APOBECs orchestrate genomic and epigenomic editing across health and disease
Authors: Karla Cervantes-Gracia, Anna Gramalla-Schmitz, Julian Weischedel, Richard Chahwan
Journal: Trends in Genetics (2021)

Genomic and epigenomic effects of apolipoprotein B mRNA editing cytosine deaminases (APOBECs) are tightly controlled and are essential for physiological immune and non-immune processes.Pathological APOBEC off-target effects are often observed because of altered catalytic activity or dysregulation, and/or synergies with other predisposing factors such as infections, inflammation, or DNA repair defects.APOBEC mutation signatures are documented in various cancers. They are also involved in autoimmune diseases, triple nucleotide repeat diseases, and diabetes, among others.Possible APOBEC signatures in aging tissues also highlight their potential contribution to this process at the genomic and epigenomic levels.Advances in gene-editing technologies combined with APOBEC mechanistic insights are ushering in the era of APOBECs as therapeutic targets, potentially closing the loop of negative versus positive gene-editing effects. APOBEC proteins can deaminate cytosine residues in DNA and RNA. This can lead to somatic mutations, DNA breaks, RNA modifications, or DNA demethylation in a selective manner. APOBECs function in various cellular compartments and recognize different nucleic acid motifs and structures. They orchestrate a wide array of genomic and epigenomic modifications, thereby affecting various cellular functions positively or negatively, including immune editing, viral and retroelement restriction, DNA damage responses, DNA demethylation, gene expression, and tissue homeostasis. Furthermore, the cumulative increase in genomic and epigenomic editing with aging could also, at least in part, be attributed to APOBEC function. We synthesize our cumulative understanding of APOBEC activity in a unifying overview and discuss their genomic and epigenomic impact in physiological, pathological, and technological contexts. APOBEC proteins can deaminate cytosine residues in DNA and RNA. This can lead to somatic mutations, DNA breaks, RNA modifications, or DNA demethylation in a selective manner. APOBECs function in various cellular compartments and recognize different nucleic acid motifs and structures. They orchestrate a wide array of genomic and epigenomic modifications, thereby affecting various cellular functions positively or negatively, including immune editing, viral and retroelement restriction, DNA damage responses, DNA demethylation, gene expression, and tissue homeostasis. Furthermore, the cumulative increase in genomic and epigenomic editing with aging could also, at least in part, be attributed to APOBEC function. We synthesize our cumulative understanding of APOBEC activity in a unifying overview and discuss their genomic and epigenomic impact in physiological, pathological, and technological contexts. The pleiotropic roles of cytosine deaminases in genomic and epigenomic editingCytosine deamination can modify the genomic code by mediating cytosine to uracil (C-to-U) conversion, thus creating U:G DNA mismatches that are subsequently consolidated by error-prone DNA repair processing. Although cytosine deamination can occur spontaneously, these reactions can be catalyzed by APOBECs (see Glossary) in a regulated process [1.Muramatsu M. et al.Specific expression of activation-induced cytidine deaminase (AID), a novel member of the RNA-editing deaminase family in germinal center B cells.J. Biol. Chem. 1999; 274: 18470-18476Abstract Full Text Full Text PDF PubMed Scopus (901) Google Scholar, 2.Mehta A. et al.Apobec-1 interacts with a 65-kDa complementing protein to edit apolipoprotein-B mRNA in vitro.J. Biol. 