cells Review Role of Alternative Splicing in Regulating Host Response to Viral Infection Kuo-Chieh Liao 1,* and Mariano A. Garcia-Blanco 2,3,4,5,* 1 Genome Institute of Singapore, A*STAR, Singapore 138672, Singapore 2 Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77550, USA 3 Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77550, USA 4 Institute of Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77550, USA 5 Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore * Correspondence: [email protected] (K.-C.L.); [email protected] (M.A.G.-B.) Abstract: The importance of transcriptional regulation of host genes in innate immunity against viral infection has been widely recognized. More recently, post-transcriptional regulatory mechanisms have gained appreciation as an additional and important layer of regulation to fine-tune host immune responses. Here, we review the functional significance of alternative splicing in innate immune responses to viral infection. We describe how several central components of the Type I and III interferon pathways encode spliced isoforms to regulate IFN activation and function. Additionally, the functional roles of splicing factors and modulators in antiviral immunity are discussed. Lastly, we discuss how cell death pathways are regulated by alternative splicing as well as the potential role of this regulation on host immunity and viral infection. Altogether, these studies highlight the importance of RNA splicing in regulating host–virus interactions and suggest a role in downregulating antiviral innate immunity; this may be critical to prevent pathological inflammation. Citation: Liao, K.-C.; Garcia-Blanco, Keywords: alternative splicing; antiviral response; innate immunity; cell death pathways M.A. Role of Alternative Splicing in Regulating Host Response to Viral Infection. Cells 2021, 10, 1720. https://doi.org/10.3390/cells10071720 1. Introduction The host response to viral infection is multifaceted and incorporates the induction Academic Editors: Marco Binder and of an antiviral transcriptional program, including the expression of interferons (IFNs) Meike Dittmann and cytokines, and the activation of cell death pathways (apoptosis, necroptosis, and pyroptosis). Among these pathways, many steps are tightly regulated at several levels to Received: 17 June 2021 ensure tissue homeostasis. In this review, we discuss the functional roles of alternative Accepted: 30 June 2021 Published: 8 July 2021 splicing and various spliced isoforms in shaping host immunity against viral infection. Pre-messenger RNA splicing is an important RNA maturation step that involves Publisher’s Note: MDPI stays neutral the joining of exons and removal of introns. The overwhelming majority of transcripts with regard to jurisdictional claims in produced by RNA polymerase II (RNAP II), including most mRNAs, contain introns and published maps and institutional affil- thus must be spliced. Splicing is carried out in cell nuclei by one of two macromolecular iations. ribonucleoprotein complexes, known as the major and the minor spliceosomes [1]. It is estimated that more than 90% of expressed human genes undergo alternative splicing (AS) [2], which enables single genes to generate multiple distinct mRNAs that can encode distinct proteins, thus greatly expanding proteome complexity. Many types of AS events have been described, and they primarily include cassette exons, mutually exclusive exons, Copyright: © 2021 by the authors. 0 0 Licensee MDPI, Basel, Switzerland. alternative 5 splice site use, alternative 3 splice site use, and intron retention. AS events This article is an open access article can be regulated in a spatiotemporal-dependent manner [1] by the combined action of distributed under the terms and cis-elements (e.g., exon splicing enhancers (ESEs)) and trans-factors (e.g., RNA binding conditions of the Creative Commons proteins) [3]. Aberrant splicing has been linked to many diseases [4,5], further underscoring Attribution (CC BY) license (https:// the importance this highly regulated process. AS and mRNA isoforms play important roles creativecommons.org/licenses/by/ in virtually all cellular processes and pathways, and it is thus not surprising that both have 4.0/). been noted to be critical for an effective antiviral response. Cells 2021, 10, 1720. https://doi.org/10.3390/cells10071720 https://www.mdpi.com/journal/cells Cells 2021, 10, x 2 of 13 elements (e.g., exon splicing enhancers (ESEs)) and trans-factors (e.g., RNA binding pro- teins) [3]. Aberrant splicing has been linked to many diseases [4,5], further underscoring the importance this highly regulated process. AS and mRNA isoforms play important roles in