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 in UV-linked cancers. Previous investigations into 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, there has yet to be a comprehensive characterization of these mechanisms on a per-TF basis. Using genome-wide maps of UV damage from human skin fibroblasts, we developed a scalable statistical framework to analyze TF-mediated mutagenic mechanisms across hundreds of TFs. We identify numerous previously unreported TFs that significantly enhance and / or inhibit damage formation in their binding sites. A systematic survey of TF-DNA complexes further revealed that positions of UV damage modulation coincide with TF-induced structural distortions that either protect or predispose DNA to photodimer formation. Additionally, we analyzed repair efficiency in TF binding sites with unprecedented resolution, identifying specific TFs and binding site positions likely to compete with repair factors. By comparing these results with skin cancer mutations, we distinguish mutation peaks driven by increased damage susceptibility versus attenuated repair, illustrating that TF-mediated mutagenesis is highly contextual and dependent on the TF, binding site position, and sequence context of the damaged locus. Our approach provides a robust statistical framework for elucidating mechanisms of mutagenic TF-binding and offers novel insights into the complex interplay between protein interactions, DNA damage, and repair.