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PMID: 23770821 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Bimodal expression of PHO84 is modulated by early termination of antisense transcription.

Nature structural & molecular biology ·Vol. 20 ·No. 7 ·2013-07-00 ·Pages 851-8

Castelnuovo M, Rahman S, Guffanti E, Infantino V, Stutz F, Zenklusen D

Abstract

Many Saccharomyces cerevisiae genes encode antisense transcripts, some of which are unstable and degraded by the exosome component Rrp6. Loss of Rrp6 results in the accumulation of long PHO84 antisense (AS) RNAs and repression of sense transcription through PHO84 promoter deacetylation. We used single-molecule resolution fluorescent in situ hybridization (smFISH) to investigate antisense-mediated transcription regulation. We show that PHO84 AS RNA acts as a bimodal switch, in which continuous, low-frequency antisense transcription represses sense expression within individual cells. Surprisingly, antisense RNAs do not accumulate at the PHO84 gene but are exported to the cytoplasm. Furthermore, rather than stabilizing PHO84 AS RNA, the loss of Rrp6 favors its elongation by reducing early transcription termination by Nrd1-Nab3-Sen1. These observations suggest that PHO84 silencing results from antisense transcription through the promoter rather than the static accumulation of antisense RNAs at the repressed gene.

MeSH Terms
DNA Helicases/physiology Exosome Multienzyme Ribonuclease Complex/physiology Gene Expression Regulation, Fungal Histone Deacetylases/physiology Histone-Lysine N-Methyltransferase/physiology In Situ Hybridization, Fluorescence Metalloendopeptidases/physiology Models, Genetic Multiprotein Complexes Nuclear Proteins/physiology Polyadenylation Polynucleotide Adenylyltransferase/physiology Promoter Regions, Genetic/genetics Proton-Phosphate Symporters/biosynthesis,genetics RNA Helicases/physiology RNA, Antisense/genetics,metabolism RNA, Fungal/genetics,metabolism RNA, Messenger/biosynthesis,metabolism RNA-Binding Proteins/physiology Saccharomyces cerevisiae/genetics Saccharomyces cerevisiae Proteins/biosynthesis,genetics,physiology Transcription, Genetic
Chemicals
Multiprotein Complexes NAB3 protein, S cerevisiae Nuclear Proteins PHO84 protein, S cerevisiae Proton-Phosphate Symporters RNA, Antisense RNA, Fungal RNA, Messenger RNA-Binding Proteins Saccharomyces cerevisiae Proteins Histone-Lysine N-Methyltransferase SET1 protein, S cerevisiae PAP1 protein, S cerevisiae Polynucleotide Adenylyltransferase Exosome Multienzyme Ribonuclease Complex RRP6 protein, S cerevisiae Metalloendopeptidases NRDC protein, human HDA1 protein, S cerevisiae Histone Deacetylases SEN1 protein, S cerevisiae DNA Helicases RNA Helicases
Authors & Affiliations
6 authors, click to expand affiliations / ORCID
Castelnuovo Manuele
Department of Cell Biology and National Center of Competence in Research "Frontiers in Genetics", University of Geneva, Switzerland.
Rahman Samir
Guffanti Elisa
Infantino Valentina
Stutz Françoise
Zenklusen Daniel
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Article Info
Journal
Nature structural & molecular biology
Abbr.
Nat Struct Mol Biol
ISSN
1545-9985
DOI
10.1038/nsmb.2598
Published
2013-07-00
Epub
2013-00-16
Pages
851-8
Language
English
Region
United States
NLM ID
101186374
PMCID
PMC4972572
Subset
IM
Grants
CIHR · 111099-1 · Canada
CIHR · MOP-BMB-232642 · Canada
External Links
PubMed source DOI: 10.1038/nsmb.2598 PMC Full Text View journal details
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