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Published, Version of Record (VoR)Open Access (License Unspecified), Open
Journal article
DNA methylation networks underlying mammalian traits
Science (American Association for the Advancement of Science), v 381(6658)
11 Aug 2023
PMID: 37561875
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
Using DNA methylation profiles (
= 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
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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- Title
- DNA methylation networks underlying mammalian traits
- Creators
- Amin Haghani - University of California, Los AngelesTodd R Robeck - SeaWorld EntertainmentJoshua Zhang - University of California, Los AngelesAke T Lu - University of California, Los AngelesJulia Ablaeva - University of RochesterVictoria A Acosta-Rodríguez - The University of Texas Southwestern Medical CenterDanielle M Adams - University of Maryland, College ParkAbdulaziz N Alagaili - King Saud UniversityJavier Almunia - Fundación A LA PARAjoy Aloysius - University of KentuckyNabil M S Amor - Laboratory of Biodiversity, Parasitology, and Ecology, University of Tunis El Manar, Tunis, TunisiaReza Ardehali - University of California, Los AngelesAdriana Arneson - University of California, Los AngelesC Scott Baker - Oregon State UniversityGareth Banks - Mary Lyon Centre at MRC HarwellKatherine Belov - The University of SydneyNigel C Bennett - University of PretoriaPeter Black - Busch Gardens Tampa, Tampa, FL, USADaniel T Blumstein - Rocky Mountain Biological LaboratoryEleanor K Bors - Oregon State UniversityCharles E Breeze - Altius Institute for Biomedical SciencesRobert T Brooke - Epigenetic Clock Development Foundation, Los Angeles, CA, USAJanine L Brown - Smithsonian Conservation Biology InstituteGerald Carter - The Ohio State UniversityAlex Caulton - University of OtagoJulie M Cavin - Dolphin Interconnect Solutions (Norway)Lisa Chakrabarti - University of NottinghamIoulia Chatzistamou - University of South CarolinaAndreas S Chavez - The Ohio State UniversityHao Chen - University of Tennessee Health Science CenterKaiyang Cheng - University of California, Los AngelesPriscila Chiavellini - Biochemistry Research Institute of La PlataOi-Wa Choi - University of California, Los AngelesShannon Clarke - AgResearchJoseph A Cook - University of New MexicoLisa N Cooper - Northeast Ohio Medical UniversityMarie-Laurence Cossette - Trent UniversityJoanna Day - Taronga Conservation Society AustraliaJoseph DeYoung - University of California, Los AngelesStacy Dirocco - SeaWorld EntertainmentChristopher Dold - SeaWorld EntertainmentJonathan L Dunnum - University of New MexicoErin E Ehmke - Duke UniversityCandice K Emmons - NOAA National Marine Fisheries Service Northwest Fisheries Science CenterStephan Emmrich - University of RochesterEbru Erbay - Bay InstituteClaire Erlacher-Reid - SeaWorld EntertainmentChris G Faulkes - Queen Mary University of LondonZhe Fei - University of California, Los AngelesSteven H Ferguson - University of ManitobaCarrie J Finno - University of California, DavisJennifer E Flower - Sea Research FoundationJean-Michel Gaillard - Laboratoire de Biométrie et Biologie EvolutiveEva Garde - Grønlands NaturinstitutLivia Gerber - Environmental Earth SciencesVadim N Gladyshev - Brigham and Women's HospitalRodolfo G Goya - Biochemistry Research Institute of La PlataMatthew J Grant - University of AucklandCarla B Green - The University of Texas Southwestern Medical CenterM Bradley Hanson - NOAA National Marine Fisheries Service Northwest Fisheries Science CenterDaniel W Hart - University of PretoriaMartin Haulena - Vancouver AquariumKelsey Herrick - SeaWorld San DiegoAndrew N Hogan - National Human Genome Research InstituteCarolyn J Hogg - The University of SydneyTimothy A Hore - University of OtagoTaosheng Huang - University at Buffalo, State University of New YorkJuan Carlos Izpisua Belmonte - Altos LabsAnna J Jasinska - University of PittsburghGareth Jones - University of BristolEve Jourdain - Norwegian Orca Survey, Andenes, NorwayOlga Kashpur - Tufts Medical CenterHarold Katcher - Yuvan Research, Mountain View, CA, USAEtsuko Katsumata - Sea WorldVimala Kaza - University of South CarolinaHippokratis Kiaris - University of South CarolinaMichael S Kobor - University of British ColumbiaPawel Kordowitzki - Nicolaus Copernicus UniversityWilliam R Koski - LGL (Canada)Michael Krützen - University of ZurichSoo Bin Kwon - University of California, Los AngelesBrenda Larison - University of California, Los AngelesSang-Goo Lee - Brigham and Women's HospitalMarianne Lehmann - Biochemistry Research Institute of La PlataJean-François Lemaître - Laboratoire de Biométrie et Biologie EvolutiveAndrew J Levine - University of California, Los AngelesXinmin Li - University of California, Los AngelesCun Li - Texas Biomedical Research InstituteAndrea R Lim - University of California, Los AngelesDavid T S Lin - University of British ColumbiaDana M Lindemann - SeaWorld EntertainmentSchuyler W Liphardt - University of New MexicoThomas J Little - University of EdinburghNicholas Macoretta - University of