Recovery of arrested replication forks by homologous recombination is error-prone

PLoS Genet. 2012;8(10):e1002976. doi: 10.1371/journal.pgen.1002976. Epub 2012 Oct 18.


Homologous recombination is a universal mechanism that allows repair of DNA and provides support for DNA replication. Homologous recombination is therefore a major pathway that suppresses non-homology-mediated genome instability. Here, we report that recovery of impeded replication forks by homologous recombination is error-prone. Using a fork-arrest-based assay in fission yeast, we demonstrate that a single collapsed fork can cause mutations and large-scale genomic changes, including deletions and translocations. Fork-arrest-induced gross chromosomal rearrangements are mediated by inappropriate ectopic recombination events at the site of collapsed forks. Inverted repeats near the site of fork collapse stimulate large-scale genomic changes up to 1,500 times over spontaneous events. We also show that the high accuracy of DNA replication during S-phase is impaired by impediments to fork progression, since fork-arrest-induced mutation is due to erroneous DNA synthesis during recovery of replication forks. The mutations caused are small insertions/duplications between short tandem repeats (micro-homology) indicative of replication slippage. Our data establish that collapsed forks, but not stalled forks, recovered by homologous recombination are prone to replication slippage. The inaccuracy of DNA synthesis does not rely on PCNA ubiquitination or trans-lesion-synthesis DNA polymerases, and it is not counteracted by mismatch repair. We propose that deletions/insertions, mediated by micro-homology, leading to copy number variations during replication stress may arise by progression of error-prone replication forks restarted by homologous recombination.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromosome Aberrations
  • DNA Helicases / metabolism
  • DNA Mismatch Repair
  • DNA Repair*
  • DNA Replication*
  • Gene Order
  • Genomic Instability
  • Homologous Recombination*
  • Inverted Repeat Sequences
  • Mutation
  • RNA-Binding Protein FUS / metabolism
  • RecQ Helicases / metabolism
  • Schizosaccharomyces / genetics
  • Schizosaccharomyces / metabolism
  • Schizosaccharomyces pombe Proteins / metabolism
  • Translocation, Genetic


  • RNA-Binding Protein FUS
  • Schizosaccharomyces pombe Proteins
  • DNA Helicases
  • RecQ Helicases
  • Rqh1 protein, S pombe

Grants and funding

This work was supported by the Institut Curie, the CNRS, ANR grants ANR-Piribio09-44854 and ANRJCJC10-1203 01, and La Ligue Contre le Cancer (comité Essonne) to SAEL. VP was funded by the ITN “Image DDR” PITN-GA-2008-215148. II was funded by the Fondation pour la Recherche Médicale (FRM) and AC by l'Association pour la Recherche sur le Cancer (ARC). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.