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Heath H, Peng S, Szmatola T, Ryan S, Bellone R, Kalbfleisch T, Petersen J, Finno C. A Comprehensive Allele Specific Expression Resource for the Equine Transcriptome. RESEARCH SQUARE 2024:rs.3.rs-4182812. [PMID: 38645140 PMCID: PMC11030527 DOI: 10.21203/rs.3.rs-4182812/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Background Allele-specific expression (ASE) analysis provides a nuanced view of cis-regulatory mechanisms affecting gene expression. Results An equine ASE analysis was performed, using integrated Iso-seq and short-read RNA sequencing data from four healthy Thoroughbreds (2 mares and 2 stallions) across 9 tissues from the Functional Annotation of Animal Genomes (FAANG) project. Allele expression was quantified by haplotypes from long-read data, with 42,900 allele expression events compared. Within these events, 635 (1.48%) demonstrated ASE, with liver tissue containing the highest proportion. Genetic variants within ASE events were in histone modified regions 64.2% of the time. Validation of allele-specific variants, using a set of 66 equine liver samples from multiple breeds, confirmed that 97% of variants demonstrated ASE. Conclusions This valuable publicly accessible resource is poised to facilitate investigations into regulatory variation in equine tissues. Our results highlight the tissue-specific nature of allelic imbalance in the equine genome.
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Heath HD, Peng S, Szmatola T, Bellone RR, Kalbfleisch T, Petersen JL, Finno CJ. A Comprehensive Allele Specific Expression Resource for the Equine Transcriptome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.31.573798. [PMID: 38260378 PMCID: PMC10802363 DOI: 10.1101/2023.12.31.573798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Background Allele-specific expression (ASE) analysis provides a nuanced view of cis-regulatory mechanisms affecting gene expression. Results In this work, we introduce and highlight the significance of an equine ASE analysis, containing integrated long- and short-read RNA sequencing data, along with insight from histone modification data, from four healthy Thoroughbreds (2 mares and 2 stallions) across 9 tissues. Conclusions This valuable publicly accessible resource is poised to facilitate investigations into regulatory variation in equine tissues and foster a deeper understanding of the impact of allelic imbalance in equine health and disease at the molecular level.
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Cappelletti E, Piras FM, Sola L, Santagostino M, Petersen JL, Bellone RR, Finno CJ, Peng S, Kalbfleisch TS, Bailey E, Nergadze SG, Giulotto E. The localization of centromere protein A is conserved among tissues. Commun Biol 2023; 6:963. [PMID: 37735603 PMCID: PMC10514049 DOI: 10.1038/s42003-023-05335-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 09/08/2023] [Indexed: 09/23/2023] Open
Abstract
Centromeres are epigenetically specified by the histone H3 variant CENP-A. Although mammalian centromeres are typically associated with satellite DNA, we previously demonstrated that the centromere of horse chromosome 11 (ECA11) is completely devoid of satellite DNA. We also showed that the localization of its CENP-A binding domain is not fixed but slides within an about 500 kb region in different individuals, giving rise to positional alleles. These epialleles are inherited as Mendelian traits but their position can move in one generation. It is still unknown whether centromere sliding occurs during meiosis or during development. Here, we first improve the sequence of the ECA11 centromeric region in the EquCab3.0 assembly. Then, to test whether centromere sliding may occur during development, we map the CENP-A binding domains of ECA11 using ChIP-seq in five tissues of different embryonic origin from the four horses of the equine FAANG (Functional Annotation of ANimal Genomes) consortium. Our results demonstrate that the centromere is localized in the same region in all tissues, suggesting that the position of the centromeric domain is maintained during development.
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Affiliation(s)
| | - Francesca M Piras
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Lorenzo Sola
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Marco Santagostino
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Jessica L Petersen
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Rebecca R Bellone
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA
| | - Carrie J Finno
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA
| | - Sichong Peng
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA
| | - Ted S Kalbfleisch
- Gluck Equine Research Center, University of Kentucky, Lexington, KY, USA
| | - Ernest Bailey
- Gluck Equine Research Center, University of Kentucky, Lexington, KY, USA
| | - Solomon G Nergadze
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Elena Giulotto
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy.
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Haghani A, Li CZ, Robeck TR, Zhang J, Lu AT, Ablaeva J, Acosta-Rodríguez VA, Adams DM, Alagaili AN, Almunia J, Aloysius A, Amor NM, Ardehali R, Arneson A, Baker CS, Banks G, Belov K, Bennett NC, Black P, Blumstein DT, Bors EK, Breeze CE, Brooke RT, Brown JL, Carter G, Caulton A, Cavin JM, Chakrabarti L, Chatzistamou I, Chavez AS, Chen H, Cheng K, Chiavellini P, Choi OW, Clarke S, Cook JA, Cooper LN, Cossette ML, Day J, DeYoung J, Dirocco S, Dold C, Dunnum JL, Ehmke EE, Emmons CK, Emmrich S, Erbay E, Erlacher-Reid C, Faulkes CG, Fei Z, Ferguson SH, Finno CJ, Flower JE, Gaillard JM, Garde E, Gerber L, Gladyshev VN, Goya RG, Grant MJ, Green CB, Hanson MB, Hart DW, Haulena M, Herrick K, Hogan AN, Hogg CJ, Hore TA, Huang T, Belmonte JCI, Jasinska AJ, Jones G, Jourdain E, Kashpur O, Katcher H, Katsumata E, Kaza V, Kiaris H, Kobor MS, Kordowitzki P, Koski WR, Krützen M, Kwon SB, Larison B, Lee SG, Lehmann M, Lemaître JF, Levine AJ, Li X, Li C, Lim AR, Lin DTS, Lindemann DM, Liphardt SW, Little TJ, Macoretta N, Maddox D, Matkin CO, Mattison JA, McClure M, Mergl J, Meudt JJ, Montano GA, Mozhui K, Munshi-South J, Murphy WJ, Naderi A, Nagy M, Narayan P, Nathanielsz PW, Nguyen NB, Niehrs C, Nyamsuren B, O’Brien JK, Ginn PO, Odom DT, Ophir AG, Osborn S, Ostrander EA, Parsons KM, Paul KC, Pedersen AB, Pellegrini M, Peters KJ, Petersen JL, Pietersen DW, Pinho GM, Plassais J, Poganik JR, Prado NA, Reddy P, Rey B, Ritz BR, Robbins J, Rodriguez M, Russell J, Rydkina E, Sailer LL, Salmon AB, Sanghavi A, Schachtschneider KM, Schmitt D, Schmitt T, Schomacher L, Schook LB, Sears KE, Seifert AW, Shafer AB, Shindyapina AV, Simmons M, Singh K, Sinha I, Slone J, Snell RG, Soltanmohammadi E, Spangler ML, Spriggs M, Staggs L, Stedman N, Steinman KJ, Stewart DT, Sugrue VJ, Szladovits B, Takahashi JS, Takasugi M, Teeling EC, Thompson MJ, Van Bonn B, Vernes SC, Villar D, Vinters HV, Vu H, Wallingford MC, Wang N, Wilkinson GS, Williams RW, Yan Q, Yao M, Young BG, Zhang B, Zhang Z, Zhao Y, Zhao P, Zhou W, Zoller JA, Ernst J, Seluanov A, Gorbunova V, Yang XW, Raj K, Horvath S. DNA methylation networks underlying mammalian traits. Science 2023; 381:eabq5693. [PMID: 37561875 PMCID: PMC11180965 DOI: 10.1126/science.abq5693] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 06/21/2023] [Indexed: 08/12/2023]
Abstract
Using DNA methylation profiles (n = 15,456) from 348 mammalian species, we constructed phyloepigenetic trees that bear marked similarities to traditional phylogenetic ones. Using unsupervised clustering across all samples, we identified 55 distinct cytosine modules, of which 30 are related to traits such as maximum life span, adult weight, age, sex, and human mortality risk. Maximum life span is associated with methylation levels in HOXL subclass homeobox genes and developmental processes and is potentially regulated by pluripotency transcription factors. The methylation state of some modules responds to perturbations such as caloric restriction, ablation of growth hormone receptors, consumption of high-fat diets, and expression of Yamanaka factors. This study reveals an intertwined evolution of the genome and epigenome that mediates the biological characteristics and traits of different mammalian species.