RochesterDewey Maddox - White Oak Conservation Center, Yulee, FL, USACraig O Matkin - North Gulf Oceanic Society, Homer, AK, USAJulie A Mattison - National Institute on AgingMatthew McClure - ABS Global, DeForest, WI, USAJune Mergl - Marineland of Canada, Niagara Falls, Ontario, CanadaJennifer J Meudt - University of Wisconsin–MadisonGisele A Montano - SeaWorld EntertainmentKhyobeni Mozhui - University of Tennessee Health Science CenterJason Munshi-South - Fordham UniversityWilliam J Murphy - Texas A&M UniversityAsieh Naderi - University of South CarolinaMartina Nagy - Museum für NaturkundePritika Narayan - University of AucklandPeter W Nathanielsz - Texas Biomedical Research InstituteNgoc B Nguyen - University of California, Los AngelesChristof Niehrs - DKFZ-ZMBH AllianceBatsaikhan Nyamsuren - Mammalogical Society of Mongolia, Ulaanbaatar, MongoliaJustine K O'Brien - Taronga Conservation Society AustraliaPerrie O'Tierney Ginn - Tufts Medical CenterDuncan T Odom - University of CambridgeAlexander G Ophir - Cornell UniversitySteve Osborn - SeaWorld EntertainmentElaine A Ostrander - National Human Genome Research InstituteKim M Parsons - NOAA National Marine Fisheries Service Northwest Fisheries Science CenterKimberly C Paul - University of California, Los AngelesAmy B Pedersen - University of EdinburghMatteo Pellegrini - University of California, Los AngelesKatharina J Peters - University of WollongongJessica L Petersen - University of Nebraska–LincolnDarren W Pietersen - University of PretoriaGabriela M Pinho - University of California, Los AngelesJocelyn Plassais - National Human Genome Research InstituteJesse R Poganik - Brigham and Women's HospitalNatalia A Prado - Adelphi UniversityPradeep Reddy - Salk Institute for Biological StudiesBenjamin Rey - Laboratoire de Biométrie et Biologie EvolutiveBeate R Ritz - UCLA HealthJooke Robbins - Center for Coastal StudiesMagdalena Rodriguez - Miami Seaquarium, Miami, FL, USAJennifer Russell - SeaWorld EntertainmentElena Rydkina - University of RochesterLindsay L Sailer - Cornell UniversityAdam B Salmon - The University of Texas Health Science Center at HoustonAkshay Sanghavi - Yuvan Research, Mountain View, CA, USAKyle M Schachtschneider - University of Illinois ChicagoDennis Schmitt - Missouri State UniversityTodd Schmitt - SeaWorld EntertainmentLars Schomacher - Institute of Molecular BiologyLawrence B Schook - University of Illinois ChicagoKaren E Sears - University of California, Los AngelesAshley W Seifert - University of KentuckyAaron B A Shafer - Trent UniversityAnastasia V Shindyapina - Brigham and Women's HospitalMelanie Simmons - Duke UniversityKavita Singh - Narsee Monjee Institute of Management StudiesIshani Sinha - University of California, Los AngelesJesse Slone - University at Buffalo, State University of New YorkRussel G Snell - University of AucklandElham Soltanmohammadi - University of South CarolinaMatthew L Spangler - University of Nebraska–LincolnMaria Spriggs - Busch Gardens Tampa, Tampa, FL, USALydia Staggs - SeaWorld EntertainmentNancy Stedman - Busch Gardens Tampa, Tampa, FL, USAKaren J Steinman - SeaWorld EntertainmentDonald T Stewart - Acadia UniversityVictoria J Sugrue - University of OtagoBalazs Szladovits - Royal Veterinary CollegeJoseph S Takahashi - Howard Hughes Medical InstituteMasaki Takasugi - University of RochesterEmma C Teeling - University College DublinMichael J Thompson - University of California, Los AngelesBill Van Bonn - Shedd AquariumSonja C Vernes - University of St AndrewsDiego Villar - Queen Mary University of LondonHarry V Vinters - University of California, Los AngelesHa Vu - University of California, Los AngelesMary C Wallingford - Tufts Medical CenterNan Wang - University of California, Los AngelesGerald S Wilkinson - University of Maryland, College ParkRobert W Williams - University of Tennessee Health Science CenterQi Yan - University of California, Los AngelesMingjia Yao - University of California, Los AngelesBrent G Young - Fisheries and Oceans CanadaBohan Zhang - Harvard UniversityZhihui Zhang - University of RochesterYang Zhao - University of RochesterPeng Zhao - University of California, Los AngelesWanding Zhou - University of PennsylvaniaJoseph A Zoller - University of California, Los AngelesJason Ernst - University of California, Los AngelesAndrei Seluanov - University of RochesterVera Gorbunova - University of RochesterX William Yang - University of California, Los AngelesKen Raj - Altos LabsSteve Horvath - University of California, Los Angeles
- Publication Details
- Science (American Association for the Advancement of Science), v 381(6658)
- Publisher
- American Association for the Advancement of Science (AAAS)
- Grant note
- 20412 / Cancer Research UK R21 DE028271 / NIDCR NIH HHS R21 AG067164 / NIA NIH HHS U34 AG068482 / NIA NIH HHS R21 AG055841 / NIA NIH HHS R21 ES024356 / NIEHS NIH HHS R01 AG050797 / NIA NIH HHS
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Biodiversity, Earth, and Environmental Science (BEES)
- Web of Science ID
- WOS:001054584400003
- Scopus ID
- 2-s2.0-85167657141
- Other Identifier
- 991021904448204721
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