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

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  • Tomasz W Turowski
  • Ewa Leśniewska
  • Clementine Delan-Forino
  • Camille Sayou
  • Magdalena Boguta
  • David Tollervey

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Original languageEnglish
Pages (from-to)933-944
Number of pages12
JournalGenome Research
Volume26
Issue number7
Early online date20 May 2016
DOIs
Publication statusPublished - Jul 2016

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.

    Research areas

  • RNA polymerase III, tRNA, UV cross-linking, RNA-protein interaction, Maf1, Nab2, exosome, transcription elongation, transcription termination, surveillance

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