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

  • Nature. 2022 Dec 21. doi: 10.1038/s41586-022-05545-9.
Magdalena P Crossley  #  1 ,  Chenlin Song  #  1 ,  Michael J Bocek  1 ,  Jun-Hyuk Choi  1  2  3 ,  Joseph Kousorous  1 ,  Ataya Sathirachinda  1 ,  Cindy Lin  4  5  6 ,  Joshua R Brickner  1 ,  Gongshi Bai  1 ,  Hannes Lans  7 ,  Wim Vermeulen  7 ,  Monther Abu-Remaileh  4  5  6 ,  Karlene A Cimprich  8
Affiliations
  • 1. Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA.
  • 2. Biometrology Group, Division of Chemical and Biological Metrology, Korea Research Institute of Standards and Science, Daejeon, South Korea.
  • 3. Department of Bio-Analytical Science, University of Science & Technology, Daejeon, South Korea.
  • 4. Department of Chemical Engineering, Stanford University, Stanford, CA, USA.
  • 5. Department of Genetics, Stanford University, Stanford, CA, USA.
  • 6. The Institute for Chemistry, Engineering & Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA, USA.
  • 7. Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands.
  • 8. Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA. [email protected].
  • # Contributed equally.
PMID: 36544021 DOI: 10.1038/s41586-022-05545-9
Abstract

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.

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