DOCSLIB.ORG

A Chromosome-Level Assembly of the Atlantic Herring –

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
A Chromosome-Level Assembly of the Atlantic Herring – bioRxiv preprint doi: https://doi.org/10.1101/668384; this version posted June 11, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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-NC-ND 4.0 International license. 1 TITLE PAGE 2 3 4 A chromosome-level assembly of the Atlantic herring – 5 detection of a supergene and other signals of selection 6 7 8 Mats E. Pettersson1, Christina M. Rochus1,*, Fan Han1,*, Junfeng Chen1, Jason Hill1, 9 Ola Wallerman1, Guangyi Fan2,3, Xiaoning Hong2,4, Qiwu Xu2, He Zhang2, 10 Shanshan Liu2, Xin Liu2,5,6, Leanne Haggerty7, Toby Hunt7, Fergal J. Martin7, Paul 11 Flicek7, Ignas Bunikis8, Arild Folkvord9,10, Leif Andersson1,11,12 12 *these authors contributed equally 13 14 15 1 Science for Life Laboratory, Department of Medical Biochemistry and 16 Microbiology, Uppsala University, Uppsala, Sweden 17 2 BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China 18 3 State Key Laboratory of Quality Research in Chinese Medicine, Institute of 19 Chinese Medical Sciences, University of Macau, Macao, China 20 4 BGI Education Center, University of Chinese Academy of Sciences, 21 Shenzhen 518083, China 22 5 BGI-Shenzhen, Shenzhen 518083, China 23 6 China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China 24 7 European Molecular Biology Laboratory, European Bioinformatics 25 Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK 1 bioRxiv preprint doi: https://doi.org/10.1101/668384; this version posted June 11, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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-NC-ND 4.0 International license. 1 8 Science for Life Laboratory Uppsala, Department of Immunology, Genetics 2 and Pathology, Uppsala University, Uppsala, Sweden. 3 9 Department of Biological Sciences, University of Bergen, Bergen, Norway. 4 10 Institute of Marine Research, Bergen, Norway. 5 11 Department of Animal Breeding and Genetics, Swedish University of 6 Agricultural Sciences, Uppsala, Sweden 7 12 Department of Veterinary Integrative Biosciences, Texas A&M University, 8 Texas, United States 2 bioRxiv preprint doi: https://doi.org/10.1101/668384; this version posted June 11, 2019. 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-NC-ND 4.0 International license. 1 ABSTRACT 2 The Atlantic herring is a model species for exploring the genetic basis for 3 ecological adaptation, due to its huge population size and extremely low genetic 4 differentiation at selectively neutral loci. However, such studies have so far been 5 hampered because of a highly fragmented genome assembly. Here, we deliver a 6 chromosome-level genome assembly based on a hybrid approach combining a de 7 novo PacBio assembly with Hi-C-supported scaffolding. The assembly comprises 8 26 autosomes with sizes ranging from 12.4 to 33.1 Mb and a total size, in 9 chromosomes, of 726 Mb. The development of a high-resolution linkage map 10 confirmed the global chromosome organization and the linear order of genomic 11 segments along the chromosomes. A comparison between the herring genome 12 assembly with other high-quality assemblies from bony fishes revealed few 13 interchromosomal but frequent intrachromosomal rearrangements. The 14 improved assembly makes the analysis of previously intractable large-scale 15 structural variation more feasible; allowing, for example, the detection of a 7.8 16 Mb inversion on chromosome 12 underlying ecological adaptation. This 17 supergene shows strong genetic differentiation between populations from the 18 northern and southern parts of the species distribution. The chromosome-based 19 assembly also markedly improves the interpretation of previously detected 20 signals of selection, allowing us to reveal hundreds of independent loci 21 associated with ecological adaptation in the Atlantic herring. 3 bioRxiv preprint doi: https://doi.org/10.1101/668384; this version posted June 11, 2019. 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-NC-ND 4.0 International license. 