High-throughput characterization of transcription factors that modulate UV damage formation and repair at single-nucleotide resolution

Genomic studies have revealed elevated damage and mutation rates in active transcription factor (TF) binding sites of UV-linked cancers. Previous research investigating the relationship between TF activity and UV DNA damage have primarily focused on select TFs or been done in aggregate across large cohorts of TFs at kilobase resolution. While collectively, there is evidence that TFs contribute to UV-induced mutagenesis by both enhancing initial damage formation and attenuating repair, no method exists to comprehensively characterize these mechanisms driving downstream mutation enrichment on a per-TF basis. Using genome-wide maps of UV damage from human skin fibroblasts, we developed a scalable statistical framework to identify and deconvolve TF-mediated mutagenic mechanisms across hundreds of TFs. We show that numerous previously unidentified TFs significantly modulate damage formation in their binding sites. Our systematic survey of TF-DNA complexes reveals that TF-induced structural distortions predispose DNA to specific photodimer types and coincide with UV damage enrichment, highlighting the role of structure in UV damage formation. Additionally, we analyzed repair efficiency in TF binding sites with unprecedented resolution, identifying specific TFs and binding site positions likely driving competition with repair factors. By comparing these results with skin cancer sample mutations, we can distinguish mutation peaks driven by increased damage susceptibility versus attenuated repair, illustrating that the mechanisms of TF-mediated mutagenesis are both TF- and position-specific. Our approach provides a robust statistical framework to elucidate the mechanisms of mutagenic TF-binding and offers novel insights into the complex interplay between protein interactions with DNA damage and repair.