Functional mutations form at CTCF-cohesin binding sites in melanoma due to uneven nucleotide excision repair across the motif. Homo sapiens

CTCF binding sites are frequently mutated in cancer, but how these mutations accumulate and whether they broadly perturb CTCF binding is not well understood. We report that skin cancers exhibit a highly-specific asymmetric mutation pattern within CTCF motifs attributable to ultraviolet irradiation and differential nucleotide excision repair (NER). CTCF binding site mutations form independent of replication timing and are enriched at sites of CTCF/cohesin complex binding, suggesting a role for cohesin in stabilizing CTCF-DNA binding and impairing NER. Performing CTCF ChIP-seq in a melanoma cell-line, we show CTCF binding site mutations to be functional by demonstrating allele-specific reduction of CTCF binding to mutant alleles. While topologically-associating domains with mutated CTCF anchors in melanoma contain differentially-expressed cancer-associated genes, CTCF motif mutations appear generally under neutral selection. However, the frequency and potential functional impact of such mutations in melanoma highlights the need to consider their impact on cellular phenotype in individual genomes. Overall design: Chromatin immunoprecipiation sequencing (ChIP-seq) against CTCF in malignant melanoma cell-line COLO829, together with IgG background control. 2 replicate experiments performed. Replicates for CTCF ChIP sequenced separately. IgG ChIP from second replicate experiment sequenced.