DOCSLIB.ORG

Literature Review and Scope of Work

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

ESRP1 is a novel marker of germ cell development and gonadal cancer Shaghayegh Saeidi Doctor of Philosophy March 2018 Department of Anatomy and Neuroscience The University of Melbourne Australia Abstract: Alternative splicing (AS) plays critical roles in controlling developmental programs. To date, there is evident that many genes splice differently during gametogenesis. Since disruption in AS may result in various reproductive disorders such as cancer, regulation of this event would be crucial during gametogenesis. The regulation of alternative splicing occurs through a network of highly combinatorial molecular interactions and numerous RNA binding proteins (RBPs) and transcription factors have been implicated in this process. Among them, ESRP1 (Epithelial Splicing Regulatory Protein) is an important cell-type specific regulator that affects the splicing of various developmental genes. Given the high level of alternative splicing during gametogenesis and the association of ESRP1 with AS, I was interested in examining the expression of ESRP1 during germ cell development and gonadal cancer. In this study by droplet digital PCR (ddPCR), I identified that Esrp1 is expressed in developing murine male and female germ cells but not somatic cells. Esrp1 also showed a high level of expression in adult mouse spermatogonia. In addition, the result of immunofluorescence experiments showed that ESRP1 protein is most highly expressed in nuclei of pre-meiotic germ cells in adult testes and co-labeled with PLZF and c-KIT. However, it did not co-localized with SOX9 in somatic cells, indicating it is germ cell specific. Furthermore, no colocalization was detected between ESRP1 and SC35 (post-transcriptional splicing marker), which suggests a probable role for ESRP1 in co-transcriptional splicing. In addition, my studies on the expression of Esrp1 in gonadal cancers showed upregulation of Esrp1 in both serous and mucinous ovarian carcinomas, its correlation with the levels of E-cadherin (CDH1) expression and coincides with switches from mesenchymal to epithelial isoforms of CD44 and FGFR2. i In testicular cancer, my data showed that Esrp1 was also up-regulated in both seminoma and mixed-germ cell testicular cancers. However, it did not regulate splicing of FGFR2 and CD44 in testicular cancers. RNA interference-mediated knockdown of ESRP1 expression in the seminoma-derived TCam-2 cell line, followed by RNA sequencing resulted in the identification of 576 novel potential splicing targets for ESRP1 in germ cell tumor cell line. IPA analyses of the data demonstrated ESRP1 regulates alternative splicing of genes that are involved in directing critical pathways involved in cell migration, morphology, and behaviors that occur during EMT. My data also showed that four mitochondrial complexes of oxidative phosphorylation are affected by differential gene expression after silencing of ESRP1. Overall, these data suggest that ESRP1 is required for germ cell development and raises the possibility that ESRP1 plays a role in splicing of mitotic and premeiotic transcripts during spermatogenesis, particularly in spermatogonia. Furthermore, my findings reveal that ESRP1 plays an important role in gonadal cancer progression by regulation of AS of numerous genes that are related to EMT. Furthermore, differential gene expression after silencing of ESRP1 suggesting that ESRP1 expression in testicular germ cells may alter ATP production and thus affect energy metabolism of these cells. ii Declaration This is to certify that 1) This thesis comprises only of my original work towards the PhD; 2) Due acknowledgement has been made in the text to all other materials used; 3) The thesis is less than 100,000 words in length, exclusive of figures, tables, bibliographies and appendices. Shaghayegh Saeidi iii Preface According to the rules and regulations that govern the Doctor of Philosophy degree at the University of Melbourne, the assessment of my contribution to this thesis was made as follows; • Chapter 3: This chapter has been published in PLoS One “Saeidi S, Shapouri F, de Iongh RU, de Iongh RU, Casagranda F, Sutherland JM, Western PS, McLaughlin EA, Familari M, Hime GR. Esrp1 is a marker of mouse fetal germ cells and is upregulated in spermatogonia. PLoS ONE. 2018; 13(1): e0190925.” I am the lead author and contributed 80% of experimental work and wrote the first draft of the entire manuscript. Chapter 4: 100% Chapter 5: 100% Chapter 6: 100% iv Acknowledgments There are many friends, family, and faculty that supported me during my PhD career. Words cannot express how much their encouragement, inspiration, and motivation has meant to me. First and foremost, I would like to thank my supervisors, Prof. Gary Hime, Dr. Mary Familari and A/Prof. Robb De Iongh for their excellent