DNA methylation networks underlying mammalian traits

Haghani, Amin; Li, Caesar Z.; Robeck, Todd R.; Zhang, Joshua; Lu, Ake T.; Ablaeva, Julia; Acosta-Rodríguez, Victoria A.; Adams, Danielle M.; Alagaili, Abdulaziz N.; Almunia, Javier; Aloysius, Ajoy; Amor, Nabil M.S.; Ardehali, Reza; Arneson, Adriana; Baker, C. Scott; Banks, Gareth; Belov, Katherine; Bennett, Nigel C.; Black, Peter; Blumstein, Daniel T.; Bors, Eleanor K.; Breeze, Charles E.; Brooke, Robert T.; Brown, Janine L.; Carter, Gerald; Caulton, Alex; Cavin, Julie M.; Chakrabarti, Lisa; Chatzistamou, Ioulia; Chavez, Andreas S.; Chen, Hao; Cheng, Kaiyang; Chiavellini, Priscila; Choi, Oi-Wa; Clarke, Shannon; Cook, Joseph A.; Cooper, Lisa N.; Cossette, Marie-Laurence; Day, Joanna; DeYoung, Joseph; Dirocco, Stacy; Dold, Christopher; Dunnum, Jonathan L.; Ehmke, Erin E.; Emmons, Candice K.; Emmrich, Stephan; Erbay, Ebru; Erlacher-Reid, Claire; Faulkes, Chris G.; Fei, Zhe; Ferguson, Steven H.; Finno, Carrie J.; Flower, Jennifer E.; Gaillard, Jean-Michel; Garde, Eva; Gerber, Livia; Gladyshev, Vadim N.; Goya, Rodolfo G.; Grant, Matthew J; Green, Carla B.; Hanson, M. Bradley; Hart, Daniel W.; Haulena, Martin; Herrick, Kelsey; Hogan, Andrew N.; Hogg, Carolyn J.; Hore, Timothy A.; Huang, Taosheng; Izpisua Belmonte, Juan Carlos; Jasinska, Anna J.; Jones, Gareth; Jourdain, Eve; Kashpur, Olga; Katcher, Harold; Katsumata, Etsuko; Kaza, Vimala; Kiaris, Hippokratis; Kobor, Michael S.; Kordowitzki, Pawel; Koski, William R.; Krützen, Michael; Kwon, Soo Bin; Larison, Brenda; Lee, Sang-Goo; Lehmann, Marianne; Lemaître, Jean-François; Levine, Andrew J.; Li, Xinmin; Li, Cun; Lim, Andrea R.; Lin, David T. S.; Lindemann, Dana M.; Liphardt, Schuyler W.; Little, Thomas J.; Macoretta, Nicholas; Maddox, Dewey; Matkin, Craig O.; Mattison, Julie A.; McClure, Matthew; Mergl, June; Meudt, Jennifer J.; Montano, Gisele A.; Mozhui, Khyobeni; Munshi-South, Jason; Murphy, William J.; Naderi, Asieh; Nagy, Martina; Narayan, Pritika; Nathanielsz, Peter W.; Nguyen, Ngoc B.; Niehrs, Christof; Nyamsuren, Batsaikhan; O’Brien, Justine K.; Ginn, Perrie O’Tierney; Odom, Duncan T; Ophir, Alexander G.; Osborn, Steve; Ostrander, Elaine A.; Parsons, Kim M.; Paul, Kimberly C.; Pedersen, Amy B.; Pellegrini, Matteo; Peters, Katharina J.; Petersen, Jessica L.; Pietersen, Darren W.; Pinho, Gabriela M.; Plassais, Jocelyn; Poganik, Jesse R.; Prado, Natalia A.; Reddy, Pradeep; Rey, Benjamin; Ritz, Beate R.; Robbins, Jooke; Rodriguez, Magdalena; Russell, Jennifer; Rydkina, Elena; Sailer, Lindsay L.; Salmon, Adam B.; Sanghavi, Akshay; Schachtschneider, Kyle M.; Schmitt, Dennis; Schmitt, Todd; Schomacher, Lars; Schook, Lawrence B.; Sears, Karen E.; Seifert, Ashley W.; Shafer, Aaron B.A.; Shindyapina, Anastasia V.; Simmons, Melanie; Singh, Kavita; Sinha, Ishani; Slone, Jesse; Snell, Russel G.; Soltanmohammadi, Elham; Spangler, Matthew L.; Spriggs, Maria; Staggs, Lydia; Stedman, Nancy; Steinman, Karen J.; Stewart, Donald T; Sugrue, Victoria J.; Szladovits, Balazs; Takahashi, Joseph S.; Takasugi, Masaki; Teeling, Emma C.; Thompson, Michael J.; Van Bonn, Bill; Vernes, Sonja C.; Villar, Diego; Vinters, Harry V.; Vu, Ha; Wallingford, Mary C.; Wang, Nan; Wilkinson, Gerald S.; Williams, Robert W.; Yan, Qi; Yao, Mingjia; Young, Brent G.; Zhang, Bohan; Zhang, Zhihui; Zhao, Yang; Zhao, Peng; Zhou, Wanding; Zoller, Joseph A.; Ernst, Jason; Seluanov, Andrei; Gorbunova, Vera; Yang, X. William; Raj, Ken; Horvath, Steve

