Figure 2: Distribution of looping interactions across cell types and their relationship with chromatin features and gene expression.
From: The long-range interaction landscape of gene promoters
a, Venn diagram showing the number of unique and overlapping looping interactions across three cell types. b, Heat map showing the enrichment/depletion of chromatin features in looping fragments compared to all interrogated fragments based on genome-wide data sets from the ENCODE consortium (Supplementary Table 7). Features include open chromatin (UW-DHS (UW, University of Washington), Duke-DHS and UNC-FAIRE (UNC, University of North Carolina; FAIRE, formaldehyde-assisted isolation of regulatory elements)); active marks (Broad Institute histone H3K4me1/2/3, H4K20me1, H3K27ac, H3K9ac); CTCF (Broad Institute CTCF ChIP peaks); inactive marks (Broad Institute histone H3K27me3); and seven-way segmentation4 (based on HMM prediction for indicated cells). We further grouped segmentation categories E and WE into ‘E class’, TSS and PF into ‘P class’, and R and T into ‘broad marks’. The colour scale represents the fold enrichment (red) or depletion (blue). The numbers listed inside each box represent P values of the significant (P < 0.05) enrichment/depletion for that mark, where (for example) E−32 indicates ×10−32 (NS, not significant, grey; two-tailed hypergeometric test and corrected for multiple testing using Bonferroni). c, Venn diagram showing the number of unique and overlapping looping distal fragments (top) and looping interactions (bottom) among four functional groups in GM12878 cells. Distal fragments are classified into four non-exclusive groups based on the seven-way segmentation. Similarly, TSS–distal fragment interactions are classified based on the functional grouping of the distal fragments. The four functional groups are E class (yellow), P class (magenta), CTCF (cyan) and unclassified (grey). d, Pie charts showing percentages and numbers of expressed/non-expressed TSSs looping or not looping to a particular group (E, P, CTCF or unclassified; coloured as in c) of distal fragments in GM12878 cells. TSSs with a CAGE value >0 are deemed expressed. Significant enrichment for expressed TSSs in the looping or non-looping categories is indicated on top (hypergeometric test; Phyper < 0.05). Significant differences in expression levels between TSS in the looping versus the non-looping category is indicated on the left (Wilcoxon signed-rank test; PWilcoxon < 0.05).
