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Program Initiatives

The Epigenomics program has transitioned from Common Fund support. For more information, please visit

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.


This initiative, issued as a cooperative agreement (U01), supported reference epigenome production centers to develop reference epigenomes of a variety of human cells. The cell types mapped were selected by the network of awardees with advice from external scientific experts, and include human embryonic stem cells, induced pluripotent stem cells, differentiating cells, differentiated cell populations, and human primary cells that are relevant to complex human disease. These epigenomic maps include information about DNA methylation, histone modifications, and associated non-coding RNAs. Functional correlates of these epigenetic marks, such as gene expression and chromatin accessibility (DNAseI hypersensitivity), were also measured. The comprehensive data sets comprising this valuable community resource are being used to understand basic biological processes as well as disease mechanisms, provide insights into epigenetic and genetic disease susceptibility, and assist in the identification of potential therapeutic targets. More information on this program can be found at


This cooperative agreement (U01) funded the Epigenomics Data Analysis and Coordination Center (EDACC), which provided data analysis and coordination for all of the Reference Epigenome Mapping Centers, as well as imported all other Roadmap Epigenomics Program data generated outside of the mapping centers. In addition, the EDACC was responsible for coordinating with the National Center for Biotechnology Information (NCBI) to develop and implement a data pipeline for transferring and tracking standardized data to NCBI for banking and public utility. The EDACC was originally funded in Fall 2008, and maintains the Human Epigenome Atlas, found at


This initiative supported technology development in two important areas of epigenetics research. The first area developed technologies that have revolutionized epigenetic profiling and/or whole epigenome studies. The second area enabled in vivo imaging of epigenetic changes in cells, tissues and eventually intact organisms. This initiative was initially launched under two separate RFAs - an R01 (research project) and an R21 (exploratory/developmental project) - both of these were funded in Fall 2008. A second RFA (R01) focused on in vivo imaging of epigenetic changes was funded in Fall 2010.


The current catalog of known epigenetic marks (as well as proteins that create, remove, and "read"; these marks) is likely incomplete. This initiative supported research aimed at identifying novel epigenetic marks and establishing their function in mammalian cells. The results of these studies were quickly translated to global epigenome mapping in human cells (conducted by the Reference Epigenome Mapping Centers). This initiative was launched in Fall 2007 under two separate RFAs - an R01 (research project) and an R21 (exploratory/developmental project), and was funded in Fall 2008.


This initiative supported research to identify fundamental epigenetic changes or epigenetic mechanisms underlying specific diseases; conditions of development or aging; or response to exposures (physical, chemical, behavioral, and social factors). This initiative was funded as a 50/50 cost share between the NIH Roadmap and specific NIH Institutes, Centers, and Offices. The Roadmap/IC co-funding mechanism fostered multiple IC involvement and ensured easy transition to individual ICs at the end of each funding period. A follow-up RFA (RFA-ES-10-002) was released as a multi-institute, Roadmap-affiliated initiative.

This page last reviewed on April 12, 2024