guidance throughout my doctoral studies. They provided me with opportunities to take on challenging projects and experiments, allowing me to mature as a scientist, all the while being ever present to help me along the way when necessary. Besides my supervisors, I would like to thank my advisory committee, Dr Peter Kitchener for his insightful comments and encouragement. I would like to thank my previous supervisor, A/Prof Reza Aflatoonian, for all his support and encouragement during my academic career. I appreciate the role you played in helping me get here. My special and heartily thanks to Franca Casagranda for helping me learn new techniques. I really appreciate your kindness and support during my PhD. My lab members, Dr Nicole Siddall, Trisha, Aviv, Arjun, James, Yoshana, Elena and Andrew. Thank you for making the lab one of the happiest labs I’ve worked in. Working alongside you guys was truly a joy. I would like to express my gratitude to my lovely friends, Kiana, Akram, Mitra, Javad, Maryam and Farhad for their unconditional friendship, support and patience throughout these years. I would like to thank my best friend Farnaz. There is no one with whom I can share my tears and fears, if you were not here. Thanks for being by my side and always giving me reasons to cheer. v I am grateful for the financial support I have received during my studies as the recipient of the Melbourne International Research Scholarship, the Melbourne International Fee Remission Scholarship and the Department of Anatomy and Neuroscience Travel Scholarship. Finally, I would like to thank my family members: my parents, my sisters, my brothers in law, my nephews (Arvin and Parsa) and my aunts. I am 100% certain (p < 0.001) that I could not have completed this journey without your love and support. I cannot possibly express how grateful I am to all of you for putting up with the emotional roller coaster that I’ve been on over the past four years. vi Publications • Saeidi S, Shapouri F, de Iongh RU, de Iongh RU, Casagranda F, Sutherland JM, Western PS, McLaughlin EA, Familari M, Hime GR. Esrp1 is a marker of mouse fetal germ cells and is upregulated in spermatogonia. PLoS ONE. 2018; 13(1): e0190925. Conference presentations • Saeidi S, Shapouri F, de Iongh RU, Casagranda F, Western PS, McLaughlin EA, Sutherland JM, Familari M, Hime GR. The role of ESRP1 during gametogenesis. Published in clinical endocrinology. 2015. Volume 84: PP-48. • Saeidi S, Shapouri F, de Iongh RU, Casagranda F, Western PS, McLaughlin EA, Sutherland JM, Familari M, Hime GR. The role of ESRP1 in mammalian germ cell development. 2016. 19th Eroupean Testis Workshop. Saint-Malo, France. vii Table of Contents Preface................................................................................................................................ iv Chapter 1. Literature review and scope of work .........................................................1 1.1. Epithelial to Mesenchymal Transition (EMT) ............................................................2 1.2. Alternative splicing (AS) during EMT .......................................................................4 1.3. Regulatory splicing factors .........................................................................................6 1.4. ESRP1 as an epithelial-specific splicing regulatory factor .........................................7 1.5. Targets of ESRP1 ......................................................................................................10 1.5.1. FGFR2 .........................................................................................................11 1.5.2. CD44 ...........................................................................................................12 1.6. Regulation of ESRP1 expression ..............................................................................14 1.7. ESRP1 function, expression, and localization ..........................................................16 1.8. Germ cell development .............................................................................................18 1.9. Alternative splicing in germ cell development .........................................................20 1.10. ESRP1 and carcinogenesis ........................................................................................23 1.11. Hypothesis.................................................................................................................25 Chapter 2. Materials and methods ..............................................................................27 2.1. Molecular biology .....................................................................................................28 2.1.1. RNA extraction ............................................................................................28
Recommended publications
  • Universidade Estadual De Campinas Instituto De Biologia

