Functions of Replication Protein A as a Sensor of R Loops and a Regulator of RNaseH1

Mol Cell. 2017 Mar 2;65(5):832-847.e4. doi: 10.1016/j.molcel.2017.01.029.


R loop, a transcription intermediate containing RNA:DNA hybrids and displaced single-stranded DNA (ssDNA), has emerged as a major source of genomic instability. RNaseH1, which cleaves the RNA in RNA:DNA hybrids, plays an important role in R loop suppression. Here we show that replication protein A (RPA), an ssDNA-binding protein, interacts with RNaseH1 and colocalizes with both RNaseH1 and R loops in cells. In vitro, purified RPA directly enhances the association of RNaseH1 with RNA:DNA hybrids and stimulates the activity of RNaseH1 on R loops. An RPA binding-defective RNaseH1 mutant is not efficiently stimulated by RPA in vitro, fails to accumulate at R loops in cells, and loses the ability to suppress R loops and associated genomic instability. Thus, in addition to sensing DNA damage and replication stress, RPA is a sensor of R loops and a regulator of RNaseH1, extending the versatile role of RPA in suppression of genomic instability.

Keywords: R loop; RNase H1; RPA; genome instability; splicing inhibitor; splicing mutation; ssDNA.

MeSH terms

  • Binding Sites
  • DNA / chemistry
  • DNA / genetics
  • DNA / metabolism*
  • Genomic Instability*
  • HEK293 Cells
  • HeLa Cells
  • Humans
  • Nucleic Acid Conformation
  • Protein Binding
  • Protein Interaction Domains and Motifs
  • RNA / chemistry
  • RNA / genetics
  • RNA / metabolism*
  • RNA Interference
  • Replication Protein A / chemistry
  • Replication Protein A / genetics
  • Replication Protein A / metabolism*
  • Ribonuclease H / chemistry
  • Ribonuclease H / genetics
  • Ribonuclease H / metabolism*
  • Structure-Activity Relationship
  • Time Factors
  • Transcription, Genetic*
  • Transfection


  • RPA1 protein, human
  • Replication Protein A
  • RNA
  • DNA
  • Ribonuclease H
  • ribonuclease HI