title: Cis-interactions between non-coding ribosomal spacers dependent on RNAP-II separate RNAP-I and RNAP-III transcription domains.
abstract: Ribosome biogenesis requires transcription of structural RNAs. In budding yeast, ribosomal units contain both 35S and 5S RNA genes separated by intergenic spacer sequences (IGS) that are transcribed by RNAP-II. IGS transcripts cause instability by promoting unequal sister chromatid recombination between repeats and are thus rapidly degraded by the exosome. Whether RNAP-II within IGS regions plays any functional role is unknown. Here we demonstrate that the bulk of RNAP-II bound to IGS sites is blocked for elongation and hence remains in a poised or stalled configuration. We describe a novel role for these stalled RNAP-II complexes in the formation of cis-interactions between the IGS of rDNA. We show that this function separates 35S and 5S RNA genes into polymerase-specific chromatin loops and demonstrate that removal of stalled RNAP-II complexes causes displacement of RNAP-III from the 5S gene region and transcriptional downregulation of 5S rRNA by spreading of RNAP-I. We conclude that stalled RNAP-II plays an active role in the cis-organisation of ribosomal repeats providing domains of polymerase specificity in the nucleolar transcription environment.
authors.affiliation: MRC Clinical Sciences Centre, Imperial College, London, UK.
authors.forename: María
authors.initials: M
authors.lastname: Mayan
authors.forename: Luis
authors.initials: L
authors.lastname: Aragón
mesh_terms: D021901:DNA, Intergenic / Q000737:chemistry / Q000378:metabolism; D004275:DNA, Ribosomal / Q000378:metabolism; D021903:DNA, Ribosomal Spacer / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000378:metabolism; D017434:Protein Structure, Tertiary; D012318:RNA Polymerase I / Q000378:metabolism*; D012319:RNA Polymerase II / Q000378:metabolism*; D012320:RNA Polymerase III / Q000378:metabolism*; D012341:RNA, Ribosomal, 5S / Q000737:chemistry / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism; D014157:Transcription Factors / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D021901:DNA, Intergenic; D004275:DNA, Ribosomal; D021903:DNA, Ribosomal Spacer; D004268:DNA-Binding Proteins; C065681:REB1 protein, S cerevisiae; D012341:RNA, Ribosomal, 5S; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors; D012319:RNA Polymerase II; D012318:RNA Polymerase I; D012320:RNA Polymerase III