1 INTRODUCTION 2 The Atlantic herring (Clupea harengus) is a model system to study the genetic 3 basis for ecological adaptation and the consequences of natural selection 4 (Martinez Barrio et al., 2016;,Lamichhaney et al., 2017). A major merit of this 5 system for evolutionary studies is the minute genetic drift due to the enormous 6 population size facilitating the detection of how natural selection affects the 7 populations. The Atlantic herring is in fact one of the most abundant vertebrates 8 on Earth, with schools comprising more than a billion individuals and an 9 estimated global population in excess of 1011 fish (Feng et al., 2017). It is also one 10 of very few marine species to successfully colonize the Baltic Sea, a brackish 11 body of water formed after the last Ice Age, giving rise to the phenotypically 12 distinct Baltic herring classified as a subspecies of the Atlantic herring. 13 Earlier work provided the first draft version of the herring genome 14 (Martinez Barrio et al., 2016), and revealed regions with strong signals of 15 selection related to both adaptation to the brackish Baltic Sea and differences in 16 spawning time between herring populations (Martinez Barrio et al., 17 2016;,Lamichhaney et al., 2017). In contrast, there is essentially no genetic 18 differentiation at selectively neutral loci even between geographically distant 19 populations, a fact documented already by isozyme and microsatellite analyses 20 (Andersson et al., 1981; Larsson et al., 2010; Limborg et al., 2012; Ryman et al., 21 1984) and verified by whole genome sequencing and Fst analysis (Lamichhaney 22 et al., 2012; Lamichhaney et al., 2017). However, while the signals of selection 23 were strong, the fragmented nature of the draft genome made it challenging to 24 determine the number of independent loci under selection as well as studying 25 the impact of large-scale inversions and other structural variations. 4 bioRxiv preprint doi: https://doi.org/10.1101/668384; this version posted June 11, 2019. 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-NC-ND 4.0 International license. 1 Here, by combining a de novo long-read assembly of an Atlantic herring 2 with long-range chromatin interaction information gathered via the Hi-C method 3 (Lieberman-Aiden et al., 2009), we remedy this fragmentation and deliver a 4 chromosome-level assembly of the herring genome comprising 26 autosomes 5 with sizes ranging from 12.4 to 33.1 Mb and a total size of 726 Mb. We also show 6 how this new assembly has a major impact on our ability to interpret the signals 7 of selection. The final assembly version is publicly available via the European 8 Nucleotide Archive (https://www.ebi.ac.uk/ena/data/view/GCA_900700415). 9 10 RESULTS 11 Compiling the hybrid assembly 12 The assembly is based on a new, de novo, assembly of an Atlantic herring, as 13 opposed to a Baltic herring used for the previously published version 1.2 14 (Martinez Barrio et al., 2016). We generated 63 Gb (approximately 75x coverage) 15 of sequence using Pacific Biosciences RSII cells and assembled the genome with 16 FALCON-unzip (Chin et al., 2016). The FALCON-unzip assembly was processed 17 through the PurgeHaplotigs pipeline (Roach et al., 2018), in order to remove 18 redundant sequences from the primary assembly. This procedure resulted in a 19 de novo assembly with a total size of 792.6 MB, a contig N50 of 1.61 Mb, 20 comparable to the scaffold N50 (1.84 Mb) of the published v1.2 genome. Thus, 21 the PacBio assembly achieves similar level of organization while eliminating a 22 substantial degree of uncertainty, as v1.2 contains close to 10% undetermined 23 bases (Ns) as compared to zero Ns in the FALCON-unzip assembly. 24 In order to obtain chromosome-level organization, a Hi-C library was 25 prepared from liver and brain tissue from the same individual as used for the 5 bioRxiv preprint doi: https://doi.org/10.1101/668384; this version posted June 11, 2019. 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-NC-ND 4.0 International license. 1 PacBio assembly, and it was sequenced on a BGISEQ-500 sequencer. Mapping 2 with Juicer v1.5.6 (Durand et al., 2016b) yielded 99 million informative Hi-C-read- 3 pairs, which were used to scaffold the PacBio de novo assembly into 4 chromosome-level organization using the 3D-DNA workflow pipeline 5 (Dudchenko et al., 2017) followed by manual correction using Juicebox v1.9.8 6 (Durand et al., 2016a). The output assembly was polished using Pilon v1.22 7 (Walker et al., 2014), based on 50x Ilumina paired-end coverage from the same 8 individual. Finally, a custom R script was applied to eliminate a set of small, 9 nearly identical repeats that were deemed likely to be redundant haplotypes 10 based on analysis of the mapped read depth of a set of Ilumina short reads from a 11 previously sequenced herring population (Martinez Barrio et al., 2016).