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Almost all APOBECs (with the exception of A3D, A2, and A4) can also edit, with varying proficiencies, the epigenomic code by deaminating 5-methylcytosine (5mC) to thymine – creating T:G mismatches – followed by error-free DNA repair [5.Chahwan R. et al.Crosstalk between genetic and epigenetic information through cytosine deamination.Trends Genet. 2010; 26: 443-448Abstract Full Text Full Text PDF PubMed Scopus (0) Google Scholar, 6.Morgan H.D. et al.Activation-induced cytidine deaminase deaminates 5-methylcytosine in DNA and is expressed in pluripotent tissues: implications for epigenetic reprogramming.J. Biol. 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Eleven APOBEC proteins have been described in humans. AID (activation-induced cytosine deaminase) is arguably the evolutionary founding member and has been extensively studied in the context of somatic hypermutation (SHM) and class-switch recombination (CSR) during antibody diversification [10.Kinoshita K. Honjo T. Linking class-switch recombination with somatic hypermutation.Nat. Rev. Mol. Cell Biol. 2001; 2: 493-503Crossref PubMed Scopus (0) Google Scholar,11.Sheppard E.C. et al.Epigenomic modifications mediating antibody maturation.Front. Immunol. 2018; 9: 355Crossref PubMed Scopus (6) Google Scholar]. APOBECs are also involved in several physiological processes including lipid metabolism (APOBEC1) [12.Navaratnam N. et al.The p27 catalytic subunit of the apolipoprotein B mRNA editing enzyme is a cytidine deaminase.J. Biol. 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Rep. 2019; 9: 3109Crossref PubMed Scopus (7) Google Scholar]. Despite their beneficial roles, dysregulation of APOBECs is associated with several diseases [17.Olson M.E. et al.APOBEC enzymes as targets for virus and cancer therapy.Cell Chem. Biol. 2018; 25: 36-49Abstract Full Text Full Text PDF PubMed Scopus (60) Google Scholar,18.Cheng A.Z. et al.APOBECs and herpesviruses.Viruses. 2021; 13: 390Crossref PubMed Scopus (1) Google Scholar]. Signatures of APOBECs feature in many cancer genomes and are considered to be potent mediators of tumorigenesis [19.Alexandrov L.B. et al.The repertoire of mutational signatures in human cancer.Nature. 2020; 578: 94-101Crossref PubMed Scopus (459) Google Scholar,20.Jiang Q. et al.Inflammation-driven deaminase deregulation fuels human pre-leukemia stem cell evolution.Cell Rep. 2021; 34108670Abstract Full Text Full Text PDF PubMed Google Scholar]. Loss-of-function mutations in APOBECs can also result in immune deficiencies or autoimmunity [7.Muramatsu M. et al.Class switch recombination and hypermutation require activation-induced cytidine deaminase (AID), a potential RNA editing enzyme.Cell. 2000; 102: 553-563Abstract Full Text Full Text PDF PubMed Google Scholar,20.Jiang Q. et al.Inflammation-driven deaminase deregulation fuels human pre-leukemia stem cell evolution.Cell Rep. 2021; 34108670Abstract Full Text Full Text PDF PubMed Google Scholar,21.Roth S.H. et al.Increased RNA editing may provide a source for autoantigens in systemic lupus erythematosus.Cell Rep. 2018; 23: 50-57Abstract Full Text Full Text PDF PubMed Scopus (33) Google Scholar]. In the following sections APOBEC family regulation (Figure 1), their genomic and epigenomic mechanisms (Figure 2), their involvement in physiology and pathology (Figure 3A–H, Key figure ), and their evolutionary and technological applications (Figure 4) are synthesized and discussed from a unifying perspective.Figure 2Genomic and epigenomic mechanisms of APOBEC deamination.Show full captionAPOBEC deaminases target DNA (blue) or RNA (green) substrates, leading to genetic (blue shading) or epigenetic changes (green shading). Both are known to be involved in healthy/physiological or disease/pathological processes. Abbreviations: HR, homologous recombination; NHEJ, non-homologous end joining; RT, reverse transcriptase. Nucleotides are depicted as N: A, C, G, or T; H: A, C, or T; R: A or G; W: A or T; Y: C or T.View Large Image