Fig. 3: Global remodeling of E-P interactions underpins functional divergence in SOL and EDL.

a APA analysis of chromatin loops in SOL (n = 16,086) and EDL (n = 12,923). Bin size: 10 kb. b Proportion of inter-TAD and intra-TAD loops. c Distribution of loop interaction types: P-S (promoter-silencer), P-P (promoter-promoter), P-E (promoter-enhancer), and P-none (promoter with no other CREs). d Overlap of genes with distinct E-P interactions (top-left). Schematic representation of E-P rewiring for Groups I–III. e The proportion of DEGs in Groups I–III. f Transcriptional changes for genes in Groups I–III. Log2 (Foldchange) represents as the change of gene expression in SOL compared to EDL. ALL (n = 15125, median = 0.0093); I (n = 27, median = −1.0220); II (n = 36, median = −1.1904); III (n = 100, median = 1.2397). Boxes represent the interquartile range with the median as a horizontal line; whiskers extend to the 5th and 95th percentiles. Significance was tested using a two-sided Wilcoxon test. g The expression and binding enrichment of Top 10 TFs enriched in I–III loops. Color scale represent original values as indicated in the color bar. h Percentage of loops with TFBS for selected TFs. i The enriched GO terms for genes in Group I–III. II_activated: GO term that more activated in Group II; III_activated: GO term that more activated in Group III; Common: GO term common in three Groups. j Chromatin interactions around TNNI1 and TNNI2 locus. Top: Virtual 4 C profile of loop contact differences. Tracks for chromatin loops, RNA-seq, ATAC-seq, CTCF, histone modifications, and TFBS are shown below. Enhancers are marked in green.