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Affiliation(s)
- Amin Haghani
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Altos Labs, San Diego, CA, USA
| | - Caesar Z. Li
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA
- Janssen Research & Development, Spring House, PA, USA
| | - Todd R. Robeck
- Zoological Operations, SeaWorld Parks and Entertainment, Orlando, FL, USA
| | - Joshua Zhang
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Ake T. Lu
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Altos Labs, San Diego, CA, USA
| | - Julia Ablaeva
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Victoria A. Acosta-Rodríguez
- Department of Neuroscience, Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Danielle M. Adams
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Abdulaziz N. Alagaili
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Javier Almunia
- Loro Parque Fundacion, Avenida Loro Parque, Puerto de la Cruz, Tenerife, Spain
| | - Ajoy Aloysius
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - Nabil M.S. Amor
- Laboratory of Biodiversity, Parasitology, and Ecology, University of Tunis El Manar, Tunis, Tunisia
| | - Reza Ardehali
- Division of Cardiology, Department of Internal Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Adriana Arneson
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - C. Scott Baker
- Marine Mammal Institute, Oregon State University, Newport, OR, USA
| | - Gareth Banks
- Mammalian Genetics Unit, MRC Harwell Institute, Harwell Science and Innovation Campus, Oxfordshire, UK
| | - Katherine Belov
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Nigel C. Bennett
- Department of Zoology and Entomology, University of Pretoria, Hatfield, South Africa
| | | | - Daniel T. Blumstein
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, USA
- The Rocky Mountain Biological Laboratory, Crested Butte, CO, USA
| | - Eleanor K. Bors
- Marine Mammal Institute, Oregon State University, Newport, OR, USA
| | | | | | - Janine L. Brown
- Center for Species Survival, Smithsonian National Zoo and Conservation Biology, Front Royal, VA, USA
| | - Gerald Carter
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Alex Caulton
- AgResearch, Invermay Agricultural Centre, Mosgiel, Otago, New Zealand
- Department of Biochemistry, University of Otago, Dunedin, Otago, New Zealand
| | - Julie M. Cavin
- Gulf World Marine Park - Dolphin Company, Panama City Beach, FL, USA
| | - Lisa Chakrabarti
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| | - Ioulia Chatzistamou
- Department of Pathology, Microbiology & Immunology, School of Medicine, University of South Carolina, Columbia, SC, USA
| | - Andreas S. Chavez
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
- Translational Data Analytics Institute, The Ohio State University, Columbus, OH, USA
| | - Hao Chen
- Department of Pharmacology, Addiction Science and Toxicology, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Kaiyang Cheng
- Medical Informatics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Priscila Chiavellini
- Biochemistry Research Institute of La Plata, Histology and Pathology, School of Medicine, University of La Plata, La Plata, Argentina
| | - Oi-Wa Choi
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Shannon Clarke
- AgResearch, Invermay Agricultural Centre, Mosgiel, Otago, New Zealand
| | - Joseph A. Cook
- University of New Mexico, Department of Biology and Museum of Southwestern Biology, Albuquerque, NM, USA
| | - Lisa N. Cooper
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, OH, USA
| | - Marie-Laurence Cossette
- Department of Environmental & Life Sciences, Trent University, Peterborough, Ontario, Canada
| | - Joanna Day
- Taronga Institute of Science and Learning, Taronga Conservation Society Australia, Mosman, New South Wales, Australia
| | - Joseph DeYoung
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | | | - Christopher Dold
- Zoological Operations, SeaWorld Parks and Entertainment, Orlando, FL, USA
| | - Jonathan L. Dunnum
- University of New Mexico, Department of Biology and Museum of Southwestern Biology, Albuquerque, NM, USA
| | | | - Candice K. Emmons
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - Stephan Emmrich
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Ebru Erbay
- Altos Labs, Bay Area Institute of Science, Redwood City, CA, USA
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | | | - Chris G. Faulkes
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Zhe Fei
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA
- Department of Statistics, University of California, Riverside, CA, USA
| | - Steven H. Ferguson
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
- Fisheries and Oceans Canada, Winnipeg, Manitoba, Canada
| | - Carrie J. Finno
- Department of Population Health and Reproduction, University of California, Davis School of Veterinary Medicine, Davis, CA, USA
| | | | - Jean-Michel Gaillard
- University of Lyon, CNRS, Laboratoire de Biometrie et Biologie Evolutive, Villeurbanne, France
| | - Eva Garde
- Greenland Institute of Natural Resources, Nuuk, Greenland
| | - Livia Gerber
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
- Australian National Wildlife Collection, CSIRO, Canberra, Australia
| | - Vadim N. Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Rodolfo G. Goya
- Biochemistry Research Institute of La Plata, Histology and Pathology, School of Medicine, University of La Plata, La Plata, Argentina
| | - Matthew J Grant
- Applied Translational Genetics Group, School of Biological Sciences, Centre for Brain Research, The University of Auckland, Auckland, New Zealand
| | - Carla B. Green
- Department of Neuroscience, Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - M. Bradley Hanson
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - Daniel W. Hart
- Department of Zoology and Entomology, University of Pretoria, Hatfield, South Africa
| | | | | | - Andrew N. Hogan
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Carolyn J. Hogg
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Timothy A. Hore
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Taosheng Huang
- Division of Human Genetics, Department of Pediatrics, University at Buffalo, Buffalo, NY, USA
| | | | - Anna J. Jasinska
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Gareth Jones
- School of Biological Sciences, University of Bristol, Bristol, UK
| | | | - Olga Kashpur
- Mother Infant Research Institute, Tufts Medical Center, Boston, MA, USA
| | | | | | - Vimala Kaza
- Peromyscus Genetic Stock Center, University of South Carolina, Columbia, SC, USA
| | - Hippokratis Kiaris
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - Michael S. Kobor
- Edwin S. H. Leong Healthy Aging Program, Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Pawel Kordowitzki
- Institute of Veterinary Medicine, Nicolaus Copernicus University, Torun, Poland
| | | | - Michael Krützen
- Evolutionary Genetics Group, Department of Anthropology, University of Zurich, Zurich, Switzerland
| | - Soo Bin Kwon
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Brenda Larison
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, USA
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA, USA
| | - Sang-Goo Lee
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Marianne Lehmann
- Biochemistry Research Institute of La Plata, Histology and Pathology, School of Medicine, University of La Plata, La Plata, Argentina
| | - Jean-François Lemaître
- University of Lyon, CNRS, Laboratoire de Biometrie et Biologie Evolutive, Villeurbanne, France
| | - Andrew J. Levine
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Xinmin Li
- Technology Center for Genomics and Bioinformatics, Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Cun Li
- Texas Pregnancy and Life-course Health Center, Southwest National Primate Research Center, San Antonio, TX, USA
- Department of Animal Science, College of Agriculture and Natural Resources, Laramie, WY, USA
| | - Andrea R. Lim
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - David T. S. Lin
- Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | | | | | - Thomas J. Little
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | | | | | - Julie A. Mattison
- Translational Gerontology Branch, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | | | - June Mergl
- Marineland of Canada, Niagara Falls, Ontario, Canada
| | - Jennifer J. Meudt
- Biomedical and Genomic Research Group, Department of Animal and Dairy Sciences, University of Wisconsin Madison, Madison, WI, USA
| | - Gisele A. Montano
- Zoological Operations, SeaWorld Parks and Entertainment, Orlando, FL, USA
| | - Khyobeni Mozhui
- Department of Preventive Medicine, University of Tennessee Health Science Center, College of Medicine, Memphis, TN, USA
| | - Jason Munshi-South
- Louis Calder Center - Biological Field Station, Department of Biological Sciences, Fordham University, Armonk, NY, USA
| | - William J. Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, TX, USA
| | - Asieh Naderi
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - Martina Nagy
- Museum fur Naturkunde, Leibniz-Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Pritika Narayan
- Applied Translational Genetics Group, School of Biological Sciences, Centre for Brain Research, The University of Auckland, Auckland, New Zealand
| | - Peter W. Nathanielsz
- Texas Pregnancy and Life-course Health Center, Southwest National Primate Research Center, San Antonio, TX, USA
- Department of Animal Science, College of Agriculture and Natural Resources, Laramie, WY, USA
| | - Ngoc B. Nguyen
- Division of Cardiology, Department of Internal Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Christof Niehrs
- Institute of Molecular Biology (IMB), Mainz, Germany
- Division of Molecular Embryology, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | | | - Justine K. O’Brien
- Taronga Institute of Science and Learning, Taronga Conservation Society Australia, Mosman, New South Wales, Australia
| | | | - Duncan T Odom
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Deutsches Krebsforschungszentrum, Division of Regulatory Genomics and Cancer Evolution, Heidelberg, Germany
| | | | | | - Elaine A. Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kim M. Parsons
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - Kimberly C. Paul
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Amy B. Pedersen
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Matteo Pellegrini
- Department Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Katharina J. Peters
- Evolutionary Genetics Group, Department of Anthropology, University of Zurich, Zurich, Switzerland
- School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia
| | | | - Darren W. Pietersen
- Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Hatfield, South Africa
| | - Gabriela M. Pinho
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Jocelyn Plassais
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jesse R. Poganik
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Natalia A. Prado
- Department of Biology, College of Arts and Science, Adelphi University, Garden City, NY, USA
- Center for Species Survival, Smithsonian Conservation Biology Institute, Front Royal, VA, USA
| | - Pradeep Reddy
- Altos Labs, San Diego, CA, USA
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Benjamin Rey
- University of Lyon, CNRS, Laboratoire de Biometrie et Biologie Evolutive, Villeurbanne, France
| | - Beate R. Ritz
