The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery (original) (raw)
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Integrative analysis of 111 reference human epigenomes
Nature, 2015
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 info...
The NIH Common Fund/Roadmap Epigenomics Program: Successes of a comprehensive consortium
Science Advances
The NIH Roadmap Epigenomics Program was launched to deliver reference epigenomic data from human tissues and cells, develop tools and methods for analyzing the epigenome, discover novel epigenetic marks, develop methods to manipulate the epigenome, and determine epigenetic contributions to diverse human diseases. Here, we comment on the outcomes from this program: the scientific contributions made possible by a consortium approach and the challenges, benefits, and lessons learned from this group science effort.
EpiExplorer: live exploration and global analysis of large epigenomic datasets
Epigenome mapping consortia are generating resources of tremendous value for studying epigenetic regulation. To maximize their utility and impact, new tools are needed that facilitate interactive analysis of epigenome datasets. Here we describe EpiExplorer, a web tool for exploring genome and epigenome data on a genomic scale. We demonstrate EpiExplorer’s utility by describing a hypothesis-generating analysis of DNA hydroxymethylation in relation to public reference maps of the human epigenome. All EpiExplorer analyses are performed dynamically within seconds, using an efficient and versatile text indexing scheme that we introduce to bioinformatics. EpiExplorer is available at http://epiexplorer.mpi-inf.mpg.de
Community Resources and Technologies Developed Through the NIH Roadmap Epigenomics Program
Methods in Molecular Biology, 2014
This chapter describes resources and technologies generated by the NIH Roadmap Epigenomics Program that may be useful to epigenomics researchers investigating a variety of diseases including cancer. Highlights include reference epigenome maps for a wide variety of human cells and tissues, the development of new technologies for epigenetic assays and imaging, the identifi cation of novel epigenetic modifi cations, and an improved understanding of the role of epigenetic processes in a diversity of human diseases. We also discuss future needs in this area including exploration of epigenomic variation between individuals, single-cell epigenomics, environmental epigenomics, exploration of the use of surrogate tissues, and improved technologies for epigenome manipulation.
High throughput profiling methods, such as microarray and RNA-seq, have generated thousands of data sets that measure gene expression changes at the whole genome level. However, from gene expression changes, we could only observe the phenomenon of the biological process. To decipher the underlying mechanisms of these phenomena, we have to understand the factors regulating gene expression. Understanding gene regulation is key to unraveling the mechanism of many biological processes, including cell development, lineage commitment and differentiation, and pathogenesis of cancers. Since gene regulation is controlled at both genetic and epigenetic levels, it is necessary to construct both genetic and epigenetic regulatory networks for these differentially expressed genes.