Fig. 4

Localised mutational processes at constitutively active binding sites of CTCF. a Histogram of CTCF binding sites with number of cell lines in ENCODE. Sites were grouped as five equal bins based on conservation across cell lines (colours). Bimodal distribution reveals a subset of sites detected in most or all cell types (in red). b Pie charts show the proportion of CTCF sites in the five bins located at chromatin loop anchors (left) and that matched the core CTCF motif (right). P values represent the enrichment in the 5th bin compared to all sites (Fisher’s exact test). The median numbers of cell lines per bin are shown in brackets. c Significance of the localised mutational enrichments in the five bins CTCF binding sites. FDR values of the RM2 analysis shown on the X-axis. Colours correspond to cancer types. d Local mutation frequency in the five bins of CTCF binding sites. Solid lines show statistically significant changes in mutation frequencies compared to flanking controls (RM2 FDR < 0.05). Loess curves were used for smoothing. e Significance of mutational enrichment in highly conserved CTCF binding sites (bins 4–5) grouped by presence or absence of core DNA-binding motif of CTCF in the sites. f Mutations in constitutively bound subsets in CTCF binding sites with and without the core CTCF DNA motifs. Oesophageal cancer (left) and liver cancer (right) are compared