Coordination of transcription-coupled repair and repair-independent release of lesion-stalled RNA polymerase II in response to transcription-blocking lesions

Elongating RNA polymerase II (PolII) will stall at transcription-blocking lesions (TBLs). Transcription coupled repair (TCR) initiated by lesion-stalled PolII is the major pathway to remove TBLs and recover transcription. However, lesion-stalled PolII also needs to be removed in the absence of TCR to allow the alternative repair machinery to access and repair TBLs. How these mutually exclusive processes are coordinated is unclear. Recently we developed Protein-Associated DNA Damage Sequencing (PADD-seq) method to investigate the interactions between PolII and UV-induced DNA lesions. With this method, we found that lesion-stalled PolII can be resolved by either TCR or p97-proteasome pathway in a repair-independent manner, both of which require CSA and ubiquitination. However, p97 is dispensable for either TCR or dissociation of PolII from damage sites in TCR-proficient cells, indicating that repair takes priority over repair-independent PolII release when TCR is applicable. Ubiquitination of RPB1-K1268 which plays a crucial role in TCR is also an important but not the sole target of p97 in repair-independent PolII release. Furthermore, the deubiquitinase activity of USP7 is involved in TCR, while it cannot abolish repair-independent PolII release. In summary, this study elucidates the fate of lesion-stalled PolII under different conditions, and may shed light on the molecular basis of genetic diseases caused by the defects of TCR genes.