Recent epigenomic studies have predicted thousands of potential enhancers in the human genome. However, there has not been systematic characterization of target promoters for these potential enhancers. Using H3K4me2 as a mark for active enhancers, we identified genome-wide Enhancer-Promoter interactions in human CD4+ T cells using ChIA-PET. Among the 6 520 long- distance chromatin interactions, we identify 2 067 enhancers that interact with 1 619 promoters and enhance their expression. These enhancers exist in accessible chromatin regions and are associated with various histone modifications and polymerase II binding. The promoters with interacting enhancers are expressed at higher levels than those without interacting enhancers, and their expression levels are positively correlated with the number of interacting enhancers. Interestingly, interacting promoters are co-expressed in a tissue-specific manner. We also find that chromosomes are organized into multiple levels of interacting domains. Our results define a global view of EP interactions and provide a data set to further understand mechanisms of enhancer targeting and long-range chromatin organization.

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National Heart, Lung, and Blood Institute
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Zhong, Chao; Cui, Kairong; Wilhelm, Christoph et al. (2016) Group 3 innate lymphoid cells continuously require the transcription factor GATA-3 after commitment. Nat Immunol 17:169-78
Zhong, Chao; Cui, Kairong; Wilhelm, Christoph et al. (2016) Erratum: Group 3 innate lymphoid cells continuously require the transcription factor GATA-3 after commitment. Nat Immunol 17:214
Ren, Gang; Cui, Kairong; Zhang, Zhiying et al. (2015) Division of labor between IRF1 and IRF2 in regulating different stages of transcriptional activation in cellular antiviral activities. Cell Biosci 5:17
Crompton, Joseph G; Narayanan, Manikandan; Cuddapah, Suresh et al. (2015) Lineage relationship of CD8(+) T cell subsets is revealed by progressive changes in the epigenetic landscape. Cell Mol Immunol :
Nakatsukasa, Hiroko; Zhang, Dunfang; Maruyama, Takashi et al. (2015) The DNA-binding inhibitor Id3 regulates IL-9 production in CD4(+) T cells. Nat Immunol :
Li, Qingtian; Wang, Helen Y; Chepelev, Iouri et al. (2014) Stage-dependent and locus-specific role of histone demethylase Jumonji D3 (JMJD3) in the embryonic stages of lung development. PLoS Genet 10:e1004524
Escobar, Thelma M; Kanellopoulou, Chrysi; Kugler, David G et al. (2014) miR-155 activates cytokine gene expression in Th17 cells by regulating the DNA-binding protein Jarid2 to relieve polycomb-mediated repression. Immunity 40:865-79
Yagi, Ryoji; Zhong, Chao; Northrup, Daniel L et al. (2014) The transcription factor GATA3 is critical for the development of all IL-7Rα-expressing innate lymphoid cells. Immunity 40:378-88
Wang, Yan; Godec, Jernej; Ben-Aissa, Khadija et al. (2014) The transcription factors T-bet and Runx are required for the ontogeny of pathogenic interferon-γ-producing T helper 17 cells. Immunity 40:355-66
Hu, Gangqing; Zhao, Keji (2014) Correlating histone modification patterns with gene expression data during hematopoiesis. Methods Mol Biol 1150:175-87

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