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA, USA
- Department of Environmental Health Sciences, UCLA Fielding School of Public Health, Los Angeles, CA, USA
| | | | | | | | - Elena Rydkina
- Department of Biology, University of Rochester, Rochester, NY, USA
| | | | - Adam B. Salmon
- The Sam and Ann Barshop Institute for Longevity and Aging Studies and Department of Molecular Medicine, UT Health San Antonio, and the Geriatric Research Education and Clinical Center, South Texas Veterans Healthcare System, San Antonio, TX, USA
| | | | - Kyle M. Schachtschneider
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, USA
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Dennis Schmitt
- College of Agriculture, Missouri State University, Springfield, MO, USA
| | | | | | - Lawrence B. Schook
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, USA
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Karen E. Sears
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, USA
| | | | - Aaron B.A. Shafer
- Department of Forensic Science, Environmental & Life Sciences, Trent University, Peterborough, Ontario, Canada
| | - Anastasia V. Shindyapina
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Kavita Singh
- Shobhaben Pratapbhai Patel School of Pharmacy & Technology Management, SVKM’S NMIMS University, Mumbai, India
| | - Ishani Sinha
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Jesse Slone
- Division of Human Genetics, Department of Pediatrics, University at Buffalo, Buffalo, NY, USA
| | - Russel G. Snell
- Applied Translational Genetics Group, School of Biological Sciences, Centre for Brain Research, The University of Auckland, Auckland, New Zealand
| | - Elham Soltanmohammadi
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | | | | | | | | | - Karen J. Steinman
- Species Preservation Laboratory, SeaWorld San Diego, San Diego, CA, USA
| | - Donald T Stewart
- Biology Department, Acadia University, Wolfville, Nova Scotia, Canada
| | | | - Balazs Szladovits
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, UK
| | - Joseph S. Takahashi
- Department of Neuroscience, Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Masaki Takasugi
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Emma C. Teeling
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin, Ireland
| | - Michael J. Thompson
- Department Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Bill Van Bonn
- Animal Care and Science Division, John G. Shedd Aquarium, Chicago, IL, USA
| | - Sonja C. Vernes
- School of Biology, The University of St. Andrews, Fife, UK
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, Netherlands
| | - Diego Villar
- Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Harry V. Vinters
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Ha Vu
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Nan Wang
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | | | - Robert W. Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, College of Medicine, Memphis, TN, USA
| | - Qi Yan
- Altos Labs, San Diego, CA, USA
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA
| | - Mingjia Yao
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA
| | | | - Bohan Zhang
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Zhihui Zhang
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Yang Zhao
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Peng Zhao
- Division of Cardiology, Department of Internal Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA
| | - Wanding Zhou
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Joseph A. Zoller
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA
| | - Jason Ernst
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Andrei Seluanov
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - Vera Gorbunova
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - X. William Yang
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | | | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Altos Labs, San Diego, CA, USA
- Altos Labs, Cambridge, UK
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5
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Batcher K, Varney S, Raudsepp T, Jevit M, Dickinson P, Jagannathan V, Leeb T, Bannasch D. Ancient segmentally duplicated LCORL retrocopies in equids. PLoS One 2023; 18:e0286861. [PMID: 37289743 PMCID: PMC10249811 DOI: 10.1371/journal.pone.0286861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 05/25/2023] [Indexed: 06/10/2023] Open
Abstract
LINE-1 is an active transposable element encoding proteins capable of inserting host gene retrocopies, resulting in retro-copy number variants (retroCNVs) between individuals. Here, we performed retroCNV discovery using 86 equids and identified 437 retrocopy insertions. Only 5 retroCNVs were shared between horses and other equids, indicating that the majority of retroCNVs inserted after the species diverged. A large number (17-35 copies) of segmentally duplicated Ligand Dependent Nuclear Receptor Corepressor Like (LCORL) retrocopies were present in all equids but absent from other extant perissodactyls. The majority of LCORL transcripts in horses and donkeys originate from the retrocopies. The initial LCORL retrotransposition occurred 18 million years ago (17-19 95% CI), which is coincident with the increase in body size, reduction in digit number, and changes in dentition that characterized equid evolution. Evolutionary conservation of the LCORL retrocopy segmental amplification in the Equidae family, high expression levels and the ancient timeline for LCORL retrotransposition support a functional role for this structural variant.
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Affiliation(s)
- Kevin Batcher
- Department of Population Health and Reproduction, University of California Davis, Davis, CA, United States of America
| | - Scarlett Varney
- Department of Population Health and Reproduction, University of California Davis, Davis, CA, United States of America
| | - Terje Raudsepp
- Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Matthew Jevit
- Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Peter Dickinson
- Department of Surgical and Radiological Sciences, University of California Davis, Davis, CA, United States of America
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Danika Bannasch
- Department of Population Health and Reproduction, University of California Davis, Davis, CA, United States of America
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6
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Peng S, Dahlgren AR, Donnelly CG, Hales EN, Petersen JL, Bellone RR, Kalbfleisch T, Finno CJ. Functional annotation of the animal genomes: An integrated annotation resource for the horse. PLoS Genet 2023; 19:e1010468. [PMID: 36862752 PMCID: PMC10013926 DOI: 10.1371/journal.pgen.1010468] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 03/14/2023] [Accepted: 01/28/2023] [Indexed: 03/03/2023] Open
Abstract
The genomic sequence of the horse has been available since 2009, providing critical resources for discovering important genomic variants regarding both animal health and population structures. However, to fully understand the functional implications of these variants, detailed annotation of the horse genome is required. Due to the limited availability of functional data for the equine genome, as well as the technical limitations of short-read RNA-seq, existing annotation of the equine genome contains limited information about important aspects of gene regulation, such as alternate isoforms and regulatory elements, which are either not transcribed or transcribed at a very low level. To solve above problems, the Functional Annotation of the Animal Genomes (FAANG) project proposed a systemic approach to tissue collection, phenotyping, and data generation, adopting the blueprint laid out by the Encyclopedia of DNA Elements (ENCODE) project. Here we detail the first comprehensive overview of gene expression and regulation in the horse, presenting 39,625 novel transcripts, 84,613 candidate cis-regulatory elements (CRE) and their target genes, 332,115 open chromatin regions genome wide across a diverse set of tissues. We showed substantial concordance between chromatin accessibility, chromatin states in different genic features and gene expression. This comprehensive and expanded set of genomics resources will provide the equine research community ample opportunities for studies of complex traits in the horse.
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Affiliation(s)
- Sichong Peng
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America
| | - Anna R. Dahlgren
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America
| | - Callum G. Donnelly
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America
| | - Erin N. Hales
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America
| | - Jessica L. Petersen
- Department of Animal Science, University of Nebraska—Lincoln, Lincoln, Nebraska, United States of America
| | - Rebecca R. Bellone
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America
| | - Ted Kalbfleisch
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, United States of America
| | - Carrie J. Finno
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America
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7
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Peng S, Magdesian KG, Dowd J, Blea J, Carpenter R, Ho W, Finno CJ. Investigation of high gamma-glutamyltransferase syndrome in California Thoroughbred racehorses. J Vet Intern Med 2022; 36:2203-2212. [PMID: 36377652 PMCID: PMC9708438 DOI: 10.1111/jvim.16582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 10/21/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Increases in serum gamma-glutamyltransferase (GGT) activity have been reported in Thoroughbred (TB) racehorses and associated with maladaptation to training but the underlying etiology remains unknown. HYPOTHESIS/OBJECTIVES Classify the etiology of high GGT syndrome in racing TBs by assessment of pancreatic enzymes, vitamin E concentrations, and both a candidate gene and whole genome association study. We hypothesized that a genetic variant resulting in antioxidant insufficiency or pancreatic dysfunction would be responsible for high GGT syndrome in TBs. ANIMALS A total of 138 California racing TBs. Amylase: n = 31 affected (serum GGT activity ≥60 IU/L), n = 52 control (serum GGT activity <40 IU/L). Lipase: n = 19 affected, n = 35 control. Serum α-tocopherol concentrations: n = 32 affected, n = 46 control. Genome-wide association study (GWAS): 36 affected, 58 control. Whole genome sequencing: n = 5 affected, n = 5 control. METHODS Biochemical and vitamin analytes were compared among cohorts. A GWAS was performed and a subset of TBs underwent whole genome sequencing to interrogate candidate genes and positional genetic regions. RESULTS Serum lipase and amylase activity and α-tocopherol concentrations did not differ between groups. No genetic variants were identified in 2 candidate genes (UGT1A1 and GGT1) that associated with the phenotype. Four single nucleotide polymorphisms (SNPs) approached a suggestive association with the phenotype (P = 2.15 × 10-5 ), defining a 100 kb region on chromosome 5 surrounding cluster of differentiation 1a (CD1A1), a transmembrane gene related to the major histocompatibility complex. CONCLUSIONS AND CLINICAL IMPORTANCE An underlying genetic etiology may exist for high GGT syndrome in racing TBs, similar to genetic disorders in humans.