Figure ViewerDownload Hi-res image Download (PPT)Figure 3Key figure. The pleiotropic role of cytosine deaminases.Show full captionThe APOBEC cytosine deaminase family members act at the genomic (blue) and epigenomic (green) levels. The deaminases are involved in many immune (lighter shades) and non-immune (darker shades) physiological (yellow) processes. When dysregulated, however, these enzymes can lead to various pathologies (orange). The APOBEC functions and effects are depicted in eight parts (A–H). (A) Genomic immune physiology. (B) Genomic non-immune physiology. (C) Genomic non-immune pathology. (D) Genomic immune pathology. (E) Epigenomic immune pathology. (F) Epigenomic non-immune pathology. (G) Epigenomic non-immune physiology. (H) Epigenomic immune physiology. Abbreviations: CSR, class-switch recombination; DSB, double-strand break; gDNA, genomic DNA; 5mC, 5-methylcytosine; miRNA, microRNA; mtDNA, mitochondrial DNA; ROS, reactive oxygen species; RT, reverse transcription; SHM, somatic hypermutation; vDNA, viral DNA.View Large Image Figure ViewerDownload Hi-res image Download (PPT)Figure 4Evolutionarily and technologically driven gene-editing applications of APOBECs.Show full caption(A) Different complexity levels of coevolution driven by APOBEC deaminases, DDR, and selective pressure over time. (B) A perspective of APOBECs as corrective and preventive tools to treat diseases at the genomic and epigenomic levels. Abbreviations: DDR, DNA damage response; TME, tumor microenvironment.View Large Image Figure ViewerDownload Hi-res image Download (PPT)APOBEC regulation: from protein domains to catalytic substrates and modulatorsAPOBEC catalytic activity is modulated by their ability to bind preferentially to nucleic acid substrates and motif signatures (WRC for AID and TC for most others); this mode of regulation could be considered as regulation by 'cis-determinants'. For the APOBEC3 (A3) subfamily it has been reported that both catalytic and non-catalytic domains interact with single-stranded DNA (ssDNA) [22.Xiao X. et al.Structural determinants of APOBEC3B non-catalytic domain for molecular assembly and catalytic regulation.nucle. 2017; 45: 7494-7506Google Scholar]. This regulates substrate deamination by guiding them to active sites in monomeric or multimeric conformations. Within the catalytic domains, positive patches distal to the active sites interact with ssDNA. In the A3F and A3G subtypes, these are reported to be crucial for binding and deamination [23.Polevoda B. et al.DNA mutagenic activity and capacity for HIV-1 restriction of the cytidine deaminase APOBEC3G depend on whether DNA or RNA binds to tyrosine 315.J. Biol. Chem. 2017; 292: 8642-8656Abstract Full Text Full Text PDF PubMed Scopus (1) Google Scholar]. The positively charged patches in the non-catalytic domain are important to boost deamination by A3F, A3G, and A3B [22.Xiao X. et al.Structural determinants of APOBEC3B non-catalytic domain for molecular assembly and catalytic regulation.nucle. 2017; 45: 7494-7506Google Scholar] (Figure 1). However, catalytic domains on their own have inconsistent deaminase activity, and the non-catalytic domains therefore have an important regulatory role.APOBECs also have a preference for specific motif sequences and substrate structures. AID preferentially binds to and targets DNA G4 quadruplex structures during transcription [24.Qiao Q. et al.AID recognizes structured DNA for class switch recombination.Mol. Cell. 2017; 67: 361-373Abstract Full Text Full Text PDF PubMed Scopus (67) Google Scholar]. G4-RNA (from transcribed switch regions) is indispensable to direct AID to its corresponding switch-region (S) target site. During CSR, ssDNA is formed by the R-loop generated through the action of RNA helicase DDX1, leading to RNA:DNA post-transcriptional events [25.Ribeiro de Almeida C. et al.RNA helicase DDX1 converts RNA G-quadruplex