학술논문
Integrative analysis of 111 reference human epigenomes
Document Type
Academic Journal
Author
Consortium, Roadmap Epigenomics; Kundaje, Anshul; Meuleman, Wouter; Ernst, Jason; Bilenky, Misha; Yen, Angela; Heravi-Moussavi, Alireza; Kheradpour, Pouya; Zhang, Zhizhuo; Wang, Jianrong; Ziller, Michael J.; Whitaker, John W.; Ward, Lucas D.; Sarkar, Abhishek; Sandstrom, Richard S.; Wu, Yi-Chieh; Pfenning, Andreas R.; Wang, Xinchen; Claussnitzer, Melina; Liu, Yaping; Harris, Alan R.; Epstein, Charles B.; Leung, Danny; Hawkins, David R.; Hong, Chibo; Mungall, Andrew J.; Chuah, Eric; Hansen, Scott R.; Bansal, Mukul S.; Dixon, Jesse R.; Feizi, Soheil; Kim, Ah-Ram; Li, Daofeng; Elliott, GiNell; Neph, Shane J.; Polak, Paz; Ray, Pradipta; Siebenthall, Kyle T.; Thurman, Robert E.; Zhou, Xin; Boyer, Laurie A.; De Jager, Philip L.; Fisher, Susan J.; Li, Wei; McManus, Michael T.; Sunyaev, Shamil; Tlsty, Thea D.; Wang, Wei; Waterland, Robert A.; Costello, Joseph F.; Hirst, Martin; Stamatoyannopoulos, John A.; Wang, Ting; Amin, Viren; Schultz, Matthew D.; Quon, Gerald; Eaton, Matthew L.; Pfenning, Andreas; Liu, Melina ClaussnitzerYaping; Coarfa, Cristian; Shoresh, Noam; Gjoneska, Elizabeta; Xie, Wei; Lister, Ryan; Moore, Richard; Tam, Angela; Canfield, Theresa K.; Kaul, Rajinder; Sabo, Peter J.; Carles, Annaick; Farh, Kai-How; Karlic, Rosa; Kulkarni, Ashwinikumar; Lowdon, Rebecca; Mercer, Tim R.; Onuchic, Vitor; Rajagopal, Nisha; Sallari, Richard C.; Sinnott-Armstrong, Nicholas A.; Stevens, Michael; Wu, Jie; Zhang, Bo; Abdennur, Nezar; Adli, Mazhar; Akerman, Martin; Barrera, Luis; Antosiewicz-Bourget, Jessica; Ballinger, Tracy; Barnes, Michael J.; Bates, Daniel; Bell, Robert J. A.; Bennett, David A.; Bianco, Katherine; Bock, Christoph; Boyle, Patrick; Brinchmann, Jan; Caballero-Campo, Pedro; Camahort, Raymond; Carrasco-Alfonso, Marlene J.; Charnecki, Timothy; Chen, Huaming; Chen, Zhao; Cheng, Jeffrey B.; Cho, Stephanie; Chu, Andy; Chung, Wen-Yu; Cowan, Chad; Deng, Qixia Athena; Deshpande, Vikram; Diegel, Morgan; Ding, Bo; Durham, Timothy; Echipare, Lorigail; Edsall, Lee; Flowers, David; Genbacev-Krtolica, Olga; Gifford, Casey; Gillespie, Shawn; Giste, Erika; Glass, Ian A.; Gnirke, Andreas; Gormley, Matthew; Gu, Hongcang; Gu, Junchen; Hafler, David A.; Hangauer, Matthew J.; Hariharan, Manoj; Hatan, Meital; Haugen, Eric; He, Yupeng; Heimfeld, Shelly; Herlofsen, Sarah; Hou, Zhonggang; Humbert, Richard; Issner, Robbyn; Jackson, Andrew R.; Jia, Haiyang; Jiang, Peng; Johnson, Audra K.; Kadlecek, Theresa; Kamoh, Baljit; Kapidzic, Mirhan; Kent, Jim; Kim, Audrey; Kleinewietfeld, Markus; Klugman, Sarit; Krishnan, Jayanth; Kuan, Samantha; Kutyavin, Tanya; Lee, Ah-Young; Lee, Kristen; Li, Jian; Li, Nan; Li, Yan; Ligon, Keith L.; Lin, Shin; Lin, Yiing; Liu, Jie; Liu, Yuxuan; Luckey, John C.; Ma, Yussanne P.; Maire, Cecile; Marson, Alexander; Mattick, John S.; Mayo, Michael; McMaster, Michael; Metsky, Hayden; Mikkelsen, Tarjei; Miller, Diane; Miri, Mohammad; Mukame, Eran; Nagarajan, Raman P.; Neri, Fidencio; Nery, Joseph; Nguyen, Tung; OʼGeen, Henriette; Paithankar, Sameer; Papayannopoulou, Thalia; Pelizzola, Mattia; Plettner, Patrick; Propson, Nicholas E.; Raghuraman, Sriram; Raney, Brian J.; Raubitschek, Anthony; Reynolds, Alex P.; Richards, Hunter; Riehle, Kevin; Rinaudo, Paolo; Robinson, Joshua F.; Rockweiler, Nicole B.; Rosen, Evan; Rynes, Eric; Schein, Jacqueline; Sears, Renee; Sejnowski, Terrence; Shafer, Anthony; Shen, Li; Shoemaker, Robert; Sigaroudinia, Mahvash; Slukvin, Igor; Stehling-Sun, Sandra; Stewart, Ron; Subramanian, Sai Lakshmi; Suknuntha, Kran; Swanson, Scott; Tian, Shulan; Tilden, Hannah; Tsai, Linus; Urich, Mark; Vaughn, Ian; Vierstra, Jeff; Vong, Shinny; Wagner, Ulrich; Wang, Hao; Wang, Tao; Wang, Yunfei; Weiss, Arthur; Whitton, Holly; Wildberg, Andre; Witt, Heather; Won, Kyoung-Jae; Xie, Mingchao; Xing, Xiaoyun; Xu, Iris; Xuan, Zhenyu; Ye, Zhen; Yen, Chia-an; Yu, Pengzhi; Zhang, Xian; Zhang, Xiaolan; Zhao, Jianxin; Zhou, Yan; Zhu, Jiang; Zhu, Yun; Ziegler, Steven; Beaudet, Arthur E.; Farnham, Peggy J.; Haussler, David; Jones, Steven J. M.; Marra, Marco A.; Thomson, James A.; Tsai, Li-Huei; Zhang, Michael Q.; Chadwick, Lisa H.; Bernstein, Bradley E.; Ecker, Joseph R.; Meissner, Alexander; Milosavljevic, Aleksandar; Ren, Bing; Kellis, Manolis
Source
Nature. Feb 19, 2015 518(7539):317-330
Subject
Language
English
ISSN
0028-0836
Abstract
The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but epigenomic studies lack a similar reference. To address this need, the NIH Roadmap Epigenomics Consortium generated the largest collection so far of human epigenomes for primary cells and tissues. Here we describe the integrative analysis of 111 reference human epigenomes generated as part of the programme, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression. We establish global maps of regulatory elements, define regulatory modules of coordinated activity, and their likely activators and repressors. We show that disease- and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease. Our results demonstrate the central role of epigenomic information for understanding gene regulation, cellular differentiation and human disease.