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Affiliation(s)
- Sichong Peng
- Department of Population Health and ReproductionUniversity of CaliforniaDavisCaliforniaUSA
| | - K. Gary Magdesian
- Department of Medicine and EpidemiologySchool of Veterinary Medicine, University of CaliforniaDavisCaliforniaUSA
| | - Joseph Dowd
- Equine Medical and Surgical GroupArcadiaCaliforniaUSA
| | - Jeffrey Blea
- Von Bleucher, Blea, Hunkin, DVM, IncSierra MadreCaliforniaUSA
| | | | - Wayne Ho
- Southern California Equine FoundationArcadiaCaliforniaUSA
| | - Carrie J. Finno
- Department of Population Health and ReproductionUniversity of CaliforniaDavisCaliforniaUSA
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8
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Kingsley NB, Sandmeyer L, Bellone RR. A review of investigated risk factors for developing equine recurrent uveitis. Vet Ophthalmol 2022; 26:86-100. [PMID: 35691017 DOI: 10.1111/vop.13002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/25/2022] [Accepted: 05/27/2022] [Indexed: 12/01/2022]
Abstract
Equine recurrent uveitis (ERU) is an ocular inflammatory disease that can be difficult to manage clinically. As such, it is the leading cause of bilateral blindness for horses. ERU is suspected to have a complex autoimmune etiology with both environmental and genetic risk factors contributing to onset and disease progression in some or all cases. Work in recent years has aimed at unraveling the primary triggers, such as infectious agents and inherited breed-specific risk factors, for disease onset, persistence, and progression. This review has aimed at encompassing those factors that have been associated, implicated, or substantiated as contributors to ERU, as well as identifying areas for which additional knowledge is needed to better understand risk for disease onset and progression. A greater understanding of the risk factors for ERU will enable earlier detection and better prognosis through prevention and new therapeutics.
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Affiliation(s)
- Nicole B Kingsley
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California - Davis, Davis, California, USA.,Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, California, USA
| | - Lynne Sandmeyer
- Department of Small Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Rebecca R Bellone
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California - Davis, Davis, California, USA.,Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, California, USA
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9
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Gurgul A, Szmatoła T, Ocłoń E, Jasielczuk I, Semik-Gurgul E, Finno CJ, Petersen JL, Bellone R, Hales EN, Ząbek T, Arent Z, Kotula-Balak M, Bugno-Poniewierska M. Another lesson from unmapped reads: in-depth analysis of RNA-Seq reads from various horse tissues. J Appl Genet 2022; 63:571-581. [PMID: 35670911 DOI: 10.1007/s13353-022-00705-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 04/27/2022] [Accepted: 05/31/2022] [Indexed: 11/25/2022]
Abstract
In recent years, a vast amount of sequencing data has been generated and large improvements have been made to reference genome sequences. Despite these advances, significant portions of reads still do not map to reference genomes and these reads have been considered as junk or artificial sequences. Recent studies have shown that these reads can be useful, e.g., for refining reference genomes or detecting contaminating microorganisms present in the analyzed biological samples. A special case of this is RNA sequencing (RNA-Seq) reads that come from tissue transcriptomes. Unmapped reads from RNA-Seq have received much less attention than those from whole-genome sequencing. In particular, in the horse, an analysis of unmapped RNA reads has not been performed yet. Thus, in this study, we analyzed the unmapped reads originating from the RNA-Seq performed through the Functional Annotation of Animal Genomes (FAANG) project in the horse, using eight different tissues from two mares. We demonstrated that unmapped reads from RNA-Seq could be easily assembled into transcripts relating to many important genes present in the sequences of other mammals. Large portions of these transcripts did not have coding potential and, thus, can be considered as non-coding RNA. Moreover, reads that were not mapped to the reference genome but aligned to the entries in NCBI database of horse proteins were enriched for biological processes that largely correspond to the functions of organ from which RNA was isolated and thus are presumably true transcripts of genes associated with cell metabolism in those tissues. In addition, a portion of reads aligned to the common pathogenic or neutral microbiota, of which the most common was Brucella spp. These data suggest that unmapped reads can be an important target for in-depth analysis that may substantially enrich results of initial RNA-Seq experiments for various tissues and organs.
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Affiliation(s)
- Artur Gurgul
- Center for Experimental and Innovative Medicine, University of Agriculture in Krakow, Rędzina 1c, 30-248, Kraków, Poland.
| | - Tomasz Szmatoła
- Center for Experimental and Innovative Medicine, University of Agriculture in Krakow, Rędzina 1c, 30-248, Kraków, Poland
| | - Ewa Ocłoń
- Center for Experimental and Innovative Medicine, University of Agriculture in Krakow, Rędzina 1c, 30-248, Kraków, Poland
| | - Igor Jasielczuk
- Center for Experimental and Innovative Medicine, University of Agriculture in Krakow, Rędzina 1c, 30-248, Kraków, Poland
| | - Ewelina Semik-Gurgul
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland
| | - Carrie J Finno
- Department of Population Health and Reproduction, University of California Davis School of Veterinary Medicine, Davis, CA, USA
| | - Jessica L Petersen
- Department of Animal Science, University of Nebraska Lincoln, Lincoln, NB, USA
| | - Rebecca Bellone
- Department of Population Health and Reproduction, University of California Davis School of Veterinary Medicine, Davis, CA, USA
- Veterinary Genetics Laboratory, University of California Davis School of Veterinary Medicine, Davis, CA, USA
| | - Erin N Hales
- Department of Population Health and Reproduction, University of California Davis School of Veterinary Medicine, Davis, CA, USA
| | - Tomasz Ząbek
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland
| | - Zbigniew Arent
- Center for Experimental and Innovative Medicine, University of Agriculture in Krakow, Rędzina 1c, 30-248, Kraków, Poland
| | - Małgorzata Kotula-Balak
- University Centre of Veterinary Medicine, University of Agriculture in Krakow, Mickiewicza 24/28, 30-059, Krakow, Poland
| | - Monika Bugno-Poniewierska
- Department of Animal Reproduction, Anatomy and Genomics, University of Agriculture in Kraków, al. Mickiewicza 24/28, 30-059, Kraków, Poland
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10
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Wang Z, Chivu AG, Choate LA, Rice EJ, Miller DC, Chu T, Chou SP, Kingsley NB, Petersen JL, Finno CJ, Bellone RR, Antczak DF, Lis JT, Danko CG. Prediction of histone post-translational modification patterns based on nascent transcription data. Nat Genet 2022; 54:295-305. [PMID: 35273399 PMCID: PMC9444190 DOI: 10.1038/s41588-022-01026-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 01/24/2022] [Indexed: 01/01/2023]
Abstract
The role of histone modifications in transcription remains incompletely understood. Here, we examine the relationship between histone modifications and transcription using experimental perturbations combined with sensitive machine-learning tools. Transcription predicted the variation in active histone marks and complex chromatin states, like bivalent promoters, down to single-nucleosome resolution and at an accuracy that rivaled the correspondence between independent ChIP-seq experiments. Blocking transcription rapidly removed two punctate marks, H3K4me3 and H3K27ac, from chromatin indicating that transcription is required for active histone modifications. Transcription was also required for maintenance of H3K27me3, consistent with a role for RNA in recruiting PRC2. A subset of DNase-I-hypersensitive sites were refractory to prediction, precluding models where transcription initiates pervasively at any open chromatin. Our results, in combination with past literature, support a model in which active histone modifications serve a supportive, rather than an essential regulatory, role in transcription.
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Affiliation(s)
- Zhong Wang
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
- School of Software Technology, Dalian University of Technology, Dalian, China
| | - Alexandra G Chivu
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Lauren A Choate
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Edward J Rice
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Donald C Miller
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Tinyi Chu
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Shao-Pei Chou
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Nicole B Kingsley
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Jessica L Petersen
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Carrie J Finno
- Department of Population Health and Reproduction, University of California, Davis, Davis, CA, USA
| | - Rebecca R Bellone
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Douglas F Antczak
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Charles G Danko
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
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11
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Horvath S, Haghani A, Peng S, Hales EN, Zoller JA, Raj K, Larison B, Robeck TR, Petersen JL, Bellone RR, Finno CJ. DNA methylation aging and transcriptomic studies in horses. Nat Commun 2022; 13:40. [PMID: 35013267 PMCID: PMC8748428 DOI: 10.1038/s41467-021-27754-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 12/07/2021] [Indexed: 12/28/2022] Open
Abstract
Cytosine methylation patterns have not yet been thoroughly studied in horses. Here, we profile n = 333 samples from 42 horse tissue types at loci that are highly conserved between mammalian species using a custom array (HorvathMammalMethylChip40). Using the blood and liver tissues from horses, we develop five epigenetic aging clocks: a multi-tissue clock, a blood clock, a liver clock and two dual-species clocks that apply to both horses and humans. In addition, using blood methylation data from three additional equid species (plains zebra, Grevy's zebras and Somali asses), we develop another clock that applies across all equid species. Castration does not significantly impact the epigenetic aging rate of blood or liver samples from horses. Methylation and RNA data from the same tissues define the relationship between methylation and RNA expression across horse tissues. We expect that the multi-tissue atlas will become a valuable resource.
