Endogenous single-strand DNA breaks at RNA polymerase II promoters in Saccharomyces cerevisiae
More about Open Access at the CrickAuthors list
Éva Hegedüs Endre Kókai Péter Nánási László Imre László Halász Rozenn Jossé Zsuzsa Antunovics Martin R Webb Aziz El Hage Yves Pommier Lóránt Székvölgyi Viktor Dombrádi Gábor SzabóAbstract
Molecular combing and gel electrophoretic studies revealed endogenous nicks with free 3'OH ends at ∼100 kb intervals in the genomic DNA (gDNA) of unperturbed and G1-synchronized Saccharomyces cerevisiae cells. Analysis of the distribution of endogenous nicks by Nick ChIP-chip indicated that these breaks accumulated at active RNA polymerase II (RNAP 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 ARS-containing IGS2 region was spared of nicks. By using a highly sensitive reverse-Southwestern blot method to map free DNA ends with 3'OH, nicks were shown to be distinct from other known rDNA breaks and linked to the regulation of rDNA silencing. Nicks in rDNA and the rest of the genome 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.
Journal details
Journal Nucleic Acids Research
Volume 46
Issue number 20
Pages 10649-10668
Available online
Publication date
Full text links
Publisher website (DOI) 10.1093/nar/gky743
Figshare View on figshare
Europe PubMed Central 30445637
Pubmed 30445637
Keywords
Related topics
Type of publication