Ribonucleotides embedded in yeast genomic DNA are targets of RNase H2 and the nucleotide excision repair system

Abstract

Increasing evidence suggests that ribonucleotides may represent one of the most common non-standard nucleotides found in genomic DNA. Therefore, it is important to understand the extent to which ribonucleotides alter genomic integrity and the cellular mechanisms that are responsible for removing them. We developed oligonucleotide-driven gene correction assays in the yeast Saccharomyces cerevisiae to show that, if not removed, mispaired and paired ribonucleotides embedded in genomic DNA serve as templates for DNA synthesis and could cause genetic change. We found that RNase H type 2 targets single paired and mispaired ribonucleotides, as well as a stretch of two or three ribonucleotides embedded in DNA, and the nucleotide excision repair system can target single paired ribonucleotides as damage.