39 36 NcadEC W2A/R14E His 64 49.89 12.59 7.27 55 45.9 9.4 5.4 47 46 Table B.4. Quantification of aggregation assays – time point 2 minute rocking (t=R2)
179
Appendix C: Sequences Used for Conservation Analysis of Protocadherin-19
>Platypus gi|620979976|ref|XP_007669727.1| PREDICTED: protocadherin-19 isoform X1 [Ornithorhynchus anatinus] LVNLKYSVDEEQRAGTVIGDVGRDARAAGFALDPRQPPPGFRVVSNSAPHLVDLDAGSGLLVTKQKIDRELLCGPSPQCPISLEVMSGS LEICAVQVEVRDLNDHAPSFPADPMELEISETASPGTRLPLDSAHDPDAGPLGVQAYELSPRDLFGLEVKTRGDGTRFAELVVERPLDRE TQARYTYRLTARDGGDPPRQGSAALTIRVTDSNDNHPVFAQPAYAVSLPEDAPPRTPVIQLNASDPDEGTNGEVVYSFGGYAGERARG LFHLDARSGLVTVGGPLDYEEARSYELDVQAKDRGPNAVPAHCKVTVHLLDVNDNAPVINLLSVHGEQVEVSEAAPPGYVIALVRASDR DAGANGRVRCRLLGSVPFRLQDYESFSTVLVDGRLDREQRDRYNLTLQARDGGAPALQSAKSFTVRVTDENDN
>AustralianGhostShark gi|632935426|ref|XP_007890046.1| PREDICTED: protocadherin-19 [Callorhinchus milii] VINLKYSIVEEERAGTLIGNIAKDAGFATSEQKVPIFRVLSNSAPHLIDINPSTGLLVTKQKIDRDLLCRQGSKCLISLEVMVNSMEICVVKVE ILDVNDNAPSFPTEQIDLEISETASPGTRVPLESAYDPDAGQFGVQSYQITPNDLFGLEIKTRGDGSRFAELVVEKELDRETQSHYSYMITA LDGGDPPNFGTTELNIKVIDSNDNYPVFDEPSYAVNVLENAPTNSLVIDLNASDPDEGTNGEIVYSFNSYVSDKTRELFKLDPRSGAITVR GHIDYEEGSIYEIDVQAKDLGPNSIPAHCKVTVNVVDVNDNVPVITLFSVNSETVEVSEAAPPGYVIGLVRVSDRDSGANGRVQCKLLGN VPFKLQEYESFYTILVDGRLDREQRDQYNLTILAKDGGSPSLQSTKSFTVKITDENDN
>FishHerring gi|831276392|ref|XP_012696135.1| PREDICTED: protocadherin-19 [Clupea harengus] LFTRTYYVKEEQPAYTKIANITQEFIDTKLAGANQSVSFRIISSSEPRWVEIDNMGVLKTKQKIDRDVVCRHNPKCVVTLELMSNTMVICV IKIEMEDLNDNAPRFPTDHIDIEISENADPGTRFPLEGASDPDSGSYGVQTYTITPNELFGLEIKTRGDGSKFAELVVEKPLDREVQSRYDY TITAEDGGDPPKSGRVKLNIKVIDSNDNNPVFDQPVYSVKVMENSPINTLVIDLNATDPDEGTNGEVRYSFNSYVSDKTREAFKIDTKTG VITVNGPLDYETTTVYEIDVQAKDLGPNSIPAHCKVNVEVLDANDNVPVINLLPVSSEIEEVSENAGPEYVIALVRVLDKDSGLNGKVKCK LLGSVPFRLQEYETFSTILVAGKLDREERDRYNLTIQAEDSGNPSLKTTKSFAVKIKDENDN
>FishGar gi|573890437|ref|XP_006632980.1| PREDICTED: protocadherin-19-like [Lepisosteus oculatus] VINLKYSVDEEERAGTVIANVAKDAKDAGFVIDPRQPSLRVISNSAPHLVDINPAGLLVTKQKIDRDIFCRQSPKCFISLEVMSNSMEICVI KVEIKDSNDNAPSFPTDHIDLEISETAAPGTRIPLEGANDPDSGIFGVQTYEITPNDLFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSYMI TALDGGEPPNFGSVELNIKVIDSNDNNPVFDEPVYTVNVMENSPINTVVIDLNATDPDEGTNGEVVYSFNSYVSEKTREVFKIDSRTGVI TVSGVLDFETMNIYEIDVQAKDLGPNSIPAHCKVTVNVMDMNDNVPVINLLSVNSELVEVSENAPLGYVIALVRVSDRDSGANGRVQC RLQGSVPFRLQEYESFSTILVDGRLDREQRDTYNLTIQAEDSGIPSLKTTKSFTVKITDENDN
>BlindCaveFish gi|992208178|ref|XP_015461177.1| PREDICTED: protocadherin-19 isoform X1 [Astyanax mexicanus] VFNLKYSVEEELRAGTKIANVTADAKVAGFALGNRQPYLRVISNSEPRWVNLSPAGLLITKQKIDRDAVCRQTPKCVVSLEVMSNSMEIC VIKIEIIDVNDNAPRFPAPRIDLEISENAAPGTRYPLESASDPDAGSNGVQTYTITPNDIFGLEIKTRGDGSKIAELVVEKMLDRESQSHYTF EITAEDGGDPPKTGTVQLNVKVLDSNDNNPVFDEPVYTVNVMENAPMNTLVIDLNATDPDEGTNGEVVYSFINFVSNLTKQMFKIDP KTGVITVNGVLDHEELRVHEIDVQAKDLGPNSIPAHCKVIVNVVDVNDNAPEIKLLSENSEMVEVSENAPLGYVIALVRVSDSDSGANGK VQCRLQGNVPFRLNEFESFSTLLVDGRLDREQRDTYNLTIVAEDSGYPPLRSSKSFAVKVTDENDN
>Zebrafish gi|229472136|gb|ACQ72596.1| protocadherin-19 isoform 1 [Danio rerio] VFNLKYTVEEELRAGTKIANVTADAKVAGFALGNRQPYLRVISNSEPRWVNLSPAGLLITKQKIDRDAVCRQTPKCFISLEVMSNSMEICV IKIEIIDVNDNAPRFPTNHIDIEISENAAPGTRFPLEGASDPDSGSNGIQTYTITPNDIFGLEIKTRGDGSKIAELVVEKTLDRETQSRYTFELT AEDGGDPPKSGTVQLNIKVIDSNDNNPVFDEPVYTVNVLENSPINTLVIDLNATDPDEGTNGEVVYSFINFVSNLTKQMFKIDPKTGVIT VNGVLDHEELHIHEIDVQAKDLGPNSIPAHCKVIVNVIDINDNAPEIKLLSENSEMVEVSENAPLGYVIALVRVSDNDSGANGKVQCRLQ GNVPFRLNEFESFSTLLVDGRLDREQRDMYNLTILAEDSGYPPLRSSKSFAVKVTDENDN
180
>FishGoldenLine gi|1020571998|ref|XP_016113863.1| PREDICTED: protocadherin-19 isoform X1 [Sinocyclocheilus grahami] VFNLKYTVEEELRAGTKIANVTADAKVAGFALGNRQPYLRVISNSEPRWVNLSPAGLLITKQKIDRDAVCRQTPKCFISLEVMSNSMEICV IKIEIIDVNDNAPRFPTNHIDIEISENAAPGTRFPLEGASDPDSGSNGIQTYTITPNDIFGLEIKTRGDGSKIAELVVEKTLDRETQSRYTFEFT AEDGGDPPKSGTVQLNIKVIDSNDNNPVFDEPVYTVNLLENSPINTLVVDLNATDPDEGTNGEVIYSFINLVSNLTKQMFKIGLKTGVITV NGVLDHEELSVHEIDVQAKDLGPNSIPAHCKVIVNVIDINDNAPEIKLLSENSEMVEVSENAPLGYVIALVRVSDSDSGANGKVQCRLQG NVPFRLNEFESFSTLLVDGRLDREQRDMYNLTILAEDSGYPPLRSSKSFAVKVTDENDN
>PikeFish gi|742234008|ref|XP_010901972.1| PREDICTED: protocadherin-19 isoform X3 [Esox lucius] VINLKYSINEEQKAGYIIGNVTKDAQTQGFAIAPRAPYLRVISNSEPRWVELSPAGLLLTHQKIDRDVACRQTAKCTVSLEVMSNSMEICV IKVEIVDLNDNAPRFPTNHIDIEISENASPGTRFPLEGASDPDSGIFGVQSYSITPNELFGLEIKTRGDGSKIAELVVQKSLDRETQSHYSYEIS AEDGGDPPKIGAVQLNIKVIDSNDNNPVFDQPVYTVNVMENSPINTLVIDLNATDPDEGTNGEVVYSFNSYVTEKTRDVFKIDPRTGIIT VNGPLDYETKHIYEIDVQAKDLGPNSIPAHCKVTVNVMDANDNPPVISLLSVNTELIEVSENAPRGYVIALVRVSDKDAGANGKVQCRL QGNVPFRLQEYESFSTILVDGRLDREQRDTYNLTIHAEDSGTPPLRATKSFVVKVTDENDN
>FishNileTilapia gi|908431029|ref|XP_013126773.1| PREDICTED: protocadherin-19 isoform X1 [Oreochromis niloticus] VINLKYGINEEMRAGSVIGNVTNDALKQGFQIAPQPPYLRVISNSHPGYVELSPAGILTAQQKIDRDVFCRQNPKCIISLEVMSNSMEICV IKVEIEDLNDNAPRFPTSHIDIEISENASPGTRFPLEGASDPDSGIFGVQSYSITPNELFGLEIKTRGDGSKIAELVVQKSLDRETQSHYTYEIS AEDGGDPPKIGAVQLNIKVIDSNDNNPVFDEPVYTVNVMENSPRNSLVIDLNATDPDEGTNGEVLYSFNSYVTEKTRDAFKIDPRTGVIT VIGDLDYETTQIYEIDVQAKDLGPNSIPAHCKVTVNVMDTNDNPPVISLLSLNTEMVEVSENAQRGYVIALVRVSDKDSGANGKVQCRL QGNVPFRLQEYESFSTILVDGRLDREQKDTYNLTIQAEDSGIPPLRATKSLVVKVTDENDN
>FishZebraMbuna gi|498963573|ref|XP_004545840.1| PREDICTED: protocadherin-19 isoform X1 [Maylandia zebra] VINLKYGINEEMRAGSVIGNVTNDALKQGFQIAPQPPYLRVISNSHPGYVELSPAGILTAQQKIDRDVFCRQNPKCIISLEVMSNSMEICV IKVEIEDLNDNAPRFPTSHIDIEISENASPGTRFPLEGASDPDSGIFGVQSYSITPNELFGLEIKTRGDGSKIAELVVQKSLDRETQSHYTYEIS AEDGGDPPKIGAVQLNIKVIDSNDNNPVFDEPVYTVNVMENSPRNSLVIDLNATDPDEGTNGEVLYSFNSYVTEKTRDAFKIDPRTGVIT VIGDLDYETTQIYEIDVQAKDLGPNSIPAHCKVTVNVMDTNDNPPVISLLSLNTEMVEVSENAQRGYVIALVRVSDKDSGANGKVQCRL QGNVPFRLQEYESFSTILVDGRLDREQKDTYNLTIQAEDSGIPPLRATKSLVVKVTDENDN
>FishMouthbrooder gi|930724046|ref|XP_014189344.1| PREDICTED: protocadherin-19 isoform X1 [Haplochromis burtoni] VINLKYGINEEMRAGSVIGNVTNDALKQGFQIAPQPPYLRVISNSHPGYVELSPAGILTAQQKIDRDVFCRQNPKCIISLEVMSNSMEICV IKVEIEDLNDNAPRFPTSHIDIEISENASPGTRFPLEGASDPDSGIFGVQSYSITPNELFGLEIKTRGDGSKIAELVVQKSLDRETQSHYTYEIS AEDGGDPPKIGAVQLNIKVIDSNDNNPVFDEPVYTVNVMENSPRNSLVIDLNATDPDEGTNGEVLYSFNSYVTEKTRDAFKIDPRTGVIT VIGDLDYETTQIYEIDVQAKDLGPNSIPAHCKVTVNVMDTNDNPPVISLLSLNTEMVEVSENAQRGYVIALVRVSDKDSGANGKVQCRL QGNVPFRLQEYESFSTILVDGRLDREQKDTYNLTIQAEDSGIPPLRATKSLVVKVTDENDN
>FishCichlid gi|923777253|ref|XP_013763739.1| PREDICTED: protocadherin-19 isoform X1 [Pundamilia nyererei] VINLKYGINEEMRAGSVIGNVTNDALKQGFQISPQPPYLRVISNSHPGYVELSPAGILTAQQKIDRDVFCRQNPKCIISLEVMSNSMEICVI KVEIEDLNDNAPRFPTSHIDIEISENASPGTRFPLEGASDPDSGIFGVQSYSITPNELFGLEIKTRGDGSKIAELVVQKSLDRETQSHYTYEIS AEDGGDPPKIGAVQLNIKVIDSNDNNPVFDEPVYTVNVMENSPRNSLVIDLNATDPDEGTNGEVLYSFNSYVTEKTRDAFKIDPRTGVIT VIGDLDYETTQIYEIDVQAKDLGPNSIPAHCKVTVNVMDTNDNPPVISLLSLNTEMVEVSENAQRGYVIALVRVSDKDSGANGKVQCRL QGNVPFRLQEYESFSTILVDGRLDREQKDTYNLTIQAEDSGIPPLRATKSLVVKVTDENDN
>FishCod gi|736301320|ref|XP_010793227.1| PREDICTED: protocadherin-19 isoform X1 [Notothenia coriiceps] VINLKYGINEEMKPGSVIGNVTKDALKQGFQIALQPPYLRVISNSEPRWVELSPAGILTTQMKIDRDVVCRQNPKCIISLEVMSNSMEICV IKVEIEDLNDNAPRFPTSHIDIEISENASPGTRFPLEGASDPDSGIFGVQSYSITPNELFGLEIKTRGDGSKIAELVVQKSLDRETQSHYSYEIS AEDGGDPPKIGAVQLNIKVIDSNDNNPVFDESVYTVNVMENSPINTLVIDLNATDPDEGPNGEVVYTFNSYVTEKTRDAFKIDSRTGIITV NGILDYETSQIFEIDIQAKDLGPNSIPAHCKVTVNVMDTNDNPPIISLLSLNTEMVEVSENAQRGYVIALVRVSDKDSGANGKVQCRLQG NVPFRLQEYESFSTILVDGRLDREQKDTYNLTIQAEDSGSPPLRATKSLVVKVSDENDN
