Integrative analysis of 111 reference human epigenomes

Integrative analysis of 111 reference human epigenomes

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 pri...

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Bibliographic Details
Main Authors: Kundaje, Anshul, Meuleman, Wouter, Ernst, Jason, Yen, Angela, Kheradpour, Pouya, Zhang, Zhizhuo, Wang, Jianrong, Ward, Lucas D., Sarkar, Abhishek Kulshreshtha, Quon, Gerald, Eaton, Matthew Lucas, Wu, Yi-Chieh, Pfenning, Andreas R., Wang, Xinchen, Claussnitzer, Melina, Liu, Yaping, Bansal, Mukul S., Kim, Ah Ram, Cowper Sal-lari, Richard, Sinnott-Armstrong, Nicholas A., Gjoneska, Elizabeta, Tsai, Li-Huei, Kellis, Manolis, Feizi- Khankandi, Soheil, Boyer, Laurie Ann
Other Authors: Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory
Format: Article
Language:en_US
Published: Nature Publishing Group 2016
Online Access:http://hdl.handle.net/1721.1/100801
https://orcid.org/0000-0002-0964-0616
https://orcid.org/0000-0003-1202-4037
https://orcid.org/0000-0002-8017-809X
https://orcid.org/0000-0002-1716-0153
https://orcid.org/0000-0003-4165-7693
https://orcid.org/0000-0002-5451-3798
https://orcid.org/0000-0002-3447-9801
https://orcid.org/0000-0002-4636-9255
https://orcid.org/0000-0002-8305-9125
https://orcid.org/0000-0003-1262-0592
https://orcid.org/0000-0002-3255-4740
https://orcid.org/0000-0001-5951-9358
https://orcid.org/0000-0003-2450-736X
https://orcid.org/0000-0002-9747-4936
https://orcid.org/0000-0003-3491-4962
https://orcid.org/0000-0002-1196-5401
Description
Summary: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.

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