Environmental Factor

October 2011


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Epigenomics data goes public

By Ed Kang
October 2011

next-generation sequencing

The consortium leverages next-generation sequencing technologies to map DNA methylation, histone modifications, chromatin accessibility, and small RNA transcripts in human embryonic stem cells as well as primary ex vivo tissues selected to represent the normal counterparts of tissues and organ systems frequently involved in human disease.

Lisa Chadwick, Ph.D.

Chadwick is one of the NIEHS administrators for the NIH Roadmap Epigenomic Mapping Consortium.(Photo courtesy of Steve McCaw)

Frederick Tyson, Ph.D.

Tyson shares responsibility as co-lead on the project. (Photo courtesy of Steve McCaw)

The NIH Roadmap Epigenomics Mapping Consortium is delivering on its promise of developing a public resource of human epigenomic data. Established around the hypothesis that epigenetics plays a critical role in human health, the mapping consortium(http://www.roadmapepigenomics.org/) Exit NIEHS is creating and cataloging reference epigenomes from a variety of normal human cells and tissues that investigators from the larger scientific community can use for their own comparisons.

The project is part of the Roadmap Epigenomics Program(http://commonfund.nih.gov/epigenomics) Exit NIEHS, an NIH Common Fund effort exploring an emerging frontier of science, which involves the study of changes in the regulation of gene activity and expression that are not dependent on gene sequence. NIEHS leads this program, along with the National Institute on Drug Abuse (NIDA). The data arising from the program will be particularly useful for environmental health scientists, because epigenetic misregulation resulting from environmental exposures is increasingly thought to be an important contributor to disease.

Mapping the human epigenome

The global analysis of epigenetic changes across the entire genome, or epigenomics, is a key focal point of the mapping activity. This has generated huge amounts of data for comparison and integration within a broad array of future studies.

Lisa Chadwick, Ph.D., and Frederick Tyson, Ph.D., program administrators in the NIEHS Division of Extramural Research and Training, are the program leads for the four Roadmap Epigenomic Mapping Centers at the Massachusetts Institute of Technology, the University of California San Francisco, the Ludwig Institute for Cancer Research, and the University of Washington.

According to Chadwick, the consortium is developing a community resource that contains epigenomic maps for a variety of adult and fetal cell and tissue types, as well as a number of embryonic and induced pluripotent stem cells. “Through the consortium, we've been successful in making protocols and data rapidly available,” said Chadwick. “There is a ton of useful information available, and we've made it easy for the scientific community to access and use it,” she said in reference to the data browsing capabilities that help users crunch data into usable form.

Chadwick sees a broader future for the data produced by the consortium. “A number of NIEHS-funded investigators have been using genome-wide association studies (GWAS) to identify susceptibility loci. The data from the mapping project have been proving to be a useful tool for interpreting GWAS hits, which often don't immediately make sense [because] they frequently land in genomic regions that don't have an obvious function. The epigenomic data that we are generating can be used to make predictions about the functional significance of these sequences.”

NIEHS will host an epigenetics mini-symposium Jan. 10, 2012, where some data from the Roadmap Epigenomic Mapping Consortium will be presented.

(Ed Kang is a public affairs specialist in the Office of Communications and Public Liaison and a regular contributor to the Environmental Factor.)

In addition to raw data, information about protocols, quality metrics,
as well as a variety of analysis tools can be found
at the following websites:

Roadmap epigenomics project (http://RoadmapEpigenomics.org)

http://RoadmapEpigenomics.org

National Center for Biotechology Information (http://ncbi.nlm.nih.gov/epigenomics)

http://ncbi.nlm.nih.gov/epigenomics

Human Epigenome Atlas (http://epigenomeatlas.org)

http://epigenomeatlas.org

Roadmap Epigenomics Visualization Hub (http://vizhub.wustl.edu)

http://vizhub.wustl.edu



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