    Universidade Estadual De Campinas Instituto De Biologia

    UNIVERSIDADE ESTADUAL DE CAMPINAS INSTITUTO DE BIOLOGIA VERÔNICA APARECIDA MONTEIRO SAIA CEREDA O PROTEOMA DO CORPO CALOSO DA ESQUIZOFRENIA THE PROTEOME OF THE CORPUS CALLOSUM IN SCHIZOPHRENIA CAMPINAS 2016 1 VERÔNICA APARECIDA MONTEIRO SAIA CEREDA O PROTEOMA DO CORPO CALOSO DA ESQUIZOFRENIA THE PROTEOME OF THE CORPUS CALLOSUM IN SCHIZOPHRENIA Dissertação apresentada ao Instituto de Biologia da Universidade Estadual de Campinas como parte dos requisitos exigidos para a obtenção do Título de Mestra em Biologia Funcional e Molecular na área de concentração de Bioquímica. Dissertation presented to the Institute of Biology of the University of Campinas in partial fulfillment of the requirements for the degree of Master in Functional and Molecular Biology, in the area of Biochemistry. ESTE ARQUIVO DIGITAL CORRESPONDE À VERSÃO FINAL DA DISSERTAÇÃO DEFENDIDA PELA ALUNA VERÔNICA APARECIDA MONTEIRO SAIA CEREDA E ORIENTADA PELO DANIEL MARTINS-DE-SOUZA. Orientador: Daniel Martins-de-Souza CAMPINAS 2016 2 Agência(s) de fomento e nº(s) de processo(s): CNPq, 151787/2F2014-0 Ficha catalográfica Universidade Estadual de Campinas Biblioteca do Instituto de Biologia Mara Janaina de Oliveira - CRB 8/6972 Saia-Cereda, Verônica Aparecida Monteiro, 1988- Sa21p O proteoma do corpo caloso da esquizofrenia / Verônica Aparecida Monteiro Saia Cereda. – Campinas, SP : [s.n.], 2016. Orientador: Daniel Martins de Souza. Dissertação (mestrado) – Universidade Estadual de Campinas, Instituto de Biologia. 1. Esquizofrenia. 2. Espectrometria de massas. 3. Corpo caloso.
  • Genetic Diagnosis and Respiratory Management Of

    Genetic Diagnosis and Respiratory Management Of

    UITNODIGING GENETIC DIAGNOSIS Voor het bijwonen van de openbare verdediging van AND RESPIRATORY het proefschrift Genetic diagnosis and respiratory management of primary ciliary dyskinesia dyskinesia ciliary of primary management respiratory and diagnosis Genetic GENETIC DIAGNOSIS MANAGEMENT OF AND RESPIRATORY MANAGEMENT OF PRIMARY CILIARY PRIMARY CILIARY DYSKINESIA DYSKINESIA Door Tamara Paff Tamara Paff dinsdag 7 november 2017 11:45 uur in de aula van de Vrije Universiteit de Boelelaan, 1105 TE Amsterdam Receptie aansluitend in Grand cafe The Basket op de VU campus Tamara Paff Johann Keplerstraat 8-1 hoog 1098 HL, Amsterdam +31645364292/ [email protected] Tamara Paff Tamara | Paranimfen Marian van der Meij [email protected] 06-15500488 Marc van der Schee [email protected] 06-40883602 14759 - Paff_R11,5_OMS_DEF.indd 1 25-09-17 10:25 UITNODIGING GENETIC DIAGNOSIS Voor het bijwonen van de openbare verdediging van AND RESPIRATORY het proefschrift Genetic diagnosis and respiratory management of primary ciliary dyskinesia dyskinesia ciliary of primary management respiratory and diagnosis Genetic GENETIC DIAGNOSIS MANAGEMENT OF AND RESPIRATORY MANAGEMENT OF PRIMARY CILIARY PRIMARY CILIARY DYSKINESIA DYSKINESIA Door Tamara Paff Tamara Paff Dag datum tijdstip in de aula van de Vrije Universiteit de Boelelaan, 1105 TE Amsterdam Receptie aansluitend in Grand cafe The Basket op de VU campus Tamara Paff Johann Keplerstraat 8-1 hoog 1098 HL, Amsterdam +31645364292/ [email protected] Tamara Paff Tamara Paranimfen Marian van der Meij | [email protected] 06-15500488 Marc van der Schee [email protected] 06-40883602 14759_TPaff_BW.indd 1 19-09-17 13:08 ProefschriftTamaraPaff_Cover+Bladwijzer.indd All Pages 15-08-17 12:47 The studies performed in this thesis were financially supported by the PCD support group (PCD belangengroep), Fonds NutsOhra, the “Dutch mudder” team and Chiesi.
  • Appendix 2. Significantly Differentially Regulated Genes in Term Compared with Second Trimester Amniotic Fluid Supernatant

