Fig. 3: Genome-wide analysis of gene–enhancer contact.
a, Chromosomes with three tracks plotted for 10-kb bins. Left to right, within each chromosome, the tracks represent the sum of 3D contact frequencies of a bin with all enhancer regions on the same chromosome (averaged across samples); the log-ratio of A versus B compartment calls across samples at that bin, where higher values imply more open chromatin (A compartment) and lower values imply more closed chromatin (B compartment); and the average TPM of genes whose TSS falls in the given bin. b, Two-dimensional density plot showing how the contact frequency of 3D chromatin interactions between a gene’s TSS and enhancers (column 1, a) relates to expression (column 3, a). c, Scatter plot showing the relationship between the A and B compartment log-ratio (column 2, a) and the contact frequency of 3D contacts with enhancers (column 1, a). d–f, Recurrent intrachromosomal contacts (green links, the height represents the frequency of interaction observed across samples) between the TSS (red dot) of FOXA1 (d), MYC (e) and AR (f), and putative enhancers (blue peaks around the outside, recurrently hypomethylated H3K27ac regions, with peak height equal to the number of hypomethylated samples). The association between putative enhancers and gene expression was measured using a t-statistic between the hypomethylation status of enhancer and gene expression (pink peaks around the outside); all P < 0.05. All t-statistics were positive.
