Genome-wide Map of R-Loop-Induced Damage Reveals How a Subset of R-Loops Contributes to Genomic Instability

Mol Cell. 2018 Aug 16;71(4):487-497.e3. doi: 10.1016/j.molcel.2018.06.037. Epub 2018 Aug 2.

Abstract

DNA-RNA hybrids associated with R-loops promote DNA damage and genomic instability. The capacity of hybrids at different genomic sites to cause DNA damage was not known, and the mechanisms leading from hybrid to damage were poorly understood. Here, we adopt a new strategy to map and characterize the sites of hybrid-induced damage genome-wide in budding yeast. We show that hybrid removal is essential for life because persistent hybrids cause irreparable DNA damage and cell death. We identify that a subset of hybrids is prone to cause damage, and the chromosomal context of hybrids dramatically impacts their ability to induce damage. Furthermore, persistent hybrids affect the repair pathway, generating large regions of single-stranded DNA (ssDNA) by two distinct mechanisms, likely resection and re-replication. These damaged regions may act as potential precursors to gross chromosomal rearrangements like deletions and duplications that are associated with R-loops and cancers.

Keywords: DNA damage; DNA-RNA hybrids; R-loops; genomic instability.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA Cleavage
  • DNA Damage
  • DNA Helicases / genetics
  • DNA Helicases / metabolism
  • DNA Replication
  • DNA, Single-Stranded / chemistry
  • DNA, Single-Stranded / genetics*
  • DNA, Single-Stranded / metabolism
  • G2 Phase Cell Cycle Checkpoints / drug effects
  • G2 Phase Cell Cycle Checkpoints / genetics
  • Gene Expression Regulation, Fungal*
  • Genome, Fungal*
  • Genomic Instability*
  • Hydroxyurea / pharmacology
  • Indoleacetic Acids / pharmacology
  • Nucleic Acid Conformation
  • Nucleic Acid Hybridization
  • RNA / chemistry
  • RNA / genetics*
  • RNA / metabolism
  • RNA Helicases / genetics
  • RNA Helicases / metabolism
  • Rad52 DNA Repair and Recombination Protein / genetics
  • Rad52 DNA Repair and Recombination Protein / metabolism
  • Saccharomyces cerevisiae / drug effects
  • Saccharomyces cerevisiae / genetics*
  • Saccharomyces cerevisiae / metabolism
  • Saccharomyces cerevisiae Proteins / genetics
  • Saccharomyces cerevisiae Proteins / metabolism

Substances

  • DNA, Single-Stranded
  • Indoleacetic Acids
  • RAD52 protein, S cerevisiae
  • Rad52 DNA Repair and Recombination Protein
  • Saccharomyces cerevisiae Proteins
  • RNA
  • SEN1 protein, S cerevisiae
  • DNA Helicases
  • RNA Helicases
  • Hydroxyurea