An autoinflammatory RIG-I variant causing Singleton-Merten syndrome associates with small non-coding Y-RNAs

Discovery Immunology, vol. 5, pp. kyag013

Abstract

Abstract Introduction The RNA sensor retinoic acid-inducible gene I (RIG-I) performs a critical role in surveying the cytoplasm for the presence of viral nucleic acids and initiating the downstream anti-viral type I interferon pathway. Through recognition of specific features, such as the presence of a 5′ tri/diphosphate motif or highly structured base-paired regions, RIG-I effectively differentiates between RNA of viral- and self-origin. In Singleton-Merten syndrome (SMS), gain-of-function variants in RIG-I lead to a breakdown in this surveillance system and results in aberrant sensing of self-RNAs and deleterious upregulation of type I interferons. The identity of the self-RNAs binding to gain-of-function RIG-I mutants has remained elusive and their elucidation would provide a greater understanding of the aetiology of SMS. Methods Here we used an infrared individual-nucleotide resolution UV-crosslinking and immunoprecipitation (irCLIP) approach to determine the RNA profile bound to a previously characterized ATPase-deficient SMS variant, RIG-IC268F. Results irCLIP identified a broad array of self-RNAs, primarily those transcribed by RNA polymerase III, that were bound to RIG-I. Subsequent native RNA immunoprecipitation confirmed a prominent and specific interaction between RIG-IC268F and Y-RNAs, a family of four structurally similar non-coding RNAs. Conclusion Manipulation of Y-RNAs alone by targeting either Y-RNA transcripts or Y-RNA stabilizing proteins was insufficient to negate RIG-I induced interferon responses, hinting at a broader profile of RNA polymerase III-derived RNAs being influential in driving the sterile activation of gain-of-function RIG-I variants.

Authors 10

1. Benjamin J. Thompson Aachen Department of Immunology, Leiden University Medical Center

   Leiden University Medical Center

   Affiliation as printed

   Department of Immunology, Leiden University Medical Center , Leiden ,

2. Christ C P Leemans Aachen Department of Immunology, Leiden University Medical Center

   Leiden University Medical Center

   Affiliation as printed

   Department of Immunology, Leiden University Medical Center , Leiden ,

3. Dennis Gravekamp Aachen Department of Immunology, Leiden University Medical Center

   Leiden University Medical Center

   Affiliation as printed

   Department of Immunology, Leiden University Medical Center , Leiden ,

4. Amarise-Jourmaine M H Silie Aachen Department of Immunology, Leiden University Medical Center

   Leiden University Medical Center

   Affiliation as printed

   Department of Immunology, Leiden University Medical Center , Leiden ,

5. Jorn E. Stok Aachen Department of Immunology, Leiden University Medical Center

   Leiden University Medical Center

   Affiliation as printed

   Department of Immunology, Leiden University Medical Center , Leiden ,

6. Jasper W. de Wolf Aachen Department of Immunology, Leiden University Medical Center

   Leiden University Medical Center

   Affiliation as printed

   Department of Immunology, Leiden University Medical Center , Leiden ,

7. Erik B. van den Akker Aachen Department of Immunology, Leiden University Medical Center

   Leiden University Medical Center

   Affiliation as printed

   Department of Immunology, Leiden University Medical Center , Leiden ,

8. Frank J. T. Staal Aachen Department of Immunology, Leiden University Medical Center

   Leiden University Medical Center

   Affiliation as printed

   Department of Immunology, Leiden University Medical Center , Leiden ,

9. Hailiang Mei Aachen Department of Biomedical Data Sciences

   Leiden University Medical Center

   Affiliation as printed

   Department of Biomedical Data Sciences, Sequencing Analysis Support Core, Leiden University Medical Center , Leiden ,

10. Annemarthe G. van der Veen corresponding Aachen Department of Immunology, Leiden University Medical Center

    Leiden University Medical Center

    Affiliation as printed

    Department of Immunology, Leiden University Medical Center , Leiden ,