    Appendix 2. Significantly Differentially Regulated Genes in Term Compared with Second Trimester Amniotic Fluid Supernatant

    Appendix 2. Significantly Differentially Regulated Genes in Term Compared With Second Trimester Amniotic Fluid Supernatant Fold Change in term vs second trimester Amniotic Affymetrix Duplicate Fluid Probe ID probes Symbol Entrez Gene Name 1019.9 217059_at D MUC7 mucin 7, secreted 424.5 211735_x_at D SFTPC surfactant protein C 416.2 206835_at STATH statherin 363.4 214387_x_at D SFTPC surfactant protein C 295.5 205982_x_at D SFTPC surfactant protein C 288.7 1553454_at RPTN repetin solute carrier family 34 (sodium 251.3 204124_at SLC34A2 phosphate), member 2 238.9 206786_at HTN3 histatin 3 161.5 220191_at GKN1 gastrokine 1 152.7 223678_s_at D SFTPA2 surfactant protein A2 130.9 207430_s_at D MSMB microseminoprotein, beta- 99.0 214199_at SFTPD surfactant protein D major histocompatibility complex, class II, 96.5 210982_s_at D HLA-DRA DR alpha 96.5 221133_s_at D CLDN18 claudin 18 94.4 238222_at GKN2 gastrokine 2 93.7 1557961_s_at D LOC100127983 uncharacterized LOC100127983 93.1 229584_at LRRK2 leucine-rich repeat kinase 2 HOXD cluster antisense RNA 1 (non- 88.6 242042_s_at D HOXD-AS1 protein coding) 86.0 205569_at LAMP3 lysosomal-associated membrane protein 3 85.4 232698_at BPIFB2 BPI fold containing family B, member 2 84.4 205979_at SCGB2A1 secretoglobin, family 2A, member 1 84.3 230469_at RTKN2 rhotekin 2 82.2 204130_at HSD11B2 hydroxysteroid (11-beta) dehydrogenase 2 81.9 222242_s_at KLK5 kallikrein-related peptidase 5 77.0 237281_at AKAP14 A kinase (PRKA) anchor protein 14 76.7 1553602_at MUCL1 mucin-like 1 76.3 216359_at D MUC7 mucin 7,
  • Precise, Pan-Cancer Discovery of Gene Fusions Reveals a Signature Of

