Journal Article

Integrative analysis of 111 reference human epigenomes

Karlic, Rosa, Hansen, R. Scott, Rajagopal, Nisha, Wang, Jianrong, Hong, Chibo, Thurman, Robert E., Haussler, David, Sabo, Peter J., Bilenky, Misha, Wang, Xinchen, Onuchic, Vitor, Leung, Danny, Shoresh, Noam, Marra, Marco A., Lister, Ryan, Meuleman, Wouter, Zhang, Bo, Kundaje, Anshul, Hawkins, R. David, Quon, Gerald, Whitaker, John W., Tlsty, Thea D., Amin, Viren, Lowdon, Rebecca, Thomson, James A., Harris, R. Alan, Wang, Ting, Beaudet, Arthur E., Gascard, Philippe, Ren, Bing, Zhou, Xin, Kulkarni, Ashwinikumar, Ecker, Joseph R., Sinnott-Armstrong, Nicholas A., Epstein, Charles B., Tam, Angela, Polak, Paz, Mungall, Andrew J., Siebenthall, Kyle T., Stevens, Michael, Liu, Yaping, Tsai, Li-Huei, Costello, Joseph F., Sandstrom, Richard S., Zhang, Michael Q., Neph, Shane J., Mercer, Tim R., Ray, Pradipta, Ernst, Jason, Schultz, Matthew D., Ward, Lucas D., Claussnitzer, Melina, Kaul, Rajinder, Wang, Wei, Waterland, Robert A., Meissner, Alexander, Zhang, Zhizhuo, Boyer, Laurie A., Sarkar, Abhishek, Wu, Yi-Chieh, Li, Wei, Eaton, Matthew L., Wu, Jie, Kellis, Manolis, Moore, Richard, Chuah, Eric, Ziller, Michael J., Feizi, Sohei

2015

Overview

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. This study describes the integrative analysis of 111 reference human epigenomes, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression; the results annotate candidate regulatory elements in diverse tissues and cell types, their candidate regulators, and the set of human traits for which they show genetic variant enrichment, providing a resource for interpreting the molecular basis of human disease. Epigenomics of human disease The goal of the NIH Roadmap Epigenomics Consortium was to generate a reference collection of human epigenomes for primary cells and tissues. This study describes the integrative analysis of 111 reference human epigenomes, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression. The results show that disease and trait-associated genetic variants are enriched in predicted 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.

• Publisher: Nature Publishing Group UK,Nature Publishing Group
• Subject: 38/43 / 38/91 / 45/15 / 631/114/2401 / 631/208/177 / 631/208/205/2138 / 631/553/2711 / Base Sequence / Cell Lineage - genetics / Cells, Cultured / Chromatin - chemistry / Chromatin - genetics / Chromatin - metabolism / Chromosomes, Human - chemistry / Chromosomes, Human - genetics / Chromosomes, Human - metabolism / Datasets as Topic / Deoxyribonucleic acid / DNA / DNA - chemistry / DNA - genetics / DNA - metabolism / DNA Methylation / Enhancer Elements, Genetic - genetics / Enzymes / Epigenesis, Genetic - genetics / Epigenetic inheritance / Epigenomics / Gene expression / Genetic diversity / Genetic research / Genetic variance / Genetic Variation - genetics / Genome, Human - genetics / Genome-Wide Association Study / Genomes / Genomics / Histones - metabolism / Human genome / Humanities and Social Sciences / Humans / multidisciplinary / Organ Specificity - genetics / Reference Values / RNA - genetics / Science