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Affiliation(s)
- Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Amin Haghani
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Sichong Peng
- Department of Population Health and Reproduction, University of California, Davis School of Veterinary Medicine, Davis, CA, USA
| | - Erin N Hales
- Department of Population Health and Reproduction, University of California, Davis School of Veterinary Medicine, Davis, CA, USA
| | - Joseph A Zoller
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ken Raj
- Radiation Effects Department, Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton, Didcot, UK
| | - Brenda Larison
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, USA
| | - Todd R Robeck
- Zoological Operations, SeaWorld Parks and Entertainment, 7007 SeaWorld Drive, Orlando, FL, USA
| | | | - Rebecca R Bellone
- Department of Population Health and Reproduction, University of California, Davis School of Veterinary Medicine, Davis, CA, USA
- Veterinary Genetics Laboratory, University of California, Davis School of Veterinary Medicine, Davis, CA, USA
| | - Carrie J Finno
- Department of Population Health and Reproduction, University of California, Davis School of Veterinary Medicine, Davis, CA, USA.
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12
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Abstract
Thoroughbred horses have been selected for racing performance for more than 400 years. Despite continued selection, race times have not improved significantly during the past 60 years, raising the question of whether genetic variation for racing performance still exists. Studies using phenotypes such as race time, money earned, and handicapping, however, demonstrate that there is extensive variation within these traits and that they are heritable. Even so, these are poor measures of racing success since Thoroughbreds race at different ages and distances and on different types of tracks, and some may not race at all. With the advent of genomic tools, DNA variants are being identified that contribute to racing success. Aside from strong associations for myostatin variants with best racing distance, weak to modest associations with racing phenotypes are reported for other genomic regions. These data suggest that diverse genetic strategies have contributed to producing a successful racehorse, and genetic variation contributing to athleticism remains important. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 10 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Ernest Bailey
- MH Gluck Equine Research Center, University of Kentucky, Lexington, Kentucky, USA; ,
| | - Jessica L Petersen
- Department of Animal Science, University of Nebraska, Lincoln, Nebraska, USA;
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13
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Peng S, Petersen JL, Bellone RR, Kalbfleisch T, Kingsley NB, Barber AM, Cappelletti E, Giulotto E, Finno CJ. Decoding the Equine Genome: Lessons from ENCODE. Genes (Basel) 2021; 12:genes12111707. [PMID: 34828313 PMCID: PMC8625040 DOI: 10.3390/genes12111707] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/24/2021] [Accepted: 10/26/2021] [Indexed: 12/23/2022] Open
Abstract
The horse reference genome assemblies, EquCab2.0 and EquCab3.0, have enabled great advancements in the equine genomics field, from tools to novel discoveries. However, significant gaps of knowledge regarding genome function remain, hindering the study of complex traits in horses. In an effort to address these gaps and with inspiration from the Encyclopedia of DNA Elements (ENCODE) project, the equine Functional Annotation of Animal Genome (FAANG) initiative was proposed to bridge the gap between genome and gene expression, providing further insights into functional regulation within the horse genome. Three years after launching the initiative, the equine FAANG group has generated data from more than 400 experiments using over 50 tissues, targeting a variety of regulatory features of the equine genome. In this review, we examine how valuable lessons learned from the ENCODE project informed our decisions in the equine FAANG project. We report the current state of the equine FAANG project and discuss how FAANG can serve as a template for future expansion of functional annotation in the equine genome and be used as a reference for studies of complex traits in horse. A well-annotated reference functional atlas will also help advance equine genetics in the pan-genome and precision medicine era.
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Affiliation(s)
- Sichong Peng
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA; (S.P.); (R.R.B.); (N.B.K.)
| | - Jessica L. Petersen
- Department of Animal Science, University of Nebraska, Lincoln, NE 68583-0908, USA; (J.L.P.); (A.M.B.)
| | - Rebecca R. Bellone
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA; (S.P.); (R.R.B.); (N.B.K.)
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Ted Kalbfleisch
- Department of Veterinary Science, Gluck Equine Research Center, University of Kentucky, Lexington, KY 40503, USA;
| | - N. B. Kingsley
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA; (S.P.); (R.R.B.); (N.B.K.)
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Alexa M. Barber
- Department of Animal Science, University of Nebraska, Lincoln, NE 68583-0908, USA; (J.L.P.); (A.M.B.)
| | - Eleonora Cappelletti
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (E.C.); (E.G.)
| | - Elena Giulotto
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (E.C.); (E.G.)
| | - Carrie J. Finno
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA; (S.P.); (R.R.B.); (N.B.K.)
- Correspondence:
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14
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Pan Z, Yao Y, Yin H, Cai Z, Wang Y, Bai L, Kern C, Halstead M, Chanthavixay G, Trakooljul N, Wimmers K, Sahana G, Su G, Lund MS, Fredholm M, Karlskov-Mortensen P, Ernst CW, Ross P, Tuggle CK, Fang L, Zhou H. Pig genome functional annotation enhances the biological interpretation of complex traits and human disease. Nat Commun 2021; 12:5848. [PMID: 34615879 PMCID: PMC8494738 DOI: 10.1038/s41467-021-26153-7] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 09/20/2021] [Indexed: 02/08/2023] Open
Abstract
The functional annotation of livestock genomes is crucial for understanding the molecular mechanisms that underpin complex traits of economic importance, adaptive evolution and comparative genomics. Here, we provide the most comprehensive catalogue to date of regulatory elements in the pig (Sus scrofa) by integrating 223 epigenomic and transcriptomic data sets, representing 14 biologically important tissues. We systematically describe the dynamic epigenetic landscape across tissues by functionally annotating 15 different chromatin states and defining their tissue-specific regulatory activities. We demonstrate that genomic variants associated with complex traits and adaptive evolution in pig are significantly enriched in active promoters and enhancers. Furthermore, we reveal distinct tissue-specific regulatory selection between Asian and European pig domestication processes. Compared with human and mouse epigenomes, we show that porcine regulatory elements are more conserved in DNA sequence, under both rapid and slow evolution, than those under neutral evolution across pig, mouse, and human. Finally, we provide biological insights on tissue-specific regulatory conservation, and by integrating 47 human genome-wide association studies, we demonstrate that, depending on the traits, mouse or pig might be more appropriate biomedical models for different complex traits and diseases.
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Affiliation(s)
- Zhangyuan Pan
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - Yuelin Yao
- MRC Human Genetics Unit at the Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Hongwei Yin
- Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China
| | - Zexi Cai
- Center for Quantitative Genetics and Genomics, Faculty of Technical Sciences, Aarhus University, Tjele, 8300, Denmark
| | - Ying Wang
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - Lijing Bai
- Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China
| | - Colin Kern
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - Michelle Halstead
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - Ganrea Chanthavixay
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | | | - Klaus Wimmers
- Leibniz-Institute for Farm Animal Biology, Dummerstorf, Germany
| | - Goutam Sahana
- Center for Quantitative Genetics and Genomics, Faculty of Technical Sciences, Aarhus University, Tjele, 8300, Denmark
| | - Guosheng Su
- Center for Quantitative Genetics and Genomics, Faculty of Technical Sciences, Aarhus University, Tjele, 8300, Denmark
| | - Mogens Sandø Lund
- Center for Quantitative Genetics and Genomics, Faculty of Technical Sciences, Aarhus University, Tjele, 8300, Denmark
| | - Merete Fredholm
- Animal Genetics, Bioinformatics and Breeding, Department of Veterinary and Animal Sciences, University of Copenhagen, Frederikgsberg C, 1870, Denmark
| | - Peter Karlskov-Mortensen
- Animal Genetics, Bioinformatics and Breeding, Department of Veterinary and Animal Sciences, University of Copenhagen, Frederikgsberg C, 1870, Denmark
| | - Catherine W Ernst
- Department of Animal Science, Michigan State University, East Lansing, MI, USA
| | - Pablo Ross
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | | | - Lingzhao Fang
- MRC Human Genetics Unit at the Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, EH4 2XU, UK.
| | - Huaijun Zhou
- Department of Animal Science, University of California, Davis, Davis, CA, USA.
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15
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Peng S, Bellone R, Petersen JL, Kalbfleisch TS, Finno CJ. Successful ATAC-Seq From Snap-Frozen Equine Tissues. Front Genet 2021; 12:641788. [PMID: 34220931 PMCID: PMC8242358 DOI: 10.3389/fgene.2021.641788] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 05/21/2021] [Indexed: 11/20/2022] Open
Abstract
An assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) has become an increasingly popular method to assess genome-wide chromatin accessibility in isolated nuclei from fresh tissues. However, many biobanks contain only snap-frozen tissue samples. While ATAC-seq has been applied to frozen brain tissues in human, its applicability in a wide variety of tissues in horse remains unclear. The Functional Annotation of Animal Genome (FAANG) project is an international collaboration aimed to provide high quality functional annotation of animal genomes. The equine FAANG initiative has generated a biobank of over 80 tissues from two reference female animals and experiments to begin to characterize tissue specificity of genome function for prioritized tissues have been performed. Due to the logistics of tissue collection and storage, extracting nuclei from a large number of tissues for ATAC-seq at the time of collection is not always practical. To assess the feasibility of using stored frozen tissues for ATAC-seq and to provide a guideline for the equine FAANG project, we compared ATAC-seq results from nuclei isolated from frozen tissue to cryopreserved nuclei (CN) isolated at the time of tissue harvest in liver, a highly cellular homogenous tissue, and lamina, a relatively acellular tissue unique to the horse. We identified 20,000-33,000 accessible chromatin regions in lamina and 22-61,000 in liver, with consistently more peaks identified using CN isolated at time of tissue collection. Our results suggest that frozen tissues are an acceptable substitute when CN are not available. For more challenging tissues such as lamina, nuclei extraction at the time of tissue collection is still preferred for optimal results. Therefore, tissue type and accessibility to intact nuclei should be considered when designing ATAC-seq experiments.