181
>Pufferfish gi|768937996|ref|XP_011609177.1| PREDICTED: protocadherin-19 isoform X1 [Takifugu rubripes] VINLKYGINEEMKPGSVIGNVTKDALKQGFQIALQPPYLRVISNSEPRWVELSPAGILTTQMKIDRDVVCRQNPKCVISLEVMSNSMEIC VIKVEIEDLNDNAPRFPTSHIDIEISENASPGTRFPLEGASDPDSGIFGVQSYSITPNELFGLEIKTRGDGSKIAELVVQKSLDRETQSHYSYEI SAEDGGDPPKIGAVQLNIKVIDSNDNNPVFDEAVYTVNVMENSPANTIVIDLNATDPDEGTNGEVVYSFHNYVTEKTRDAFKIDPRTGII TVNGVLDYETAQIYEIDVQAKDLGPNSIPAHCKVTVNVMDTNDNPPVISLLSLNTEMVEVSENAQRGYVIALVRVSDKDSGANGKVQC RLQGNVPFRLQEYESFSTILVDGRLDREQKDTYNLTIQAEDSGIPPLRATKSLVVKVTDENDN
>FishMinnow gi|974053082|ref|XP_015244031.1| PREDICTED: protocadherin-19 isoform X1 [Cyprinodon variegatus] VINLKYGINEEMKPGSVIGNVTRDALKQGFQIAPQPPYLRVISNSEPRWVELSPAGILTTQMKIDRDVVCRQNPKCIISLEVMSNSMEIC VIKVEIQDLNDNAPRFPTSHIDIEISENASPGTRFPLEGASDPDSGIFGVQSYSITPNELFGLEIKTRGDGSKIAELVVQKSLDRETQSHYSYEI SAEDGGDPPKIGAVQLNIKVIDSNDNNPVFDEPVYTVNVMENSPVNTLVIDLNATDPDEGTNGEVVYSFNSYVTEKTREAFKIDPRTGII TVNGVLDYETTQIYEIDVQAKDLGPNSIPAHCKVTVNVMDTNDNPPVISLLSLNTEMVEVSENAQRGYVIALVRVSDKDSGANGKVKCT LQGNVPFKLQEYESFSTILVDGRLDREQKDTFNLTIQAEDSGIPQLRATKSLVVKVTDENDN
>FishFundulus gi|831520348|ref|XP_012717246.1| PREDICTED: protocadherin-19 isoform X3 [Fundulus heteroclitus] VINLKYGINEEMKPGSVIGNVTRDALKQGFQIAPQPPYLRVISNSEPRWVELSPAGILTTQMKIDRDVVCRQNPKCIISLEVMSNSMEIC VIKVEIEDLNDNAPRFPTSHIDLEISENASPGTRFPLEGASDPDSGIFGVQSYSITPNELFGLEIKTRGDGSKIAELVVQKSLDRETQSHYTYEI SAEDGGEPPKIGAVQLNIKVIDSNDNNPVFDEPVYTVNVMENSPVNTLVIDLNATDPDEGTNGEVVYSFNSYVTEKTREAFKIDPRTGIIT VNGVLDYEATQIYEIDVQAKDLGPNSIPAHCKVTVNVMDTNDNPPVISLLSLNTEMVEVSENAQRGYVIALVRVSDKDSGANGKVKCTL QGNVPFRLQEYESFSTILVDGRLDREQKDTFNLTIQAEDSGIPQLRATKSLVVKVTDENDN
>FishSailfin gi|961839858|ref|XP_014887029.1| PREDICTED: protocadherin-19 isoform X1 [Poecilia latipinna] VINLKYGINEEMKPGSVIGNVTRDALKQGFQIAPQPPYLRVISNSEPRWVELSPAGILTTQMKIDRDVVCRQNPKCIISLEVMSNSMEIC VIKVEIEDLNDNAPRFPTSHIDIEISENASPGTRFPLEGASDPDSGIFGVQSYSITPNELFGLEIKTRGDGSKIAELVVQKSLDRETQSHYTYEI SAEDGGDPPKIGAVQLNIKVIDSNDNNPVFDEPVYTVNVMENSPVNTLVIDLNATDPDEGTNGEVVYSFNSYVTEKTREAFKIDPRTGII TVNSVLDYETTKIYEIDVQAKDLGPNSIPAHCKVTVNVMDTNDNPPVISLLSLNTEMVEVSENAQRGYVIALVRVSDKDSGANGKVKCT LQGNVPFRLQEYESFSTILVDGKLDREQKDTFNLTIQAEDSGIPQLRATKSLVVKVTDENDN
>FishRice gi|765132009|ref|XP_011478203.1| PREDICTED: protocadherin-19 isoform X1 [Oryzias latipes] VINLKYGINEEMKPGSVIGNVTKDALKQGFQIAPQPPYLRVISNSEPRWVELSPAGILTTQMKIDRDVVCRQNPKCIISLEVMSNSMEICV IKVEIEDLNDNAPKFPTSHIDIEISENASPGTRFPLEGASDPDSGIFGVQSYSITPNELFGLEIKTRGDGSKIAELVVQKSLDRETQSHYTYEIS AEDGGDPPKIGAVQLNIKVIDSNDNNPVFDESVYTVNVMENSPINTLVIDLNATDPDEGTNGEVVYSFNSYVTEKTREAFKIDPRTGIITV NGVLDYETSQIYEIDVQAKDLGPNSIPAHCKVTVNVMDTNDNPPVISLLSLNTEMVEVSENAQRGYVIALVRVSDKDSGANGKVQCRL QGNVPFRLQEYESFSTILVDGKLDREQKDTFNLTIQAEDSGTPPLRATKSLVVKVTDENDN
>FishTurquoiseKillifish gi|1007705818|ref|XP_015803078.1| PREDICTED: protocadherin-19 isoform X1 [Nothobranchius furzeri] VINLKYGINEEMKPGSVIGNVTKDALKQGFQIAPQPPYLRVISNSEPRWVELSPAGILTTQMKIDRDVVCRQNPKCIISLEVMSNSMEICV IKVEIEDLNDNAPRFPTSHIDLEISENASPGTRFPLEGASDPDSGMFGVQSYSITPNELFGLEIKTRGDGSKIAELVVQKSLDRETQSHYTYE ISAEDGGDPPKIGAVQLNIKVIDSNDNNPVFDEPVYTVNVMENSPINTLVIDLNATDPDEGTNGEVVYSFNSYVTEKTREAFKIDPRTGII TVNGVLDYETTQIYEIDVQAKDLGPNSIPAHCKVTVNVMDTNDNPPVISLLSLNTEMVEVSENAQRGYVIALVRVSDKDSGANGKVQC RLQGNVPFRLQEYESFSTILVDGRLDREQKDTYNLTIQAEDSGTPPLRVTKSLVVKVTDENDN
>FishKillefish gi|928075037|ref|XP_013887442.1| PREDICTED: protocadherin-19 isoform X1 [Austrofundulus limnaeus] VINLKYGINEEMKPGSVIGNVTKDALKQGFQIAPSPPYLRVISNSEPRWVELSPAGILTTQMKIDRDVVCRQTPKCIISLEVMSNSMEICVI KVEIEDLNDNAPRFPTSHIDLEISENASPGTRFPLEGASDPDSGIFGVQSYSITPNELFGLEIKTRGDGSKIAELVVQKSLDRETQSHYTYEIS AEDGGDPPKIGAVQLNIKVIDSNDNNPVFDEPVYTVNVMENSPINTLVIDLNATDPDEGTNGEIVYSFNSYVTEKTREAFKIDPRTGIITV NGILDYEATQIYEIDVQAKDLGPNSIPAHCKVTVNVMDTNDNPPVISLLSLNTEMVEVSENAQRGYVIALVRVSDKDSGANGKVQCRLQ GNVPFRLQEYESFSTILVDGRLDREQKDTYNLTIQAEDSGSPPLRATKSLVVKVTDENDN
>NakedMoleRat gi|351711409|gb|EHB14328.1| Protocadherin-19 [Heterocephalus glaber] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDSRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDGAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSF RIIALDGGDPPRLGTVGLSIKVTDSNDNNPVFSESTYSVSVPENSPPNTPVIRLNASDPDEGTNGQVIYSFYGYVNDRTRELFHIDPHSGL VTVTGALDYEEGHEYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSELVEVSESSPPGYVIALVRVSDRDSGLNGRVQCR LLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSAKSFTVLITDENDN 182
>Pika gi|504157446|ref|XP_004590273.1| PREDICTED: protocadherin-19 [Ochotona princeps] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLITKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSFR ITALDGGDPPHLGTVGLSIKVTDSNDNNPVFGESTYAVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHSGL VTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQCR LLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSAKSFTVRITDENDN
>SquirrelMonkey gi|725597696|ref|XP_010349138.1| PREDICTED: protocadherin-19 isoform X3 [Saimiri boliviensis boliviensis] LINLKYSVEEEQRAGTVIANVAKDARDAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNEMFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSF RITALDGGDPPRLGTVGLNIKVTDSNDNNPVFGESTYTVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHS GLVTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQ CRLLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSAKSFTVLITDENDN
>Marmoset gi|296235955|ref|XP_002763118.1| PREDICTED: protocadherin-19 isoform X3 [Callithrix jacchus] LINLKYSVEEEQRAGTVIANVAKDARDAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNEMFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSF RITALDGGDPPRLGTVGLNIKVTDSNDNNPVFGESTYTVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHS GLVTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQ CRLLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSAKSFTVLITDENDN
>MonkeyNancy gi|817298036|ref|XP_012319466.1| PREDICTED: protocadherin-19 isoform X1 [Aotus nancymaae] LINLKYSVEEEQRAGTVIANVAKDARDAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNEMFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSF RITALDGGDPPRLGTVGLNIKVTDSNDNNPVFGESTYTVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHS GLVTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQ CRLLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSAKSFTVLITDENDN
>Baboon gi|685617101|ref|XP_009196181.1| PREDICTED: protocadherin-19 isoform X1 [Papio anubis] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSFR ITALDGGDPPRLGTVGLSIKVTDSNDNNPVFSESTYSVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHSGL VTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQCR LLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSAKSFTVLITDENDN
>monkey gi|388454671|ref|NP_001252617.1| protocadherin-19 precursor [Macaca mulatta] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDSRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQMELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYS FRITALDGGDPPRLGTVGLSIKVTDSNDNNPVFSESTYSVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHS GLVTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQ CRLLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSAKSFTVLITDENDN
