Promoter-capture HiC data sets used

We obtained promoter-capture HiC data for GM12878 and CD34⁺ cells in human from ref. ⁵¹ and H9 cells from ref. ⁸⁹ and mouse embryonic cells (mESCs) and mouse fetal liver cells (FLCs) from ref. ⁷⁴. The processed significant promoter—other end-fragment interactions were directly obtained from the authors’ supplementary data. The corresponding promoter gene expression data for GM12878 and CD34⁺ cells are obtained from NIH Epigenomics Roadmap project, and for mESC and FLC are obtained from the ENCODE project. To find the target genes interacting with candidate silencer elements, we overlapped silencer elements with other end fragments. Then, we looked at the expression distribution of those target genes in the respective cell type. Similarly, we overlapped active enhancers with other end fragments to find enhancer interacting genes. We defined active enhancers as DHS overlapping both H3K4me1 and H3K27ac (DHS + H3K4me1 + H3K27ac).