Fig. 5

Comparison of OCSs and DHSs in HCT116 cells and correlation of CTCF binding with open chromatin regions. a Venn diagram showing the overlap between the OCSs and DHSs identified using NicE-seq and DNase-seq (ENCODE) for fixed HCT116 cells. b Correlation of tag enrichment (RPKM) for peaks common to NicE-seq and DNase-seq was determined using the Pearson’s linear correlation method for HCT116 cells. A linear regression line was also plotted. c A heat map showing the distribution of common peaks between NicE-seq and DNase-seq in a ±3-kb window for HCT116 cells. d A Venn diagram showing the overlap between ChIP-CTCF peaks (ENCODE), OCSs, and DHSs identified using NicE-seq and DNase-seq (ENCODE). e A heat map representing the distribution of ChIP-CTCF peaks in a ±3-kb window across ChIP-CTCF, NicE-seq, and DNase-seq data sets reveals similar patterns for enrichment of tag densities. f A heat map showing the correlation of peaks unique to ChIP-CTCF in a ±3-kb window with occupancy of RNA pol II revealed no enrichment for RNA pol II, suggesting the region is transcriptionally inactive. g A heat map showing the correlation of peaks common to ChIP-CTCF, NicE-seq, and DNase-seq data sets in a ±3-kb window with occupancy of RNA pol II revealed significant enrichment for RNA pol II, suggesting the region is transcriptionally active. h A heat map showing the correlation of peaks common to ChIP-CTCF and NicE-seq data sets in a ±3-kb window with occupancy of RNA pol II revealed enrichment for RNA pol II, suggesting the region is transcriptionally active. i A heat map showing the correlation of peaks common to ChIP-CTCF and DNase-seq data sets in a ±3-kb window with occupancy of RNA pol II revealed low enrichment for RNA pol II