>Monkey gi|388454671|ref|NP_001252617.1| protocadherin-19 precursor [Macaca mulatta] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDSRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQMELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYS FRITALDGGDPPRLGTVGLSIKVTDSNDNNPVFSESTYSVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHS GLVTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQ CRLLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSAKSFTVLITDENDN
183
>MacaqueMonkeylike gi|544521854|ref|XP_005594161.1| PREDICTED: protocadherin-19 isoform X3 [Macaca fascicularis] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDSRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQMELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYS FRITALDGGDPPRLGTVGLSIKVTDSNDNNPVFSESTYSVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHS GLVTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQ CRLLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSAKSFTVLITDENDN
>MacaquePigtailed gi|795483655|ref|XP_011770105.1| PREDICTED: protocadherin-19 isoform X3 [Macaca nemestrina] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDSRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQMELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYS FRITALDGGDPPRLGTVGLSIKVTDSNDNNPVFSESTYSVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHS GLVTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQ CRLLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSAKSFTVLISDENDN
>DrillBaboonlike gi|795172846|ref|XP_011842950.1| PREDICTED: protocadherin-19 isoform X2 [Mandrillus leucophaeus] LINLKYSIEEEQRAGTVIANVAKDAREAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSFR ITALDGGDPPRLGTVGLSIKVTDSNDNNPVFSESTYSVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHSGL VTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQCR LLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSAKSFTVLITDENDN
>Mangabey gi|795336907|ref|XP_011929066.1| PREDICTED: protocadherin-19 isoform X3 [Cercocebus atys] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQMELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYS FRITALDGGDPPRLGTVGLSIKVTDSNDNNPVFSESTYSVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHS GLVTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQ CRLLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSAKSFTVLITDENDN
>chimp gi|694985556|ref|XP_009437627.1| PREDICTED: protocadherin-19 [Pan troglodytes] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSFR ITALDGGDPPRLGTVGLSIKVTDSNDNNPVFSESTYAVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHSGL VTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQCR LLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSAKSFTVLITDENDN
>MonkeyColobus gi|795141350|ref|XP_011792655.1| PREDICTED: protocadherin-19 isoform X2 [Colobus angolensis palliatus] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDQLCRQSPKCIISLEVMSSSMEI CVIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSF RITALDGGDPPRLGTVGLSIKVTDSNDNNPVFSESTYAVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHSG LVTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQC RLLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSAKSFTVLITDENDN
>GibbonMonkeylike gi|332254730|ref|XP_003276485.1| PREDICTED: protocadherin-19 isoform X2 [Nomascus leucogenys] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSFR ITALDGGDPPRLGTVGLSIKVTDSNDNNPVFSESTYTVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHSGL VTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQCR LLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSAKSFTVLISDENDN
184
>Human gi|296434287|ref|NP_001171809.1| protocadherin-19 isoform c precursor [Homo sapiens] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSFR ITALDGGDPPRLGTVGLSIKVTDSNDNNPVFSESTYAVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHSGL VTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQCR LLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSAKSFTVLITDENDN
>Gorilla gi|426396637|ref|XP_004064538.1| PREDICTED: protocadherin-19 isoform 2 [Gorilla gorilla gorilla] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSFR ITALDGGDPPRLGTVGLSIKVTDSNDNNPVFSESTYAVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHSGL VTVTGVLDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQCR LLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSAKSFTVLITDENDN
>Orangutan gi|297710519|ref|XP_002831924.1| PREDICTED: protocadherin-19 [Pongo abelii] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSFR ITALDGGDPPRLGTVGLSIKVTDSNDNNPVFSESTYSVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHSGL VTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQCR LLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSAKSFTVLITDENDN
>ShrewCommon gi|505836249|ref|XP_004611703.1| PREDICTED: protocadherin-19 isoform X1 [Sorex araneus] LINLKYSVEEEQRAGTVIANVAKDARDAGFAMDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEI CVIKVEIKDLNDNAPSFPAGQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYN FRITALDGGDPPHMGTVGLSIKVTDSNDNNPVFGQSNYAVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDP HSGLVTVIGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDTGLNGR VQCRLLGNVPFRLQEYESFSTILVDGRLDREQHEQYNLTIQARDGGVPMLQSAKSFTVRITDENDN
>DamaraMolerat gi|676279624|gb|KFO33567.1| Protocadherin-19 [Fukomys damarensis] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPTFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDREIQSHYNFR ITALDGGDPPHLGTVGLSIKVTDSNDNNPVFGESTYSVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHSGL VTVTGALDYEEGNVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQCR LLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDSGVPMLQSAKSFTVRITDENDN
>Vole gi|532031590|ref|XP_005358727.1| PREDICTED: protocadherin-19 isoform X2 [Microtus ochrogaster] LINLKYSVEEEQRAGTVIANVAKDAREAGFAMDPRQASTFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQNPKCIISLEVMSSSMEI CVIKVEIKDLNDNAPSFPTAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKNLDRETQSHYN FRITALDGGDPPHMGTAGLSIKVTDSNDNNPVFGESSYSVSVPENSPPNTPVIRLNASDPDEGTNGQVIYSFYGYANDHTRELFQIDPHS GLVTVTGALDYEEGQVYELDVQAKDLGPNSIPAHCKVTVSILDTNDNPPIINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQC RLLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDSGVPTLQSAKSFTVRITDENDN
>HedgehogEuropean gi|617655069|ref|XP_007535321.1| PREDICTED: protocadherin-19 isoform X1 [Erinaceus europaeus] LINLKYSVEEEQRAGTVIANVAKDARDAGFALDPRQASAFRVVSNSAPHLVDINPNSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEI CVIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDREKQSHYN FRITALDGGDPPHLGTVGLSIKVTDSNDNNPVFGESTYSVSVPENSPPNTPVIRLNASDPDEGTNGQVIYSFYGYVNDHTRELFQIDPHS GLVTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDHDSGLNGRVQ CRLLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSAKSFTVRITDENDN
>RodentDegu gi|507696329|ref|XP_004643384.1| PREDICTED: protocadherin-19 isoform X2 [Octodon degus] LINLKYSVEEEQRAGTVIANVAKDAREAGFGLDSRQASAFRVVSNSAPHLVDINPGSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETESHYSFR ITALDGGDPPRLGTVGLSIKVTDSNDNNPVFGESTYSVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHSGL VTVTGALDYEESRVYELDVQAKDLGPNSIPAHCKITVNVLDTNDNPPIINLLSVNSELVEVSENAPPGYVIALVRVSDRDSGHNGRVQCR LMGSVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSAKSFTVRITDENDN
