We propose to work cooperatively with other Mapping Centers and the Data Coordination Center (EDACC) funded by this Roadmap mechanism to comprehensively map epigenomes of select human cells with significant relevance to complex human disease. Our group, consisting of scientists at UCSF, UC Davis, UCSC and the British Columbia Genome Sciences Centre has the broad expertise that this project requires. We will focus on cells relevant to human health and complex disease including cells from the blood, brain, breast and U.S. Government-approved lines of human embryonic stem cells (aim 1). We will incorporate high quality, homogeneous cells from males and females, and two predominant racial groups, and biological replicates of each cell type. Production of comprehensive maps will include 6 histone modifications selected for their opposing roles in regulating active and inactive chromatin (aim 2), DNA methylation (aim 3) and miRNA and gene expression (aim 4). This epigenetic data, along with genetic and expression data will be integrated using advanced informatics (aim 5) to address fundamental roles of epigenetics in differentiation, maintenance of cell-type identity and gene expression. Our cell and data production pipeline will incorporate verification and data validation with independent methods, and will operate under a model motivated by increased data production and decrease cost. We summarize the analysis capacity of our instruments and our explicit strategy for data sharing of our proposed REMC-generated resources including biological specimens, protocols, data, software tools and intellectual resources. We envision that our group in conjunction with the other REMC teams, the EDACC, ENCODE, future EHHD (Epigenetics of Human Health and Disease) centers and the NIH Roadmap program will develop methods, tools and reference epigenome maps for the research community that will make the promise of epigenetics in understand and treating human complex disease a reality. Our reference epigenomes will enable new disciplines including human population epigenetics, comparative epigenomics, neuroepigenetics, and therapeutic epigenetics for tissue regeneration and reversal of disease.

Public Health Relevance

The epigenome is the dynamic interface between our changing environment and the static genome, and understanding it is a goal of immense importance to human health. We will map reference cell epigenomes of the brain, breast, blood and approved embryonic stem cells, inclusive of males and females and different racial groups. This cooperative work will transform our understanding of the short and long-lasting consequences of environment impact on human health and disease.

National Institute of Health (NIH)
National Institute of Environmental Health Sciences (NIEHS)
Research Project--Cooperative Agreements (U01)
Project #
Application #
Study Section
Special Emphasis Panel (ZRG1-CB-P (50))
Program Officer
Tyson, Frederick L
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of California San Francisco
Schools of Medicine
San Francisco
United States
Zip Code
Pan, Deng; Roy, Somdutta; Gascard, Philippe et al. (2016) SOX2, OCT3/4 and NANOG expression and cellular plasticity in rare human somatic cells requires CD73. Cell Signal 28:1923-1932
Yao, Lijing; Shen, Hui; Laird, Peter W et al. (2015) Inferring regulatory element landscapes and transcription factor networks from cancer methylomes. Genome Biol 16:105
Elliott, GiNell; Hong, Chibo; Xing, Xiaoyun et al. (2015) Intermediate DNA methylation is a conserved signature of genome regulation. Nat Commun 6:6363
Li, Daofeng; Zhang, Bo; Xing, Xiaoyun et al. (2015) Combining MeDIP-seq and MRE-seq to investigate genome-wide CpG methylation. Methods 72:29-40
Roadmap Epigenomics Consortium; Kundaje, Anshul; Meuleman, Wouter et al. (2015) Integrative analysis of 111 reference human epigenomes. Nature 518:317-30
Yao, Lijing; Berman, Benjamin P; Farnham, Peggy J (2015) Demystifying the secret mission of enhancers: linking distal regulatory elements to target genes. Crit Rev Biochem Mol Biol 50:550-73
Zhou, Xin; Li, Daofeng; Zhang, Bo et al. (2015) Epigenomic annotation of genetic variants using the Roadmap Epigenome Browser. Nat Biotechnol 33:345-6
Gascard, Philippe; Bilenky, Misha; Sigaroudinia, Mahvash et al. (2015) Epigenetic and transcriptional determinants of the human breast. Nat Commun 6:6351
Zhou, Xin; Li, Daofeng; Lowdon, Rebecca F et al. (2014) methylC Track: visual integration of single-base resolution DNA methylation data on the WashU EpiGenome Browser. Bioinformatics 30:2206-7
Blattler, Adam; Yao, Lijing; Witt, Heather et al. (2014) Global loss of DNA methylation uncovers intronic enhancers in genes showing expression changes. Genome Biol 15:469

Showing the most recent 10 out of 41 publications