DNA methylation networks underlying mammalian traits
Amin Haghani(University of California, Los Angeles), Caesar Z. Li(Texas Biomedical Research Institute), Caesar Z. Li(Texas Biomedical Research Institute), Todd R. Robeck(SeaWorld Entertainment), Joshua Zhang(University of California, Los Angeles), Ake T. Lu(University of California, Los Angeles), Julia Ablaeva(University of Rochester), Victoria A. Acosta-Rodríguez(University of Maryland, College Park), Danielle M. Adams(King Saud University), Abdulaziz N. Alagaili(King Saud University), Javier Almunia(University of Kentucky), Ajoy Aloysius(University of Kentucky), Nabil Amor(University of California, Los Angeles), Reza Ardehali(University of California, Los Angeles), A Arneson(Oregon State University), C. Scott Baker(Oregon State University), Gareth Banks(The University of Sydney), Katherine Belov(The University of Sydney), Nigel C. Bennett(University of Pretoria), Peter McL. Black(University of California, Los Angeles), Daniel T. Blumstein(Oregon State University), Eleanor K. Bors(Oregon State University), Charles E. Breeze(Altius Institute for Biomedical Sciences), Robert T. Brooke(Smithsonian Conservation Biology Institute), Janine L. Brown(Smithsonian Conservation Biology Institute), Gerald G. Carter(AgResearch), Alex Caulton(AgResearch), Julie M. Cavin(University of Nottingham), Lisa Chakrabarti(University of Nottingham), Ioulia Chatzistamou(University of South Carolina), Andreas S. Chavez(University of Tennessee Health Science Center), Hao Chen(University of Tennessee Health Science Center), Kaiyang Cheng(University of California, Los Angeles), Priscila Chiavellini(University of California, Los Angeles), Oi‐Wa Choi(University of California, Los Angeles), Shannon Clarke(AgResearch), Joseph A. Cook(New Mexico Museum of Natural History and Science), Lisa Noelle Cooper(Trent University), Marie‐Laurence Cossette(Taronga Conservation Society Australia), Joanna Day(University of California, Los Angeles), Joseph DeYoung(SeaWorld Entertainment), Stacy DiRocco(SeaWorld Entertainment), Christopher Dold(SeaWorld Entertainment), Jonathan L. Dunnum(Duke University), Erin E. Ehmke(NOAA National Marine Fisheries Service), Candice K. Emmons(NOAA National Marine Fisheries Service), Stephan Emmrich(Cedars-Sinai Medical Center), Ebru Erbay(Cedars-Sinai Medical Center), Claire Erlacher‐Reid(SeaWorld Entertainment), Chris G. Faulkes(University of California, Riverside), Zhe Fei(University of California, Riverside), Steven H. Ferguson(Fisheries and Oceans Canada), Carrie J. Finno(Sea Research Foundation), Jennifer E. Flower(Université Claude Bernard Lyon 1), Jean‐Michel Gaillard(Université Claude Bernard Lyon 1), Eva Garde(Commonwealth Scientific and Industrial Research Organisation), Livia Gerber(Brigham and Women's Hospital), Vadim N. Gladyshev(Brigham and Women's Hospital), Rodolfo G. Goya(University of Auckland), Matthew J. Grant(University of Auckland), Carla B. Green(NOAA National Marine Fisheries Service), M. Bradley Hanson(NOAA National Marine Fisheries Service), Daniel W. Hart(Vancouver Aquarium), Martin Haulena(SeaWorld Entertainment), Kelsey Herrick(National Institutes of Health), Andrew N. Hogan(The University of Sydney), Carolyn J. Hogg(The University of Sydney), Timothy A. Hore(University at Buffalo, State University of New York), Taosheng Huang(Altos Labs), Juan Carlos Izpisúa Belmonte(University of California, Los Angeles), Anna J. Jasinska(University of California, Los Angeles), Gareth Jones(University of Bristol), Eve Jourdain(Tufts Medical Center), Olga Kashpur(Tufts Medical Center), Harold L. Katcher, Etsuko Katsumata(University of South Carolina), Vimala Kaza(University of South Carolina), Hippokratis Kiaris(University of British Columbia), Michael S. Kobor(University of British Columbia), Paweł Kordowitzki(Nicolaus Copernicus University), William R. Koski(University of Zurich), Michael Krützen(University of California, Los Angeles), Soo Bin Kwon(University of California, Los Angeles), Brenda Larison(Brigham and Women's Hospital), Sang‐Goo Lee(Brigham and Women's Hospital), Marianne Lehmann(Université Claude Bernard Lyon 1), Jean‐François Lemaître(Université Claude Bernard Lyon 1), Andrew J. Levine(University of California, Los Angeles), Xinmin Li(Texas Biomedical Research Institute), Cun Li(Texas Biomedical Research Institute), Cun Li(Texas Biomedical Research Institute), Andrea R. Lim(SeaWorld Entertainment), David Lin(University of British Columbia), Dana M. Lindemann(SeaWorld Entertainment), Schuyler Liphardt(University of New Mexico), Thomas J. Little(University of Edinburgh), Nicholas Macoretta(University of