    Precise, Pan-Cancer Discovery of Gene Fusions Reveals a Signature Of

    bioRxiv preprint doi: https://doi.org/10.1101/178061; this version posted August 18, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 Precise, pan-cancer discovery of gene fusions reveals a signature of selection in primary 2 tumors 3 4 Donald Eric Freeman1,3,Gillian Lee Hsieh1, Jonathan Michael Howard1, Erik Lehnert2, Julia 5 Salzman1,3,4* 6 7 Author affiliation 8 1Stanford University Department of Biochemistry, 279 Campus Drive, Stanford, CA 94305 9 2Seven Bridges Genomics, 1 Main Street, Suite 500, Cambridge MA 02142 10 3Stanford University Department of Biomedical Data Science, Stanford, CA 94305-5456 11 4Stanford Cancer Institute, Stanford, CA 94305 12 13 *Corresponding author [email protected] 14 15 Short Abstract: 16 The eXtent to which gene fusions function as drivers of cancer remains a critical open question 17 in cancer biology. In principle, transcriptome sequencing provided by The Cancer Genome 18 Atlas (TCGA) enables unbiased discovery of gene fusions and post-analysis that informs the 19 answer to this question. To date, such an analysis has been impossible because of 20 performance limitations in fusion detection algorithms. By engineering a new, more precise, 21 algorithm and statistical approaches to post-analysis of fusions called in TCGA data, we report 22 new recurrent gene fusions, including those that could be druggable; new candidate pan-cancer 23 oncogenes based on their profiles in fusions; and prevalent, previously overlooked, candidate 24 oncogenic gene fusions in ovarian cancer, a disease with minimal treatment advances in recent 25 decades.
  • Hominin-Specific NOTCH2 Paralogs Expand Human Cortical Neurogenesis

    Hominin-Specific NOTCH2 Paralogs Expand Human Cortical Neurogenesis

    bioRxiv preprint doi: https://doi.org/10.1101/221358; this version posted November 17, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Hominin-specific NOTCH2 paralogs expand human cortical neurogenesis through regulation of Delta/Notch interactions. Ikuo K. Suzuki1,2, David Gacquer1, Roxane Van Heurck1,2, Devesh Kumar1,2, Marta Wojno1,2, Angéline Bilheu1,2, Adèle Herpoel1,2, Julian Chéron1,2, Franck Polleux6, Vincent Detours1, and Pierre Vanderhaeghen1,2,3,4,5*. 1 Université Libre de Bruxelles (ULB), Institute for Interdisciplinary Research (IRIBHM), B-1070 Brussels, Belgium 2 ULB Institute of Neuroscience (UNI), B-1070 Brussels, Belgium 3 WELBIO, Université Libre de Bruxelles, B-1070 Brussels, Belgium 4 VIB, Center for Brain and Disease Research, B-3000 Leuven, Belgium 5 University of Leuven (KU Leuven), Department of Neurosciences, B-3000 Leuven, Belgium 6 Department of Neuroscience, Columbia University Medical Center, Columbia University, New York, NY 10027, USA *Correspondence and Lead Contact: [email protected] Keywords Human brain development, human brain evolution, neurogenesis, Notch pathway, cerebral cortex bioRxiv preprint doi: https://doi.org/10.1101/221358; this version posted November 17, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Summary The human cerebral cortex has undergone rapid expansion and increased complexity during recent evolution. Hominid-specific gene duplications represent a major driving force of evolution, but their impact on human brain evolution remains unclear.
  • Supplementary Table 1

    Supplementary Table 1

    Supplementary Table 1. 492 genes are unique to 0 h post-heat timepoint. The name, p-value, fold change, location and family of each gene are indicated. Genes were filtered for an absolute value log2 ration 1.5 and a significance value of p ≤ 0.05. Symbol p-value Log Gene Name Location Family Ratio ABCA13 1.87E-02 3.292 ATP-binding cassette, sub-family unknown transporter A (ABC1), member 13 ABCB1 1.93E-02 −1.819 ATP-binding cassette, sub-family Plasma transporter B (MDR/TAP), member 1 Membrane ABCC3 2.83E-02 2.016 ATP-binding cassette, sub-family Plasma transporter C (CFTR/MRP), member 3 Membrane ABHD6 7.79E-03 −2.717 abhydrolase domain containing 6 Cytoplasm enzyme ACAT1 4.10E-02 3.009 acetyl-CoA acetyltransferase 1 Cytoplasm enzyme ACBD4 2.66E-03 1.722 acyl-CoA binding domain unknown other containing 4 ACSL5 1.86E-02 −2.876 acyl-CoA synthetase long-chain Cytoplasm enzyme family member 5 ADAM23 3.33E-02 −3.008 ADAM metallopeptidase domain Plasma peptidase 23 Membrane ADAM29 5.58E-03 3.463 ADAM metallopeptidase domain Plasma peptidase 29 Membrane ADAMTS17 2.67E-04 3.051 ADAM metallopeptidase with Extracellular other thrombospondin type 1 motif, 17 Space ADCYAP1R1 1.20E-02 1.848 adenylate cyclase activating Plasma G-protein polypeptide 1 (pituitary) receptor Membrane coupled type I receptor ADH6 (includes 4.02E-02 −1.845 alcohol dehydrogenase 6 (class Cytoplasm enzyme EG:130) V) AHSA2 1.54E-04 −1.6 AHA1, activator of heat shock unknown other 90kDa protein ATPase homolog 2 (yeast) AK5 3.32E-02 1.658 adenylate kinase 5 Cytoplasm kinase AK7
  • Interlocus Gene Conversion Events Introduce Deleterious Mutations Into at Least 1% of Human Genes Associated with Inherited Disease