185
>BatVesper gi|1016642962|ref|XP_016051176.1| PREDICTED: protocadherin-19 isoform X3 [Miniopterus natalensis] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDMLCRQSPKCIISLEVMSSSMEI CVIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSF RITALDGGDPPHLGTVGLNIKVTDSNDNNPVFSESTYSVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHSG LVTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVNILDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQC RLLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSAKSFTVRITDENDN
>Mouse gi|157426849|ref|NP_001098715.1| protocadherin-19 isoform a precursor [Mus musculus] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSFR ITALDGGDPPHMGTVGLSIKVTDSNDNNPVFGESTYSVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHSG LVTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPIINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQCR LLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDSGVPMLQSAKSFTVRITDENDN
>MousePrairieDeer gi|589947607|ref|XP_006986473.1| PREDICTED: protocadherin-19 [Peromyscus maniculatus bairdii] LINLKYSVEEEQRAGTVIANVAKDAREAGFAMDTRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEI CVIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSF RITALDGGDPPHLGTVGLSIKVTDSNDNNPVFGESTYSVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHSG LVTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSILDTNDNPPIINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQCR LLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDSGVPMLQSAKSFIVRITDENDN
>Rat gi|281306738|ref|NP_001162600.1| protocadherin-19 precursor [Rattus norvegicus] LINLKYSVEEEQRAGTVIANVAKDAREAGFAMDTRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEI CVIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSF RITALDGGDPPHMGTVGLTIKVTDSNDNNPVFGESTYSVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHS GLVTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPIINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQ CRLLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDSGVPMLQSAKSFTVRITDENDN
>HamsterGolden gi|524941921|ref|XP_005072565.1| PREDICTED: protocadherin-19 isoform X3 [Mesocricetus auratus] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSFR ITALDGGDPPHLGTVGLSIKVTDSNDNNPVFGESTYSVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHSGL VTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPIINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQCRL LGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDSGVPMLQSAKSFTVRITDENDN
>batChinese gi|432098502|gb|ELK28221.1| Protocadherin-19 [Myotis davidii] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSFR ITALDGGDPPHLGTVGLSIKVTDSNDNNPVFGESTYSVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDHTRELFQIDPHSGL VTVTGTLDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQCR LLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSAKSFTVRITDENDN
>BatBrown gi|641729159|ref|XP_008154759.1| PREDICTED: protocadherin-19 isoform X3 [Eptesicus fuscus] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSFR ITALDGGDPPHLGTVGLSIKVTDSNDNNPVFGESTYSVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDHTRELFQIDPHSGL VTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQCR LLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSAKSFTVRITDENDN
>WaterBuffalo gi|594105420|ref|XP_006075665.1| PREDICTED: protocadherin-19-like isoform X2 [Bubalus bubalis] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSFR ITALDGGDPPHLGTVGLSIKVTDSNDNNPVFGESTYSVSVPENSPPNTPVIRLNATDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHSGL VTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQCR LLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSAKSFTVRITDENDN 186
>cow gi|741905642|ref|XP_010800707.1| PREDICTED: protocadherin-19 isoform X3 [Bos taurus] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSFR ITALDGGDPPHLGTVGLSIKVTDSNDNNPVFGESTYSVSVPENSPPNTPVIRLNATDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHSGL VTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQCR LLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSAKSFTVRITDENDN
>SheepMouflon gi|803285084|ref|XP_012002201.1| PREDICTED: protocadherin-19 isoform X4 [Ovis aries musimon] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSFR ITALDGGDPPHLGTVGLSIKVTDSNDNNPVFGESTYSVSVPENSPPNTPVIRLNATDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHSGL VTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQCR LLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSAKSFTVRITDENDN
>Alpaca gi|560976030|ref|XP_006210310.1| PREDICTED: protocadherin-19 isoform X2 [Vicugna pacos] LINLKYSVEEEQRAGTVIANVAKDARDAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLDIKTRGDGSRFAELVVEKSLDRETQSHYSF RITALDGGDPPHLGTVGLSIKVTDSNDNNPVFGESTYSVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHSG LVTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQC RLLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDSGVPMLQSAKSFTVRITDENDN
>WhaleMinke gi|594666907|ref|XP_007181522.1| PREDICTED: protocadherin-19 isoform X1 [Balaenoptera acutorostrata scammoni] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPATQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSFR ITALDGGDPPHLGTVGLSIKVTDSNDNNPVFGESTYSVTVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHSGL VTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQCR LLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSSKSFTVRITDENDN
>SpermWhale gi|593727610|ref|XP_007109739.1| PREDICTED: protocadherin-19 isoform X1 [Physeter catodon] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDMLCRQSPKCIISLEVMSSSMEI CVIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSF RITALDGGDPPHLGTVGLSIKVTDSNDNNPVFGESTYSVTVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHSG LVTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQC RLLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSSKSFTVRITDENDN
>WhaleKiller gi|466076610|ref|XP_004283572.1| PREDICTED: protocadherin-19 isoform X2 [Orcinus orca] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSFR ITALDGGDPPHLGTVGLSIKVTDSNDNNPVFGESTYLVTVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHSGL VTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQCR LLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSSKSFTVRITDENDN
>dolphin gi|466076610|ref|XP_004283572.1| PREDICTED: protocadherin-19 isoform X2 [Orcinus orca] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSFR ITALDGGDPPHLGTVGLSIKVTDSNDNNPVFGESTYLVTVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHSGL VTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQCR LLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSSKSFTVRITDENDN
187
>DolphinFreshwater gi|602715660|ref|XP_007468031.1| PREDICTED: protocadherin-19 isoform X3 [Lipotes vexillifer] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSFR ITALDGGDPPHLGTVGLSIKVTDSNDNNPVFGESTYSVTVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHSGL VTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQCR LLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSSKSFTVRITDENDN
