Fig. 6: p53 drives the formation of promoter-enhancer interactions or uses pre-established ones to control gene transcription over distance.

A Percentage of significant promoter interactions (CHiCAGO score ≥ 5) gained, lost, and maintained between Nut 1 h and Nut 0 h time points (left) and Nut 10 h, and Nut 0 h time points (right) respectively. The three interaction sets shown are comparing the total interactomes (total); comparing promoter interactions with non-promoter regions (promoter with other-end or P-OE); and comparing interactomes with a p53 binding site present at either end (p53). Nut 0 h refers to control cells prior to p53 activation. B Upset plot showing the overlap between p53 binding sites and p53 distal target genes found at maintained, gained and lost interactions between Nut 1 h and Nut 0 h time points (left) and Nut 10 h and Nut 0 h time points (right). C Gene set enrichment analysis of gene sets from the Molecular Signatures Database (MSigDB) with significant enrichment (p-adj <0.05) in one or more p53 distal target gene groups defined by the interaction dynamism between Nut 1 h and Nut 0 h (left) and Nut 10 h and Nut 0 h time points (right). Bubble size indicates the number of genes found enriched for a given gene set. p values were calculated using a hypergeometric distribution test (or one-sided Fisher exact test) and adjusted for multiple comparisons using Benjamini-Hochberg (BH). D Interaction landscape of JAG2’s gene promoter (blue shade) showing dynamic interactions (arcs) with two p53-bound enhancers (red asterisk and pink shade) located 186 kb and 185 kb away. H3K27ac profiles along p53 activation are represented at the top. Peak tips colored in black represent a peak going over the scale limit. Arrows symbolize gene placement and orientation along the genomic window. E Interaction landscape of BRD7’s gene promoter (blue shade) showing stable interactions (arcs) with a p53-bound enhancer (red asterisk and pink shade). H3K27ac profiles along p53 activation are represented at the top. Peak tips colored in black represent a peak going over the scale limit. Arrows symbolize gene placement and orientation along the genomic window.