Fig. 2: Characterization of the 3D Chromatin Organization in SOL and EDL.

a Compartment switching between SOL and EDL. b The expression changes of genes located within regions that underwent the compartment switch. A-to-B (n = 576, median = 0.163); B-to-A (n = 536, median = −0.0529); stable (n = 11581, median = 0.0071). c SIM1 gene locus underwent a B-to-A switch from SOL to EDL, with higher expression in EDL than SOL. Tracks for RNA-seq and ATAC-seq signal, and histone modification are shown. d Overlap of TAD boundaries between SOL and EDL. e Pearson correlation coefficient was calculated between the insulation scores of TADs (n = 2981) in SOL and EDL. Statistical significance was assessed using a two-sided Pearson correlation test. f The distribution of DEGs and CREs in changed TADs and cTADs. g Gene expression levels in cTADs (n = 2376) with relatively low, medium, or high D-scores. h The enriched GO terms for genes within the cTADs with higher D-scores in EDL (EDL) and cTADs with higher D-scores in SOL (SOL). Significance was tested using binomial test. i Representative cTAD with different D-scores in two tissues. Top: Hi-C contact heatmaps of the genomic region containing MYH2 gene locus. D-scores of cTAD were marked. Middle: TAD boundaries and genome browser tracks of PC1 values. Bottom: tracks for RNA-seq and ATAC-seq signal, CTCF, and histone modification. For (b and g), 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 (b) and two-sided Kruskal–Wallis test (g).