>cat gi|410988977|ref|XP_004000746.1| PREDICTED: protocadherin-19 isoform X2 [Felis catus] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSF HITALDGGDPPHLGTVGLSIKVTDSNDNNPVFGESTYAVSVPENSPSSTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHSG LVTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQC RLLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSAKSFTVRITDENDN
>Ferret gi|511915858|ref|XP_004777234.1| PREDICTED: protocadherin-19 isoform X2 [Mustela putorius furo] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSFR ITALDGGDPPHLGTVGLSIKVTDSNDNNPVFGESTYAVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDHTRELFQIDPHSGL VTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQCR LLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSAKSFTVRITDENDN
>walrus gi|472382152|ref|XP_004410462.1| PREDICTED: protocadherin-19 isoform X3 [Odobenus rosmarus divergens] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSFR ITALDGGDPPHLGTVGLSIKVTDSNDNNPVFGESTYAVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHSGL VTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQCR LLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSAKSFTVRITDENDN
>dog gi|545558674|ref|XP_005641608.1| PREDICTED: protocadherin-19 isoform X1 [Canis lupus familiaris] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSF HITALDGGDPPHLGTVGLSIKVTDSNDNNPVFGESTYAVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHS GLVTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSEMVEVSESAPPGYVIALVRVSDRDSGLNARV QCRLLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSAKSFTVRITDENDN
>panda bear gi|301787013|ref|XP_002928922.1| PREDICTED: protocadherin-19 isoform X1 [Ailuropoda melanoleuca] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSFR ITALDGGDPPHLGTVGLSIKVTDSNDNNPVFGESTYAVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHSGL VTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQCR LLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDSGVPMLQSAKSFTVRITDENDN
>Armadillo gi|488547693|ref|XP_004465351.1| PREDICTED: protocadherin-19 isoform X1 [Dasypus novemcinctus] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDNAYDPDSGIFGVQTYELTPNELFGLDIKTRGDGSRFAELVVEKSLDRETQSHYNF RMTALDGGDPPHLGTVGLSIRVTDSNDNNPVFGESTYAVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPH SGLVTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRV QCRLLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSAKSFTVRITDENDN
188
>guinea pig gi|514463186|ref|XP_003471009.2| PREDICTED: protocadherin-19 isoform X1 [Cavia porcellus] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSFR ITALDGGDPPHLGTVGLSIKVTDSNDNNPVFGESTYVVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHSGL VTVTGALDYEEGRVYELDVQAKDLGPNSIPAHCKVTVNVLDTNDNPPIINLLSVNSELVEVSESAPAGYVIALVRVSDRDSGLNGRVQCR LLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSAKSFTVRITDENDN
>elephant gi|344296750|ref|XP_003420067.1| PREDICTED: protocadherin-19 [Loxodonta africana] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDSRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSFR ITALDGGDPPHLGTVGLSIKVTDSNDNNPVFGESTYAVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYANDHTRELFQIDPHSGL VTVTGALDYEEGHVYELDVQARDLGPNSIPAHCKVTVSILDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQCR LLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPTLQSAKSFTVRITDENDN
>Chinchilla gi|533188044|ref|XP_005406986.1| PREDICTED: protocadherin-19 isoform X2 [Chinchilla lanigera] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSFR ITALDGGDPPHMGTVGLSIKVTDSNDNNPVFGESTYAVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHSG LVTVTGDLDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQC RLLGSVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSAKSFTVRITDENDN
>Mole gi|586477209|ref|XP_006869149.1| PREDICTED: protocadherin-19-like isoform X2 [Chrysochloris asiatica] LINLKYSVEEEQRAGTVIANVAKDALEAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSFR ITALDGGDPPHLGTVGLSIKVTDSNDNNPVFGESTYAVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHSGL VTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPIINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQCRL LGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSAKSFTVRITDENDN
>Galago gi|395850619|ref|XP_003797877.1| PREDICTED: protocadherin-19 isoform X1 [Otolemur garnettii] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSFR ITALDGGDPPHLGTVGLSIKVTDSNDNNPVFGESTYSVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHSGL VTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQCR LLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSAKSFTVRITDENDN
>Lemur gi|826309942|ref|XP_012505497.1| PREDICTED: protocadherin-19 isoform X2 [Propithecus coquereli] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSFR ITALDGGDPPHLGTVGLSIKVTDSNDNNPVFGESTYSVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHSGL VTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQCR LLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSAKSFTVRITDENDN
>LemurGrayMouse gi|829779337|ref|XP_012622834.1| PREDICTED: protocadherin-19 isoform X5 [Microcebus murinus] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSFR ITALDGGDPPHLGTVGLSIKVTDSNDNNPVFGESTYSVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHSGL VTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQCR LLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSAKSFTVRITDENDN
>HedgehogLesser gi|507683671|ref|XP_004711250.1| PREDICTED: protocadherin-19 isoform X2 [Echinops telfairi] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSFR ITALDGGDPPHLGTVGLSIKVTDSNDNNPVFGESTYAVSVPENSLPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHSGL ITVTGELDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPIINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQCRL LGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSAKSFTVRITDENDN
189
>aardvark gi|634879844|ref|XP_007950361.1| PREDICTED: protocadherin-19 [Orycteropus afer afer] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLDIKTRGDGSRFAELVVEKSLDRETQSHYSF RITALDGGDPPRLGTVGLSIKVTDSNDNNPVFGESTYAVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHSG LITVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQCR LLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSAKSFTVRITDENDN
>AfricanRodent gi|847038905|ref|XP_012806731.1| PREDICTED: protocadherin-19 isoform X2 [Jaculus jaculus] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSFR ITALDGGDPPHLGTVGLSIKVTDSNDNNPVFGESTYAVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHSGL VTVTGVLDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQCR LLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDSGVPMLQSAKSFTVRITDENDN
>MoleStarnosed gi|507956665|ref|XP_004685693.1| PREDICTED: protocadherin-19 isoform X2 [Condylura cristata] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSFR ITALDGGDPPHLGTVGLSIKVTDSNDNNPVFGESTYAVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHSGL VTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPIINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQCRL LGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSAKSFTVRITDENDN
>KangarooRat gi|852803504|ref|XP_012890545.1| PREDICTED: protocadherin-19 isoform X3 [Dipodomys ordii] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSFR ITALDGGDPPHLGTVGLSIKVTDSNDNNPVFGESTYAVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHSGL VTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQCR LLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSAKSFTVRITDENDN
>Tarsier gi|640816692|ref|XP_008065163.1| PREDICTED: protocadherin-19 isoform X2 [Tarsius syrichta] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSFR ITALDGGDPPHMGTVGLSIKVTDSNDNNPVFGESTYAVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHSG LVTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQC RLLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGMPMLQSAKSFTVRITDENDN
>bat gi|431895727|gb|ELK05148.1| Protocadherin-19 [Pteropus alecto] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSFR ITALDGGEPPHLGTVGLSIKVTDSNDNNPVFGESTYSVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHSGL VTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQCR LLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSAKSFTVRITDENDN
>BatFruit gi|1012278423|ref|XP_015987000.1| PREDICTED: protocadherin-19 isoform X2 [Rousettus aegyptiacus] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSFR ITALDGGEPPHLGTVGLSIKVTDSNDNNPVFGESTYSVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHSGL VTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVVDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQC RLLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSAKSFTVRITDENDN
>MarmotAlpine gi|984131667|ref|XP_015357790.1| PREDICTED: protocadherin-19 [Marmota marmota marmota] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSFR ITALDGGDPPHLGTVGLSIKVTDSNDNNPVFGESTYAVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHSGL VTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQCR LLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSAKSFTVRITDENDN
190
>Manatee gi|471379606|ref|XP_004377600.1| PREDICTED: protocadherin-19 isoform X2 [Trichechus manatus latirostris] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSFR ITALDGGDPPHLGTVGLSIKVTDSNDNNPVFGESTYAVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHSGL VTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQCR LLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSAKSFTVRITDENDN
>Squirrel gi|532092270|ref|XP_005331819.1| PREDICTED: protocadherin-19 isoform X2 [Ictidomys tridecemlineatus] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYNF RITALDGGDPPHLGTVGLSIKVTDSNDNNPVFGESTYAVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHS GLVTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPIINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQ CRLLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSAKSFTVRITDENDN
>horse gi|545229209|ref|XP_005614384.1| PREDICTED: protocadherin-19 isoform X2 [Equus caballus] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSFR ITALDGGDPPHLGTVGLSIKVTDSNDNNPVFGESTYAVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHSAL VTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQCR LLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSAKSFTVRITDENDN
>Rhinoceros gi|478533854|ref|XP_004441064.1| PREDICTED: protocadherin-19 isoform 2 [Ceratotherium simum simum] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSFR ITALDGGDPPHLGTVGLSIKVTDSNDNNPVFGESTYAVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHSGL VTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQCR LLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSAKSFTVRITDENDN
>FishCoelacanth gi|557003890|ref|XP_006003957.1| PREDICTED: protocadherin-19 isoform X1 [Latimeria chalumnae] VINLKYSVDEEQRAGTVIANIAKDSKEAGFVIDPRQSSFRVISNSAPLLVDINPSGLLVTKQKIDRDLLCRQNLKCQISLEVMSSTMEICVIK VEIKDLNDNAPSFPTDQIDLEISETANPGTKIPLESAYDPDSGNFGVQTYEITPNDLFGLEIKTRGDGSRFAELVVERALDRETQSHYSYMI TALDGGDPPNFGTVELNIKVIDSNDNNPVFDEAAYIVNIPENSPVNTPVIDLNATDPDEGTNGEILYSFNSYVADKTRDLFKIDPQTGLISV NGAIDYEEGHIYEIDVQAKDLGPNSIPAHCKVTVNVIDVNDNVPVINLLPVNSEMVEVSENAPPGYVIALVRVSDRDSGTNGRVQCKLL GNVPFRSQEYESFSTILVDGRLDREQRDQYNLTILARDNGNPTLQSTKSFTVKITDENDN
>frog gi|847158231|ref|XP_012824695.1| PREDICTED: protocadherin-19 isoform X1 [Xenopus tropicalis] LINLKYTVEEEQRAGTVIANVAKDAKDAGFVLDPRQPAFRVVSNSASHLVDINASGLLVTKQKIDRDMLCRQIPKCVISLEVMSNSMEIC VIKVEIKDLNDNAPSFPTDQIDLEISETASPGTRIPLESAYDPDSGNYGVQTYEITPNDLFGLEIKTRGDGSRFAELVVEKALDRETQSHYSYI ITALDGGDPSNFGTVELNIKVIDSNDNNPMFEEAAYTVNVPENSALNTMVIDLNATDPDEGTNGEIVYSFNSYVSDKTRELFKIDPKTGV ITVSGAIDYEEGHVYEIDVQAKDLGPNSIPAHCKVTVNVLDMNDNVPVINLLSVNSEVVEVSENAPPGYVIALVRVSDKDSGINGRVLCK LLGSVPFRLQEYESFSTILVDGRLDREQRDQYNLTIQAKDSGNPSLQSTKSFTVRITDENDN
>turtle gi|465969103|gb|EMP31953.1| Protocadherin-19 [Chelonia mydas] LINLKYSVDEEQRAGTVIANIGKDAREAGFVLAPRQPAAFRVVSNSAPHLVDISPGSGLLVTKQKIDRDLLCRQSPKCVISLEVMSSSMEIC VIKLEIKDLNDNAPSFPTDQIELEISETASPGTRVPLESAYDPDSGSFGVQSYELTPNDLFGLETKTRGDGSRFAELVVERSLDRETQSHYSY LLTALDGGDPPNFGTVELSIRVIDSNDNNPLFEEPAYAVSVPENAPPGTPLLRLNASDPDEGTNGQVLYSFHSYVSERARQLFHLDPQSG LLSVSGAVDYEEGHSYELDVQAKDLGPNSIPAHCKVTVSVQDANDNPPLINLLSVNSELVEVSESAPPGYVIALVRVSDHDSGANGRVQ CKLLGSVPFRLQEYESFSTILVDGRLDREQRDQYNLTIQARDNGVPSLQATKSFTVKITDENDN
191
>snakeKingCobra gi|602652330|ref|XP_007432538.1| PREDICTED: protocadherin-19-like [Python bivittatus] LINLKYSVEEEQRAGTVIANIAKDARDAGFVLDPRQPTAFRVVSNSAPHLVDINPGSGLLVTKQKIDRDLLCRQSPKCVISLEVMSSSMEI CVIKLEIKDLNDNAPSFPTDQIALEISETASPGTRVPLESAYDPDSGSFGVQSYEITPNDLFGLETKTRGDGSRFAELVVEKSLDRETQSHYS YMITALDGGDPPNFGTVELTIRVIDSNDNNPLFEEPSYTVSVLENAPPGTPVIRLNATDPDEGTNGQVLYSIHSYVSEKARDLFQINPQTG LITVTGAIDYEEGHAYELDVQAKDLGPNSIPAHCKVTVTVQDANDNPPLINLLSVNSELVEVSENAPPGYVIALVRVSDRDAGANGRVQC KLLGNVPFRLQEYESFSTILVDGRLDREQRDQYNLTIQAKDNGIPSLQATKSFTVKITDENDN
>ostrich gi|697512175|ref|XP_009683261.1| PREDICTED: protocadherin-19 [Struthio camelus australis] LINLKYSVEEEQRAGTVIANVAKDARDAGFVLDSRQPTAFRVVSNSAPHLVDISPGSGLLVTKQKIDRDLLCRQSPKCVISLEVMSSSMEI CVIKLEIKDLNDNAPSFPTDQIELEISETASPGTRVPLESAYDPDSGSFGVQSYEITPNDLFGLETKTRGDGSRFAELVVEKSLDRETQSHYS YVITALDGGDPPNFGTVELSIRVIDSNDNNPLFEEPAYTVSVPENSPPGTPVIRLNASDPDEGTNGQVLYSFHSYVSERARELFQIDPQSG LITVSGAIDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSIQDANDNPPLINLLSVNSELVEVSENAPPGYVIALVRVSDRDSGANGRVQC KLLGNVPFRLQEYESFSTILVDGRLDREQRDQYNLTIQARDNGVPSLQATKSFTVKITDENDN
>Alligator gi|564243840|ref|XP_006278693.1| PREDICTED: protocadherin-19-like isoform X2 [Alligator mississippiensis] LINLKYSVEEEQRAGTVIANVAKDAREAGFVLDPRQPAAFRVVSNSAPHLVDINPGSGLLVTKQKIDRDLLCRQSPKCVISLEVMSSSMEI CVIKLEIKDLNDNAPSFPTDQIELEISETASPGTRVPLESAYDPDSGSFGVQSYQITPNDLFGLETKIRGDGSRFAELVVEKSLDRETQSHYS YLITALDGGDPPNLGTVELSIRVIDSNDNNPLFEELAYTVSVPENAPPGTPLLRLNASDPDEGTNGQVLYSFHSYVSERARDLFQIDPQSG LITVSGAIDYEEGHVYELDVQAKDLGPNSIPAHCKVTVTVQDANDNPPLINLLSVNSELVEVSENAPPGYVIALVRVSDRDSGANGRVQC KLLGNVPFRLQEYESFSTILVDGRLDREQRDQYNLTIQAKDNGIPSLQATKSFTVKITDENDN
