Role for RNA:DNA hybrids in origin-independent replication priming in a eukaryotic system

Proc Natl Acad Sci U S A. 2015 May 5;112(18):5779-84. doi: 10.1073/pnas.1501769112. Epub 2015 Apr 20.


DNA replication initiates at defined replication origins along eukaryotic chromosomes, ensuring complete genome duplication within a single S-phase. A key feature of replication origins is their ability to control the onset of DNA synthesis mediated by DNA polymerase-α and its intrinsic RNA primase activity. Here, we describe a novel origin-independent replication process that is mediated by transcription. RNA polymerase I transcription constraints lead to persistent RNA:DNA hybrids (R-loops) that prime replication in the ribosomal DNA locus. Our results suggest that eukaryotic genomes have developed tools to prevent R-loop-mediated replication events that potentially contribute to copy number variation, particularly relevant to carcinogenesis.

Keywords: RNA:DNA hybrids; RNase H; replication; ribosomal DNA; topoisomerase 1.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins
  • Camptothecin / chemistry
  • Carcinogenesis / metabolism
  • Cell Cycle
  • Cell Separation
  • Chromosomes / chemistry
  • DNA / chemistry*
  • DNA Copy Number Variations
  • DNA Replication*
  • DNA, Ribosomal / chemistry*
  • Electrophoresis, Gel, Two-Dimensional
  • Flow Cytometry
  • Gene Dosage
  • Genomic Instability*
  • Humans
  • Hydroxyurea / chemistry
  • Luminescent Proteins
  • Methyl Methanesulfonate / chemistry
  • Mutation
  • RNA / chemistry*
  • Replication Origin
  • Ribonuclease H / chemistry*
  • Saccharomyces cerevisiae / metabolism


  • Bacterial Proteins
  • DNA, Ribosomal
  • Luminescent Proteins
  • yellow fluorescent protein, Bacteria
  • RNA
  • DNA
  • Methyl Methanesulfonate
  • Ribonuclease H
  • Hydroxyurea
  • Camptothecin