Integrative analysis of 111 reference human epigenomes Open


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.

DOI: 10.1038/nature14248

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@article{Consortium2015IntegrativeAO, title={Integrative analysis of 111 reference human epigenomes Open}, author={Roadmap Epigenomics Consortium and Anshul Kundaje and Wouter Meuleman and Jason Ernst and Misha Bilenky and Angela Yen and Alireza Heravi Moussavi and Pouya Kheradpour and ZhiZhuo Zhang and Jianrong Wang and Michael J. Ziller and Viren Amin and John W. Whitaker and Matthew D. Schultz and Lucas D. Ward and Abhishek Sarkar and Gerald Quon and Richard S. Sandstrom and Matthew L. Eaton and Yi-Chieh Wu and Andreas R. Pfenning and Xinchen Wang and Melina Claussnitzer and Yaping Liu and Cristian Coarfa and R. Alan Harris and Noam Shoresh and Charles B. Epstein and Elizabeta Gjoneska and Danny Leung and Wei Xie and R. David Hawkins and Ryan Lister and Chibo Hong and Philippe Gascard and Andrew J. Mungall and Richard A. Moore and Eric Chuah and Angela Tam and Theresa K. Canfield and R. Scott Hansen and Rajinder Kaul and Peter J. Sabo and Mukul S. Bansal and Annaick Carles and Jesse R. Dixon and Kai-How Farh and Soheil Feizi and Rosa Karlic and Ah-Ram Kim and Ashwinikumar Kulkarni and Daofeng Li and Rebecca F. Lowdon and GiNell Elliott and Tim R. Mercer and Shane J. Neph and Vitor Onuchic and Paz Polak and Nisha Rajagopal and Pradipta Ray and Richard C. Sallari and Kyle T. Siebenthall and Nicholas A. Sinnott-Armstrong and Michael Stevens and Robert E. Thurman and Jie Wu and Bo Zhang and Xin Zhou and Arthur E. Beaudet and Laurie A. Boyer and Philip L. De Jager and Peggy J. Farnham and Susan J. Fisher and David Haussler and Steven J. M. Jones and Wei Li and Marco A. Marra and Michael T. McManus and Shamil R. Sunyaev and James A. Thomson and Thea D. Tlsty and Li-Huei Tsai and Wei Wang and Robert A. Waterland and Michael Q. Zhang and Lisa H. Chadwick and Bradley E. Bernstein and Joseph F. Costello and Joseph R. Ecker and Martin Hirst and Alexander Meissner and Aleksandar Milosavljevic and Bing Ren and John A. Stamatoyannopoulos and Ting Wang and Manolis Kellis}, journal={Nature}, year={2015}, volume={518 7539}, pages={317-30} }