The Rad4 homologue YDR314C is essential for strand-specific repair of RNA polymerase I-transcribed rDNA in Saccharomyces cerevisiae.

Summary The Saccharomyces cerevisiae protein Rad4 is involved in damage recognition in nucleotide excision repair (NER). In RNA polymerase II-transcribed regions Rad4 is essential for both NER subpathways global genome repair (GGR) and transcription coupled repair (TCR). In ribosomal DNA (rDNA), however, the RNA polymerase I-transcribed strand can be repaired in the absence of Rad4. In Saccharomyces cerevisiae the YDR314C protein shows homology to Rad4. The possible involvement of YDR314C in NER was studied by analysing strand-specific cyclobutane pyrimidine dimer (CPD) removal in both RNA pol I- and RNA pol II-transcribed genes. Here we show that the Rad4-independent repair of rDNA is dependent on YDR314C. Moreover, in Rad4 proficient cells preferential repair of the transcribed strand of RNA pol I-transcribed genes was lost after deletion of YDR314C, demonstrating that Rad4 cannot replace YDR314C. CPD removal from the RNA pol II-transcribed RPB2 gene was unaffected in ydr314c mutants. We conclude that the two homologous proteins Rad4 and YDR314C are both involved in NER and probably have a similar function, but operate at different loci in the genome and are unable to replace each other.