**3. Epigenetic regulation during viral infections**

As intracellular parasites that lack critical cellular components for replication, protein synthesis, metabolism, and energy production, viruses are incapable of self-maintenance. Therefore, they strictly rely on the cellular machineries of the host cell for their propagation, including the host's epigenetic factors [23]. Viruses hijack the epigenetic regulation mechanisms for multiple reasons. Firstly, several molecular processes such as viral genome replication, transcription of viral proteins and the packaging of new viral particles may simultaneously take place within a single host cell. The existence and coordination of distinct viral genome states allowing these molecular processes are often orchestrated by the machineries of epigenetic regulation [1]. Secondly, as key regulators of gene expression, epigenetic factors are required for the transcription of viral proteins. Especially for viruses encompassing large genomes such as Herpesviruses, epigenetic regulation ensures that only the relevant set of genes are expressed in accordance with the stage of infection [24]. Lastly, the genetic material of DNA viruses is either found in a eukaryotic chromatinlike state in the viral particle or gets packaged within the host cell, making it a target for epigenetic regulation. For instance, the DNA of polyomaviruses (such as Simian Virus 40 – SV40) exists as chromatin throughout their life cycle and is regulated by histone modifications, RNAi, and nucleosome positioning [25, 26]. Similarly, the linear DNA of adenoviruses is packaged by viral proteins that are similar to histones, namely protein VII, which then get replaced by histones upon viral entry into the host [27].

There are three main outcomes of viral exploitation of epigenetic mechanisms, which are the restriction of viral replication by the host immunity and its evasion, regulation of viral latency and the enhancing of viral mRNA function.

#### **3.1 Epigenetic mechanisms of host repression and viral immune evasion**

Epigenetic mechanisms can alter gene expression patterns in the cell in response to environmental stimuli, enabling them to quickly adapt to external changes. As important external stimuli that induce cellular response, viral infections are often confronted by epigenetic alterations within the host cell to repress viral replication and gene expression [28]. Upon entry into the host cell, viral DNA rapidly gets packaged and heterochromatinized, inhibiting viral gene transcription. The epigenetic restriction of viral activity is considered as an innate immune response, which further participates in inducing adaptive immunity and apoptosis in the infected cells [23]. On the other hand, viruses have also developed epigenetic strategies to counteract and evade the cellular antiviral response both by suppressing host immunity and by creating a suitable environment for viral replication [28].

Viral DNA is distinguished and targeted for epigenetic repression by two main mechanisms involving pro-myelocytic leukemia nuclear bodies (PML-NBs) and interferon-inducible protein 16 (IFI16). PML-NBs consist of PML proteins and several epigenetics factors such as transcriptional co-repressors and histone

#### *Epigenetic Regulation Mechanisms in Viral Infections: A Special Focus on COVID-19 DOI: http://dx.doi.org/10.5772/intechopen.98866*

chaperons, which constitute a regulatory hub for gene expression. In alpha-herpes virus HSV-1, histone variant H3.3 carrying repressive histone modifications (e.g. H3K9me3) is incorporated into the viral DNA via PML-NB-associated histone chaperons HIRA, Daxx and ATRX [29, 30]. In hepatitis B virus, Smc5/6 proteins, together with PML-NBs, provide viral inhibition. In overcoming host repression, both herpesviruses and the hepatitis B virus target PML-NBs for degradation and dispersion of the effector proteins. In herpesviruses, the viral protein VP16 interacts with host proteins HCF-1 and Oct-1 to recruit histone demethylases LSD1 and JMJD2 for the removal of previously established repressive H3K9me3 marks [31, 32]. Next, activating H3K4me3 marks are deposited by histone methyltransferases Set1 and MLL1 to allow the transcription of viral immediate early protein ICP0 [33]. As an E3 ubiquitin ligase, ICP0 targets PML-NB for ubiquitylation and degradation, which subsequently releases Daxx and ATRX from the vicinity of viral DNA [34]. Likewise, pp71 protein in beta-herpesvirus HCMV, BNRF1 protein in Epstein–Barr virus and HBx protein in hepatitis B virus exert similar functions in disassembling the PML-NBs and avoiding the repressive mechanisms of the host [35–37].

Foreign DNA is recognized by several factors in the host cell, which trigger the induction of innate immunity and the secretion of cytokines and chemokines. IFI16 acts as an innate immune DNA sensor for viral DNA and induces inflammasome activation [38]. In addition to its key role in stimulating interferon-β secretion, IFI16 contributes to the restriction of viral propagation via deposition of repressive histone marks to the viral DNA and displacing transcription factors from viral gene promoters [39, 40]. Similar to the viral evasion of PML-NB-mediated host repression, IFI16 can be degraded by the ICP0 protein in HSV-1 and its repressive activity can be blocked by HCMV proteins [41, 42]. Furthermore, IFI16 itself is subjected to epigenetic regulation, in which its acetylation by p300 may provide another layer of modulating transcriptional activity [43].

Another viral mechanism that provides escape from recognition and elimination by the host immune system makes use of viral miRNAs that share sequence homology with cellular mRNAs and miRNAs. By specifically targeting and silencing transcripts for host proteins that might function as inhibitors of viral replication, such as regulators of antiviral immunity, viruses can avoid host repression [44]. Viral miRNAs have also been attributed additional roles in regulating viral protein expression and controlling viral replication [45]. The biogenesis of viral miRNAs relies solely on the cellular machineries of the host; whereby the host RNA polymerases, ribonucleases and endonucleases act in cohort to transcribe and process the viral miRNA precursors into mature viral miRNAs [46]. Viral miRNAs are detected in several types of viruses, including but not limited to the frequent human infectors such as Epstein Barr virus, herpes B virus, human cytomegalovirus, human immunodeficiency virus 1, herpes simplex virus 1 and 2, Kaposi sarcoma-associated herpesvirus and simian virus 40. Currently, there are more than 300 viral miRNA precursors and more than 500 mature viral miRNAs available in the miRBase collection [47].

Lastly, viral infections can induce global alterations in histone modifications or the chromatin composition of the host, resulting in distinct epigenetic landscapes. For instance, E1A protein in adenoviruses interacts with lysine acetyltransferases p300/CBP to preferentially block histone acetylation and to repress a set of genes that would normally inhibit infection [48]. Likewise, protein VII can act as a histone mimic due to its structural resemblance to histones and change the host chromatin composition. It also binds to high-mobility group proteins (HMGBs) and tethers them to chromatin, inhibiting their release that typically acts as a danger signal to activate immune system in response to inflammatory stimulus [49].

#### **3.2 Epigenetic regulation of viral latency**

Viral invasions often fail to achieve successful propagation and production of infectious progeny due to several reasons such as host repression, deficiency in host resources and failure to replicate the viral genome properly [50]. In contrast to the lytic infections that produce and release infectious progeny via host cell lysis, latent infections result in the stable maintenance of viral genome within the host cell without expression of viral antigens and production of viral particles. When viruses infect non-permissive cells, they repurpose the epigenetic mechanisms of host repression to enter a dormant state, which would allow establishment of long-term infections while avoiding the host adaptive immune response [51]. The majority of viruses that can achieve latency belongs to the families of herpesviruses and retroviruses. While herpesviruses accomplish latency by means of epigenetic repression, retroviruses reverse transcribe their RNA genome into DNA and integrate it to the host genome for viral persistence.

Latent infections are reversible, as it is possible to reactivate viral replication and switch to lytic infection under permissive conditions. The decision between a lytic and a latent infection requires the expression of distinct sets of genes, indicating epigenetic regulation [1]. During the establishment of latency, viral gene expression is tightly controlled in a temporal manner, in which the latency genes are first turned on and then partially turned off to limit the production of viral antigens while the lytic gene foci are heterochromatinized for transcriptional repression [23]. The silencing of lytic gene expression in latent infections is mainly orchestrated by the action of transcriptional corepressor complex Co-REST and the Polycomb complex [52–54]. Consequently, the viral genome is enriched in repressive histone marks such as H3K27me3 and H3K9me3, which are excluded from the latency related genes [50]. Likewise, activating histone methylations (e.g. H3K4me3) are found at the transcript start sites and the regulatory regions of latency genes [55]. Interestingly, viral genomes can harbor bivalent chromatin states consisting of both activating and repressive histone marks that enable transition between latent and lytic phases [56]. Formation of higher-order chromatin structures via chromatin organizing factor CTCF is implicated in the regulation of latency as well [57]. In addition to the host-driven mechanisms, viral proteins BNRF1, HCF1 and VP16 participate in the recruitment of histone chaperons and histone deacetylases to prevent lytic gene expression [58, 59].

In order to be stably maintained within the host cell through several rounds of cell division, the viral genome forms minichromosomes (episomes) and segregates along the host chromosomes following replication [1]. For this purpose, the viral episome is tethered to the host metaphase chromatin via viral proteins, replicated by the host replication machinery and the newly synthesized episomes are equally divided between the daughter cells prior to the completion of cell division [50]. The cellular targets of viral episome tethering includes AT-rich DNA, histones and other chromatin associated factors [60–62]. The formation of episomes also serves to protect viral genome integrity via formation of "endless" i.e., circular genomes [50].

#### **3.3 Enhanced viral mRNA function**

Viral RNAs are heavily modified by the covalent addition of functional groups that are similar to cellular mRNAs; however, some of these modifications are found in significantly higher levels in viruses than eukaryotes. Recent studies attributed important roles for RNA modifications in promoting viral replication, through enhanced stability of viral transcripts, increased efficiency of translation and escaping immune recognition [1]. N6-methyladenosine (m6 A) constitutes a major source of RNA

*Epigenetic Regulation Mechanisms in Viral Infections: A Special Focus on COVID-19 DOI: http://dx.doi.org/10.5772/intechopen.98866*

modifications, which is deposited by METTL3 and recognized by the YTH domain of YTHDC1, YTHDC2, YTHDF1, YTHDF2 and YTHDF3 proteins [63]. m6 A has been shown to promote viral gene expression and replication, as well as to enhance immune evasion [64–66]. Mutations that alter m6 A deposition sites and thereby reduce m6 A levels result in a substantial decrease in viral pathogenicity, suggesting a novel strategy that could be used in engineering vaccines based on attenuated viruses [65]. 5-methylcytidine (m5 C) is another abundant RNA modification. It is catalyzed mainly by NSUN2 and its loss causes decreased translation efficiency of HIV-1 transcripts [67]. N4-acetylcytidine (ac4 C) is set by NAT10 and is found both in viral and cellular RNAs. Previous reports have established a link between ac4 C and improved stability and translation efficiency of viral transcripts and indicated that its loss at even 3′-untranslated regions of viral mRNAs leads to reduced levels of viral transcription and protein synthesis [23]. 2ʹO-methylation is a distinct type of RNA modification, in the sense that it can be deposited by the nucleolar protein FTSJ3 on either one of the three types of ribonucleotides (A, U and G) and on cytidine residues possibly by an unknown mechanism. Viruses that lack 2ʹO-methylation due to depletion of FTSJ3 activity trigger the cytoplasmic viral RNA sensor MDA5, implicating 2ʹO-methylation as a viral mechanism of escaping recognition by the host immune system [68].
