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Presenting the Epigenome Roadmap

Epigenetics is implicated not just in the normal functioning of a cell and development but also in disease. Availability of the human genome sequence was a prerequisite for studies of genetic variation and its association with disease. The NIH Roadmap Epigenomics Program was created to provide a similar reference for genome-wide analyses of epigenetic changes — the epigenome.

Epigenome roadmap A Nature special issue nature.com/epigenomeroadmap

The result is a public data resource containing information on DNA methylation, histone modifications, chromatin accessibility and small RNAs in stem cells and primary cell lines selected to represent tissues and organs frequently involved in disease. This effort now culminates in the publication — here and elsewhere — of a considerable body of research papers.

On page 317 of this issue, the Roadmap Epigenomics Consortium describes the integrative analysis of 111 reference human epigenomes generated to establish global maps of regulatory elements. On page 350, Ren and colleagues describe the first human haplotype–resolved epigenomes, and show how they vary across tissues and among individuals.

Bernstein, Hafler and colleagues (page 337) present a fine-mapping strategy for genetic and epigenetic causal variants in 21 autoimmune diseases. On page 365, Tsai, Kellis and colleagues describe and compare hippocampal epigenomes of Alzheimer's disease patients with those of relevant mouse models. Stamatoyannopoulos, Sunyaev and colleagues (page 360) show how cell-of-origin chromatin organization shapes the mutational landscape of cancer.

Finally, three papers (pages 344, 355 and 331) dissect the role of epigenetic regulation in stem cell differentiation. Meissner and colleagues describe context-dependent rewiring of transcriptional regulation during differentiation of stem cells; Elkabetz, Meissner and colleagues studied regulatory networks during neural differentiation; while Ren and colleagues describe chromatin architecture changes during stem cell differentiation.

Research in this issue is accompanied by an online collection — the Epigenome Roadmap — which unites research from across Nature Publishing Group journals, as well as news stories and multimedia. Exploration of research papers is enhanced by 'threads', which highlight topics discussed in more than one paper.

We acknowledge the exclusive financial support of Illumina in producing this online collection. As always, Nature has full responsibility for all editorial content.

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Skipper, M., Eccleston, A., Gray, N. et al. Presenting the Epigenome Roadmap. Nature 518, 313 (2015). https://doi.org/10.1038/518313a

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