    Interlocus Gene Conversion Events Introduce Deleterious Mutations Into at Least 1% of Human Genes Associated with Inherited Disease

    Supplemental Material for: Interlocus gene conversion events introduce deleterious mutations into at least 1% of human genes associated with inherited disease Claudio Casola1, Ugne Zekonyte1, Andrew D. Phillips2, David N. Cooper2, and Matthew W. Hahn1,3 1Department of Biology and 3School of Informatics and Computing, Indiana University, Bloomington, IN 47405 2 Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, United Kingdom. Corresponding author: Claudio Casola Department of Biology, Indiana University 1001 East 3rd Street, Bloomington, IN 47405 Phone: 812-856-7016 Fax: 812-855-6705 Email: [email protected] 1 Methods Validation of disease alleles originating from interlocus gene conversion All candidate IGC-derived disease alleles identified by our BLAST searches were further examined to identify high-confidence IGC events. Such alleles required at least one disease-associated mutation plus another mutation to be shared by the IGC donor sequence. In addition, we excluded from our data set those cases where hypermutable CpG sites constituted all the diagnostic mutations. After careful examination of the available literature, we also disregarded several putative IGC events that were deemed likely to represent experimental artifacts. In particular, we identified several cases where primer pairs, which were originally considered to have amplified a single genomic locus or cDNA transcript, also appeared to be capable of amplifying sequences paralogous to the target genes. Such instances included disease alleles from the genes CFC1 (Bamford et al. 2000), GPD2 (Novials et al. 1997) and HLA-DRB1 (Velickovic et al. 2004). In the first two of these cases, we noted that the primer pairs that had been originally designed to amplify the genes specifically, also perfectly matched the paralogous gene CFC1B and an unlinked processed pseudogene of GPD2, respectively.
  • The Driver of Extreme Human-Specific Olduvai Repeat Expansion Remains Highly Active in the Human

    The Driver of Extreme Human-Specific Olduvai Repeat Expansion Remains Highly Active in the Human

    Genetics: Early Online, published on November 21, 2019 as 10.1534/genetics.119.302782 1 The Driver of Extreme Human-Specific Olduvai Repeat Expansion Remains Highly Active in the Human 2 Genome 3 Ilea E. Heft,1,* Yulia Mostovoy,2,* Michal Levy-Sakin,2 Walfred Ma,2 Aaron J. Stevens,3 Steven 4 Pastor,4 Jennifer McCaffrey,4 Dario Boffelli,5 David I. Martin,5 Ming Xiao,4 Martin A. Kennedy,3 5 Pui-Yan Kwok,2,6,7 and James M. Sikela1 6 7 1Department of Biochemistry and Molecular Genetics, and Human Medical Genetics and 8 Genomics Program, University of Colorado School of Medicine, Aurora CO 80045 9 2Cardiovascular Research Institute, 6Department of Dermatology, and 7Institute for Human 10 Genetics, University of California, San Francisco, San Francisco, CA, USA 11 3Department of Pathology, University of Otago, Christchurch, New Zealand 8140 12 4School of Biomedical Engineering, Drexel University, Philadelphia, PA 19104 13 5Children's Hospital Oakland Research Institute, Oakland, CA, 94609 14 15 Corresponding author: James M. Sikela: [email protected] 16 *Ilea E. Heft and Yulia Mostovoy contributed equally to this article. 17 1 Copyright 2019. 18 Abstract 19 Sequences encoding Olduvai protein domains (formerly DUF1220) show the greatest 20 human lineage-specific increase in copy number of any coding region in the genome and have 21 been associated, in a dosage-dependent manner, with brain size, cognitive aptitude, autism, 22 and schizophrenia. Tandem intragenic duplications of a three-domain block, termed the Olduvai 23 triplet, in four NBPF genes in the chromosomal 1q21.1-.2 region are primarily responsible for 24 the striking human-specific copy number increase.
  • DUF1220-Domain Copy Number Implicated in Human Brain-Size Pathology and Evolution