Load more

Recommended publications
  • The LRRC8A:C Heteromeric Channel Is a Cgamp Transporter and the Dominant
    bioRxiv preprint doi: https://doi.org/10.1101/2020.02.13.948273; this version posted February 14, 2020. 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. The LRRC8A:C Heteromeric Channel Is a cGAMP Transporter and the Dominant cGAMP Importer in Human Vasculature Cells Lauren J. Lahey1,2, Xianlan Wen3, Rachel E. Mardjuki2,4, Volker Böhnert2,5, Christopher Ritchie2,5, Jacqueline A. Carozza2,4, Gaelen T. Hess2,6, Merritt Maduke3, Michael C. Bassik2,6, and Lingyin Li2,5,7,* 1Biophysics Program, 2Stanford ChEM-H, 3Department of Molecular and Cellular Physiology, 4Department of Chemistry, 5Department of Biochemistry, 6Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 USA. 7Lead Contact *Correspondence: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2020.02.13.948273; this version posted February 14, 2020. 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 Extracellular 2'3'-cyclic-GMP-AMP (cGAMP) is an immunotransmitter secreted by cancer cells and taken up by host cells to activate the anti-cancer STING pathway. No cGAMP exporter has been identified, and SLC19A1, a recently identified cGAMP importer, does not account for the import actiVity in most cell types. Here, we identify the LRRC8A:C heteromeric channel, a volume-regulated anion channel (VRAC), as a cGAMP transporter. This channel mediates cGAMP import or export depending on the cGAMP chemical gradient. cGAMP influences anion influx through VRAC, indicating it is likely a direct substrate of the channel.
    [Show full text]
  • Selective Transport of Neurotransmitters and Modulators by Distinct Volume-Regulated LRRC8 Anion Channels Darius Lutter1,2,3, Florian Ullrich1,2, Jennifer C
    © 2017. Published by The Company of Biologists Ltd | Journal of Cell Science (2017) 130, 1122-1133 doi:10.1242/jcs.196253 RESEARCH ARTICLE Selective transport of neurotransmitters and modulators by distinct volume-regulated LRRC8 anion channels Darius Lutter1,2,3, Florian Ullrich1,2, Jennifer C. Lueck1,2,3, Stefan Kempa2 and Thomas J. Jentsch1,2,4,* ABSTRACT volume regulation (Jentsch, 2016; Nilius et al., 1997; Pedersen In response to swelling, mammalian cells release chloride and et al., 2016). This plasma membrane channel, which appears to be organic osmolytes through volume-regulated anion channels expressed in all cells, is normally closed but can be activated by cell swelling or other cellular signaling cascades. In most cells, VRAC (VRACs). VRACs are heteromers of LRRC8A and other LRRC8 − isoforms (LRRC8B to LRRC8E), which are co-expressed in HEK293 opening leads to an efflux of Cl , which, together with an efflux of + + and most other cells. The spectrum of VRAC substrates and its K through independent K channels, lowers the intracellular dependence on particular LRRC8 isoforms remains largely unknown. osmolarity and, by secondarily driving water efflux, results in We show that, besides the osmolytes taurine and myo-inositol, regulatory volume decrease. Cell swelling also stimulates an efflux ‘ ’ myo LRRC8 channels transport the neurotransmitters glutamate, of organic osmolytes such as -inositol, taurine and glutamate. aspartate and γ-aminobutyric acid (GABA) and the co-activator It was controversial whether this release occurs through VRAC or D-serine. HEK293 cells engineered to express defined subsets of through a distinct channel named VSOAC (for volume-sensitive LRRC8 isoforms were used to elucidate the subunit-dependence organic osmolyte/anion channel) (Jackson and Strange, 1993; of transport.
