The DNA damage response acts as a safeguard against harmful DNA-RNA hybrids of different origins

EMBO Rep. 2019 Sep;20(9):e47250. doi: 10.15252/embr.201847250. Epub 2019 Jul 24.


Despite playing physiological roles in specific situations, DNA-RNA hybrids threat genome integrity. To investigate how cells do counteract spontaneous DNA-RNA hybrids, here we screen an siRNA library covering 240 human DNA damage response (DDR) genes and select siRNAs causing DNA-RNA hybrid accumulation and a significant increase in hybrid-dependent DNA breakage. We identify post-replicative repair and DNA damage checkpoint factors, including those of the ATM/CHK2 and ATR/CHK1 pathways. Thus, spontaneous DNA-RNA hybrids are likely a major source of replication stress, but they can also accumulate and menace genome integrity as a consequence of unrepaired DSBs and post-replicative ssDNA gaps in normal cells. We show that DNA-RNA hybrid accumulation correlates with increased DNA damage and chromatin compaction marks. Our results suggest that different mechanisms can lead to DNA-RNA hybrids with distinct consequences for replication and DNA dynamics at each cell cycle stage and support the conclusion that DNA-RNA hybrids are a common source of spontaneous DNA damage that remains unsolved under a deficient DDR.

Keywords: ATM; ATR; DNA damage response; R loop; post-replicative repair.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Cycle / genetics
  • Cell Cycle / physiology
  • DNA Damage / genetics
  • DNA Damage / physiology*
  • DNA Replication / genetics
  • DNA Replication / physiology
  • DNA, Single-Stranded / genetics
  • DNA, Single-Stranded / metabolism
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / metabolism
  • Discoidin Domain Receptors / genetics
  • Discoidin Domain Receptors / metabolism
  • Flow Cytometry
  • HeLa Cells
  • Humans
  • Models, Biological
  • Phosphoric Diester Hydrolases / genetics
  • Phosphoric Diester Hydrolases / metabolism
  • Real-Time Polymerase Chain Reaction
  • Signal Transduction / genetics
  • Signal Transduction / physiology
  • Ubiquitin-Conjugating Enzymes / genetics
  • Ubiquitin-Conjugating Enzymes / metabolism


  • DNA, Single-Stranded
  • DNA-Binding Proteins
  • UBE2A protein, human
  • UBE2B protein, human
  • Ubiquitin-Conjugating Enzymes
  • Discoidin Domain Receptors
  • Phosphoric Diester Hydrolases
  • TDP2 protein, human