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Program Snapshot

The Epigenomics program has transitioned from Common Fund support. Common Fund programs are strategic investments that achieve a set of high-impact goals within a 5-10 year timeframe. At the conclusion of each program, deliverables transition to other sources of support or use within the scientific community.

Please note that since the Epigenomics program is no longer supported by the Common Fund, the program website is being maintained as an archive and will not be updated on a regular basis.

The Epigenomics program was supported by the Common Fund from 2008 to 2017. Currently, Roadmap-developed datasets are available through the Roadmap Epigenomics Mapping Consortium website, the ENCODE website, IHEC, and the Baylor Epigenome Atlas. During the period of program funding, there was a significant increase in the funding and study of Epigenomics, a diversification in topics of funded Epigenomics projects, and an increase in the types of diseases linked to epigenomic changes.

Highlights of the Epigenomics program’s major accomplishments are:

  • Completion of 111 reference epigenomes in a variety of healthy human cells and tissues
  • Development of mammalian whole genome bisulfite sequencing for DNA methylation determination
  • Development of epigenomic metadata and data standards that have been adopted by the scientific community
  • Enabling human in vivo epigenetic enzyme imaging using PET
  • Advancing functional epigenomic manipulation using CRISPR
  • Generation of over 2,600 data sets used to predict tissue-specific patterns of human disease
  • Discovered new epigenetic marks, including novel histone modifications

The Common Fund's Epigenomics Program generated a set of reference epigenomes and new research tools, technologies, datasets, and infrastructure that accelerated our understanding of how genome-wide chemical and non-chemical modifications to DNA and the proteins DNA wraps around regulate gene activity without altering the DNA sequence itself and what role these modifications play in health and disease.

The Roadmap Epigenomics program issued its first round of awards in 2008. The program issued 77 awards and produced 111 reference maps of epigenomic modifications in a variety of healthy human cells and tissues, as well as other resources and tools that are extensively used by the biomedical research community. The Roadmap datasets are available through the Roadmap Epigenomics Mapping Consortium website, the ENCODE website, IHEC), and the Baylor Epigenome Atlas. Over 230 publications have cited use of Roadmap Epigenomics program data, with publications covering a wide range of topics. The Roadmap Epigenomics program became a founding member of the International Human Epigenome Consortium (IHEC) in 2010, which has significantly enhanced global funding and coordination of epigenomic research. Roadmap Epigenomics awardees published over 800 peer-reviewed articles. An integrative analysis paper, together with more than 20 companion papers, was published in a 2015 special edition of Nature. Program funding ended in 2017.

A Scientific Illustration of How Epigenetic Mechanisms Can Affect Health

Epigenomics is a quickly growing frontier of science focusing on DNA modifications and modifications of proteins associated with DNA.  These modifications occur “on top of” the genome and can be associated with changes in gene activity without alteration of the underlying DNA sequence, or “genetic blueprint.” The Common Fund-supported NIH Roadmap Epigenomics Program focused on characterizing the occurrence and potential functions of these modifications in normal development and in a wide variety of diseases.

There are many types of epigenomic modifications and their occurrence across the human genome has not been well-characterized.  Therefore, one component of the program was mapping these modifications across the entire genome of many different human cell types. These include stem cells and a range of primary cell types and tissues (e.g. cells and tissues from blood, lung, heart, gastrointestinal tract, and brain).  These epigenomic maps are available to the entire scientific community for use in their own research projects through the National Center for Biotechnology Information at the NIH ( More can be learned about the Epigenomics mapping effort, including the relevant protocols used to obtain data and the numerous publications generated thus far, through the Common Fund Roadmap Epigenomics Program Website) .

The generation of these epigenomic maps for different cellular states is beginning to allow scientists to: (1) identify which epigenomic modifications are the most informative to map; (2) predict the functions of particular regions of the genome; and (3) provide a glimpse of how the epigenomes of distinct cell and tissue types differ. These data sets can also be used to help identify genetic loci and epigenomic changes associated with different diseases.

The Epigenomics Program also supported individual research projects examining the role of epigenetic regulation in a wide variety of diseases and conditions (see the Funded Research for specific research projects under initiative RFA-RM-08-017). In addition, the program supported the discovery of new epigenetic modifications that may play a role in human health, as well as new technologies that permit enhanced epigenetic analyses, including the imaging of epigenetic changes in vivo. Surveys of Epigenomics program staff, funded researchers, and external scientific experts found that all groups considered this a very successful program based on the quality of knowledge and products generated.

The NIH Roadmap Epigenomics Program joined the International Human Epigenome Consortium (IHEC), a growing international effort to coordinate worldwide epigenome mapping and to disseminate experimental standards for epigenome characterization, in 2010.  Read more about IHEC at:

Read more about the program initiatives

NIH Roadmap Epigenomics

Information about the data, protocols, reagents, and analytical tools generated by the Epigenomics Program, including over 100 comprehensive reference epigenomic datasets from hundreds of human cell types and tissues, can be found on the Roadmap Epigenomics Website.

New Resources from the Roadmap Epigenomics Program

Researchers report a large suite of driver and reporter transgenic mouse lines for a wide range of applications, greatly expanding the selection of high-precision genetic tools to study cell types in the mouse brain.

Epigenomes Around the World

The Epigenomics Program is part of the International Human Epigenome Consortium that aims to coordinate worldwide epigenome mapping and characterization efforts. 

Creative Mind

Anshul Kundaje was recently featured on the NIH Director's Blog. He led the integrative analysis of the Roadmap Epigenomics data as part of a team funded by the NIH Common Fund Epigenomics Program.

A Roadmap to the Living Genome

Learn more about Epigenomics grantee John Stamatoyannopoulos’ lecture “A Roadmap to the Living Genome,” in which he presents research describing new epigenomic maps for a wide variety of normal human cell/tissue types; insights into the genomic patterning of epigenomic features; and encoding of cellular state, maturity, and fate information within epigenomic landscapes.

Watch the video “A Roadmap to the Living Genome” or view the slides from the Epigenomics presentation to the NIH Council of Councils.

This page last reviewed on June 4, 2024