>BirdFlycatcher gi|524996133|ref|XP_005045860.1| PREDICTED: protocadherin-19 [Ficedula albicollis] LVNLKYSVEEEQRAGTVIANVAKDARDAGFVLDPRQPAAFRVVSNSAPHLVDISPGSGLLVTKQKIDRDLLCRQSPKCVISLEVMSSSME ICVIKLEIKDLNDNAPSFPTDQIELEISETASPGTRVPLESAYDPDSGSFGVQSYEITPNDLFGLETKTRGDGSRFAELVVEKSLDRETQSHYS YVITALDGGDPPNFGTVELSIRVIDSNDNNPLFEEPAYTVSVPENAPPGTPVIRLNASDPDEGTNGQVLYSFHSYVSERARELFQIDPQSG LITVSGAIDYEEGHVYELDVQAKDLGPNSIPAHCKVTISVQDANDNPPLINLLSVNSELVEVSENAPLGYVIALVRVSDRDSGANGRVQCK LLGNVPFRLQEYESFSTILVDGRLDREQRDQYNLTIQARDNGIPSLQATKSFTVKITDENDN
>chicken gi|148747842|ref|NP_001092077.1| protocadherin-19 precursor [Gallus gallus] LVNLKYSVEEEQRAGTVIANIAKDARDAGFVIDPRQPTAFRVVSNSAPHLVDINPGSGLLVTKQKIDRDLLCRQSPKCVISLEVMSSSMEI CVIKLEIKDLNDNAPSFPTDQIELEISETASPGTRVPLESAYDPDSGSFGVQSYQITPNDLFGLETKTRGDGSRFAELVVEKSLDRETQSHYS YVITALDGGDPPNFGTVELSIRVIDSNDNNPLFEEPAYTVSVPENAPPGTPVIRLNASDPDEGTNGQVLYSFHSYVSDRARELFQIDPQSG LITVSGAIDYEEGHVYELDVQAKDLGPNSIPAHCKVTISVQDANDNPPLINLLSVNSELVEVSENAPPGYVIALVRVSDRDSGANGRVQC KLLGNVPFRLQEYESFSTILVDGRLDREQRDQYNLTIQAKDNGVPSLQATKSFTVKITDENDN
>BirdQuail gi|1003768398|ref|XP_015715882.1| PREDICTED: protocadherin-19 isoform X1 [Coturnix japonica] LVNLKYSVEEEQRAGTVIANVAKDARDAGFVIDPRQPTAFRVVSNSAPHLVDINPGSGLLVTKQKIDRDLLCRQSPKCVISLEVMSSSMEI CVIKLEIKDLNDNAPSFPTDQIELEISETASPGTRVPLESAYDPDSGSFGVQSYQITPNDLFGLETKTRGDGSRFAELVVEKSLDRETQSHYS YVITALDGGDPPNFGTVELSIRVIDSNDNNPLFEEPAYTVSVPENAPPGTPVIRLNASDPDEGTNGQVLYSFHSYVSDRARELFQIDPQSG LITVSGAIDYEEGHVYELDVQAKDLGPNSIPAHCKVTISVQDANDNPPLINLLSVNSELVEVSENAPPGYVIALVRVSDRDSGANGRVQC KLLGNVPFRLQEYESFSTILVDGRLDREQRDQYNLTIQAKDNGVPSLQATKSFTVKITDENDN
>BirdCrestedIbis gi|694845366|ref|XP_009463652.1| PREDICTED: protocadherin-19 [Nipponia nippon] LVNLKYSVEEEQRAGTVIANVAKDARDAGFVLDPRQPAAFRVVSNSAPHLVDISPGSGLLVTKQKIDRDLLCRQSPKCVISLEVMSSSME ICVIKLEIKDLNDNAPSFPTDQIELEISETASPGTRVPLESAYDPDSGSFGVQSYEITPNDLFGLETKTRGDGSRFAELVVEKSLDRETQSHYS YVITALDGGDPPNFGTVELSIRVIDSNDNNPLFEEPAYTVSVPENAPPGTPVIRLNASDPDEGTNGQVLYSFHSYVSERARELFQIDPQSG LITVSGAIDYEEGHVYELDVQAKDMGPNSIPAHCKVTISVQDANDNPPLINLLSVNSELVEVSENAPPGYVIALVRVSDRDSGANGRVQC KLLGNVPFRLQEYESFSTILVDGRLDREQRDQYNLTIQAKDNGVPSLQATKSFTVKITDENDN
>BirdCommonStaring gi|959073949|ref|XP_014740474.1| PREDICTED: protocadherin-19 [Sturnus vulgaris] LVNLKYSVEEEQRAGTVIANVAKDARDAGFVLDPRQPAAFRVVSNSAPHLVDISPGSGLLVTKQKIDRDLLCRQSPKCVISLEVMSSSME ICVIKLEIKDLNDNAPSFPTDQIELEISETASPGTRVPLESAYDPDSGSFGVQSYEITPNDLFGLETKTRGDGSRFAELVVEKSLDRETQSHYS YVITALDGGDPPNFGTVELSIRVIDSNDNNPLFEEPAYTVSVPENAPPGTPVIRLNASDPDEGTNGQVLYSFHSYVSERARELFQIDPQSG LITVSGAIDYEEGHVYELDVQAKDLGPNSIPAHCKVTISVQDANDNPPLINLLSVNSELVEVSENAPLGYVIALVRVSDRDSGANGRVQCK LLGNVPFRLQEYESFSTILVDGRLDREQRDQYNLTIQARDNGIPSLQATKSFTVKITDENDN
192
>BaldEagle gi|729748455|ref|XP_010570737.1| PREDICTED: protocadherin-19 [Haliaeetus leucocephalus] LVNLKYSVEEEQRAGTVIANVAKDARDAGFVLDPRQPAAFRVVSNSAPHLVDISPGSGLLVTKQKIDRDLLCRQSPKCVISLEVMSSSME ICVIKLEIKDLNDNAPSFPTDQIELEISETASPGTRVPLESAYDPDSGSFGVQSYEITPNDLFGLETKTRGDGSRFAELVVEKSLDRETQSHYS YVITALDGGDPPNFGTVELSIRVIDSNDNNPLFEEPAYTVSVPENAPPGTPVIRLNASDPDEGTNGQVLYSFHSYVSERARELFQIDPQSG LITVSGAIDYEEGHVYELDVQAKDLGPNSIPAHCKVTISVQDANDNPPLINLLSVNSELVEVSENAPPGYVIALVRVSDRDSGANGRVQC KLLGNVPFRLQEYESFSTILVDGRLDREQRDQYNLTIQAKDNGVPSLQATKSFTVKITDENDN
>GoldenEagle gi|768363097|ref|XP_011578766.1| PREDICTED: protocadherin-19 [Aquila chrysaetos canadensis] LVNLKYSVEEEQRAGTVIANVAKDARDAGFVLDPRQPAAFRVVSNSAPHLVDISPGSGLLVTKQKIDRDLLCRQSPKCVISLEVMSSSME ICVIKLEIKDLNDNAPSFPTDQIELEISETASPGTRVPLESAYDPDSGSFGVQSYEITPNDLFGLETKTRGDGSRFAELVVEKSLDRETQSHYS YVITALDGGDPPNFGTVELSIRVIDSNDNNPLFEEPAYTVSVPENAPPGTPVIRLNASDPDEGTNGQVLYSFHSYVSERARELFQIDPQSG LITVSGAIDYEEGHVYELDVQAKDLGPNSIPAHCKVTISVQDANDNPPLINLLSVNSELVEVSENAPPGYVIALVRVSDRDSGANGRVQC KLLGNVPFRLQEYESFSTILVDGRLDREQRDQYNLTIQAKDNGVPSLQATKSFTVKITDENDN
>BirdFalcon gi|529425926|ref|XP_005232798.1| PREDICTED: protocadherin-19 [Falco peregrinus] LVNLKYSVEEEQRAGTVIANVAKDARDAGFVLDPRQPTAFRVVSNSAPHLVDISPGSGLLVTKQKIDRDLLCRQSPKCVISLEVMSSSMEI CVIKLEIKDLNDNAPSFPTDQIELEISETASPGTRVPLESAYDPDSGSFGVQSYEITPNDLFGLETKTRGDGSRFAELVVEKSLDRETQSHYS YVITALDGGDPPNFGTVELSIRVIDSNDNNPLFEEPAYTVSVPENSPPGTPVIRLNASDPDEGTNGQVLYSFHSYVSDRARELFQIDPQSG LITVSGAIDYEEGHVYELDVQAKDLGPNSIPAHCKVTISVQDANDNPPLINLLSVNSELVEVSENAPPGYVIALVRVSDRDSGANGRVQC KLLGNVPFRLQEYESFSTILVDGRLDREQRDQYNLTIQAKDNGVPSLQATKSFTVKITDENDN
>BirdRuff gi|960990709|ref|XP_014810790.1| PREDICTED: protocadherin-19 [Calidris pugnax] LVNLKYSVEEEQRAGTVIANVAKDARDAGFVLDPRQPTAFRVVSNSAPHLVDISPGSGLLVTKQKIDRDLLCRQSPKCVISLEVMSSSMEI CVIKLEIKDLNDNAPSFPTDQIELEISETASPGTRVPLESAYDPDSGSFGVQSYEITPNDLFGLETKTRGDGSRFAELVVEKSLDRETQSHYS YVITALDGGDPPNFGTVELSIRVIDSNDNNPLFEEPAYTVSVPENAPPGTPVIRLNASDPDEGTNGQVLYSFHSYVSERARELFQIDPQSG LITVSGAIDYEEGHVYELDVQAKDLGPNSIPAHCKVTISVQDANDNPPLINLLSVNSELVEVSENAPPGYVIALVRVSDRDSGANGRVQC KLLGNVPFRLQEYESFSTILVDGRLDREQRDQYNLTIQAKDNGVPSLQATKSFTVKITDENDN
>BirdGroundTit gi|543365623|ref|XP_005526171.1| PREDICTED: protocadherin-19 [Pseudopodoces humilis] LVNLKYSVEEEQRAGTVIANVAKDARDAGFVLDPRQPAAFRVVSNSAPHLVDISPGSGLLVTKQKIDRDLLCRQSPKCVISLEVMSSSME ICVIKLEIKDLNDNAPSFPTDQIELEISETASPGTRVPLESAYDPDSGSFGVQSYEITPNDLFGLETKTRGDGSRFAELVVEKSLDRETQSHYS YVITALDGGDPPNFGTVELSIRVIDSNDNNPLFEEPAYTVSVPENAPPGTPVIRLNASDPDEGTNGQVLYSFHSYVSERARELFQIDPQSG LITVSGAIDYEEGHVYELDVQAKDLGPNSIPAHCKVTISVQDANDNPPLINLLSVNSELVEVSENAPPGYVIALVRVSDRDSGANGRVQC KLLGNVPFRLQEYESFSTILVDGRLDREQRDQYNLTIQARDNGIPSLQATKSFTVKITDENDN
>BirdSparrow gi|929510832|ref|XP_014127252.1| PREDICTED: protocadherin-19 isoform X1 [Zonotrichia albicollis] LVNLKYSVEEEQRAGTVIANVAKDARDAGFVLDPRQPAAFRVVSNSAPHLVDISPGSGLLVTKQKIDRDLLCRQSPKCVISLEVMSSSME ICVIKLEIKDLNDNAPSFPTDQIELEISETASPGTRVPLESAYDPDSGSFGVQSYEITPNDLFGLETKTRGDGSRFAELVVEKSLDRETQSHYS YVITALDGGDPPNFGTVELSIRVIDSNDNNPLFEEPAYTVSVPENAPPGTPVIRLNASDPDEGTNGQVLYSFHSYVSERARELFQIDPQSG LITVSGAIDYEEGHVYELDVQAKDLGPNSIPAHCKVTISVQDANDNPPLINLLSVNSELVEVSENAPPGYVIALVRVSDRDSGANGRVQC KLLGNVPFRLQEYESFSTILVDGRLDREQRDQYNLTIQARDNGIPSLQATKSFTVKITDENDN
193
Appendix D: Sequences Used for Conservation Analysis between Protocadherin Family
Members
>pcdh19ECdr gi|229472136|gb|ACQ72596.1| protocadherin-19 isoform 1 [Danio rerio] VFNLKYTVEEELRAGTKIANVTADAKVAGFALGNRQPYLRVISNSEPRWVNLSPAGLLITKQKIDRDAVCRQTPKCFISLEVMSNSMEICV IKIEIIDVNDNAPRFPTNHIDIEISENAAPGTRFPLEGASDPDSGSNGIQTYTITPNDIFGLEIKTRGDGSKIAELVVEKTLDRETQSRYTFELT AEDGGDPPKSGTVQLNIKVIDSNDNNPVFDEPVYTVNVLENSPINTLVIDLNATDPDEGTNGEVVYSFINFVSNLTKQMFKIDPKTGVIT VNGVLDHEELHIHEIDVQAKDLGPNSIPAHCKVIVNVIDINDNAPEIKLLSENSEMVEVSENAPLGYVIALVRVSDNDSGANGKVQCRLQ GNVPFRLNEFESFSTLLVDGRLDREQRDMYNLTILAEDSGYPPLRSSKSFAVKVTDENDN
>pcdh19EC gi|296434287|ref|NP_001171809.1| protocadherin-19 isoform c precursor [Homo sapiens] LINLKYSVEEEQRAGTVIANVAKDAREAGFALDPRQASAFRVVSNSAPHLVDINPSSGLLVTKQKIDRDLLCRQSPKCIISLEVMSSSMEIC VIKVEIKDLNDNAPSFPAAQIELEISEAASPGTRIPLDSAYDPDSGSFGVQTYELTPNELFGLEIKTRGDGSRFAELVVEKSLDRETQSHYSFR ITALDGGDPPRLGTVGLSIKVTDSNDNNPVFSESTYAVSVPENSPPNTPVIRLNASDPDEGTNGQVVYSFYGYVNDRTRELFQIDPHSGL VTVTGALDYEEGHVYELDVQAKDLGPNSIPAHCKVTVSVLDTNDNPPVINLLSVNSELVEVSESAPPGYVIALVRVSDRDSGLNGRVQCR LLGNVPFRLQEYESFSTILVDGRLDREQHDQYNLTIQARDGGVPMLQSAKSFTVLITDENDN
>pcdh18EC gi|14589929|ref|NP_061908.1| protocadherin-18 isoform 1 precursor [Homo sapiens] KNLKYRIYEEQRVGSVIARLSEDVADVLLKLPNPSTVRFRAMQRGNSPLLVVNEDNGEISIGATIDREQLCQKNLNCSIEFDVITLPTEHLQ LFHIEVEVLDINDNSPQFSRSLIPIEISESAAVGTRIPLDSAFDPDVGENSLHTYSLSANDFFNIEVRTRTDGAKYAELIVVRELDRELKSSYEL QLTASDMGVPQRSGSSILKISISDSNDNSPAFEQQSYIIQLLENSPVGTLLLDLNATDPDEGANGKIVYSFSSHVSPKIMETFKIDSERGHLT LFKQVDYEITKSYEIDVQAQDLGPNSIPAHCKIIIKVVDVNDNKPEININLMSPGKEEISYIFEGDPIDTFVALVRVQDKDSGLNGEIVCKLH GHGHFKLQKTYENNYLILTNATLDREKRSEYSLTVIAEDRGTPSLSTVKHFTVQINDINDN
