title: Nuclear RNA Decay Pathways Aid Rapid Remodeling of Gene Expression in Yeast.
abstract: In budding yeast, the nuclear RNA surveillance system is active on all pre-mRNA transcripts and modulated by nutrient availability. To test the role of nuclear surveillance in reprogramming gene expression, we identified transcriptome-wide binding sites for RNA polymerase II and the exosome cofactors Mtr4 (TRAMP complex) and Nab3 (NNS complex) by UV crosslinking immediately following glucose withdrawal (0, 4, and 8 min). In glucose, mRNA binding by Nab3 and Mtr4 was mainly restricted to promoter-proximal sites, reflecting early transcription termination. Following glucose withdrawal, many growth-related mRNAs showed reduced transcription but increased Nab3 binding, accompanied by downstream recruitment of Mtr4, and oligo(A) tailing. We conclude that transcription termination is followed by TRAMP-mediated RNA decay. Upregulated transcripts evaded increased surveillance factor binding following glucose withdrawal. Some upregulated genes showed use of alternative transcription starts to bypass strong NNS binding sites. We conclude that nuclear surveillance pathways regulate both positive and negative responses to glucose availability.
authors.affiliation: Wellcome Trust Centre for Cell Biology, University of Edinburgh, Michael Swann Building, King's Buildings, Edinburgh EH9 3BF, Scotland.
authors.forename: Stefan
authors.initials: S
authors.lastname: Bresson
authors.affiliation: Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
authors.forename: Alex
authors.initials: A
authors.lastname: Tuck
authors.affiliation: Wellcome Trust Centre for Cell Biology, University of Edinburgh, Michael Swann Building, King's Buildings, Edinburgh EH9 3BF, Scotland.
authors.forename: Desislava
authors.initials: D
authors.lastname: Staneva
authors.affiliation: Wellcome Trust Centre for Cell Biology, University of Edinburgh, Michael Swann Building, King's Buildings, Edinburgh EH9 3BF, Scotland. Electronic address: d.tollervey@ed.ac.uk.
authors.forename: David
authors.initials: D
authors.lastname: Tollervey
mesh_terms: D000222:Adaptation, Physiological; D001665:Binding Sites; D002467:Cell Nucleus / Q000378:metabolism*; D053487:DEAD-box RNA Helicases / Q000235:genetics / Q000378:metabolism; D015966:Gene Expression Regulation, Fungal; D005947:Glucose / Q000172:deficiency / Q000378:metabolism; D009687:Nuclear Proteins / Q000235:genetics / Q000378:metabolism; D011485:Protein Binding; D012319:RNA Polymerase II / Q000235:genetics / Q000378:metabolism; D012323:RNA Processing, Post-Transcriptional; D020871:RNA Stability; D012331:RNA, Fungal / Q000235:genetics / Q000378:metabolism*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism*; D015138:RNA, Nuclear / Q000235:genetics / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism; D013997:Time Factors; D014158:Transcription, Genetic
chemical_list: C090564:NAB3 protein, S cerevisiae; D009687:Nuclear Proteins; D012331:RNA, Fungal; D012333:RNA, Messenger; D015138:RNA, Nuclear; D016601:RNA-Binding Proteins; D029701:Saccharomyces cerevisiae Proteins; D012319:RNA Polymerase II; C101004:MTR4 protein, S cerevisiae; D053487:DEAD-box RNA Helicases; D005947:Glucose
keywords: RNA exosome; RNA polymerase II; RNA surveillance; gene expression