Abstract
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.
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Acknowledgements
We thank our colleagues Brian Abraham, Alika Maunakea and Daniel Kraushaar for critical reading of the manuscript and Thomas Ried for suggestions. The paired-end sequencing was performed by the DNA Sequencing Core Facility of National Heart, Lung and Blood Institute (NHLBI). This work was supported by the Division of Intramural Research, NHLBI, National Institutes of Health, USA.
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( Supplementary information is linked to the online version of the paper on the Cell Research website.)
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Supplementary information, Table S1
The list of 6520 intra-chromosomal interactions (XLSX 532 kb)
Supplementary information, Table S2
PCR primer sequences for 3C-PCR (PDF 55 kb)
Supplementary information, Table S3
PCR primer sequences for the reporter assays (PDF 52 kb)
Supplementary information, Figure S1
Miscellaneous analyses. (PDF 207 kb)
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Chepelev, I., Wei, G., Wangsa, D. et al. Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization. Cell Res 22, 490–503 (2012). https://doi.org/10.1038/cr.2012.15
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DOI: https://doi.org/10.1038/cr.2012.15
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