    [Show full text]
  • The LRRC8A:C Heteromeric Channel Is a Cgamp Transporter and the Dominant Cgamp Importer in Human Vasculature Cells
    bioRxiv preprint doi: https://doi.org/10.1101/2020.02.13.948273; this version posted March 27, 2020. 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. The LRRC8A:C Heteromeric Channel Is a cGAMP Transporter and the Dominant cGAMP Importer in Human Vasculature Cells Lauren J. Lahey1,2, Xianlan Wen3, Rachel E. Mardjuki2,4, Volker Böhnert2,5, Gaelen T. Hess2,6, Christopher Ritchie2,5, Jacqueline A. Carozza2,4, Merritt Maduke3, Michael C. Bassik2,6, and Lingyin Li2,5,7,* 1Biophysics Program, 2Stanford ChEM-H, 3Department of Molecular and Cellular Physiology, 4Department of Chemistry, 5Department of Biochemistry, 6Department of Genetics, Stanford University, School of Medicine, Stanford, CA 94305 USA. 7Lead Contact *Correspondence: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2020.02.13.948273; this version posted March 27, 2020. 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 Extracellular 2'3'-cyclic-GMP-AMP (cGAMP) is an immunotransmitter secreted by cancer cells and taken up by host cells to activate the anti-cancer STING pathway. No cGAMP exporter has been identified, and SLC19A1, a recently identified cGAMP importer, does not account for the import actiVity in most cell types. Here, we identify the LRRC8A:C heteromeric channel, a volume-regulated anion channel (VRAC), as a cGAMP transporter. This channel mediates cGAMP import or export depending on the cGAMP chemical gradient, and channel activation or inhibition modulates cGAMP transport.
    [Show full text]
  • The M1 Aminopeptidase NPEPPS Is a Novel Regulator of Cisplatin Sensitivity
    bioRxiv preprint doi: https://doi.org/10.1101/2021.03.04.433676; this version posted March 4, 2021. 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-NC-ND 4.0 International license. 1 The M1 aminopeptidase NPEPPS is a 2 novel regulator of cisplatin sensitivity 3 4 Robert T. Jones1,15, Andrew Goodspeed1,3,15, Maryam C. Akbarzadeh2,4,16, Mathijs Scholtes2,16, 5 Hedvig Vekony1, Annie Jean1, Charlene B. Tilton1, Michael V. Orman1, Molishree Joshi1,5, 6 Teemu D. Laajala1,6, Mahmood Javaid7, Eric T. Clambey8, Ryan Layer7,9, Sarah Parker10, 7 Tokameh Mahmoudi2,11, Tahlita Zuiverloon2,*, Dan Theodorescu12,13,14,*, James C. Costello1,3,* 8 9 1Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, 10 USA 11 2 Department of Urology, Erasmus MC Cancer Institute, Erasmus University Medical Center 12 Rotterdam, Rotterdam, The Netherlands 13 3University of Colorado Comprehensive Cancer Center, University of Colorado Anschutz 14 Medical Campus, Aurora, CO, USA 15 4Stem Cell and Regenerative Medicine Center of Excellence, Tehran University of Medical 16 Sciences, Tehran, Iran 17 5Functional Genomics Facility, University of Colorado Anschutz Medical Campus, Aurora, CO, 18 USA 19 6Department of Mathematics and Statistics, University of Turku, Turku, Finland. 20 7Computer Science Department, University of Colorado, Boulder 21 8Department of Anesthesiology, University
    [Show full text]
  • Genome-Wide Association and Gene Enrichment Analyses of Meat Sensory Traits in a Crossbred Brahman-Angus
