title: Global analysis of transcriptionally engaged yeast RNA polymerase III reveals extended tRNA transcripts.
abstract: RNA polymerase III (RNAPIII) synthesizes a range of highly abundant small stable RNAs, principally pre-tRNAs. Here we report the genome-wide analysis of nascent transcripts attached to RNAPIII under permissive and restrictive growth conditions. This revealed strikingly uneven polymerase distributions across transcription units, generally with a predominant 5' peak. This peak was higher for more heavily transcribed genes, suggesting that initiation site clearance is rate-limiting during RNAPIII transcription. Down-regulation of RNAPIII transcription under stress conditions was found to be uneven; a subset of tRNA genes showed low response to nutrient shift or loss of the major transcription regulator Maf1, suggesting potential "housekeeping" roles. Many tRNA genes were found to generate long, 3'-extended forms due to read-through of the canonical poly(U) terminators. The degree of read-through was anti-correlated with the density of U-residues in the nascent tRNA, and multiple, functional terminators can be located far downstream. The steady-state levels of 3'-extended pre-tRNA transcripts are low, apparently due to targeting by the nuclear surveillance machinery, especially the RNA binding protein Nab2, cofactors for the nuclear exosome, and the 5'-exonuclease Rat1.
authors.affiliation: Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, Scotland; Institute of Biotechnology, Faculty of Chemistry, Warsaw University of Technology, 00-664 Warsaw, Poland;
authors.forename: Tomasz W
authors.initials: TW
authors.lastname: Turowski
authors.affiliation: Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland.
authors.forename: Ewa
authors.initials: E
authors.lastname: Leśniewska
authors.affiliation: Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, Scotland;
authors.forename: Clementine
authors.initials: C
authors.lastname: Delan-Forino
authors.affiliation: Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, Scotland;
authors.forename: Camille
authors.initials: C
authors.lastname: Sayou
authors.affiliation: Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland.
authors.forename: Magdalena
authors.initials: M
authors.lastname: Boguta
authors.affiliation: Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, Scotland;
authors.forename: David
authors.initials: D
authors.lastname: Tollervey
mesh_terms: D015966:Gene Expression Regulation, Fungal; D016681:Genome, Fungal; D012320:RNA Polymerase III / Q000502:physiology*; D012343:RNA, Transfer / Q000235:genetics* / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000201:enzymology* / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000502:physiology*; D017423:Sequence Analysis, RNA; D013728:Terminator Regions, Genetic; D014158:Transcription, Genetic
chemical_list: D029701:Saccharomyces cerevisiae Proteins; D012343:RNA, Transfer; D012320:RNA Polymerase III