R-loop-derived cytoplasmic RNA-DNA hybrids activate an immune response

Nature. 2023 Jan;613(7942):187-194. doi: 10.1038/s41586-022-05545-9. Epub 2022 Dec 21.


R-loops are RNA-DNA-hybrid-containing nucleic acids with important cellular roles. Deregulation of R-loop dynamics can lead to DNA damage and genome instability1, which has been linked to the action of endonucleases such as XPG2-4. However, the mechanisms and cellular consequences of such processing have remained unclear. Here we identify a new population of RNA-DNA hybrids in the cytoplasm that are R-loop-processing products. When nuclear R-loops were perturbed by depleting the RNA-DNA helicase senataxin (SETX) or the breast cancer gene BRCA1 (refs. 5-7), we observed XPG- and XPF-dependent cytoplasmic hybrid formation. We identify their source as a subset of stable, overlapping nuclear hybrids with a specific nucleotide signature. Cytoplasmic hybrids bind to the pattern recognition receptors cGAS and TLR3 (ref. 8), activating IRF3 and inducing apoptosis. Excised hybrids and an R-loop-induced innate immune response were also observed in SETX-mutated cells from patients with ataxia oculomotor apraxia type 2 (ref. 9) and in BRCA1-mutated cancer cells10. These findings establish RNA-DNA hybrids as immunogenic species that aberrantly accumulate in the cytoplasm after R-loop processing, linking R-loop accumulation to cell death through the innate immune response. Aberrant R-loop processing and subsequent innate immune activation may contribute to many diseases, such as neurodegeneration and cancer.

Publication types

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

MeSH terms

  • Apoptosis
  • Cytoplasm* / immunology
  • Cytoplasm* / metabolism
  • DNA Helicases / genetics
  • DNA Helicases / metabolism
  • DNA* / chemistry
  • DNA* / immunology
  • Genes, BRCA1
  • Humans
  • Innate Immunity Recognition*
  • Multifunctional Enzymes / genetics
  • Multifunctional Enzymes / metabolism
  • Mutation
  • Neoplasms
  • Nucleic Acid Heteroduplexes* / chemistry
  • Nucleic Acid Heteroduplexes* / immunology
  • R-Loop Structures* / immunology
  • RNA Helicases / genetics
  • RNA Helicases / metabolism
  • RNA* / chemistry
  • RNA* / immunology
  • Spinocerebellar Ataxias / genetics


  • cGAS protein, human
  • DNA
  • DNA excision repair protein ERCC-5
  • DNA Helicases
  • IRF3 protein, human
  • Multifunctional Enzymes
  • Nucleic Acid Heteroduplexes
  • RNA
  • RNA Helicases
  • SETX protein, human
  • TLR3 protein, human
  • xeroderma pigmentosum group F protein