>pcdh17EC gi|94538350|ref|NP_001035519.1| protocadherin-17 precursor [Homo sapiens] LKNLNYSVPEEQGAGTVIGNIGRDARLQPGLPPAERGGGGRSKSGSYRVLENSAPHLLDVDADSGLLYTKQRIDRESLCRHNAKCQLSLE VFANDKEICMIKVEIQDINDNAPSFSSDQIEMDISENAAPGTRFPLTSAHDPDAGENGLRTYLLTRDDHGLFGLDVKSRGDGTKFPELVI QKALDREQQNHHTLVLTALDGGEPPRSATVQINVKVIDSNDNSPVFEAPSYLVELPENAPLGTVVIDLNATDADEGPNGEVLYSFSSYVP DRVRELFSIDPKTGLIRVKGNLDYEENGMLEIDVQARDLGPNPIPAHCKVTVKLIDRNDNAPSIGFVSVRQGALSEAAPPGTVIALVRVTD RDSGKNGQLQCRVLGSVPFKLEENYDNFYTVVTDRPLDRETQDEYNVTIVARDGGSPPLNSTKSFAIKILDENDN
>pcdh10EC gi|14589916|ref|NP_116586.1| protocadherin-10 isoform 1 precursor [Homo sapiens] QLHYTVQEEQEHGTFVGNIAEDLGLDITKLSARGFQTVPNSRTPYLDLNLETGVLYVNEKIDREQICKQSPSCVLHLEVFLENPLELFQVEI EVLDINDNPPSFPEPDLTVEISESATPGTRFPLESAFDPDVGTNSLRDYEITPNSYFSLDVQTQGDGNRFAELVLEKPLDREQQAVHRYVL TAVDGGGGQRTGTALLTIRVLDSNDNVPAFDQPVYTVSLPENSPPGTLVIQLNATDPDEGQNGEVVYSFSSHISPRARELFGLSPRTGRL EVSGELDYEESPVYQVYVQAKDLGPNAVPAHCKVLVRVLDANDNAPEISFSTVKEAVSEGAAPGTVVALFSVTDRDSEENGQVQCELLG DVPFRLKSSFKNYYTIVTEAPLDREAGDSYTLTVVARDRGEPALSTSKSIQVQVSDVNDN
>pcdh8EC gi|6631102|ref|NP_002581.2| protocadherin-8 isoform 1 precursor [Homo sapiens] KTVRYSTFEEDAPGTVIGTLAEDLHMKVSGDTSFRLMKQFNSSLLRVREGDGQLTVGDAGLDRERLCGQAPQCVLAFDVVSFSQEQFR LVHVEVEVRDVNDHAPRFPRAQIPVEVSEGAAVGTRIPLEVPVDEDVGANGLQTVRLAEPHSPFRVELQTRADGAQCADLVLLQELDR ESQAAYSLELVAQDGGRPPRSATAALSVRVLDANDHSPAFPQGAVAEVELAEDAPVGSLLLDLDAADPDEGPNGDVVFAFGARTPPEA RRLFRLDPRSGRLTLAGPVDYERQDTYELDVRAQDRGPGPRAATCKVIVRIRDVNDNAPDIAITPLAAPGTPEAGATSLVPEGAARESLV ALVSTSDRDSGANGQVRCALYGHEHFRLQPAYAGSYLVVTAASLDRERIAEYNLTLVAEDRGAPPLRTVRPYTVRVGDENDN
194
>pcdh11EC gi|14589920|ref|NP_116750.1| protocadherin-11 X-linked isoform c precursor [Homo sapiens] QEKNYTIREEMPENVLIGDLLKDLNLSLIPNKSLTTAMQFKLVYKTGDVPLIRIEEDTGEIFTTGARIDREKLCAGIPRDEHCFYEVEVAILPD EIFRLVKIRFLIEDINDNAPLFPATVINISIPENSAINSKYTLPAAVDPDVGINGVQNYELIKSQNIFGLDVIETPEGDKMPQLIVQKELDREEK DTYVMKVKVEDGGFPQRSSTAILQVSVTDTNDNHPVFKETEIEVSIPENAPVGTSVTQLHATDADIGENAKIHFSFSNLVSNIARRLFHLN ATTGLITIKEPLDREETPNHKLLVLASDGGLMPARAMVLVNVTDVNDNVPSIDIRYIVNPVNDTVVLSENIPLNTKIALITVTDKDADHNG RVTCFTDHEIPFRLRPVFSNQFLLETAAYLDYESTKEYAIKLLAADAGKPPLNQSAMLFIKVKDENDN
>pcdh9EC gi|45243534|ref|NP_982354.1| protocadherin-9 isoform 1 precursor [Homo sapiens] QELIYTIREELPENVPIGNIPKDLNISHINAATGTSASLVYRLVSKAGDAPLVKVSSSTGEIFTTSNRIDREKLCAGASYAEENECFFELEVVILP NDFFRLIKIKIIVKDTNDNAPMFPSPVINISIPENTLINSRFPIPSATDPDTGFNGVQHYELLNGQSVFGLDIVETPEGEKWPQLIVQQNLD REQKDTYVMKIKVEDGGTPQKSSTAILQVTVSDVNDNRPVFKEGQVEVHIPENAPVGTSVIQLHATDADIGSNAEIRYIFGAQVAPATK RLFALNNTTGLITVQRSLDREETAIHKVTVLASDGSSTPARATVTINVTDVNDNPPNIDLRYIISPINGTVYLSEKDPVNTKIALITVSDKDTD VNGKVICFIEREVPFHLKAVYDNQYLLETSSLLDYEGTKEFSFKIVASDSGKPSLNQTALVRVKLEDENDN
>pcdh7EC gi|291084612|ref|NP_001166994.1| protocadherin-7 isoform d precursor [Homo sapiens] KQLLRYRLAEEGPADVRIGNVASDLGIVTGSGEVTFSLESGSEYLKIDNLTGELSTSERRIDREKLPQCQMIFDENECFLDFEVSVIGPSQS WVDLFEGQVIVLDINDNTPTFPSPVLTLTVEENRPVGTLYLLPTATDRDFGRNGIERYELLQEPRSSVFELQVADTPDGEKQPQLIVKGAL DREQRDSYELTLRVRDGGDPPRSSQAILRVLITDVNDNSPRFEKSVYEADLAENSAPGTPILQLRAADLDVGVNGQIEYVFGAATESVRR LLRLDETSGWLSVLHRIDREEVNQLRFTVMARDRGQPPKTDKATVVLNIKDENDNVPSIEIRKIGRIPLKDGVANVAEDVLVDTPIALVQ VSDRDQGENGVVTCTVVGDVPFQLKPASDTEGDQNKKKYFLHTSTPLDYEATREFNVVIVAVDSGSPSLSSNNSLIVKVGDTNDN
>pcdh1EC gi|27754771|ref|NP_002578.2| protocadherin-1 isoform 1 precursor [Homo sapiens] TRVVYKVPEEQPPNTLIGSLAADYGFPDVGHLYKLEVGAPYLRVDGKTGDIFTTETSIDREGLRECQNQLPGDPCILEFEVSITDLVQNGSP RLLEGQIEVQDINDNTPNFASPVITLAIPENTNIGSLFPIPLASDRDAGPNGVASYELQAGPEAQELFGLQVAEDQEEKQPQLIVMGNLD RERWDSYDLTIKVQDGGSPPRASSALLRVTVLDTNDNAPKFERPSYEAELSENSPIGHSVIQVKANDSDQGANAEIEYTFHQAPEVVRRL LRLDRNTGLITVQGPVDREDLSTLRFSVLAKDRGTNPKSARAQVVVTVKDMNDNAPTIEIRGIGLVTHQDGMANISEDVAEETAVALVQ VSDRDEGENAAVTCVVAGDVPFQLRQASETGSDSKKKYFLQTTTPLDYEKVKDYTIEIVAVDSGNPPLSSTNSLKVQVVDVNDN
>pcdhgC5 gi|18087751|ref|NP_291061.1| protocadherin gamma-C5 precursor [Mus musculus] QLRYSVVEESEPGTLVGNVAQDLGLKGTDLLSRRLRLGSEENGRYFSLSLVSGALAVSQKIDRESLCGASTSCLLPVQVVTEHPLELTRVEV EILDLNDNSPSFATPDREMRISESAAPGARFPLDSAQDPDVGTNTVSFYTLSPNSHFSLHVKTLKDGKLFPELVLEQQLDRETQARHQLV LTAVDGGTPARSGTSLISVIVLDVNDNAPTFQSSVLRVGLPENTPPGTLLLRLNATDPDEGTNGQLDYSFGDHTSETVKNLFGLDPSSGAI HVLGPVDFEESNFYEIHARARDQGQPAMEGHCVIQVDVGDANDNPPEVLLASLVNPVLESTPVGTVVGLFNVRDRDSGRNGEVSLKT SPNLPFQIKPSENHYSLLTSQPLDREATSHYTIELLASDAGSPPLHTHLTLRLNISDVNDN
>pcdhgC3 gi|18087747|ref|NP_291059.1| protocadherin gamma subfamily C, 3 precursor [Mus musculus] STIIHYEILEERERGFPVGNVVTDLGLDLGSLSARRLRVVSGASRRFFEVNWETGEMFVNDRLDREELCGTLPSCTVTLELVVENPLELFSA EVVVQDINDNNPSFPTGEMKLEISEALAPGTRFPLESAHDPDVGSNSLQTYELSHNEYFALRVQTREDGTKYAELVLERALDWEREPSV QLVLTALDGGTPARSATLPIRITVLDANDNAPAFNQSLYRARVREDAPPGTRVAQVLATDLDEGLNGEIVYSFGSHNRAGVRELFALDLV TGVLTIKGRLDFEDTKLHEIYIQAKDKGANPEGAHCKVLVEVVDVNDNAPEITVTSVYSPVPEDAPLGTVIALLSVTDLDAGENGLVTCEV PPGLPFSLTSSLKNYFTLKTSAALDRETMPEYNLSITARDSGIPSLSALTTVKVQVSDINDN
>pcdhgA8 gi|18087767|ref|NP_291069.1| protocadherin gamma-A8 precursor [Mus musculus] QIRYSVPEETDKGTVVGNISKDLGLEPRELAERGVRIVSRGRSQLFSLNPRGGSLVTAGRIDREELCAQSTPCLVNINILVEEKGKLFGVEIEI TDINDNNPKFHVGDLEVKINEIAAPGARYPLPEAVDPDVGINSLQSYQLSPNRHFSLHLQTGDDGTINPELVLERTLDREEEPTHHLVLTA SDGGEPRRSSTALIQITVLDTNDNAPVFDQPVYRVKVLENVAPGTLLLTVRASDPDEGVNGKVTYKFRKINEKQSLLFHLHENTGEMTVA KNLDYEECSLYEMEIQAEDVGALLGRSKVIIMVEDVNDNRPEVTITSLFNPVLENSLPGTVIAFLNVHDQDSGKNGQVVCYTHDNLPFKL EKSIDNYYRLVTWKYLDREKVSTYNITVIASDLGAPPLSTETYIALTVADTNDN
>pcdhgA1 gi|18087753|ref|NP_291062.1| protocadherin gamma-A1 precursor [Mus musculus] GNIRYSVPEETDKGSFVGSIAKDLGLETRELMERGIRIVSRGRSQLFSLNPRSGSLVTAGRIDREELCAQSTPCVVSFNILMEDEMKLLPIEV EIIDINDNTPQFQLEELELKMSEITTPGTRIPLPLGQDLDVGINSLQSYQLSANPHFSLDVQQGPEGPQQPEMVLQRPLDREKDAVHYLV LTASDGGSPIHSGTLQIHVQVVDVNDNPPAFTKAEYHVSVPENVPLGTRLLKVNATDPDEGANGRVTYSFHKVDHSVVRKFQLDAYTG ELSNKEPLDFEEYKVYPMEIQAQDGAGLMARAKVLVTVLDVNDNAPEVGITSVTNTVPENFPPGTTIALISVHDQDADNNGHITCSIPG NLPFKLEKLVDNYYRLVTERTLDREQSSRHNITITATDQGTPPLSTQAHISLLVTDINDN
195
>pcdhb1 gi|16716425|ref|NP_444356.1| protocadherin beta-1 precursor [Mus musculus] ATIRYSVAEEMESGSFVANVAKDLGLEVGKLAERGARLVAEGNRLHFRLHRKTGDLFVKEKLDREALCGKSDPCVLHFEIILAEPLQSFRV EVRVFDINDNAPVFLNKEPLLKIPESTPLGSRFPLQSAQDLDVGLNGLQNYTLSANTYFHLHTRFRSHGPKYAELVLDNPLDREAQPEVNL TITAVDGGSPPKSGTANIRVVVLDVNDHVPQFSRLVYRAQVPENSDNGSLVVVVTATDLDEGTNKQITYSLAENPEAVLRTFLVDPQTG EVRLRGPLDFEMIETYDIDIQATDGGGLSAHSKVLVEVVDVNDNPPEVTISSVSSPLPEDSALQTVVALFTIRDRDVRVGGKITCFLKEDLP FVVKHTFRNSYSLVTDRSLDREDVSSYNITLVAMDTGPPNLSTETVIEVVIADVNDN
>pcdhaC2 gi|51092283|ref|NP_001003672.1| protocadherin alpha-C2 precursor [Mus musculus] QLRYSVPEEQSPGALVGNVARALGLELRRLGPGCLRINHLGAPSPRYLELDLTNGALFVNERIDREALCEQRPRCLLSLEVLAHNPVAVSAI EVEILDINDNSPRFPRPDYQLQVSESVAPGARFHIESAQDPDVGANSVQTYELSPSEHFELDLKPLQENSKVLELVLRKGLDREQTALHYL VLTAVDGGIPARSGTAQIAVRVLDTNDNSPAFDQSTYRVQLREDAPPGTLVVKLNASDPDEGSNGELRYSLSSYTSDRERQLFSIDVTTG EVRVSGTLDYEESSSYQIYVQATDRGPVPMAGHCKVLVDIIDVNDNAPEVVLTDLYSPVPEDVALNTVVALLSVNDQDSGSNRKVSLGL EASLPFRLNGFGNSYTLVVSGPLDRERVAAYNITVTATDGGVPPLTSQRTLQVEISDINDN
196