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Integrative analysis of 111 reference human epigenomes.


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.

SUBMITTER: Roadmap Epigenomics Consortium 

PROVIDER: S-EPMC4530010 | biostudies-literature | 2015 Feb

REPOSITORIES: biostudies-literature

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Integrative analysis of 111 reference human epigenomes.

Kundaje Anshul A   Meuleman Wouter W   Ernst Jason J   Bilenky Misha M   Yen Angela A   Heravi-Moussavi Alireza A   Kheradpour Pouya P   Zhang Zhizhuo Z   Wang Jianrong J   Ziller Michael J MJ   Amin Viren V   Whitaker John W JW   Schultz Matthew D MD   Ward Lucas D LD   Sarkar Abhishek A   Quon Gerald G   Sandstrom Richard S RS   Eaton Matthew L ML   Wu Yi-Chieh YC   Pfenning Andreas R AR   Wang Xinchen X   Claussnitzer Melina M   Liu Yaping Y   Coarfa Cristian C   Harris R Alan RA   Shoresh Noam N   Epstein Charles B CB   Gjoneska Elizabeta E   Leung Danny D   Xie Wei W   Hawkins R David RD   Lister Ryan R   Hong Chibo C   Gascard Philippe P   Mungall Andrew J AJ   Moore Richard R   Chuah Eric E   Tam Angela A   Canfield Theresa K TK   Hansen R Scott RS   Kaul Rajinder R   Sabo Peter J PJ   Bansal Mukul S MS   Carles Annaick A   Dixon Jesse R JR   Farh Kai-How KH   Feizi Soheil S   Karlic Rosa R   Kim Ah-Ram AR   Kulkarni Ashwinikumar A   Li Daofeng D   Lowdon Rebecca R   Elliott GiNell G   Mercer Tim R TR   Neph Shane J SJ   Onuchic Vitor V   Polak Paz P   Rajagopal Nisha N   Ray Pradipta P   Sallari Richard C RC   Siebenthall Kyle T KT   Sinnott-Armstrong Nicholas A NA   Stevens Michael M   Thurman Robert E RE   Wu Jie J   Zhang Bo B   Zhou Xin X   Beaudet Arthur E AE   Boyer Laurie A LA   De Jager Philip L PL   Farnham Peggy J PJ   Fisher Susan J SJ   Haussler David D   Jones Steven J M SJ   Li Wei W   Marra Marco A MA   McManus Michael T MT   Sunyaev Shamil S   Thomson James A JA   Tlsty Thea D TD   Tsai Li-Huei LH   Wang Wei W   Waterland Robert A RA   Zhang Michael Q MQ   Chadwick Lisa H LH   Bernstein Bradley E BE   Costello Joseph F JF   Ecker Joseph R JR   Hirst Martin M   Meissner Alexander A   Milosavljevic Aleksandar A   Ren Bing B   Stamatoyannopoulos John A JA   Wang Ting T   Kellis Manolis M  

Nature 20150201 7539


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, D  ...[more]

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