Nucleotide excision repair and photolyase preferentially repair the nontranscribed strand of RNA polymerase III-transcribed genes in Saccharomyces cerevisiae

Abstract

A high-resolution primer extension technique was used to study the relationships between repair, transcription, and mutagenesis in RNA polymerase III transcribed genes in Saccharomyces cerevisiae. The in vivo repair of UV-induced DNA damage by nucleotide excision repair (NER) and by photoreactivation is shown to be preferential for the nontranscribed strand (NTS) od the SNR6 gene. This is in contrast to RNA polymerase II genes in which the NER is preferential for the transcribed strand (TS). The repair- strand bias observed in SNR6 was abolished by inactivation of transcription in a snr6Δ2 mutant, showing a contribution od RNA polymerase III transcription in this phenomenon. The same strand bias for NER (slow in TS, fast in NTS) was discovered in the SUP4 gene, but only outside of the intragenic promoter element (box A). Unexpectedly, the repair in the transcribed box A was similar on both strands. The strand specificity as well as the repair heterogeneity determined in the transcribed strand ot the SUP4 gene, correlate well with the previously reported site- and strand-specific mutagenesis in this gene. These findings present a novel view regarding the relationships between DNA repair, mutagenesis, and transcription.