The RNA polymerase III-RIG-I axis in antiviral immunity and inflammation

Abstract

Nucleic acid sensors survey subcellular compartments for atypical or mislocalized RNA or DNA, ultimately triggering innate immune responses. Retinoic acid-inducible gene-I (RIG-I) is part of the family of cytoplasmic RNA receptors that can detect viruses. A growing literature demonstrates that mammalian RNA polymerase III (Pol III) transcribes certain viral or cellular DNA sequences into immunostimulatory RIG-I ligands, which elicits antiviral or inflammatory responses. Dysregulation of the Pol III-RIG-I sensing axis can lead to human diseases including severe viral infection outcomes, autoimmunity, and tumor progression. Here, we summarize the newly emerging role of viral and host-derived Pol III transcripts in immunity and also highlight recent advances in understanding how mammalian cells prevent unwanted immune activation by these RNAs to maintain homeostasis.

Keywords: RIG-I; RNA polymerase III; antiviral immunity; cancer; inflammation.

Figure 1.. RIG-I agonists and signal transduction

A, In the absence of an agonist, RIG-I remains in an auto-repressed conformation in which the CARDs are sequestered by the helicase domain [101]. Ser/Thr phosphorylation in the CARDs also aids in repressing RIG-I downstream signaling. CARD dephosphorylation by the protein phosphatase-1(PP1)-PPP1R12C complex is a prerequisite for RIG-I signaling and can be driven by disturbances to the actin cytoskeleton during virus infection [102, 103]. MAVS activation requires RIG-I tetramerization that is facilitated by K63-linked ubiquitination mediated by several E3 ligases including TRIM25 and Riplet [104, 105]. Another mechanism promoting RIG-I oligomerization is ATP-driven translocation from the 5′ end to the interior of the dsRNA, thereby re-exposing the 5′ end and allowing recruitment of another RIG-I molecule [106]. Upon its activation, MAVS forms prion-like aggregates amplifying the signaling cascade that results in the recruitment of inhibitor of NF-κB kinase (IKK) family members (IKKε or TBK1, and IKKα/β/γ) [107]. Eventually, paracrine or autocrine IFN-I/III effects lead to upregulation of IFN-stimulated genes (ISGs) through JAK-STAT signaling and create a milieu impeding efficient virus replication. B, Structural domains of RIG-I. C, Molecular features of bona fide RIG-I agonists. Abbreviations: p, phosphorylation marks. Ub, ubiquitination. This Figure was created using Biorender.com

Figure 2.. Molecular mechanisms to prevent activation of innate immunity by host-derived RNAs.

Eukaryotic RNA modifications including 7-methylated guanosine (m7G), 2′-O methylation, pseudouridine, 2-thiouridine and 5-methylcytidine have been shown to impede RNA recognition by several sensors including RIG-I [21, 22] (left panel). Moreover, adenosine alterations such as deamidation (inosine) by ADAR1 or N6-methyadenosine (m6A) prevent aberrant formation of cytosolic dsRNAs including transposable elements (TEs) [–25] (left panel). TEs are also transcriptionally repressed through epigenetic regulation, indirectly shown by anticancer treatments inhibiting histone methyltransferases (G9A, SETDB1, EZH2), histone demethylases (LSD1), and DNA methyltransferases (DNMTs) [–29] (middle panel). In addition, immunostimulatory RNAs can be processed post-transcription such as the removal of 5′-PPP by DUSP11 and RNase P (middle panel). Endogenous RNAs can also be actively metabolized by the mitochondrial degradosome (SUV3 and PNPase), Dicer, and the RNA helicase SKIV2L [–32] (middle panel). The importance of intron metabolism has been shown by spliceosome-targeted therapies (PRMT inhibitors) that result in immunostimulatory intron-retained mRNAs as a source of endogenous immunostimulatory dsRNAs [33, 34] (middle panel). In addition, numerous RBPs can prevent immune recognition by shielding endogenous RNAs or by enhancing their metabolism [, , –39] (right panel). ERVs, endogenous retroviruses; LINEs, long interspersed nuclear elements; SINEs, short interspersed nuclear elements; IR-Alu, inverted-repeat Alu; mt, mitochondrial; DNMTs, DNA methyltransferases; PRMTs, protein arginine methyltransferases. This Figure was created using Biorender.com

Key Figure, Figure 3.. Pol III transcripts activating RIG-I during virus infection, cancer and inflammation.

Pol III transcripts can serve as RIG-I agonists and trigger antiviral defense programs or inflammatory responses. A, Pol III transcribes sequences in the viral DNA genome of EBV, adenovirus and varicella zoster virus (VZV) to generate immunostimulatory EBERs, VA RNAs and VZV RNA, respectively [7, 40, 54]. B, Nuclear-replicating viruses including, HSV-1, EBV and IAV induce the expression and nuclear-to-cytosolic redistribution of the cellular Pol III transcript RNA5SP141. In addition, these viruses trigger RNA5SP141 ‘unshielding’ in the cytosol through virus host shutoff mechanisms that ultimately repress TST and MRPL18 protein abundances [6, 57]. C, Infection-dependent reduction of DUSP11 by KSHV and HIV-1 results in the accumulation of triphosphorylated Pol III transcripts [9]. D, NSUN2 depletion decreases m5C modification of H1 RNA, which stimulates the transcription of Pol III transcripts that induce RIG-I activation and suppresses replication of RNA viruses. E, NOTCH1-MYC signaling induced by cancer cells can activate stromal cells and enhances Pol III-mediated transcription of 7SL RNA, which in its protein-unbound form is subsequently sorted into exosomes and can drive RIG-I activation in recipient cancer cells [68]. F and G, Loss of DUSP11 or TDP-43 causes the accumulation of immunostimulatory Pol III transcripts that trigger inflammatory responses [38, 72]. This Figure was created using Biorender.com