    Proceedings of the World Congress on Genetics Applied to Livestock Production, 11. 124 Genome-wide association and gene enrichment analyses of meat tenderness in an Angus-Brahman cattle population J.D. Leal-Gutíerrez1, M.A. Elzo1, D. Johnson1 & R.G. Mateescu1 1 University of Florida, Department of Animal Sciences, 2250 Shealy Dr, 32608 Gainesville, Florida, United States. [email protected] Summary The objective of this study was to identify genomic regions associated with meat tenderness related traits using a whole-genome scan approach followed by a gene enrichment analysis. Warner-Bratzler shear force (WBSF) was measured on 673 steaks, and tenderness and connective tissue were assessed by a sensory panel on 496 steaks. Animals belong to the multibreed Angus-Brahman herd from University of Florida and range from 100% Angus to 100% Brahman. All animals were genotyped with the Bovine GGP F250 array. Gene enrichment was identified in two pathways; the first pathway is involved in negative regulation of transcription from RNA polymerase II, and the second pathway groups several cellular component of the endoplasmic reticulum membrane. Keywords: tenderness, gene enrichment, regulation of transcription, cell growth, cell proliferation Introduction Identification of quantitative trait loci (QTL) for any complex trait, including meat tenderness, is the first most important step in the process of understanding the genetic architecture underlying the phenotype. Given a large enough population and a dense coverage of the genome, a genome-wide association study (GWAS) is usually successful in uncovering major genes and QTLs with large and medium effect on these type of traits. Several GWA studies on Bos indicus (Magalhães et al., 2016; Tizioto et al., 2013) or crossbred beef cattle breeds (Bolormaa et al., 2011b; Hulsman Hanna et al., 2014; Lu et al., 2013) were successful at identifying QTL for meat tenderness; and most of them include the traditional candidate genes µ-calpain and calpastatin.
    [Show full text]
  • Leucine-Rich Repeat Containing 8A Contributes to the Expansion Of
    © 2020. Published by The Company of Biologists Ltd | Biology Open (2020) 9, bio048264. doi:10.1242/bio.048264 RESEARCH ARTICLE Leucine-rich repeat containing 8A contributes to the expansion of brain ventricles in zebrafish embryos Yen-Tzu Tseng1, Chun-Lin Ko1, Chia-Teng Chang1, Yen-Hua Lee1, Wei-Chun Huang Fu2 and I-Hsuan Liu1,3,4,* ABSTRACT outwardly rectifying Cl− current and consequently an RVD when The sodium osmotic gradient is necessary for the initiation of brain cells were exposed to hypotonic solutions (Cahalan and Lewis, 1988; ventricle inflation, but a previous study predicted that organic and Hazama and Okada, 1988). Later, organic osmolytes such as inorganic osmolytes play equivalently important roles in osmotic taurine were considered accountable for at least half of the total homeostasis in astrocytes. To test whether organic osmoregulation RVD, and hence a putative volume-sensitive organic osmolyte/anion also plays a role in brain ventricle inflation, the core component for channel (VSOAC) was proposed for this activity (Garcia-Romeu volume-regulated anion and organic osmolyte channel, lrrc8a,was et al., 1991; Jackson and Strange, 1993; Strange and Jackson, 1995). investigated in the zebrafish model. RT-PCR and whole-mount in situ Due to the pharmacological similarity and controversial experimental hybridization indicated that both genes were ubiquitously expressed results, the question of whether VRAC is identical to VSOAC was through to 12 hpf, and around the ventricular layer of neural tubes and once a highly debated issue (Díaz et al., 1993; Kirk and Kirk, 1994; the cardiogenic region at 24 hpf. Knocking down either one lrrc8a Lambert and Hoffmann, 1994; Sanchez-Olea et al., 1995; Shennan paralog with morpholino oligos resulted in abnormalities in circulation et al., 1994).
