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The SKIV2L RNA exosome limits activation of the RIG-I-like receptors

Nature Immunology volume 15, pages 839–845 (2014)Cite this article

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Abstract

Sensors of the innate immune system that detect intracellular nucleic acids must be regulated to prevent inappropriate activation by endogenous DNA and RNA. The exonuclease Trex1 regulates the DNA-sensing pathway by metabolizing potential DNA ligands that trigger it. However, an analogous mechanism for regulating the RIG-I-like receptors (RLRs) that detect RNA remains unknown. We found here that the SKIV2L RNA exosome potently limited the activation of RLRs. The unfolded protein response (UPR), which generated endogenous RLR ligands through the cleavage of cellular RNA by the endonuclease IRE-1, triggered the production of type I interferons in cells depleted of SKIV2L. Humans with deficiency in SKIV2L had a type I interferon signature in their peripheral blood. Our findings reveal a mechanism for the intracellular metabolism of immunostimulatory RNA, with implications for specific autoimmune disorders.

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Figure 1: SKIV2L is a negative regulator of the RLR-mediated antiviral response.
Figure 2: The UPR activates an antiviral response in cells depleted of SKIV2L.
Figure 3: SKIV2L specifically regulates the MAVS-dependent antiviral response.
Figure 4: SKIV2L-deficient humans have a robust type I interferons signature.
Figure 5: Different roles for SKIV2L and TTC37 in the regulation of RLRs.

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Acknowledgements

We thank M. Gale, Jr. (University of Washington) for Mavs−/− mice, and members of the Stetson laboratory for discussions. Supported by the National Institute of Allergy and Infectious Disease (AI084914 to D.B.S.), the Nuclease Immune Mediated Brain and Lupus-like conditions (NIMBL) project of the European Union Seventh Framework Programme 2007-2013 (241779 to Y.J.C. and D.B.S.), the Lupus Research Institute (D.B.S.), the Cancer Research Institute (E.E.G.) and the Rita Allen Foundation (D.B.S.).

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Authors and Affiliations

  1. Department of Immunology, University of Washington School of Medicine, Seattle, Washington, USA

    Sterling C Eckard, Elizabeth E Gray & Daniel B Stetson

  2. Manchester Academic Health Science Centre, University of Manchester, Genetic Medicine, Manchester, UK

    Gillian I Rice & Yanick J Crow

  3. UMR_S 910, Inserm-Faculte´ de Medecine, Aix-Marseille Universite, Marseille, France

    Alexandre Fabre & Catherine Badens

  4. AP-HM, Service de Pediatrie Multidisciplinaire, Hopital d'Enfants de la Timone, Marseille, France

    Alexandre Fabre

  5. AP-HM, Laboratoire de Genetique Moleculaire, Hopital d'Enfants de la Timone, Marseille, France

    Catherine Badens

  6. Liver Unit, Birmingham Children's Hospital, Birmingham, UK

    Jane L Hartley

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Contributions

S.C.E. did all experiments with mouse cells; G.I.R. and Y.J.C. did the ISG analysis of human cells and helped write the manuscript; A.F., C.B. and J.L.H. obtained peripheral blood samples from patients with THES and control subjects, provided intellectual input and insights into human THES and helped write the manuscript; E.E.G. developed the Lenti-CRISPR system; and S.C.E. and D.B.S. designed the study and wrote the manuscript.

Corresponding author

Correspondence to Daniel B Stetson.

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The authors declare no competing financial interests.

Integrated supplementary information

Supplementary Figure 1 Restriction fragment length polymorphism (RFLP) analysis of mouse fibroblasts in which Ern1 was targeted.

(a) MEFs immortalized with SV40 Large T antigen were transduced with lentiviruses encoding CAS9 alone, or CAS9 plus one of two guide RNAs targeting the murine Ern1 gene. Genomic DNA was isolated at the indicated times post selection of transduced cells, amplified with PCR primers flanking the targeted site, and digested with the indicated restriction enzymes. For guide RNA 1 (top), the digested wild-type DNA results in products of 191 bp and 103 bp. Targeted alleles are resistant to BsajI digestion and are ~294 bp, with a concomitant loss of the wild-type digestion products. For guide RNA 2 (bottom), the digested wild-type allele results in products of 157 bp and 96 bp. The targeted alleles are resistant to MlucI digestion and are ~253 bp. The asterisk in the bottom panel denotes a MlucI digestion product of the PCR that is outside the targeted region.

(b) A schematic view of the restriction enzyme sites within amplified genomic DNA for each guide RNA. The NHEJ product denotes insertions/deletions at the CRISPR/CAS9 target site that disrupt the restriction enzyme site.

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Eckard, S., Rice, G., Fabre, A. et al. The SKIV2L RNA exosome limits activation of the RIG-I-like receptors. Nat Immunol 15, 839–845 (2014). https://doi.org/10.1038/ni.2948

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