Molecular Cell
Volume 72, Issue 6, 20 December 2018, Pages 942-954.e7
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Article
Repression of Divergent Noncoding Transcription by a Sequence-Specific Transcription Factor

https://doi.org/10.1016/j.molcel.2018.10.018Get rights and content
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Highlights

  • Expression of divergent noncoding RNAs is repressed by Rap1

  • Rap1 prevents initiation of divergent noncoding transcription near its binding sites

  • Rap1 provides directionality toward productive transcription

Summary

Many active eukaryotic gene promoters exhibit divergent noncoding transcription, but the mechanisms restricting expression of these transcripts are not well understood. Here, we demonstrate how a sequence-specific transcription factor represses divergent noncoding transcription at highly expressed genes in yeast. We find that depletion of the transcription factor Rap1 induces noncoding transcription in a large fraction of Rap1-regulated gene promoters. Specifically, Rap1 prevents transcription initiation at cryptic promoters near its binding sites, which is uncoupled from transcription regulation in the protein-coding direction. We further provide evidence that Rap1 acts independently of previously described chromatin-based mechanisms to repress cryptic or divergent transcription. Finally, we show that divergent transcription in the absence of Rap1 is elicited by the RSC chromatin remodeler. We propose that a sequence-specific transcription factor limits access of basal transcription machinery to regulatory elements and adjacent sequences that act as divergent cryptic promoters, thereby providing directionality toward productive transcription.

Keywords

yeast
RSC
promoter
Rap1
transcription
divergent
noncoding RNA
transcription factor
repression
directionality

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