    DUF1220-Domain Copy Number Implicated in Human Brain-Size Pathology and Evolution

    ARTICLE DUF1220-Domain Copy Number Implicated in Human Brain-Size Pathology and Evolution Laura J. Dumas,1 Majesta S. O’Bleness,1 Jonathan M. Davis,1,2 C. Michael Dickens,1 Nathan Anderson,1 J.G. Keeney,1 Jay Jackson,1 Megan Sikela,1 Armin Raznahan,3 Jay Giedd,3 Judith Rapoport,3 Sandesh S.C. Nagamani,4 Ayelet Erez,4 Nicola Brunetti-Pierri,5,6 Rachel Sugalski,7 James R. Lupski,4 Tasha Fingerlin,2 Sau Wai Cheung,4 and James M. Sikela1,* DUF1220 domains show the largest human-lineage-specific increase in copy number of any protein-coding region in the human genome and map primarily to 1q21, where deletions and reciprocal duplications have been associated with microcephaly and macro- cephaly, respectively. Given these findings and the high correlation between DUF1220 copy number and brain size across primate line- À ages (R2 ¼ 0.98; p ¼ 1.8 3 10 6), DUF1220 sequences represent plausible candidates for underlying 1q21-associated brain-size pathol- ogies. To investigate this possibility, we used specialized bioinformatics tools developed for scoring highly duplicated DUF1220 sequences to implement targeted 1q21 array comparative genomic hybridization on individuals (n ¼ 42) with 1q21-associated micro- cephaly and macrocephaly. We show that of all the 1q21 genes examined (n ¼ 53), DUF1220 copy number shows the strongest asso- ciation with brain size among individuals with 1q21-associated microcephaly, particularly with respect to the three evolutionarily conserved DUF1220 clades CON1(p ¼ 0.0079), CON2 (p ¼ 0.0134), and CON3 (p ¼ 0.0116). Interestingly, all 1q21 DUF1220-encoding genes belonging to the NBPF family show significant correlations with frontal-occipital-circumference Z scores in the deletion group.
  • High Resolution Measurement of DUF1220 Domain Copy Number from Whole Genome Sequence Data David P

    High Resolution Measurement of DUF1220 Domain Copy Number from Whole Genome Sequence Data David P

    Astling et al. BMC Genomics (2017) 18:614 DOI 10.1186/s12864-017-3976-z METHODOLOGYARTICLE Open Access High resolution measurement of DUF1220 domain copy number from whole genome sequence data David P. Astling1, Ilea E. Heft1, Kenneth L. Jones2 and James M. Sikela1* Abstract Background: DUF1220 protein domains found primarily in Neuroblastoma BreakPoint Family (NBPF) genes show the greatest human lineage-specific increase in copy number of any coding region in the genome. There are 302 haploid copies of DUF1220 in hg38 (~160 of which are human-specific) and the majority of these can be divided into 6 different subtypes (referred to as clades). Copy number changes of specific DUF1220 clades have been associated in a dose-dependent manner with brain size variation (both evolutionarily and within the human population), cognitive aptitude, autism severity, and schizophrenia severity. However, no published methods can directly measure copies of DUF1220 with high accuracy and no method can distinguish between domains within a clade. Results: Here we describe a novel method for measuring copies of DUF1220 domains and the NBPF genes in which they are found from whole genome sequence data. We have characterized the effect that various sequencing and alignment parameters and strategies have on the accuracy and precision of the method and defined the parameters that lead to optimal DUF1220 copy number measurement and resolution. We show that copy number estimates obtained using our read depth approach are highly correlated with those generated by ddPCR for three representative DUF1220 clades. By simulation, we demonstrate that our method provides sufficient resolution to analyze DUF1220 copy number variation at three levels: (1) DUF1220 clade copy number within individual genes and groups of genes (gene-specific clade groups) (2) genome wide DUF1220 clade copies and (3) gene copy number for DUF1220-encoding genes.
  • Functional Investigations of Duf1220 Protein Domains

