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

Nat Struct Mol Biol. 2013 Jul;20(7):851-8. doi: 10.1038/nsmb.2598. Epub 2013 Jun 16.


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.

Publication types

  • Research Support, Non-U.S. Gov't

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
  • Proton-Phosphate Symporters / genetics*
  • RNA Helicases / physiology
  • RNA, Antisense / genetics*
  • RNA, Antisense / metabolism
  • RNA, Fungal / genetics*
  • RNA, Fungal / metabolism
  • RNA, Messenger / biosynthesis
  • RNA, Messenger / metabolism
  • RNA-Binding Proteins / physiology
  • Saccharomyces cerevisiae / genetics*
  • Saccharomyces cerevisiae Proteins / biosynthesis
  • Saccharomyces cerevisiae Proteins / genetics*
  • Saccharomyces cerevisiae Proteins / physiology
  • Transcription, Genetic*


  • 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