Arginine methylation of the DDX5 helicase RGG/RG motif by PRMT5 regulates resolution of RNA:DNA hybrids

EMBO J. 2019 Aug 1;38(15):e100986. doi: 10.15252/embj.2018100986. Epub 2019 Jun 21.

Abstract

Aberrant transcription-associated RNA:DNA hybrid (R-loop) formation often causes catastrophic conflicts during replication, resulting in DNA double-strand breaks and genomic instability. Preventing such conflicts requires hybrid dissolution by helicases and/or RNase H. Little is known about how such helicases are regulated. Herein, we identify DDX5, an RGG/RG motif-containing DEAD-box family RNA helicase, as crucial player in R-loop resolution. In vitro, recombinant DDX5 resolves R-loops in an ATP-dependent manner, leading to R-loop degradation by the XRN2 exoribonuclease. DDX5-deficient cells accumulate R-loops at loci with propensity to form such structures based on RNA:DNA immunoprecipitation (DRIP)-qPCR, causing spontaneous DNA double-strand breaks and hypersensitivity to replication stress. DDX5 associates with XRN2 and resolves R-loops at transcriptional termination regions downstream of poly(A) sites, to facilitate RNA polymerase II release associated with transcriptional termination. Protein arginine methyltransferase 5 (PRMT5) binds and methylates DDX5 at its RGG/RG motif. This motif is required for DDX5 interaction with XRN2 and repression of cellular R-loops, but not essential for DDX5 helicase enzymatic activity. PRMT5-deficient cells accumulate R-loops, resulting in increased formation of γH2AX foci. Our findings exemplify a mechanism by which an RNA helicase is modulated by arginine methylation to resolve R-loops, and its potential role in regulating transcription.

Keywords: Arginine methylation; DDX5; RGG/RG motif; RNA helicase; XRN2.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Motifs
  • Arginine / metabolism
  • Cell Line
  • DEAD-box RNA Helicases / chemistry*
  • DEAD-box RNA Helicases / metabolism*
  • DNA / metabolism
  • Exoribonucleases / metabolism
  • HEK293 Cells
  • Humans
  • Methylation
  • Protein-Arginine N-Methyltransferases / genetics
  • Protein-Arginine N-Methyltransferases / metabolism*
  • RNA / chemistry*
  • RNA / metabolism
  • RNA Polymerase II / metabolism

Substances

  • RNA
  • DNA
  • Arginine
  • PRMT5 protein, human
  • Protein-Arginine N-Methyltransferases
  • RNA Polymerase II
  • Exoribonucleases
  • XRN2 protein, human
  • Ddx5 protein, human
  • DEAD-box RNA Helicases