structures into R-Loops to promote IgH class switch recombination.Mol. Cell. 2018; 70: 650-662Abstract Full Text Full Text PDF PubMed Scopus (66) Google Scholar]. It has been suggested that AID multimerizes during CSR when interacting with G4 structures [24.Qiao Q. et al.AID recognizes structured DNA for class switch recombination.Mol. Cell. 2017; 67: 361-373Abstract Full Text Full Text PDF PubMed Scopus (67) Google Scholar]. The ribonucleoprotein (RNP) binding proteins, HnRNP-K and -L, have been proposed as cofactors that support and regulate AID deamination during SHM and CSR [26.Mondal S. et al.Functional requirements of AID's higher order structures and their interaction with RNA-binding proteins.Proc. Natl. Acad. Sci. U. S. A. 2016; 113: E1545-E1554Crossref PubMed Scopus (0) Google Scholar]. The affinity of A3A is also higher for DNA and RNA hairpins [27.Silvas T.V. et al.Substrate sequence selectivity of APOBEC3A implicates intra-DNA interactions.Sci. Rep. 2018; 8: 7511Crossref PubMed Scopus (26) Google Scholar].By contrast, an inhibitory role has been attributed to RNA structures bound to the A3G, A3H, and AID catalytic domains. The action of RNase has long been described as being crucial for AID ssDNA deamination [28.Bransteitter R. et al.Activation-induced cytidine deaminase deaminates deoxycytidine on single-stranded DNA but requires the action of RNase.Proc. Natl. Acad. Sci. U. S. A. 2003; 100: 4102-4107Crossref PubMed Scopus (548) Google Scholar]. RNA binding promotes the dissociation of A3G multimers and restricts its deamination capacity, possibly mediated by ssDNA and ssRNA binding competition [23.Polevoda B. et al.DNA mutagenic activity and capacity for HIV-1 restriction of the cytidine deaminase APOBEC3G depend on whether DNA or RNA binds to tyrosine 315.J. Biol. Chem. 2017; 292: 8642-8656Abstract Full Text Full Text PDF PubMed Scopus (1) Google Scholar]. RNA binding to A3H also inhibits and regulates its deaminase activity [29.Shaban N.M. et al.The antiviral and cancer genomic DNA deaminase APOBEC3H is regulated by an RNA-mediated dimerization mechanism.Mol. Cell. 2018; 69: 75-86Abstract Full Text Full Text PDF PubMed Scopus (2) Google Scholar] (Figure 1). Notably, RNA binding to A3H loops 1 and 7 (adjacent to the A3H catalytic pocket) changes A3H structure. Residues from these loops are known to regulate 5mC deamination by A3A and A3G [30.Ito F. et al.Family-wide comparative analysis of cytidine and methylcytidine deamination by eleven human APOBEC proteins.J. Mol. Biol. 2017; 429: 1787-1799Crossref PubMed Scopus (33) Google Scholar]. In A3H, it is proposed that RNA must be released from loops 1 and 7 for the enzyme to identify, bind to, and deaminate ssDNA/mC [31.Ito F. et al.Understanding the structure, multimerization, subcellular localization and mc selectivity of a genomic mutator and anti-HIV factor APOBEC3H.Sci. Rep. 2018; 8: 3763Crossref PubMed Scopus (25) Google Scholar].Phosphorylation is also considered to be an important APOBEC post-translational modulator. Phosphorylation of AID Ser38 residue promotes CSR; it is essential for AID and replication protein A complex 2 (RPA2) binding (Figure 1). By contrast, Thr27 phosphorylation inhibits its deaminase activity [32.Basu U. et al.The AID antibody diversification enzyme is regulated by protein kinase a phosphorylation.Nature. 