Fig. 2: Chromatin regulatory domains (CRDs) and gene–enhancer interactions.

a Distribution of lengths is shown for CTCF-mediated chromatin loops (ChIA-PET; n = 21,805). b The fraction of differentially H3K27ac modified peaks are shown per CRD. Peaks were classified as higher in PAH (red), healthy (blue), or unchanged (grey) if their log2 fold change value was above 0.5, below −0.5, or between −0.5 and 0.5 respectively. c Schematic of the approach for determining CRDs: H3K27ac peaks at the two boundaries of CTCF-mediated ChIA-PET loops are positively correlated (p-value < 0.05). d P-value distribution of Pearson correlation coefficients (R) between H3K27ac signals located at opposite anchor points within the same CTCF loop; R > 0 (red bars) and R < 0 (blue bars). e P-value distribution of Pearson correlation coefficients (R) of H3K27ac signal and expression of genes that are within the same CTCF loop; R > 0 (red bars), R < 0 (green bars) and randomly located H3K27ac signals (blue bars). f GO terms that are enriched among the genes that are connected to differentially H3K27-acetylated enhancers within CRDs. Some of the GO terms have very similar sets of genes and are thus not completely independent. g For each number of enhancers (x-axis) the fraction of genes within CRDs (orange) and within non-CRD ChIA-PET loops (blue) are shown. h Examples of ChIA-PET data is shown for two genes also shown in Fig. 1f (additional genes shown in Supplementary Fig. 3e). CRD-ChIA PET loops are shown in red, correlation-based enhancer-gene interactions are shown in green and non-CRD ChIA-PET loops are shown in grey. Source data for a–b, d–e, h are provided in Source Data File.