# Endogenous RNA cleavage products that activate the RIG-I dependent interferon response

> **NIH NIH F30** · UNIVERSITY OF COLORADO DENVER · 2020 · $33,761

## Abstract

Project summary/abstract
 Type I interferons (IFN) are potent antiviral cytokines whose expression must be tightly regulated to
combat infection without driving the development of inflammatory and autoimmune pathologies. Upregulation
of type I IFN is pathogenic in a group of monogenic disorders termed type I interferonopathies and the majority
are caused by mutations in genes involved in nucleic acid metabolism. Defects in RNA metabolism can result
in aberrant activation of innate immune RNA sensors by cellular RNAs, initiating type I interferon expression.
Chronic type I IFN signaling activates a signature of interferon stimulated gene (ISG) expression associated
with autoimmune and autoinflammatory disease. Furthermore, ISG expression is highly heterogeneous and
this heterogeneity directs immune cell state and function.
 Retinoic acid-inducible gene I (RIG-I) is a RNA innate immune sensor that recognizes double-stranded
RNAs with 5´-triphosphates – a unique feature of viral RNA replication – to initiate type I IFN expression.
Mutations in the RNA exosome (3´à5 degradation) cofactor SKIV2L cause the rare multisystem disorder
trichohepatoenteric syndrome; and people with this disorder and SKIV2L mutations have a type I IFN
signature. In cells that don't express SKIV2L, activation of the unfolded protein response (UPR) also initiates
type I IFN expression dependent on a RIG-I mediated signaling. The RNA endoribonuclease Ire1 cleaves ER-
localized mRNAs during the UPR as part of Regulated IRE1-Dependent Decay (RIDD), producing RNA
fragments with 5´-hydroxyl and 2´,3´-cyclic phosphate ends. We hypothesize that SKIV2L is required during
RIDD to target Ire1 cleaved ER-targeted mRNAs for degradation to prevent activation of a RIG-I dependent
type I interferon response. Currently, the RNAs that initiate this response and the consequences of the
activated ISG program are unknown.
 The tools needed to comprehensively identify endogenous cleaved RNAs and direct RIG-I-RNA
interactions have limited our understanding of endogenous RNA detection by RIG-I. Our aims are to (1) identify
Ire1 cleaved RNAs targeted by SKIV2L for degradation to prevent RIG-I-dependent IFN induction using a novel
RNA end-sequencing method to directly identify RNAs cleaved by Ire1 in SKIV2L mutant cells during RIDD;
and (2) characterize heterogeneous ISG expression induced by direct activation of RIG-I by Ire1 cleaved RNAs
using a cross-linking and immunoprecipitation method to capture and sequence RIG-I bound RNAs and single
cell RNA sequencing to profile transcriptional and cellular heterogeneity of the ISG response induced by these
endogenous RNAs. These studies will facilitate efforts to understand the molecular basis of endogenous RNA
detection by RIG-I and contribute to a developing paradigm highlighting the critical role of RNA sensing by
innate immune regulators in interferon-mediated autoinflammatory and autoimmune disease.

## Key facts

- **NIH application ID:** 9999280
- **Project number:** 5F30AI140615-02
- **Recipient organization:** UNIVERSITY OF COLORADO DENVER
- **Principal Investigator:** Rachel Ancar
- **Activity code:** F30 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $33,761
- **Award type:** 5
- **Project period:** 2019-05-01 → 2023-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9999280

## Citation

> US National Institutes of Health, RePORTER application 9999280, Endogenous RNA cleavage products that activate the RIG-I dependent interferon response (5F30AI140615-02). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/9999280. Licensed CC0.

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