2005; 438: 508-511Crossref PubMed Scopus (212) Google Scholar]. The same outcome has been described for A3B Thr214 and A3G Thr218 phosphorylation [33.Matsumoto T. et al.Protein kinase A inhibits tumor mutator APOBEC3B through phosphorylation.Sci. Rep. 2019; 9: 8307Crossref PubMed Scopus (8) Google Scholar]. Furthermore, Thr32 phosphorylation reduces A3G affinity for HIV viral infectivity factor (Vif), decreasing its degradation rate [34.Shirakawa K. et al.Phosphorylation of APOBEC3G by protein kinase A regulates its interaction with HIV-1 Vif.Nat. Struct. Mol. Biol. 2008; 15: 1184-1191Crossref PubMed Scopus (0) Google Scholar], highlighting the importance of the dual roles of phosphorylation in APOBECs.APOBEC induction can also depend on 'trans-determinants'. APOBEC often depends on environmental factors, which occur transiently throughout a lifetime, leading to the accumulation of what is now termed 'episodic' rather than consistent mutational APOBEC events [35.Petljak M. et al.Characterizing mutational signatures in human cancer cell lines reveals episodic APOBEC mutagenesis.Cell. 2019; 176: 1282-1294Abstract Full Text Full Text PDF PubMed Scopus (118) Google Scholar]. Proinflammatory cytokines (IFN-α/β, TNF-α, IL-1β, and IL-6) are well-known enhancers of A3s expression. Moreover, alternative splicing can also control APOBEC function through the generation of isoforms (e.g., A3A, B, H, and F). A3B splice variants can restrain mutagenic A3B1 expression [36.Banday A.R. et al.Isoform-specific characterization implicates alternative splicing in APOBEC3B as a mechanism restricting APOBEC-mediated mutagenesis.Commun. Biol. 2021; 4: 386PubMed Google Scholar]. A3H function can be diversified by alternative splicing into three isoforms: non-functional, maintained function, and enhanced viral restriction function [37.Ebrahimi D. et al.Genetic and mechanistic basis for APOBEC3H alternative splicing, retrovirus restriction, and counteraction by HIV-1 protease.Nat. Commun. 2018; 9: 4137Crossref PubMed Scopus (18) Google Scholar].The localization of APOBECs is another important factor that regulates their activity. They tend to be localized either within the cytoplasm or the nucleus. Thus, cytoplasmic signals (e.g., for A1, AID) or viral byproducts (e.g., for A3G) can regulate APOBEC activity. In addition, heat-shock proteins (Hsp70/90) can also stabilize AID in the cytoplasm by inhibiting its ubiquitylation and proteasomal degradation [38.Orthwein A. et al.Regulation of activation-induced deaminase stability and antibody gene diversification by Hsp90.J. Exp. Med. 2010; 207: 2751-2765Crossref PubMed Scopus (75) Google Scholar]. USP49 was also reported to stabilize A3G by hindering and removing the HIV Vif A3G ubiquitination mark, thereby enhancing A3G activity [39.Pan T. et al.USP49 potently stabilizes APOBEC3G protein by removing ubiquitin and inhibits HIV-1 replication.eLife. 2019; 8e48318Crossref PubMed Scopus (7) Google Scholar]. APOBECs can also be enclosed in P-bodies (e.g., A3G and F). A3G association in large RNP complexes suppresses its catalytic activity, but a moderate increase in A3G expression was found to decrease the formation of processing bodies (P-bodies) and promote stress-resistance [40.Yoshino S. et al.EXOSC9 depletion attenuates P-body formation, stress resistance, and tumorigenicity of cancer cells.Sci. Rep. 2020; 10: 9275Crossref PubMed Scopus (1) Google Scholar]. Recent data suggest that depletion of exosome component 9 (EXOSC9; P-body formation factor) induces A3G overexpression, thus aiding APOBEC regulation positively [40.Yoshino S. et al.EXOSC9 depletion attenuates P-body formation, stress resistance, and tumorigenicity of cancer cells.Sci. Rep. 2020; 10: 9275Crossref PubMed Scopus (1) Google Scholar].In parallel, inhibition of long interspersed nuclear repeat 1 (LINE-1) and endogenous retrovirus (ERV) retroelements through G-to-A hypermutation has been long attributed to A3s (Figure 2, Figure 3B). Thus, the cofactors for APOBECs involved in retroelement restriction are also of interest. RPA is involved in LINE-1-retroelement integration and protects ssDNA during target-site primer reverse transcription from deamination in vitro, but its recent association with A3A suggests that RPA guides them both to integration sites and restricts retrotransposition [41.Miyoshi T. et al.Poly(ADP-ribose) polymerase 2 recruits replication protein A to sites of LINE-1 integration to