Single-Molecule Imaging Reveals a Switch between Spurious and Functional ncRNA Transcription

Mol Cell. 2015 Nov 19;60(4):597-610. doi: 10.1016/j.molcel.2015.09.028. Epub 2015 Nov 5.


Eukaryotic transcription is pervasive, and many of the resulting RNAs are non-coding. It is unknown whether ubiquitous transcription is functional or simply reflects stochastic transcriptional noise. By single-molecule visualization of the dynamic interplay between coding and non-coding transcription at the GAL locus in living yeast cells, we show that antisense GAL10 ncRNA transcription can switch between functional and spurious under different conditions. During galactose induction, GAL10 sense transcription occurs in short stochastic bursts, which are unaffected by transcription of antisense GAL10 ncRNA, even when both are present simultaneously at the same locus. In contrast, when GAL10 is not induced, ncRNA transcription is critical to prevent transcriptional leakage of GAL1 and GAL10. Suppression of ncRNA transcription by strand-specific CRISPR/dCas9 results in transcriptional leakage of the inducer GAL1, leading to a more sensitive transcription activation threshold, an alteration of metabolic switching, and a fitness defect in competition experiments.

Publication types

  • Research Support, N.I.H., Intramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Clustered Regularly Interspaced Short Palindromic Repeats
  • Galactokinase / genetics*
  • Galactose / metabolism
  • Gene Expression Regulation, Fungal
  • Operon
  • RNA, Fungal / genetics*
  • RNA, Long Noncoding / genetics*
  • Saccharomyces cerevisiae / genetics*
  • Saccharomyces cerevisiae Proteins / genetics*
  • Trans-Activators / genetics*
  • Transcription, Genetic


  • GAL10 protein, S cerevisiae
  • RNA, Fungal
  • RNA, Long Noncoding
  • Saccharomyces cerevisiae Proteins
  • Trans-Activators
  • GAL1 protein, S cerevisiae
  • Galactokinase
  • Galactose

Associated data

  • GEO/GSE72032