Integrative analysis of 111 reference human epigenomes

Kundaje, A., Meuleman, W., Ernst, J., Bilenky, M., Yen, A., Heravi-Moussavi, A., Kheradpour, P., Zhang, Z., Wang, J., Ziller, M. J., Amin, V., Whitaker, J. W., Schultz, M. D., Ward, L. D., Sarkar, A., Quon, G., Sandstrom, R. S., Eaton, M. L., Wu, Y. C., Pfenning, A. R., Wang, X., Claussnitzer, M., Liu, Y., Coarfa, C., Harris, R. A., Shoresh, N., Epstein, C. B., Gjoneska, E., Leung, D., Xie, W., Hawkins, R. D., Lister, R., Hong, C., Gascard, P., Mungall, A. J., Moore, R., Chuah, E., Tam, A., Canfield, T. K., Hansen, R. S., Kaul, R., Sabo, P. J., Bansal, M. S., Carles, A., Dixon, J. R., Farh, K. H., Feizi, S., Karlic, R., Kim, A. R., Kulkarni, A., Li, D., Lowdon, R., Elliott, G., Mercer, T. R., Neph, S. J., Onuchic, V., Polak, P., Rajagopal, N., Ray, P., Sallari, R. C., Siebenthall, K. T., Sinnott-Armstrong, N. A., Stevens, M., Thurman, R. E., Wu, J., Zhang, B., Zhou, X., Beaudet, A. E., Boyer, L. A., De Jager, P. L., Farnham, P. J., Fisher, S. J., Haussler, D., Jones, S. J., Li, W., Marra, M. A., McManus, M. T., Sunyaev, S., Thomson, J. A., Tlsty, T. D., Tsai, L. H., Wang, W., Waterland, R. A., Zhang, M. Q., Chadwick, L. H., Bernstein, B. E., Costello, J. F., Ecker, J. R., Hirst, M., Meissner, A., Milosavljevic, A., Ren, B., Stamatoyannopoulos, J. A., Wang, T., Kellis, M. (February 2015) Integrative analysis of 111 reference human epigenomes. Nature, 518 (7539). pp. 317-30. ISSN 0028-0836

URL: http://www.ncbi.nlm.nih.gov/pubmed/25693563
DOI: 10.1038/nature14248

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.

Item Type: Paper
Subjects: bioinformatics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > epigenetics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > epigenetics
CSHL Authors:
Communities: CSHL labs > Zhang lab
Depositing User: Matt Covey
Date: 19 February 2015
Date Deposited: 27 Feb 2015 18:04
Last Modified: 27 Feb 2015 18:04
Related URLs:
URI: http://repository.cshl.edu/id/eprint/31246

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