virtually all cellular processes and pathways, and it is thus not surprising that both have been noted to be critical for an effective antiviral response. Cells 2021, 10, 1720 2 of 12 2. Alternative RNA Splicing and Its Isoforms in Type I and III IFN Responses The antiviral response initiates when cellular pattern recognition receptors (PRRs) detect2. Alternative pathogen-associated RNA Splicing molecular and Its Isoforms patterns in (PAMPs). Type I and Cytosolic III IFN Responses retinoic acid-inducible gene I (RIG-I)The antiviral and melanoma response initiates differentiation- when cellularassociated pattern protein recognition 5 (MDA-5) receptors sense (PRRs) double- strandeddetect pathogen-associated RNA (dsRNA) (RIG-I molecular specifically patterns detects (PAMPs). 5′-triphosphate Cytosolic retinoic or acid-inducible5′-diphosphate of RNAgene molecules) I (RIG-I) and and melanoma undergo differentiation-associated conformational changes protein to associate 5 (MDA-5) with sense the downstream double- 0 0 mitochondrialstranded RNA antiviral (dsRNA) signaling (RIG-I specifically protein (MAVS). detects 5 -triphosphateSubsequently, or MAVS 5 -diphosphate associates of with TANKRNA Binding molecules) Kinase and undergo1 (TBK1) conformational and I-kappa-B changes kinase toepsilon associate (IKK withε), thepromoting downstream the phos- phorylationmitochondrial of interferon antiviral signaling regulatory protein factor (MAVS). 3 (IRF3) Subsequently, and interferon MAVS associatesregulatory with factor 7 TANK Binding Kinase 1 (TBK1) and I-kappa-B kinase epsilon (IKK"), promoting the (IRF7). These two transcription factors translocate to the nucleus and drive the transcrip- phosphorylation of interferon regulatory factor 3 (IRF3) and interferon regulatory factor 7 tion(IRF7). and production These two transcription of Type I factorsand Type translocate III interferon to the nucleus (IFN) andmRNAs. drive the The transcription cytosolic DNA sensor,and productioncyclic GMP-AMP of Type Isynthase and Type (cGAS), III interferon can detect (IFN) DNA mRNAs. in the The cytoplasm cytosolic DNAas PAMP, whensensor, DNA cyclic viruses GMP-AMP infect cells synthase and produce (cGAS), can the detectcyclic DNAdinucleotide in the cytoplasm 2′,3′-cyclic as GMP–AMP PAMP, (2′,3when′-cGAMP) DNA viruses [6]. This infect secondary cells and producemessenger the cyclicin turn dinucleotide activates 2ER-resident0,30-cyclic GMP–AMP stimulator of 0 0 interferon(2 ,3 -cGAMP) genes [(STING)6]. This secondary and leads messenger to TBK1-dependent in turn activates IRF3 ER-resident phosphorylation stimulator for of Type I andinterferon III IFN production. genes (STING) It is and important leads to TBK1-dependent to note that cGAS IRF3 has phosphorylation been shown to for also Type respond I to andRNA III virus IFN production. infection, Itprobably is important due to to note the that cytoplasmic cGAS has been release shown of tohost also mitochondrial respond to RNA virus infection, probably due to the cytoplasmic release of host mitochondrial DNA [7]. Additionally, membrane-bound Toll-like receptor 3 (TLR3) can recognize DNA [7]. Additionally, membrane-bound Toll-like receptor 3 (TLR3) can recognize dsRNA dsRNAin the in endosomal the endosomal compartments. compartments. Ligand detectionLigand detection by TLR3 triggersby TLR3 its triggers association its association with withthe the TIR-domain-containing TIR-domain-containing adapter-inducing adapter-inducing interferon- interferon-β (TRIF)β adaptor (TRIF) andadaptor induces and in- ducesTBK1/IKK TBK1/IKK"-dependentε-dependent IRF3 phosphorylation.IRF3 phosphorylation. All of theseAll of processes these processes culminate culminate in the in thetranscriptional transcriptional induction induction of Typeof Type I and I and III IFNIII IFN genes genes and and the productionthe production of these of these IFNs IFNs (Figure(Figure 1).1). FigureFigure 1. Alternative 1. Alternative splicing splicing in inthe the host host Type Type I Iand and Type IIIIII IFN IFN response. response. AS AS isoforms isoforms that that upregulate upregulate the antiviral the antiviral responseresponse are shown are shown in green, in green, and and th thoseose that that downregulate downregulate thethe antiviral antiviral response response are are shown shown in red. in red. Newly synthesized Type I and III IFNs are secreted and activate downstream signaling in both autocrine- and paracrine-dependent manners. These two classes of IFNs bind to Cells 2021, 10, 1720 3 of 12 different membrane receptors. Type I IFNs bind to interferon alpha and beta receptor subunits 1 and 2 (IFNAR1 and IFNAR2), whereas Type III IFNs utilize the interferon