RNA polymerase III regulates cytosolic RNA:DNA hybrids and intracellular microRNA expression

J Biol Chem. 2015 Mar 20;290(12):7463-73. doi: 10.1074/jbc.M115.636365. Epub 2015 Jan 26.


RNA:DNA hybrids form in the nuclei and mitochondria of cells as transcription-induced R-loops or G-quadruplexes, but exist only in the cytosol of virus-infected cells. Little is known about the existence of RNA:DNA hybrids in the cytosol of virus-free cells, in particular cancer or transformed cells. Here, we show that cytosolic RNA:DNA hybrids are present in various human cell lines, including transformed cells. Inhibition of RNA polymerase III (Pol III), but not DNA polymerase, abrogated cytosolic RNA:DNA hybrids. Cytosolic RNA:DNA hybrids bind to several components of the microRNA (miRNA) machinery-related proteins, including AGO2 and DDX17. Furthermore, we identified miRNAs that are specifically regulated by Pol III, providing a potential link between RNA:DNA hybrids and the miRNA machinery. One of the target genes, exportin-1, is shown to regulate cytosolic RNA:DNA hybrids. Taken together, we reveal previously unknown mechanism by which Pol III regulates the presence of cytosolic RNA:DNA hybrids and miRNA biogenesis in various human cells.

Keywords: Antibody S9.6; Cancer; DNA Damage; Innate Immunity; MicroRNA (miRNA); RNA Polymerase III; RNA Transport; RNA:DNA Hybrid; RNase H.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Cell Line, Tumor
  • Cytosol / metabolism
  • DNA / genetics*
  • DNA Damage
  • Humans
  • Mass Spectrometry
  • MicroRNAs / genetics*
  • Nucleic Acid Hybridization*
  • Oligonucleotide Array Sequence Analysis
  • RNA / genetics*
  • RNA Polymerase III / metabolism*
  • RNA, Small Interfering


  • MicroRNAs
  • RNA, Small Interfering
  • RNA
  • DNA
  • RNA Polymerase III