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DNA damage poses a constant threat to genome integrity and 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 cyclobutane pyrimidine dimers (CPDs), and initiating repair through transcription-coupled nucleotide excision repair (TC-NER). In proliferating cells, RNA polymerase I (Pol I), responsible for ribosomal RNA synthesis, dominates transcriptional output. Using structural and molecular analyses, we found that Pol I stalls at CPDs due to interactions near its active site, requiring ERCC6 (CSB) to displace the stalled complex and enable repair. Our investigation revealed that TLK1 and its downstream kinase NEK1 regulate ERCC6 through phosphorylation of conserved residues within a “hydroxy patch” essential for ATPase and DNA-binding activity. Mutational disruption of this phosphorylation 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. Comparative analysis with yeast orthologs, studying traditional TC-NER of coding genes, suggests this mechanism is evolutionarily conserved, underscoring a unified strategy across eukaryotes to coordinate transcriptional recovery and genome maintenance following genotoxic stress.