Extended Data Figure 3: Mutation rate at DHS sites.
From: Nucleotide excision repair is impaired by binding of transcription factors to DNA
a–c, Mutation rate centred in DHS sites in melanomas is shown for all DHS genome wide (a), a subset of DHS regions overlapping promoters (2.5kb from TSS) (b) and DHS regions outside promoters (c). Within b and c, the first row shows the mutation rate in regions that do not contain sequences of any overlapping TFBS (noTFBS), neither predicted TFBS (from PIQ31, corresponding to 1,284 different motifs) or known TFBS (mapped from ENCODE28 ChIP-seq analysis, corresponding to 109 TFs). The second row contains only predicted TFBS (predTFBS), removing any sequences that overlap the known TFBS. The third row contains the subset of sequences that overlap with all predicted TFBS, without removing the known ones (predTFBSall). The last row contains the subset of sequences with known TFBS. The barplot at the right of each panel compares the mutation rate in the DHS and the flank for each group of regions, and the P value (from chi-square test) shows the enrichment of mutation rate between two groups. The increase in predicted TFBS is, as expected, lower than that observed within the TFBS mapped by ENCODE (DHS-promoter-TFBS), reflecting the lower precision in the mapping of the predictions compared to mapping by ChIP-seq. The zero coordinate in the x axis corresponds to the DHS peak mid-point, and the magenta line above it represents the average size of DHS (~150 nt).
