Endogenous DNA breaks were detected at RNA polymerase II promoters and are likely to contribute to genomic instability. Éva Hegedüs et al., Nucleic Acids Research, 2018, 1, DOI: 10.1093/nar/gky743
Molecular combing and gel electrophoretic studies revealed endogenous single-strand breaks, nicks with free 3′OH ends at ∼100 kb intervals in the genomic DNA of unperturbed and G1-synchronized Saccharomyces cerevisiae cells. These breaks accumulated at active RNA polymerase II promoters, reminiscent of the promoter-proximal transient DNA breaks of higher eukaryotes. Similar periodicity of endogenous nicks was found within the ribosomal rDNA cluster, involving every ∼10th of the tandemly repeated 9.1 kb units of identical sequence. Nicks were mapped by Southern blotting to a few narrow regions within the affected units. Three of them were overlapping the RNAP II promoters, while the region directing rDNA replication was spared of nicks. By using a highly sensitive method to map free DNA ends with 3′OH, they were shown to be distinct from other known rDNA breaks and linked to transcriptional regulation at the locus. Nicks were typically found at the ends of combed DNA molecules, occasionally together with R-loops, comprising a major pool of vulnerable sites that are connected with transcriptional regulation and are likely to contribute to genomic instability.