facilitate retrotransposition.Mol. Cell. 2019; 75: 1286-1298Abstract Full Text Full Text PDF PubMed Scopus (0) Google Scholar]. A3C, A3D/E, and A3H also restrict retrotransposition, the former by creating dimers and all by interacting with LINE-1 ORF1p in an RNA-dependent manner, suggesting interplay with LINE-1 RNP [42.Feng Y. et al.Deamination-independent restriction of LINE-1 retrotransposition by APOBEC3H.Sci. Rep. 2017; 7: 10881Crossref PubMed Scopus (16) Google Scholar]. In addition, extracellular vesicles secreted by cells expressing A3G and A3F can also restrict retrotransposition [43.Khatua A.K. et al.Inhibition of LINE-1 and Alu retrotransposition by exosomes encapsidating APOBEC3G and APOBEC3F.Virology. 2010; 400: 68-75Crossref PubMed Scopus (0) Google Scholar] (Figure 1, green).Genomic and epigenomic contributions of APOBECs to immune physiologySeveral APOBECs belong to the class of IFN response genes and are upregulated upon pathogen encounter in immune and non-immune cells. In adaptive and innate immunity, they act at both the genomic and epigenomic levels.In germinal center B cells, AID is upregulated and mediates SHM and CSR of immunoglobulin genes. Thus, AID produces mutations and double-strand breaks (DSBs) in DNA, which enables B cells to produce functional and high-affinity antibodies against pathogens (Figure 2, Figure 3A) (reviewed in [44.Yeap L.S. Meng F.L. Cis- and trans-factors affecting AID targeting and mutagenic outcomes in antibody diversification.Adv. Immunol. 2019; 141: 51-103Crossref PubMed Scopus (9) Google Scholar]). AID also mediates DNA demethylation and increases methylation diversity during the differentiation of naïve B cells in germinal centers [45.Dominguez P.M. et al.DNA methylation dynamics of germinal center B cells are mediated by AID.Cell Rep. 2015; 12: 2086-2098Abstract Full Text Full Text PDF PubMed Google Scholar]. Although these results indicate a contribution of AID deaminase activity, direct proof of AID involvement remains elusive. Further epigenomic changes are attributed to the APOBEC A3A and A3G, which facilitate antiviral cell responses by editing host and pathogen RNAs (Figure 3H). A3A was reported to deaminate several host mRNAs to promote proinflammatory (M1) macrophage polarization activated by viral infection, IFN, and hypoxia [46.Alqassim E.Y. et al.RNA editing enzyme APOBEC3A promotes pro-inflammatory M1 macrophage polarization.Commun. Biol. 2021; 4: 102Crossref PubMed Scopus (1) Google Scholar] (Figure 3H). Moreover, A3A and A3G host mRNA editing leads to altered levels of cellular proteins which are required for a successful viral life cycle [47.Sharma S. et al.The double-domain cytidine deaminase APOBEC3G is a cellular site-specific RNA editing enzyme.Sci. Rep. 2016; 6: 39100Crossref PubMed Scopus (41) Google Scholar]. However, a direct connection between the host RNA editing and the virus-restricting and proinflammatory functions of A3A remains to be fully elucidated.APOBEC deaminases further restrict DNA viruses and retroviruses directly in an editing-dependent manner (extensively reviewed in [48.Xu W.K. et al.The role of APOBECs in viral replication.Microorganisms. 2020; 8: 1899Crossref Scopus (5) Google Scholar]) (Figure 3A). Recently, studies on coronaviruses (CoVs) and rubella also indicated an involvement of APOBECs in RNA virus restriction. A study on human CoV-NL63 showed inhibition of virus replication mediated by A3C, A3F, and A3H, but could not detect hypermutation of the RNA genome in in vitro assays [49.Milewska A. et al.APOBEC3-mediated restriction of RNA virus replication.Sci. Rep. 2018; 8: 5960Crossref PubMed Scopus (40) Google Scholar]. However, the RNA genome of coronaviruses is highly U/A-rich [50.Pyrc K. et al.Genome structure and transcriptional regulation of human coronavirus NL63.Virol. J. 2004; 1: 7Crossref PubMed Scopus (0) Google Scholar], and mutation analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus shows predominant C-to-U transitions in which UCN hotspot motifs are preferentially targeted [51.Klimczak L.J. et al.Similarity between mutation spectra in hypermutated genomes of rubella virus and in SARS-CoV-2 genomes accumulated during the COVID-19 pandemic.PLoS One. 2020; 15e0237689Crossref PubMed Scopus (11) Google Scholar,52.Simmonds P. Rampant C→U hypermutation in the genomes of SARS-CoV-2 and other coronaviruses: causes and consequences for their short- and long-term evolutionary trajectories.mSphere. 