Volume 22, No 3, Mar 2012

ISSN: 1001-0602 
EISSN: 1748-7838 2018 
impact factor 17.848* 
(Clarivate Analytics, 2019)

Volume 22 Issue 3, March 2012: 490-503

ORIGINAL ARTICLES

Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization

Iouri Chepelev^1,*, Gang Wei^1,*, Dara Wangsa², Qingsong Tang¹ and Keji Zhao¹

¹Systems Biology Center, National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA
²Section of Cancer Genomics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA Correspondence: Keji Zhao,(+1-301-496-2098;)

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 EP interactions in human CD4⁺ T cells. 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. The Gene Expression Omnibus accession number for the raw and analyzed chromatin interaction data is GSE32677.

Cell Research (2012) 22:490-503. doi:10.1038/cr.2012.15; published online 24 January 2012

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