Nascent RNA signaling to yeast RNA Pol II during transcription elongation

PLoS One. 2018 Mar 23;13(3):e0194438. doi: 10.1371/journal.pone.0194438. eCollection 2018.


Transcription as the key step in gene expression is a highly regulated process. The speed of transcription elongation depends on the underlying gene sequence and varies on a gene by gene basis. The reason for this sequence dependence is not known in detail. Recently, our group studied the cross talk between the nascent RNA and the transcribing RNA polymerase by screening the Escherichia coli genome for RNA sequences with high affinity to RNA Pol by performing genomic SELEX. This approach led to the identification of RNA polymerase-binding APtamers termed "RAPs". RAPs can have positive and negative effects on gene expression. A subgroup is able to downregulate transcription via the activity of the termination factor Rho. In this study, we used a similar SELEX setup using yeast genomic DNA as source of RNA sequences and highly purified yeast RNA Pol II as bait and obtained almost 1300 yeast-derived RAPs. Yeast RAPs are found throughout the genome within genes and antisense to genes, they are overrepresented in the non-transcribed strand of yeast telomeres and underrepresented in intergenic regions. Genes harbouring a RAP are more likely to show lower mRNA levels. By determining the endogenous expression levels as well as using a reporter system, we show that RAPs located within coding regions can reduce the transcript level downstream of the RAP. Here we demonstrate that RAPs represent a novel type of regulatory RNA signal in Saccharomyces cerevisiae that act in cis and interfere with the elongating transcription machinery to reduce the transcriptional output.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Fungal Proteins / genetics
  • Fungal Proteins / metabolism*
  • RNA Polymerase II / genetics
  • RNA Polymerase II / metabolism*
  • RNA, Fungal / biosynthesis*
  • RNA, Fungal / genetics
  • Saccharomyces cerevisiae / genetics
  • Saccharomyces cerevisiae / metabolism*
  • Signal Transduction / physiology*
  • Transcription Elongation, Genetic / physiology*


  • Fungal Proteins
  • RNA, Fungal
  • RNA Polymerase II

Grant support

This work was supported by the Austrian Science Fund ( FWF grants n° F4301 and F4308 (to RS); and the Vienna RNA Doctoral School DK W1207-B09) supported by the Austrian Science fund FWF. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript