title: Genome-wide distribution of RNA-DNA hybrids identifies RNase H targets in tRNA genes, retrotransposons and mitochondria.
abstract: During transcription, the nascent RNA can invade the DNA template, forming extended RNA-DNA duplexes (R-loops). Here we employ ChIP-seq in strains expressing or lacking RNase H to map targets of RNase H activity throughout the budding yeast genome. In wild-type strains, R-loops were readily detected over the 35S rDNA region, transcribed by Pol I, and over the 5S rDNA, transcribed by Pol III. In strains lacking RNase H activity, R-loops were elevated over other Pol III genes, notably tRNAs, SCR1 and U6 snRNA, and were also associated with the cDNAs of endogenous TY1 retrotransposons, which showed increased rates of mobility to the 5'-flanking regions of tRNA genes. Unexpectedly, R-loops were also associated with mitochondrial genes in the absence of RNase H1, but not of RNase H2. Finally, R-loops were detected on actively transcribed protein-coding genes in the wild-type, particularly over the second exon of spliced ribosomal protein genes.
authors.affiliation: Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom.
authors.forename: Aziz
authors.initials: A
authors.lastname: El Hage
authors.affiliation: Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom.
authors.forename: Shaun
authors.initials: S
authors.lastname: Webb
authors.affiliation: Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom.
authors.forename: Alastair
authors.initials: A
authors.lastname: Kerr
authors.affiliation: Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom.
authors.forename: David
authors.initials: D
authors.lastname: Tollervey
mesh_terms: D043603:DNA-(Apurinic or Apyrimidinic Site) Lyase / Q000235:genetics; D016681:Genome, Fungal; D008928:Mitochondria / Q000235:genetics*; D012318:RNA Polymerase I / Q000235:genetics; D012320:RNA Polymerase III / Q000235:genetics; D012342:RNA, Small Nuclear / Q000235:genetics; D012343:RNA, Transfer / Q000235:genetics; D018626:Retroelements / Q000235:genetics*; D016914:Ribonuclease H / Q000235:genetics*; D012441:Saccharomyces cerevisiae; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics; D014158:Transcription, Genetic
chemical_list: D012342:RNA, Small Nuclear; D018626:Retroelements; D029701:Saccharomyces cerevisiae Proteins; C405486:U6 small nuclear RNA; D012343:RNA, Transfer; D012318:RNA Polymerase I; D012320:RNA Polymerase III; D016914:Ribonuclease H; D043603:DNA-(Apurinic or Apyrimidinic Site) Lyase; C101825:NTG1 protein, S cerevisiae