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

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.

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-I^C268F.

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-I^C268F and Y-RNAs, a family of four structurally similar non-coding RNAs.

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.