Elevated pyrimidine dimer formation at distinct genomic bases underlie promoter mutation hotspots in UV-exposed cancers

Sequencing of whole cancer genomes has revealed an abundance of recurrent mutations in gene-regulatorypromoter regions, in particular in melanoma where strong mutation hotspots areobserved adjacent to ETS-family transcription factor (TF) binding sites. While sometimesinterpreted as functional driver events, these mutations have also been suggested to be due tolocally inhibited DNA repair or, alternatively, increased propensity for UV damage formation.Here, we provide evidence that base-specific elevations in the efficacy of UV formation underliethese signals. First, we find that UV light induces mutations preferably at a known ETS promoterhotspot in cultured cells even in the absence of global or transcription-coupled nucleotideexcision repair (NER), ruling out inhibited repair. Further, by genome-wide mapping ofcyclobutane pyrimidine dimers (CPDs) shortly after UV exposure and thus before DNA repair,we find that ETS-site-related mutation hotspots coincide with a strong position-specific increasein CPD formation frequency. While inhibited NER appears to underlie a general increase insomatic mutation burden in TF binding sites, our results show that most prominent individualrecurrent bases are instead caused by elevated DNA damage formation, thus explaining a keyphenomenon in whole-genome cancer analyses.