doi:10.1126/science.abq5693

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DNA methylation networks underlying mammalian traits

2023
By Haghani, Amin ; Li, Caesar Z. ; Robeck, Todd R. ; ...
Source: Science, 381(6658)

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Haghani, Amin ; Li, Caesar Z. ; Robeck, Todd R. ; Zhang, Joshua ; Lu, Ake T. ; ... More +

Haghani, Amin ; Li, Caesar Z. ; Robeck, Todd R. ; Zhang, Joshua ; Lu, Ake T. ; Ablaeva, Julia ; Acosta-Rodríguez, Victoria A. ; Adams, Danielle M. ; Alagaili, Abdulaziz N. ; Almunia, Javier ; Aloysius, Ajoy ; Amor, Nabil M.S. ; Ardehali, Reza ; Arneson, Adriana ; Baker, C. Scott ; Banks, Gareth ; Belov, Katherine ; Bennett, Nigel C. ; Black, Peter ; Blumstein, Daniel T. ; Bors, Eleanor K. ; Breeze, Charles E. ; Brooke, Robert T. ; Brown, Janine L. ; Carter, Gerald ; Caulton, Alex ; Cavin, Julie M. ; Chakrabarti, Lisa ; Chatzistamou, Ioulia ; Chavez, Andreas S. ; Chen, Hao ; Cheng, Kaiyang ; Chiavellini, Priscila ; Choi, Oi-Wa ; Clarke, Shannon ; Cook, Joseph A. ; Cooper, Lisa N. ; Cossette, Marie-Laurence ; Day, Joanna ; DeYoung, Joseph ; Dirocco, Stacy ; Dold, Christopher ; Dunnum, Jonathan L. ; Ehmke, Erin E. ; Emmons, Candice K. ; Emmrich, Stephan ; Erbay, Ebru ; Erlacher-Reid, Claire ; Faulkes, Chris G. ; Fei, Zhe ; Ferguson, Steven H. ; Finno, Carrie J. ; Flower, Jennifer E. ; Gaillard, Jean-Michel ; Garde, Eva ; Gerber, Livia ; Gladyshev, Vadim N. ; Goya, Rodolfo G. ; Grant, Matthew J ; Green, Carla B. ; Hanson, M. Bradley ; Hart, Daniel W. ; Haulena, Martin ; Herrick, Kelsey ; Hogan, Andrew N. ; Hogg, Carolyn J. ; Hore, Timothy A. ; Huang, Taosheng ; Izpisua Belmonte, Juan Carlos ; Jasinska, Anna J. ; Jones, Gareth ; Jourdain, Eve ; Kashpur, Olga ; Katcher, Harold ; Katsumata, Etsuko ; Kaza, Vimala ; Kiaris, Hippokratis ; Kobor, Michael S. ; Kordowitzki, Pawel ; Koski, William R. ; Krützen, Michael ; Kwon, Soo Bin ; Larison, Brenda ; Lee, Sang-Goo ; Lehmann, Marianne ; Lemaître, Jean-François ; Levine, Andrew J. ; Li, Xinmin ; Li, Cun ; Lim, Andrea R. ; Lin, David T. S. ; Lindemann, Dana M. ; Liphardt, Schuyler W. ; Little, Thomas J. ; Macoretta, Nicholas ; Maddox, Dewey ; Matkin, Craig O. ; Mattison, Julie A. ; McClure, Matthew ; Mergl, June ; Meudt, Jennifer J. ; Montano, Gisele A. ; Mozhui, Khyobeni ; Munshi-South, Jason ; Murphy, William J. ; Naderi, Asieh ; Nagy, Martina ; Narayan, Pritika ; Nathanielsz, Peter W. ; Nguyen, Ngoc B. ; Niehrs, Christof ; Nyamsuren, Batsaikhan ; O’Brien, Justine K. ; Ginn, Perrie