NEK1 Phosphorylation Modulates ERCC6 in Transcription-Coupled Nucleotide Excision Repair

DNA damage must be efficiently repaired to sustain cell survival. During transcription, RNA polymerases (RNAPs) serve as sentinels of genome health by detecting bulky DNA lesions, such as UV-induced CPDs, and initiating TC-NER. TC-NER has been most investigated for Pol II, and depends on coordinated interaction of numerous NER proteins, including the central translocase ERCC6(CSB), largely to dislodge the stalled EC. However, this basic mechanism is not unique to Pol II. RNA polymerase I, responsible for ribosomal RNA synthesis, dominates transcriptional output. Using structural and molecular analyses, we found that Pol I known to be stalled at CPDs due to interactions near its active site, requires ERCC6 (CSB) to displace the stalled EC and enable repair, whose activity we now show depends heavily on multiple phosphorylations of the “hydroxy patch”. TLK1 and its downstream kinase NEK1 regulate ERCC6 through phosphorylation of conserved residues within a “hydroxy patch” essential for ATPase and DNA interactions. Mutational disruption of this phosphorylation ‘core’ impaired Pol I transcription recovery and pre-rRNA processing following UV exposure. These findings uncover a TLK1–NEK1–ERCC6 regulatory axis linking DNA repair, ribosome biogenesis, and the integrated stress response that results in cell cycle progression delay and major reprogramming of the transcriptional repertoire. Comparative analysis with yeast orthologs, studying traditional TC-NER of protein-coding genes, suggests this mechanism is evolutionarily conserved.