    [Show full text]
  • Molecular Architecture Underlying Fluid Absorption by the Developing Inner
    RESEARCH ARTICLE Molecular architecture underlying fluid absorption by the developing inner ear Keiji Honda1†, Sung Huhn Kim2‡, Michael C Kelly3, Joseph C Burns3§, Laura Constance2, Xiangming Li2#, Fei Zhou2, Michael Hoa4, Matthew W Kelley3, Philine Wangemann2*, Robert J Morell5, Andrew J Griffith1* 1Molecular Biology and Genetics Section, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, United States; 2Anatomy and Physiology Department, Kansas State University, Manhattan, United States; 3Developmental Neuroscience Section, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, United States; 4Auditory Development and Restoration Program, National Institute on *For correspondence: Deafness and Other Communication Disorders, National Institutes of Health, [email protected] (PW); Bethesda, United States; 5Genomics and Computational Biology Core, National [email protected] (AJG) Institute on Deafness and Other Communication Disorders, National Institutes of Present address: Health, Bethesda, United States †Otolaryngology Department, Tsuchiura Kyodo General Hospital, Tsuchiura, Japan; ‡Department of Abstract Mutations of SLC26A4 are a common cause of hearing loss associated with Otorhinolaryngology, Head and enlargement of the endolymphatic sac (EES). Slc26a4 expression in the developing mouse Neck Surgery, Yonsei University College of Medicine, Seoul, endolymphatic sac is required for acquisition of normal inner ear structure and function. Here, we Korea; §Decibel Therapeutics, show that the mouse endolymphatic sac absorbs fluid in an SLC26A4-dependent fashion. Fluid Cambridge, United States; absorption was sensitive to ouabain and gadolinium but insensitive to benzamil, bafilomycin and #Technique R and D-Drug S3226. Single-cell RNA-seq analysis of pre- and postnatal endolymphatic sacs demonstrates two Substance, GlaxoSmithKline types of differentiated cells.
    [Show full text]
  • Quantitative Trait Loci Mapping of Macrophage Atherogenic Phenotypes
    QUANTITATIVE TRAIT LOCI MAPPING OF MACROPHAGE ATHEROGENIC PHENOTYPES BRIAN RITCHEY Bachelor of Science Biochemistry John Carroll University May 2009 submitted in partial fulfillment of requirements for the degree DOCTOR OF PHILOSOPHY IN CLINICAL AND BIOANALYTICAL CHEMISTRY at the CLEVELAND STATE UNIVERSITY December 2017 We hereby approve this thesis/dissertation for Brian Ritchey Candidate for the Doctor of Philosophy in Clinical-Bioanalytical Chemistry degree for the Department of Chemistry and the CLEVELAND STATE UNIVERSITY College of Graduate Studies by ______________________________ Date: _________ Dissertation Chairperson, Johnathan D. Smith, PhD Department of Cellular and Molecular Medicine, Cleveland Clinic ______________________________ Date: _________ Dissertation Committee member, David J. Anderson, PhD Department of Chemistry, Cleveland State University ______________________________ Date: _________ Dissertation Committee member, Baochuan Guo, PhD Department of Chemistry, Cleveland State University ______________________________ Date: _________ Dissertation Committee member, Stanley L. Hazen, MD PhD Department of Cellular and Molecular Medicine, Cleveland Clinic ______________________________ Date: _________ Dissertation Committee member, Renliang Zhang, MD PhD Department of Cellular and Molecular Medicine, Cleveland Clinic ______________________________ Date: _________ Dissertation Committee member, Aimin Zhou, PhD Department of Chemistry, Cleveland State University Date of Defense: October 23, 2017 DEDICATION I dedicate this work to my entire family. In particular, my brother Greg Ritchey, and most especially my father Dr. Michael Ritchey, without whose support none of this work would be possible. I am forever grateful to you for your devotion to me and our family. You are an eternal inspiration that will fuel me for the remainder of my life. I am extraordinarily lucky to have grown up in the family I did, which I will never forget.
