Elf1 promotes TC-NER in yeast by using its C-terminal domain to bind TFIIH

Transcription coupled-nucleotide excision repair (TC-NER) repairs DNA lesions that stall RNA polymerase II (Pol II) transcription. Here, we show that the C-terminal domain (CTD) of elongation factor-1 (Elf1) plays a critical role in TC-NER in yeast. Analysis of genome-wide repair of UV-induced cyclobutane pyrimidine dimers (CPDs) using CPD-seq indicates that the Elf1 CTD is required for efficient Rad26-dependent and Rad26-independent TC-NER across the yeast genome. The Elf1-CTD is also important for TC-NER in rad16∆ cells deficient in GG-NER. Finally, we show that a mutant in the Elf1-CTD (elf1-Y99A) that disrupts binding to a subunit of TFIIH affects Rad26-independent repair in a rad26∆ mutant background. We used the CPD-seq method to map UV-induced cyclobutane pyrimidine dimers (CPDs) a single nucleotide resolution across the yeast genome, both immediately after UV-radiation (UV 0hr) and following 2 hours of repair (UV 2hr). The no UV control represents unirradated sample. These experiments were performed in different mutant backgrounds, including mutants in Elf1.