    Functional Investigations of Duf1220 Protein Domains

    FUNCTIONAL INVESTIGATIONS OF DUF1220 PROTEIN DOMAINS by JONATHON G. KEENEY B.A., University of Colorado Boulder, 2006 A thesis submitted to the Faculty of the Graduate School of the University of Colorado in partial fulfillment of the requirements for the degree of Doctor of Philosophy Neuroscience Program 2014 ii This thesis for the Doctor of Philosophy degree by Jonathon G. Keeney has been approved for the Neuroscience Program by S. Rock Levinson, Chair Thomas Finger David Pollock Diego Restrepo Matthew Taylor James Sikela, Advisor Date __5/9/14__ iii Keeney, Jonathon G. (Ph.D., Neuroscience) Functional Investigations of DUF1220 Protein Domains Thesis directed by Professor James Sikela ABSTRACT Copy number expansion of genetic content is a powerful way in which species adapt to environments, and a powerful mechanism by which novel genes are generated. DUF1220 domains were previously identified as showing the largest human lineage- specific increase in copy number of any protein coding sequence with the human genome. While the function of DUF1220 domains remains obscure, the Sikela lab has identified a strong correlation between increasing DUF1220 copy number and increases in both brain size and cortical neuron number within great apes. In addition, a significant association has been reported between reduction and gain of DUF1220 copy number and brain size in microcephaly and macrocephaly, respectively . This thesis investigates the function of DUF1220 domains by further investigating the correlation between DUF1220 copy number and several physical brain measurements within anthropoid primates (monkey, ape and human). The spatiotemporal expression pattern in human fetal brain tissue was then evaluated, and suggested a role in neural progenitor expansion.
  • Endocrine System Local Gene Expression

    Endocrine System Local Gene Expression

    Copyright 2008 By Nathan G. Salomonis ii Acknowledgments Publication Reprints The text in chapter 2 of this dissertation contains a reprint of materials as it appears in: Salomonis N, Hanspers K, Zambon AC, Vranizan K, Lawlor SC, Dahlquist KD, Doniger SW, Stuart J, Conklin BR, Pico AR. GenMAPP 2: new features and resources for pathway analysis. BMC Bioinformatics. 2007 Jun 24;8:218. The co-authors listed in this publication co-wrote the manuscript (AP and KH) and provided critical feedback (see detailed contributions at the end of chapter 2). The text in chapter 3 of this dissertation contains a reprint of materials as it appears in: Salomonis N, Cotte N, Zambon AC, Pollard KS, Vranizan K, Doniger SW, Dolganov G, Conklin BR. Identifying genetic networks underlying myometrial transition to labor. Genome Biol. 2005;6(2):R12. Epub 2005 Jan 28. The co-authors listed in this publication developed the hierarchical clustering method (KP), co-designed the study (NC, AZ, BC), provided statistical guidance (KV), co- contributed to GenMAPP 2.0 (SD) and performed quantitative mRNA analyses (GD). The text of this dissertation contains a reproduction of a figure from: Yeo G, Holste D, Kreiman G, Burge CB. Variation in alternative splicing across human tissues. Genome Biol. 2004;5(10):R74. Epub 2004 Sep 13. The reproduction was taken without permission (chapter 1), figure 1.3. iii Personal Acknowledgments The achievements of this doctoral degree are to a large degree possible due to the contribution, feedback and support of many individuals. To all of you that helped, I am extremely grateful for your support.