    [Show full text]
  • The Pdx1 Bound Swi/Snf Chromatin Remodeling Complex Regulates Pancreatic Progenitor Cell Proliferation and Mature Islet Β Cell
    Page 1 of 125 Diabetes The Pdx1 bound Swi/Snf chromatin remodeling complex regulates pancreatic progenitor cell proliferation and mature islet β cell function Jason M. Spaeth1,2, Jin-Hua Liu1, Daniel Peters3, Min Guo1, Anna B. Osipovich1, Fardin Mohammadi3, Nilotpal Roy4, Anil Bhushan4, Mark A. Magnuson1, Matthias Hebrok4, Christopher V. E. Wright3, Roland Stein1,5 1 Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 2 Present address: Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 3 Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 4 Diabetes Center, Department of Medicine, UCSF, San Francisco, California 5 Corresponding author: [email protected]; (615)322-7026 1 Diabetes Publish Ahead of Print, published online June 14, 2019 Diabetes Page 2 of 125 Abstract Transcription factors positively and/or negatively impact gene expression by recruiting coregulatory factors, which interact through protein-protein binding. Here we demonstrate that mouse pancreas size and islet β cell function are controlled by the ATP-dependent Swi/Snf chromatin remodeling coregulatory complex that physically associates with Pdx1, a diabetes- linked transcription factor essential to pancreatic morphogenesis and adult islet-cell function and maintenance. Early embryonic deletion of just the Swi/Snf Brg1 ATPase subunit reduced multipotent pancreatic progenitor cell proliferation and resulted in pancreas hypoplasia. In contrast, removal of both Swi/Snf ATPase subunits, Brg1 and Brm, was necessary to compromise adult islet β cell activity, which included whole animal glucose intolerance, hyperglycemia and impaired insulin secretion. Notably, lineage-tracing analysis revealed Swi/Snf-deficient β cells lost the ability to produce the mRNAs for insulin and other key metabolic genes without effecting the expression of many essential islet-enriched transcription factors.
    [Show full text]
  • SUPPORTING INFORMATION for Regulation of Gene Expression By
    SUPPORTING INFORMATION for Regulation of gene expression by the BLM helicase correlates with the presence of G4 motifs Giang Huong Nguyen1,2, Weiliang Tang3, Ana I. Robles1, Richard P. Beyer4, Lucas T. Gray5, Judith A. Welsh1, Aaron J. Schetter1, Kensuke Kumamoto1,6, Xin Wei Wang1, Ian D. Hickson2,7, Nancy Maizels5, 3,8 1 Raymond J. Monnat, Jr. and Curtis C. Harris 1Laboratory of Human Carcinogenesis, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, U.S.A; 2Department of Medical Oncology, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, U.K.; 3Department of Pathology, University of Washington, Seattle, WA U.S.A.; 4 Center for Ecogenetics and Environmental Health, University of Washington, Seattle, WA U.S.A.; 5Department of Immunology and Department of Biochemistry, University of Washington, Seattle, WA U.S.A.; 6Department of Organ Regulatory Surgery, Fukushima Medical University, Fukushima, Japan; 7Cellular and Molecular Medicine, Nordea Center for Healthy Aging, University of Copenhagen, Denmark; 8Department of Genome Sciences, University of WA, Seattle, WA U.S.A. SI Index: Supporting Information for this manuscript includes the following 19 items. A more detailed Materials and Methods section is followed by 18 Tables and Figures in order of their appearance in the manuscript text: 1) SI Materials and Methods 2) Figure S1. Study design and experimental workflow. 3) Figure S2. Immunoblot verification of BLM depletion from human fibroblasts. 4) Figure S3. PCA of mRNA and miRNA expression in BLM-depleted human fibroblasts. 5) Figure S4. qPCR confirmation of mRNA array data. 6) Table S1. BS patient and control detail.
