Genome-wide mapping of protein-DNA damage interaction by PADD-seq

The interactions between proteins and DNA damage are critical for the mechanistic studies of DNA repair and damage response. However, due to the relatively random distributions of UV-induced damage and other DNA bulky adducts, it is challenging to measure the interactions between proteins and these lesions across the genome. Therefore, we developed Protein Associated DNA Damage Sequencing (PADD-seq) to delineate genome-wide protein-DNA damage interaction at base resolution by detecting lesions in protein-bound DNA fragments. Using this method, we observed that RNA polymerase II (PolII) was blocked by damage in template strands, and the interaction declined within 2 h in transcription coupled repair-proficient cells. In contrast, it was clearly shown that PolII was restrained at damage sites in the absence of CSB. In conclusion, this new method provides a powerful tool to monitor the dynamics of protein-DNA damage interaction at genomic level, and promotes the comprehensive research for DNA repair and damage response.