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Global analysis of transcriptionally engaged yeast RNA polymerase III reveals extended tRNA transcripts

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 distribution...

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Autores principales: Turowski, Tomasz W., Leśniewska, Ewa, Delan-Forino, Clementine, Sayou, Camille, Boguta, Magdalena, Tollervey, David
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937561/
https://www.ncbi.nlm.nih.gov/pubmed/27206856
http://dx.doi.org/10.1101/gr.205492.116
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author Turowski, Tomasz W.
Leśniewska, Ewa
Delan-Forino, Clementine
Sayou, Camille
Boguta, Magdalena
Tollervey, David
author_facet Turowski, Tomasz W.
Leśniewska, Ewa
Delan-Forino, Clementine
Sayou, Camille
Boguta, Magdalena
Tollervey, David
author_sort Turowski, Tomasz W.
collection PubMed
description 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.
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spelling pubmed-49375612016-07-22 Global analysis of transcriptionally engaged yeast RNA polymerase III reveals extended tRNA transcripts Turowski, Tomasz W. Leśniewska, Ewa Delan-Forino, Clementine Sayou, Camille Boguta, Magdalena Tollervey, David Genome Res Research 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. Cold Spring Harbor Laboratory Press 2016-07 /pmc/articles/PMC4937561/ /pubmed/27206856 http://dx.doi.org/10.1101/gr.205492.116 Text en © 2016 Turowski et al.; Published by Cold Spring Harbor Laboratory Press http://creativecommons.org/licenses/by/4.0/ This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
spellingShingle Research
Turowski, Tomasz W.
Leśniewska, Ewa
Delan-Forino, Clementine
Sayou, Camille
Boguta, Magdalena
Tollervey, David
Global analysis of transcriptionally engaged yeast RNA polymerase III reveals extended tRNA transcripts
title Global analysis of transcriptionally engaged yeast RNA polymerase III reveals extended tRNA transcripts
title_full Global analysis of transcriptionally engaged yeast RNA polymerase III reveals extended tRNA transcripts
title_fullStr Global analysis of transcriptionally engaged yeast RNA polymerase III reveals extended tRNA transcripts
title_full_unstemmed Global analysis of transcriptionally engaged yeast RNA polymerase III reveals extended tRNA transcripts
title_short Global analysis of transcriptionally engaged yeast RNA polymerase III reveals extended tRNA transcripts
title_sort global analysis of transcriptionally engaged yeast rna polymerase iii reveals extended trna transcripts
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937561/
https://www.ncbi.nlm.nih.gov/pubmed/27206856
http://dx.doi.org/10.1101/gr.205492.116
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