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Affiliation(s)
- Sichong Peng
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Rebecca Bellone
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Jessica L. Petersen
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Theodore S. Kalbfleisch
- Department of Veterinary Science, Gluck Equine Research Center, University of Kentucky, Lexington, KY, United States
| | - Carrie J. Finno
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
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16
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Kingsley NB, Hamilton NA, Lindgren G, Orlando L, Bailey E, Brooks S, McCue M, Kalbfleisch TS, MacLeod JN, Petersen JL, Finno CJ, Bellone RR. "Adopt-a-Tissue" Initiative Advances Efforts to Identify Tissue-Specific Histone Marks in the Mare. Front Genet 2021; 12:649959. [PMID: 33841506 PMCID: PMC8033197 DOI: 10.3389/fgene.2021.649959] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/01/2021] [Indexed: 12/13/2022] Open
Affiliation(s)
- N B Kingsley
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States.,Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Natasha A Hamilton
- Faculty of Science, School of Life and Environmental Science, University of Sydney, Camperdown, NSW, Australia
| | - Gabriella Lindgren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Livestock Genetics, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Ludovic Orlando
- Centre d'Anthropobiologie et Génomique de Toulouse (CAGT), Faculté de Médecine Purpan, Université Toulouse III-Paul Sabatier, Toulouse, France
| | - Ernie Bailey
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY, United States
| | - Samantha Brooks
- Department of Animal Sciences, University of Florida, Gainesville, FL, United States
| | - Molly McCue
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, United States
| | - T S Kalbfleisch
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY, United States
| | - James N MacLeod
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY, United States
| | - Jessica L Petersen
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Carrie J Finno
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Rebecca R Bellone
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States.,Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
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17
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Kern C, Wang Y, Xu X, Pan Z, Halstead M, Chanthavixay G, Saelao P, Waters S, Xiang R, Chamberlain A, Korf I, Delany ME, Cheng HH, Medrano JF, Van Eenennaam AL, Tuggle CK, Ernst C, Flicek P, Quon G, Ross P, Zhou H. Functional annotations of three domestic animal genomes provide vital resources for comparative and agricultural research. Nat Commun 2021; 12:1821. [PMID: 33758196 PMCID: PMC7988148 DOI: 10.1038/s41467-021-22100-8] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 03/01/2021] [Indexed: 01/31/2023] Open
Abstract
Gene regulatory elements are central drivers of phenotypic variation and thus of critical importance towards understanding the genetics of complex traits. The Functional Annotation of Animal Genomes consortium was formed to collaboratively annotate the functional elements in animal genomes, starting with domesticated animals. Here we present an expansive collection of datasets from eight diverse tissues in three important agricultural species: chicken (Gallus gallus), pig (Sus scrofa), and cattle (Bos taurus). Comparative analysis of these datasets and those from the human and mouse Encyclopedia of DNA Elements projects reveal that a core set of regulatory elements are functionally conserved independent of divergence between species, and that tissue-specific transcription factor occupancy at regulatory elements and their predicted target genes are also conserved. These datasets represent a unique opportunity for the emerging field of comparative epigenomics, as well as the agricultural research community, including species that are globally important food resources.
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Affiliation(s)
- Colin Kern
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - Ying Wang
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - Xiaoqin Xu
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - Zhangyuan Pan
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - Michelle Halstead
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - Ganrea Chanthavixay
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - Perot Saelao
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - Susan Waters
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - Ruidong Xiang
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, VIC, Australia
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Amanda Chamberlain
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Ian Korf
- Genome Center, University of California, Davis, Davis, CA, USA
| | - Mary E Delany
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - Hans H Cheng
- USDA-ARS, Avian Disease and Oncology Laboratory, East Lansing, MI, USA
| | - Juan F Medrano
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | | | - Chris K Tuggle
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | - Catherine Ernst
- Department of Animal Science, Michigan State University, East Lansing, MI, USA
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Gerald Quon
- Department of Molecular and Cellular Biology, University of California, David, Davis, CA, USA
| | - Pablo Ross
- Department of Animal Science, University of California, Davis, Davis, CA, USA.
| | - Huaijun Zhou
- Department of Animal Science, University of California, Davis, Davis, CA, USA.
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18
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Donnelly CG, Bellone RR, Hales EN, Nguyen A, Katzman SA, Dujovne GA, Knickelbein KE, Avila F, Kalbfleisch TS, Giulotto E, Kingsley NB, Tanaka J, Esdaile E, Peng S, Dahlgren A, Fuller A, Mienaltowski MJ, Raudsepp T, Affolter VK, Petersen JL, Finno CJ. Generation of a Biobank From Two Adult Thoroughbred Stallions for the Functional Annotation of Animal Genomes Initiative. Front Genet 2021; 12:650305. [PMID: 33763124 PMCID: PMC7982670 DOI: 10.3389/fgene.2021.650305] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 02/15/2021] [Indexed: 12/27/2022] Open
Abstract
Following the successful creation of a biobank from two adult Thoroughbred mares, this study aimed to recapitulate sample collection in two adult Thoroughbred stallions as part of the Functional Annotation of the Animal Genome (FAANG) initiative. Both stallions underwent thorough physical, lameness, neurologic, and ophthalmic (including electroretinography) examinations prior to humane euthanasia. Epididymal sperm was recovered from both stallions immediately postmortem and cryopreserved. Aseptically collected full thickness skin biopsies were used to isolate, culture and cryopreserve dermal fibroblasts. Serum, plasma, cerebrospinal fluid, urine, and gastrointestinal content from various locations were collected and cryopreserved. Under guidance of a board-certified veterinary anatomic pathologist, 102 representative tissue samples were collected from both horses. Whole tissue samples were flash-frozen and prioritized tissues had nuclei isolated and cryopreserved. Spatially contemporaneous samples of each tissue were submitted for histologic examination. Antemortem and gross pathologic examination revealed mild abnormalities in both stallions. One stallion (ECA_UCD_AH3) had unilateral thoracic limb lameness and bilateral chorioretinal scars. The second stallion (ECA_UCD_AH4) had subtle symmetrical pelvic limb ataxia, symmetrical prostatomegally, and moderate gastrointestinal nematodiasis. DNA from each was whole-genome sequenced and genotyped using the GGP Equine 70K SNP array. The genomic resources and banked biological samples from these animals augments the existing resource available to the equine genomics community. Importantly we may now improve the resolution of tissue-specific gene regulation as affected by sex, as well as add sex-specific tissues and gametes.
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Affiliation(s)
- Callum G Donnelly
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Rebecca R Bellone
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States.,Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Erin N Hales
- Morris Animal Foundation, Denver, CO, United States
| | - Annee Nguyen
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Scott A Katzman
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Ghislaine A Dujovne
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Kelly E Knickelbein
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Felipe Avila
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Ted S Kalbfleisch
- Gluck Equine Research Center, University of Kentucky, Lexington, KY, United States
| | - Elena Giulotto
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Nicole B Kingsley
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Jocelyn Tanaka
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Elizabeth Esdaile
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Sichong Peng
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Anna Dahlgren
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Anna Fuller
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Michael J Mienaltowski
- Department of Animal Science, College of Agricultural and Environmental Sciences, University of California, Davis, Davis, CA, United States
| | - Terje Raudsepp
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, United States
| | - Verena K Affolter
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Jessica L Petersen
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Carrie J Finno
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
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19
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Hisey EA, Hermans H, Lounsberry ZT, Avila F, Grahn RA, Knickelbein KE, Duward-Akhurst SA, McCue ME, Kalbfleisch TS, Lassaline ME, Back W, Bellone RR. Whole genome sequencing identified a 16 kilobase deletion on ECA13 associated with distichiasis in Friesian horses. BMC Genomics 2020; 21:848. [PMID: 33256610 PMCID: PMC7706231 DOI: 10.1186/s12864-020-07265-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 11/23/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Distichiasis, an ocular disorder in which aberrant cilia (eyelashes) grow from the opening of the Meibomian glands of the eyelid, has been reported in Friesian horses. These misplaced cilia can cause discomfort, chronic keratitis, and corneal ulceration, potentially impacting vision due to corneal fibrosis, or, if secondary infection occurs, may lead to loss of the eye. Friesian horses represent the vast majority of reported cases of equine distichiasis, and as the breed is known to be affected with inherited monogenic disorders, this condition was hypothesized to be a simply inherited Mendelian trait. RESULTS A genome wide association study (GWAS) was performed using the Axiom 670 k Equine Genotyping array (MNEc670k) utilizing 14 cases and 38 controls phenotyped for distichiasis. An additive single locus mixed linear model (EMMAX) approach identified a 1.83 Mb locus on ECA5 and a 1.34 Mb locus on ECA13 that reached genome-wide significance (pcorrected = 0.016 and 0.032, respectively). Only the locus on ECA13 withstood replication testing (p = 1.6 × 10- 5, cases: n = 5 and controls: n = 37). A 371 kb run of homozygosity (ROH) on ECA13 was found in 13 of the 14 cases, providing evidence for a recessive mode of inheritance. Haplotype analysis (hapQTL) narrowed the region of association on ECA13 to 163 kb. Whole-genome sequencing data from 3 cases and 2 controls identified a 16 kb deletion within the ECA13 associated haplotype (ECA13:g.178714_195130del). Functional annotation data supports a tissue-specific regulatory role of this locus. This deletion was associated with distichiasis, as 18 of the 19 cases were homozygous (p = 4.8 × 10- 13). Genotyping the deletion in 955 horses from 54 different breeds identified the deletion in only 11 non-Friesians, all of which were carriers, suggesting that this could be causal for this Friesian disorder. CONCLUSIONS This study identified a 16 kb deletion on ECA13 in an intergenic region that was associated with distichiasis in Friesian horses. Further functional analysis in relevant tissues from cases and controls will help to clarify the precise role of this deletion in normal and abnormal eyelash development and investigate the hypothesis of incomplete penetrance.
