Fig. 7: SSTEs and DSEs exhibit distinct distribution preference within higher-order chromatin structures.
From: Quantitative analysis of cis-regulatory elements in transcription with KAS-ATAC-seq
a Table presenting the enriched transcription factors (TFs) motifs identified on DSEs in mESCs. The hypergeometric test was used to calculate the p-values. b Stacked bar plot showing the distribution of different ENCODE-defined candidate cis-regulatory elements (CREs) across M-SSTEs, W-SSTEs, and DSEs in mESCs. The ENCODE-defined candidate CREs include DNase I H3K4me3, distal enhancers, proximal enhancers, promoters, and CTCF binding sites. c Vertical bar plot showing the percentage of S-SSTEs, D-SSTEs, and DSEs located within TADs or at TAD boundaries. d Metagene profiles showing the averaged read density of CTCF ChIP-seq data across S-SSTEs (n = 3247), D-SSTEs (n = 15,536), and DSEs (n = 12,999) in mESCs. e Metagene profiles showing the averaged read density of KAS-ATAC-seq data across SSTEs within TADs or at TAD boundaries in mESCs. f, Snapshot of UCSC genome browser tracks showing the Hi-C-seq, CTCF ChIP-seq, Cohesin ChIP-seq, ATAC-seq, KAS-ATAC-seq, GRO-seq, NET-CAGE, RNA Pol II and Cohesin ChIA-PET data in mESCs across a representative region (chr1:53,767,262-58,437,774) with prominent topologically associating domains (TADs). TADs are marked by dashed red lines and their boundaries are highlighted in pink. g, h Vertical bar plot illustrating the percentages of promoters, S-SSTEs, D-SSTEs, and DSEs linked to long-range interaction loops defined by RNA Pol II (g) and CTCF (h) ChIA-PET data in mESCs.
