The Npl3 hnRNP prevents R-loop-mediated transcription-replication conflicts and genome instability

Genes Dev. 2013 Nov 15;27(22):2445-58. doi: 10.1101/gad.229880.113.


Transcription is a major obstacle for replication fork (RF) progression and a cause of genome instability. Part of this instability is mediated by cotranscriptional R loops, which are believed to increase by suboptimal assembly of the nascent messenger ribonucleoprotein particle (mRNP). However, no clear evidence exists that heterogeneous nuclear RNPs (hnRNPs), the basic mRNP components, prevent R-loop stabilization. Here we show that yeast Npl3, the most abundant RNA-binding hnRNP, prevents R-loop-mediated genome instability. npl3Δ cells show transcription-dependent and R-loop-dependent hyperrecombination and genome-wide replication obstacles as determined by accumulation of the Rrm3 helicase. Such obstacles preferentially occur at long and highly expressed genes, to which Npl3 is preferentially bound in wild-type cells, and are reduced by RNase H1 overexpression. The resulting replication stress confers hypersensitivity to double-strand break-inducing agents. Therefore, our work demonstrates that mRNP factors are critical for genome integrity and opens the option of using them as therapeutic targets in anti-cancer treatment.

Keywords: DNA damage response; Npl3; R loops; hnRNPs; transcription-associated genome instability; transcription–replication conflicts.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • 3' Flanking Region
  • DNA Damage
  • DNA Helicases / genetics
  • DNA Helicases / metabolism
  • DNA Replication / genetics*
  • Gene Deletion
  • Genome, Fungal
  • Genomic Instability / genetics*
  • Heterogeneous-Nuclear Ribonucleoproteins / genetics
  • Heterogeneous-Nuclear Ribonucleoproteins / metabolism
  • Mutagens / pharmacology
  • Nuclear Proteins / genetics*
  • Nuclear Proteins / metabolism*
  • RNA-Binding Proteins / genetics*
  • RNA-Binding Proteins / metabolism*
  • Saccharomyces cerevisiae / drug effects
  • Saccharomyces cerevisiae / genetics*
  • Saccharomyces cerevisiae / metabolism*
  • Saccharomyces cerevisiae Proteins / genetics*
  • Saccharomyces cerevisiae Proteins / metabolism*
  • Transcription, Genetic / genetics*


  • Heterogeneous-Nuclear Ribonucleoproteins
  • Mutagens
  • NPL3 protein, S cerevisiae
  • Nuclear Proteins
  • RNA-Binding Proteins
  • Saccharomyces cerevisiae Proteins
  • Rrm3 protein, S cerevisiae
  • DNA Helicases