O’Tierney ; Odom, Duncan T ; Ophir, Alexander G. ; Osborn, Steve ; Ostrander, Elaine A. ; Parsons, Kim M. ; Paul, Kimberly C. ; Pedersen, Amy B. ; Pellegrini, Matteo ; Peters, Katharina J. ; Petersen, Jessica L. ; Pietersen, Darren W. ; Pinho, Gabriela M. ; Plassais, Jocelyn ; Poganik, Jesse R. ; Prado, Natalia A. ; Reddy, Pradeep ; Rey, Benjamin ; Ritz, Beate R. ; Robbins, Jooke ; Rodriguez, Magdalena ; Russell, Jennifer ; Rydkina, Elena ; Sailer, Lindsay L. ; Salmon, Adam B. ; Sanghavi, Akshay ; Schachtschneider, Kyle M. ; Schmitt, Dennis ; Schmitt, Todd ; Schomacher, Lars ; Schook, Lawrence B. ; Sears, Karen E. ; Seifert, Ashley W. ; Shafer, Aaron B.A. ; Shindyapina, Anastasia V. ; Simmons, Melanie ; Singh, Kavita ; Sinha, Ishani ; Slone, Jesse ; Snell, Russel G. ; Soltanmohammadi, Elham ; Spangler, Matthew L. ; Spriggs, Maria ; Staggs, Lydia ; Stedman, Nancy ; Steinman, Karen J. ; Stewart, Donald T ; Sugrue, Victoria J. ; Szladovits, Balazs ; Takahashi, Joseph S. ; Takasugi, Masaki ; Teeling, Emma C. ; Thompson, Michael J. ; Van Bonn, Bill ; Vernes, Sonja C. ; Villar, Diego ; Vinters, Harry V. ; Vu, Ha ; Wallingford, Mary C. ; Wang, Nan ; Wilkinson, Gerald S. ; Williams, Robert W. ; Yan, Qi ; Yao, Mingjia ; Young, Brent G. ; Zhang, Bohan ; Zhang, Zhihui ; Zhao, Yang ; Zhao, Peng ; Zhou, Wanding ; Zoller, Joseph A. ; Ernst, Jason ; Seluanov, Andrei ; Gorbunova, Vera ; Yang, X. William ; Raj, Ken ; Horvath, Steve Less -
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NMFS (National Marine Fisheries Service) ; NWFSC (Northwest Fisheries Science Center)

NMFS (National Marine Fisheries Service) ; NWFSC (Northwest Fisheries Science Center) Less -
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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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Multidisciplinary
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Science, 381(6658)
DOI:

https://doi.org/10.1126/science.abq5693
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0036-8075;1095-9203;
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American Association for the Advancement of Science (AAAS)
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Journal Article
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urn:sha256:c9e37864ae9a2a40c7a93b46d50d8c82624ec103876db9e5d55415e441994e43
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DNA methylation networks underlying mammalian traits

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