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Review
. 2021 May;102(5):001603.
doi: 10.1099/jgv.0.001603.

Discovering antiviral restriction factors and pathways using genetic screens

Chloe E Jones  1 , Wenfang S Tan  2 , Finn Grey  2 , David J Hughes  1
Affiliations
Review

Discovering antiviral restriction factors and pathways using genetic screens

Chloe E Jones et al. J Gen Virol. 2021 May.

Abstract

Viral infections activate the powerful interferon (IFN) response that induces the expression of several hundred IFN stimulated genes (ISGs). The principal role of this extensive response is to create an unfavourable environment for virus replication and to limit spread; however, untangling the biological consequences of this large response is complicated. In addition to a seemingly high degree of redundancy, several ISGs are usually required in combination to limit infection as individual ISGs often have low to moderate antiviral activity. Furthermore, what ISG or combination of ISGs are antiviral for a given virus is usually not known. For these reasons, and since the function(s) of many ISGs remains unexplored, genome-wide approaches are well placed to investigate what aspects of this response result in an appropriate, virus-specific phenotype. This review discusses the advances screening approaches have provided for the study of host defence mechanisms, including clustered regularly interspaced short palindromic repeats/CRISPR associated protein 9 (CRISPR/Cas9), ISG expression libraries and RNA interference (RNAi) technologies.

Keywords: CRISPR/Cas9; Innate immunity; RNAi; antiviral immunity; genome-wide screens; interferon.

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Conflict of interest statement

The authors declare that there are no conflicts of interest

Figures

Fig. 1.
Fig. 1.
Antiviral factors identified using screening methods. A schematic illustrating a selection of antiviral factors identified during genome-wide screening. Each antiviral factor is attributed to a stage in the viral life cycle corresponding to literature references throughout this review [52, 53, 63, 65, 69, 85, 87, 141]; it should be noted that many ISGs have been seen to act at additional stages. The key indicates the screening type used to identify each example: (c), clustered regularly interspaced short palindromic repeats/CRISPR associated protein 9 (CRISPR/Cas9), (o), Overexpression, (r), RNA interference (RNAi). Abbreviations used: HCV; Hepatitis C Virus, SARS-CoV-2; Severe Acute Respiratory Syndrome Coronavirus 2, IAV; Influenza A Virus, HIV; Human Immunodeficiency Virus, HCMV; Human Cytomegalovirus, EBOV; Ebola Virus, YFV; Yellow Fever Virus, DENV; Dengue Virus, ZIKV; Zika Virus, WNV; West Nile Virus, BUNV; Bunyavirus. Created with biorender.com biorender.com.
Fig. 2.
Fig. 2.
Different approaches to CRISPR/Cas9 screening based on Cas9 variation. In CRISPR/Cas9 KO screens, a single guide RNA targets the Cas9 endonuclease protein to a specific locus in the coding sequence of a gene leading to a double strand break in the DNA. This activates the cellular DNA damage response; primarily, the imprecise non-homologous end-joining pathway that introduces INDELs resulting in gene knockout. For CRISPR activation (CRISPRa) and CRISPR interference (CRISPRi) screens, fusion of either a transcriptional activator or repressor domain to a catalytically inactive Cas9 subunit results in overexpression or inhibition of gene expression, respectively. Created with biorender.com.
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