2020; 5e00408-20Crossref PubMed Google Scholar]. Interestingly, RNA viruses in invertebrates – where APOBECs are absent – do not manifest a marked increase in C-to-U mutations [53.Rosani U. et al.A-to-I editing of Malacoherpesviridae RNAs supports the antiviral role of ADAR1 in mollusks.BMC Evol. Biol. 2019; 19: 149Crossref PubMed Scopus (5) Google Scholar,54.Rosani U. et al.A needle in a haystack: tracing bivalve-associated viruses in high-throughput transcriptomic data.Viruses. 2019; 11: 205Crossref Scopus (6) Google Scholar]. Furthermore, analysis of the RNA secondary structure elements surrounding the mutated Cs strongly indicate A3A as a potential candidate [51.Klimczak L.J. et al.Similarity between mutation spectra in hypermutated genomes of rubella virus and in SARS-CoV-2 genomes accumulated during the COVID-19 pandemic.PLoS One. 2020; 15e0237689Crossref PubMed Scopus (11) Google Scholar]. Rigorous high-resolution sequencing of SARS-CoV-2 during the pandemic provides a large number of accurate virus genome sequences that enable real-time monitoring of virus–host evolution. The contribution of APOBECs to host–virus coevolution is under investigation, and whether APOBEC-induced mutations contribute to immune escape or drug resistance of the virus has been debated (Box 1). Apart from APOBEC-mediated virus genome editing, various publications report deamination-independent restriction mechanisms, and APOBECs may therefore interfere with the replication and transcription of viral genomes by binding to viral proteins and RNAs or by blocking viral polymerases (reviewed in [48.Xu W.K. et al.The role of APOBECs in viral replication.Microorganisms. 2020; 8: 1899Crossref Scopus (5) Google Scholar]).Box 1The contribution of APOBEC to host–virus coevolutionViruses are predicted to have fewer APOBEC motifs in their genomes because of innate immune APOBEC deaminase editing of viral genomes over a protracted evolutionary timescale (see Figure 4A in main text). APOBECs have varying target sequence biases (see Figure 1 in main text); therefore, reduced APOBEC motif representations might differ depending on each virus. For example, γ-herpesviruses EBV and Kaposi sarcoma-associated herpesvirus (KSHV) exhibit a reduction in 5′-TC motifs that are preferentially edited by A3A/B [119.Martinez T. et al.Evolutionary effects of the AID/APOBEC family of mutagenic enzymes on human gamma-herpesviruses.Virus Evol. 2019; 5vey040Crossref PubMed Scopus (8) Google Scholar]. By contrast, 5′-CCC motifs which are edited by A3G are over-represented, albeit not hypermutated [119.Martinez T. et al.Evolutionary effects of the AID/APOBEC family of mutagenic enzymes on human gamma-herpesviruses.Virus Evol. 2019; 5vey040Crossref PubMed Scopus (8) Google Scholar]. Herpesvirus genomes might be protected from A3G editing because A3G (i) preferentially edits retroviruses, and (ii) is mainly located in the cytoplasm; it therefore might not be recruited and incorporated into virions. However, viruses cannot completely avoid APOBEC target motifs, especially in functionally important sequences. Therefore, some viruses have evolved proteins or miRNAs to inhibit, block, or sequester APOBEC proteins or to downregulate their expression. For instance, HIV Vif was demonstrated to mark A3 enzymes for degradation as well as to in