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Affiliation(s)
- E A Hisey
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA
| | - H Hermans
- Department of Clinical Sciences, Utrecht University, Yalelaan 112-114, NL-3584, CM, Utrecht, The Netherlands
| | - Z T Lounsberry
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA
| | - F Avila
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA
| | - R A Grahn
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA
| | - K E Knickelbein
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA
- Veterinary Medical Teaching Hospital, University of California-Davis, Davis, CA, USA
| | - S A Duward-Akhurst
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, MN, USA
| | - M E McCue
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, MN, USA
| | - T S Kalbfleisch
- Department of Veterinary Science, Gluck Equine Research Center, University of Kentucky, Lexington, KY, USA
| | - M E Lassaline
- Department of Clinical Sciences and Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - W Back
- Department of Clinical Sciences, Utrecht University, Yalelaan 112-114, NL-3584, CM, Utrecht, The Netherlands
- Department of Surgery and Anaesthesia of Domestic Animals, Ghent University, Merelbeke, Belgium
| | - R R Bellone
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA.
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA.
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20
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Orlando L. The Evolutionary and Historical Foundation of the Modern Horse: Lessons from Ancient Genomics. Annu Rev Genet 2020; 54:563-581. [PMID: 32960653 DOI: 10.1146/annurev-genet-021920-011805] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The domestication of the horse some 5,500 years ago followed those of dogs, sheep, goats, cattle, and pigs by ∼2,500-10,000 years. By providing fast transportation and transforming warfare, the horse had an impact on human history with no equivalent in the animal kingdom. Even though the equine sport industry has considerable economic value today, the evolutionary history underlying the emergence of the modern domestic horse remains contentious. In the last decade, novel sequencing technologies have revolutionized our capacity to sequence the complete genome of organisms, including from archaeological remains. Applied to horses, these technologies have provided unprecedented levels of information and have considerably changed models of horse domestication. This review illustrates how ancient DNA, especially ancient genomes, has inspired researchers to rethink the process by which horses were first domesticated and then diversified into a variety of breeds showing a range of traits that are useful to humans.
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Affiliation(s)
- Ludovic Orlando
- Laboratoire d'Anthropobiologie Moléculaire et Imagerie de Synthèse, Faculté de Médecine Purpan, Université Toulouse III-Paul Sabatier, 31000 Toulouse, France;
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21
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Rivas VN, Magdesian KG, Fagan S, Slovis NM, Luethy D, Javsicas LH, Caserto BG, Miller AD, Dahlgren AR, Peterson J, Hales EN, Peng S, Watson KD, Khokha MK, Finno CJ. A nonsense variant in Rap Guanine Nucleotide Exchange Factor 5 (RAPGEF5) is associated with equine familial isolated hypoparathyroidism in Thoroughbred foals. PLoS Genet 2020; 16:e1009028. [PMID: 32986719 PMCID: PMC7544121 DOI: 10.1371/journal.pgen.1009028] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 10/08/2020] [Accepted: 08/05/2020] [Indexed: 11/18/2022] Open
Abstract
Idiopathic hypocalcemia in Thoroughbred (TB) foals causes tetany and seizures and is invariably fatal. Based upon the similarity of this disease with human familial hypoparathyroidism and occurrence only in the TB breed, we conducted a genetic investigation on two affected TB foals. Familial hypoparathyroidism was identified, and pedigree analysis suggested an autosomal recessive (AR) mode of inheritance. We performed whole-genome sequencing of the two foals, their unaffected dams and four unaffected, unrelated TB horses. Both homozygosity mapping and an association analysis were used to prioritize potential genetic variants. Of the 2,808 variants that significantly associated with the phenotype using an AR mode of inheritance (P<0.02) and located within a region of homozygosity, 1,507 (54%) were located in a 9.7 Mb region on chr4 (44.9-54.6 Mb). Within this region, a nonsense variant (RAPGEF5 c.2624C>A,p.Ser875*) was significantly associated with the hypoparathyroid phenotype (Pallelic = 0.008). Affected foals were homozygous for the variant, with two additional affected foals subsequently confirmed in 2019. Necropsies of all affected foals failed to identify any histologically normal parathyroid glands. Because the nonsense mutation in RAPGEF5 was near the C-terminal end of the protein, the impact on protein function was unclear. Therefore, we tested the variant in our Xenopus overexpression model and demonstrated RAPGEF5 loss-of-function. This RAPGEF5 variant represents the first genetic variant for hypoparathyroidism identified in any domestic animal species.
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Affiliation(s)
- Victor N. Rivas
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America
| | - K. Gary Magdesian
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America
| | - Sophia Fagan
- Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale School of Medicine, Yale University, New Haven, Connecticut, United States of America
| | - Nathan M. Slovis
- Hagyard Equine Medical Hospital, Lexington, Kentucky, United States of America
| | - Daniela Luethy
- Department of Clinical Studies–New Bolton Center, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Laura H. Javsicas
- Rhinebeck Equine L.L.P., Rhinebeck, New York, United States of America
| | | | - Andrew D. Miller
- Department of Biomedical Sciences, Section of Anatomic Pathology, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Anna R. Dahlgren
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America
| | - Janel Peterson
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America
| | - Erin N. Hales
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America
| | - Sichong Peng
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America
| | - Katherine D. Watson
- Department of Anatomic Pathology, Veterinary Medical Teaching Hospital, University of California-Davis, Davis, California, United States of America
| | - Mustafa K. Khokha
- Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale School of Medicine, Yale University, New Haven, Connecticut, United States of America
| | - Carrie J. Finno
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America
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22
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Dahlgren AR, Scott EY, Mansour T, Hales EN, Ross PJ, Kalbfleisch TS, MacLeod JN, Petersen JL, Bellone RR, Finno CJ. Comparison of Poly-A + Selection and rRNA Depletion in Detection of lncRNA in Two Equine Tissues Using RNA-seq. Noncoding RNA 2020; 6:E32. [PMID: 32825772 PMCID: PMC7549351 DOI: 10.3390/ncrna6030032] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/17/2020] [Accepted: 08/18/2020] [Indexed: 12/14/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are untranslated regulatory transcripts longer than 200 nucleotides that can play a role in transcriptional, post-translational, and epigenetic regulation. Traditionally, RNA-sequencing (RNA-seq) libraries have been created by isolating transcriptomic RNA via poly-A+ selection. In the past 10 years, methods to perform ribosomal RNA (rRNA) depletion of total RNA have been developed as an alternative, aiming for better coverage of whole transcriptomic RNA, both polyadenylated and non-polyadenylated transcripts. The purpose of this study was to determine which library preparation method is optimal for lncRNA investigations in the horse. Using liver and cerebral parietal lobe tissues from two healthy Thoroughbred mares, RNA-seq libraries were prepared using standard poly-A+ selection and rRNA-depletion methods. Averaging the two biologic replicates, poly-A+ selection yielded 327 and 773 more unique lncRNA transcripts for liver and parietal lobe, respectively. More lncRNA were found to be unique to poly-A+ selected libraries, and rRNA-depletion identified small nucleolar RNA (snoRNA) to have a higher relative expression than in the poly-A+ selected libraries. Overall, poly-A+ selection provides a more thorough identification of total lncRNA in equine tissues while rRNA-depletion may allow for easier detection of snoRNAs.