    [Show full text]
  • Structure of the Human Volume Regulated Anion Channel
    RESEARCH ARTICLE Structure of the human volume regulated anion channel Jennifer M Kefauver1,2, Kei Saotome1,2†, Adrienne E Dubin1†, Jesper Pallesen2, Christopher A Cottrell2, Stuart M Cahalan1‡, Zhaozhu Qiu3§#, Gunhee Hong1, Christopher S Crowley2,4, Tess Whitwam1, Wen-Hsin Lee2, Andrew B Ward2*, Ardem Patapoutian1* 1Department of Neuroscience, Howard Hughes Medical Institute, The Scripps Research Institute, La Jolla, United States; 2Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, United States; 3Genomics Institute of the Novartis Research Foundation, San Diego, United States; 4Department of Dermatology, University of California, San Diego, San Diego, United States *For correspondence: [email protected] (ABW); [email protected] (AP) Abstract SWELL1 (LRRC8A) is the only essential subunit of the Volume Regulated Anion Channel † (VRAC), which regulates cellular volume homeostasis and is activated by hypotonic solutions. These authors contributed equally to this work SWELL1, together with four other LRRC8 family members, potentially forms a vastly heterogeneous cohort of VRAC channels with different properties; however, SWELL1 alone is also functional. Here, ‡ Present address: Vertex we report a high-resolution cryo-electron microscopy structure of full-length human homo- Pharmaceuticals, San Diego, hexameric SWELL1. The structure reveals a trimer of dimers assembly with symmetry mismatch United States; §Department of between the pore-forming domain and the cytosolic leucine-rich repeat (LRR) domains. Importantly, Physiology, Johns Hopkins mutational analysis demonstrates that a charged residue at the narrowest constriction of the University School of Medicine, Baltimore, United States; homomeric channel is an important pore determinant of heteromeric VRAC. Additionally, a #Solomon H. Snyder Department mutation in the flexible N-terminal portion of SWELL1 affects pore properties, suggesting a of Neuroscience, Johns Hopkins putative link between intracellular structures and channel regulation.
    [Show full text]
  • Whole Exome Sequencing Identifies APCDD1 and HDAC5 Genes As Potentially Cancer Predisposing in Familial Colorectal Cancer
    International Journal of Molecular Sciences Article Whole Exome Sequencing Identifies APCDD1 and HDAC5 Genes as Potentially Cancer Predisposing in Familial Colorectal Cancer Diamanto Skopelitou 1,2,3,4, Beiping Miao 1,2,3, Aayushi Srivastava 1,2,3,4, Abhishek Kumar 1,5,6, Magdalena Ku´swik 7, Dagmara Dymerska 7, Nagarajan Paramasivam 8, Matthias Schlesner 9 , Jan Lubinski 7, Kari Hemminki 1,10,11, Asta Försti 1,2,3 and Obul Reddy Bandapalli 1,2,3,4,* 1 Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; [email protected] (D.S.); [email protected] (B.M.); [email protected] (A.S.); [email protected] (A.K.); [email protected] (K.H.); [email protected] (A.F.) 2 Hopp Children’s Cancer Center (KiTZ), 69120 Heidelberg, Germany 3 Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany 4 Medical Faculty, Heidelberg University, 69120 Heidelberg, Germany 5 Institute of Bioinformatics, International Technology Park, Bangalore 560066, India 6 Manipal Academy of Higher Education (MAHE), Manipal 576104, India 7 Department of Genetics and Pathology, Pomeranian Medical University, 71252 Szczecin, Poland; [email protected] (M.K.); [email protected] (D.D.); [email protected] (J.L.) 8 Computational Oncology, Molecular Diagnostics Program, National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany; [email protected] 9 Bioinformatics and Omics Data Analytics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Citation: Skopelitou, D.; Miao, B.; [email protected] 10 Srivastava, A.; Kumar, A.; Ku´swik, Cancer Epidemiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany 11 Biomedical Center, Faculty of Medicine in Pilsen, Charles University in Prague, 30605 Pilsen, Czech Republic M.; Dymerska, D.; Paramasivam, N.; * Correspondence: [email protected]; Tel.: +49-6221-421809 Schlesner, M.; Lubinski, J.; Hemminki, K.; et al.
    [Show full text]