R-loop mediated transcription-associated recombination in trf4Δ mutants reveals new links between RNA surveillance and genome integrity

PLoS One. 2013 Jun 7;8(6):e65541. doi: 10.1371/journal.pone.0065541. Print 2013.


To get further insight into the factors involved in the maintenance of genome integrity we performed a screening of Saccharomyces cerevisiae deletion strains inducing hyperrecombination. We have identified trf4, a gene encoding a non-canonical polyA-polymerase involved in RNA surveillance, as a factor that prevents recombination between DNA repeats. We show that trf4Δ confers a transcription-associated recombination phenotype that is mediated by the nascent mRNA. In addition, trf4Δ also leads to an increase in the mutation frequency. Both genetic instability phenotypes can be suppressed by overexpression of RNase H and are exacerbated by overexpression of the human cytidine deaminase AID. These results suggest that in the absence of Trf4 R-loops accumulate co-transcriptionally increasing the recombination and mutation frequencies. Altogether our data indicate that Trf4 is necessary for both mRNA surveillance and maintenance of genome integrity, serving as a link between RNA and DNA metabolism in S. cerevisiae.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine Deaminase / metabolism
  • Biocatalysis
  • DNA-Directed DNA Polymerase / chemistry
  • DNA-Directed DNA Polymerase / genetics*
  • DNA-Directed DNA Polymerase / metabolism
  • Genome, Fungal / genetics*
  • Genomic Instability / genetics
  • Humans
  • Mutation / genetics*
  • Nucleic Acid Conformation*
  • Phenotype
  • Polyadenylation / genetics
  • Protein Structure, Tertiary
  • RNA, Fungal / genetics
  • RNA, Fungal / metabolism*
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • Recombination, Genetic*
  • Saccharomyces cerevisiae / genetics
  • Saccharomyces cerevisiae Proteins / chemistry
  • Saccharomyces cerevisiae Proteins / genetics*
  • Saccharomyces cerevisiae Proteins / metabolism
  • Transcription, Genetic*


  • RNA, Fungal
  • RNA, Messenger
  • Saccharomyces cerevisiae Proteins
  • DNA-Directed DNA Polymerase
  • PAP2 protein, S cerevisiae
  • Adenosine Deaminase

Grant support

This work was supported by grants from the Spanish Ministry of Science and Research (BFU2010-16372 and Consolider Ingenio 2010 CSD2007-00015), Junta de Andalucía (CVI-4567) and European Union (FEDER). SG was the recipient of a predoctoral training grant from the Spanish Ministry of Health. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.