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Affiliation(s)
- Anna R. Dahlgren
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA; (A.R.D.); (T.M.); (E.N.H.); (R.R.B.)
| | - Erica Y. Scott
- Department of Animal Science, College of Agricultural and Environmental Sciences, University of California Davis, Davis, CA 95616, USA; (E.Y.S.); (P.J.R.)
| | - Tamer Mansour
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA; (A.R.D.); (T.M.); (E.N.H.); (R.R.B.)
| | - Erin N. Hales
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA; (A.R.D.); (T.M.); (E.N.H.); (R.R.B.)
| | - Pablo J. Ross
- Department of Animal Science, College of Agricultural and Environmental Sciences, University of California Davis, Davis, CA 95616, USA; (E.Y.S.); (P.J.R.)
| | - Theodore S. Kalbfleisch
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40546, USA; (T.S.K.); (J.N.M.)
| | - James N. MacLeod
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40546, USA; (T.S.K.); (J.N.M.)
| | - Jessica L. Petersen
- Department of Animal Science, University of Nebraska Lincoln, Lincoln, NE 68583, USA;
| | - Rebecca R. Bellone
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA; (A.R.D.); (T.M.); (E.N.H.); (R.R.B.)
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA
| | - Carrie J. Finno
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA; (A.R.D.); (T.M.); (E.N.H.); (R.R.B.)
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23
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Abstract
The sequencing and assembly of a reference genome for the horse has been revolutionary for investigation of horse health and performance. Next-generation sequencing (NGS) methods represent a second revolution in equine genomics. Researchers can align and compare DNA and RNA sequencing data to the reference genome to explore variation that may contribute or be attributed to disease. NGS has also facilitated the translation of research discovery to clinically relevant applications. This article discusses the history and development of NGS, details some of the available sequencing platforms, and describes currently available applications in the context of both discovery and clinical settings.
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MacLeod JN, Kalbfleisch TS. Genetics, Genomics, and Emergent Precision Medicine 12 Years After the Equine Reference Genome Was Published. Vet Clin North Am Equine Pract 2020; 36:173-181. [PMID: 32654780 DOI: 10.1016/j.cveq.2020.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
The first equine reference genome was completed in 2007 and published in 2009. This major accomplishment has enabled equine science to advance in ways that broadly parallel the transformative impact that genomics has had on many animal species including humans. A conceptual overview of reference genomes, genome annotation, and the major implications for equine science is presented. The relationship between genomic sequencing and the accelerating application of precision P4 medicine is discussed in the context of human and equine patients. Emergent technologies built on the foundation of genomic sequencing and rapidly gaining traction in research and clinical settings are introduced.
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Affiliation(s)
- James N MacLeod
- Department of Veterinary Science, Gluck Equine Research Center, University of Kentucky, Lexington, KY 40546-0099, USA.
| | - Theodore S Kalbfleisch
- Department of Veterinary Science, Gluck Equine Research Center, University of Kentucky, Lexington, KY 40546-0099, USA
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25
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Gao S, Nanaei HA, Wei B, Wang Y, Wang X, Li Z, Dai X, Wang Z, Jiang Y, Shao J. Comparative Transcriptome Profiling Analysis Uncovers Novel Heterosis-Related Candidate Genes Associated with Muscular Endurance in Mules. Animals (Basel) 2020; 10:ani10060980. [PMID: 32512843 PMCID: PMC7341310 DOI: 10.3390/ani10060980] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 05/24/2020] [Accepted: 06/02/2020] [Indexed: 11/25/2022] Open
Abstract
Simple Summary Mules have better and greater muscle endurance than hinnies and their parents. However, the molecular mechanisms underlying heterosis in their muscles are still much less understood. In this study, we conducted comparative transcriptome and alternative splicing analysis on the heterosis mechanism of muscular endurance in mules. Our results showed that 8 genes were significantly enriched in the “muscle contraction” pathway. In addition, 68% of the genes with alternative splicing events from the mule muscle tissue were validated by the long transcript reads generated from PacBio sequencing platform. Our findings provide a research foundation for studying the genetic basis of heterosis in mules. Abstract Heterosis has been widely exploited in animal and plant breeding programs to enhance the productive traits of hybrid progeny from two breeds or species. However, its underlying genetic mechanisms remain enigmatic. Transcriptome profiling analysis can be used as a method for exploring the mechanism of heterosis. Here, we performed genome-wide gene expression and alternative splicing (AS) analyses in different tissues (muscle, brain, and skin) from crosses between donkeys and horses. Our results indicated that 86.1% of the differentially expressed genes (DEGs) and 87.2% of the differential alternative splicing (DAS) genes showed over-dominance and dominance in muscle. Further analysis showed that the “muscle contraction” pathway was significantly enriched for both the DEGs and DAS genes in mule muscle tissue. Taken together, these DEGs and DAS genes could provide an index for future studies of the genetic and molecular mechanism of heterosis in the hybrids of donkey and horse.
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26
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Functionally Annotating Regulatory Elements in the Equine Genome Using Histone Mark ChIP-Seq. Genes (Basel) 2019; 11:genes11010003. [PMID: 31861495 PMCID: PMC7017286 DOI: 10.3390/genes11010003] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/10/2019] [Accepted: 12/16/2019] [Indexed: 01/02/2023] Open
Abstract
One of the primary aims of the Functional Annotation of ANimal Genomes (FAANG) initiative is to characterize tissue-specific regulation within animal genomes. To this end, we used chromatin immunoprecipitation followed by sequencing (ChIP-Seq) to map four histone modifications (H3K4me1, H3K4me3, H3K27ac, and H3K27me3) in eight prioritized tissues collected as part of the FAANG equine biobank from two thoroughbred mares. Data were generated according to optimized experimental parameters developed during quality control testing. To ensure that we obtained sufficient ChIP and successful peak-calling, data and peak-calls were assessed using six quality metrics, replicate comparisons, and site-specific evaluations. Tissue specificity was explored by identifying binding motifs within unique active regions, and motifs were further characterized by gene ontology (GO) and protein–protein interaction analyses. The histone marks identified in this study represent some of the first resources for tissue-specific regulation within the equine genome. As such, these publicly available annotation data can be used to advance equine studies investigating health, performance, reproduction, and other traits of economic interest in the horse.
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27
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Raudsepp T, Finno CJ, Bellone RR, Petersen JL. Ten years of the horse reference genome: insights into equine biology, domestication and population dynamics in the post-genome era. Anim Genet 2019; 50:569-597. [PMID: 31568563 PMCID: PMC6825885 DOI: 10.1111/age.12857] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2019] [Indexed: 12/14/2022]
Abstract
The horse reference genome from the Thoroughbred mare Twilight has been available for a decade and, together with advances in genomics technologies, has led to unparalleled developments in equine genomics. At the core of this progress is the continuing improvement of the quality, contiguity and completeness of the reference genome, and its functional annotation. Recent achievements include the release of the next version of the reference genome (EquCab3.0) and generation of a reference sequence for the Y chromosome. Horse satellite‐free centromeres provide unique models for mammalian centromere research. Despite extremely low genetic diversity of the Y chromosome, it has been possible to trace patrilines of breeds and pedigrees and show that Y variation was lost in the past approximately 2300 years owing to selective breeding. The high‐quality reference genome has led to the development of three different SNP arrays and WGSs of almost 2000 modern individual horses. The collection of WGS of hundreds of ancient horses is unique and not available for any other domestic species. These tools and resources have led to global population studies dissecting the natural history of the species and genetic makeup and ancestry of modern breeds. Most importantly, the available tools and resources, together with the discovery of functional elements, are dissecting molecular causes of a growing number of Mendelian and complex traits. The improved understanding of molecular underpinnings of various traits continues to benefit the health and performance of the horse whereas also serving as a model for complex disease across species.
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Affiliation(s)
- T Raudsepp
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Research, Texas A&M University, College Station, TX, 77843, USA
| | - C J Finno
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - R R Bellone
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA.,School of Veterinary Medicine, Veterinary Genetics Laboratory, University of California-Davis, Davis, CA, 95616, USA
| | - J L Petersen
- Department of Animal Science, University of Nebraska, Lincoln, NE, 68583-0908, USA
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Improved reference genome for the domestic horse increases assembly contiguity and composition. Commun Biol 2018; 1:197. [PMID: 30456315 PMCID: PMC6240028 DOI: 10.1038/s42003-018-0199-z] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 10/16/2018] [Indexed: 11/30/2022] Open
Abstract
Recent advances in genomic sequencing technology and computational assembly methods have allowed scientists to improve reference genome assemblies in terms of contiguity and composition. EquCab2, a reference genome for the domestic horse, was released in 2007. Although of equal or better quality compared to other first-generation Sanger assemblies, it had many of the shortcomings common to them. In 2014, the equine genomics research community began a project to improve the reference sequence for the horse, building upon the solid foundation of EquCab2 and incorporating new short-read data, long-read data, and proximity ligation data. Here, we present EquCab3. The count of non-N bases in the incorporated chromosomes is improved from 2.33 Gb in EquCab2 to 2.41 Gb in EquCab3. Contiguity has also been improved nearly 40-fold with a contig N50 of 4.5 Mb and scaffold contiguity enhanced to where all but one of the 32 chromosomes is comprised of a single scaffold. Theodore Kalbfleisch et al. present an improved genome assembly for the domestic horse by combining short- and long-read data, as well as proximity ligation data. They improve contiguity of the assembly by 40-fold, with a 10-fold reduction in gaps.
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