Rochester), Dewey Maddox(National Institutes of Health), Craig O. Matkin, Julie A. Mattison(National Institutes of Health), Matthew McClure(University of Wisconsin–Madison), June Mergl(SeaWorld Entertainment), Jennifer J. Meudt(University of Wisconsin–Madison), Gisele Montano(SeaWorld Entertainment), Khyobeni Mozhui(University of Tennessee Health Science Center), Jason Munshi‐South(University of South Carolina), William J. Murphy(Museum für Naturkunde), Asieh Naderi(University of Auckland), Martina Nagy(Texas Biomedical Research Institute), Pritika Narayan(University of Auckland), Peter W. Nathanielsz(Texas Biomedical Research Institute), Ngoc B. Nguyen(University of California, Los Angeles), Christof Niehrs(Heidelberg University), Nyamsuren Batsaikhan(Tufts Medical Center), Justine K. O’Brien(University of Cambridge), Perrie O’Tierney-Ginn(Tufts Medical Center), Duncan T. Odom(SeaWorld Entertainment), Alexander G. Ophir(National Institutes of Health), Steve Osborn(NOAA National Marine Fisheries Service), Elaine A. Ostrander(National Institutes of Health), Kim M. Parsons(NOAA National Marine Fisheries Service), Kimberly C. Paul(University of California, Los Angeles), Amy B. Pedersen(University of Zurich), Matteo Pellegrini(University of Nebraska–Lincoln), Katharina J. Peters(University of Zurich), Jessica L. Petersen(University of Nebraska–Lincoln), Darren W. Pietersen(National Institutes of Health), Gabriela Medeiros de Pinho(Brigham and Women's Hospital), Jocelyn Plassais(National Institutes of Health), Jesse R. Poganik(Brigham and Women's Hospital), Natalia A. Prado(Université Claude Bernard Lyon 1), Pradeep Reddy(Salk Institute for Biological Studies), Benjamin Rey(Université Claude Bernard Lyon 1), Beate Ritz(University of California, Los Angeles), Jooke Robbins(SeaWorld Entertainment), Magdalena Rodríguez(University of Rochester), Jennifer Russell(SeaWorld Entertainment), Elena Rydkina(South Texas Veterans Health Care System), Lindsay L. Sailer(Cornell University), Adam B. Salmon(University of Illinois Urbana-Champaign), Akshay Sanghavi(Missouri State University), Kyle M. Schachtschneider(SeaWorld Entertainment), Dennis Schmitt(Missouri State University), Todd L. Schmitt(SeaWorld Entertainment), Lars Schomacher(University of California, Los Angeles), Lawrence B. Schook(University of Kentucky), Karen E. Sears(University of California, Los Angeles), Ashley W. Seifert(Brigham and Women's Hospital), Aaron B. A. Shafer(Duke University), Anastasia V. Shindyapina(Brigham and Women's Hospital), Melanie Simmons(University of California, Los Angeles), Kavita Singh(Narsee Monjee Institute of Management Studies), Ishani Sinha(University of Auckland), Jesse Slone(University of South Carolina), Russel G. Snell(University of Nebraska–Lincoln), Elham Soltanmohammadi(University of South Carolina), Matthew L Spangler(University of Nebraska–Lincoln), Maria Spriggs, Lydia Staggs(SeaWorld Entertainment), Nancy Stedman(Acadia University), Karen J. Steinman(SeaWorld Entertainment), Donald T. Stewart(Royal Veterinary College), Victoria J Sugrue(Howard Hughes Medical Institute), Balázs Szladovits(Royal Veterinary College), Joseph S. Takahashi(University College Dublin), Masaki Takasugi(University of California, Los Angeles), Emma C. Teeling(University College Dublin), Michael J. Thompson(University of California, Los Angeles), Bill Van Bonn(Queen Mary University of London), Sonja C. Vernes(University of California, Los Angeles), Diego Villar(University of California, Los Angeles), Harry V. Vinters(Tufts Medical Center), Ha Vu(University of California, Los Angeles), Mary C. Wallingford(Tufts Medical Center), Nan Wang(University of Tennessee Health Science Center), Gerald S. Wilkinson(University of California, Los Angeles), Robert W. Williams(University of Tennessee Health Science Center), Qi Yan(Fisheries and Oceans Canada), M. Yao(Brigham and Women's Hospital), Brent G. Young(Fisheries and Oceans Canada), Bohan Zhang(Brigham and Women's Hospital), Zhihui Zhang(University of California, Los Angeles), Yang Zhao(Children's Hospital of Philadelphia), Peng Zhao(University of California, Los Angeles), Wanding Zhou(Children's Hospital of Philadelphia), Joseph A. Zoller(University of California, Los Angeles), Jason Ernst(University of California, Los Angeles), Andrei Seluanov(University of California, Los Angeles), Vera Gorbunova(University of Rochester), X. William Yang(University of California, Los Angeles), Ken Raj, Steve Horvath(University of California, Los Angeles)
Cited by 130Open Access
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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