The mechanism by which herpes simplex virus 1 (HSV-1) establishes latency in sensory neurons is largely unknown. Recent studies indicate that epigenetic modifications of the chromatin associated with the latent genome may play a key role in the transcriptional control of lytic genes during latency. In this study, we found both constitutive and facultative types of heterochromatin to be present on the latent HSV-1 genome. Deposition of the facultative marks trimethyl H3K27 and histone variant macroH2A varied at different sites on the genome, whereas the constitutive marker trimethyl H3K9 did not. In addition, we show that in the absence of the latency-associated transcript (LAT), the latent genome shows a dramatic increase in trimethyl H3K27, suggesting that expression of the LAT during latency may act to promote an appropriate heterochromatic state that represses lytic genes but is still poised for reactivation. Due to the presence of the mark trimethyl H3K27, we examined whether Polycomb group proteins, which methylate H3K27, were present on the HSV-1 genome during latency. Our data indicate that Bmi1, a member of the Polycomb repressive complex 1 (PRC1) maintenance complex, associates with specific sites in the genome, with the highest level of enrichment at the LAT enhancer. To our knowledge, these are the first data demonstrating that a virus can repress its gene transcription to enter latency by exploiting the mechanism of Polycomb-mediated repression.After primary infection by herpes simplex virus 1 (HSV-1) in mucosal epithelia, the virus enters sensory neurons, where it can persist as a transcriptionally silent extrachromosomal episome (19). The only abundant transcription that occurs during latency is from a diploid gene in the repeat long segment of the virus that produces the latency-associated transcript (LAT), an 8.3-to 8.5-kb noncoding RNA (20, 21). The LAT is detectably expressed in only one-third of neurons that contain latent HSV genomes (9, 16). Following a reactivation stimulus, some of the latent genomes can exit this state to actively express lytic transcripts and produce new virus. The mechanism by which the genome establishes and maintains this latent state is currently unknown, although it is hypothesized that the reversible nature of the latent phase involves the constant interplay between cellular and viral factors that either keep the viral genome repressed or allow for reactivation.Recent studies have shed light on epigenetic modifications to the HSV-1 genome during the establishment and maintenance of latency. As the genome enters the latent phase in the mouse, an accumulation of the histone mark dimethyl H3 lysine 9 (diMe H3K9), historically known as a transcriptionally repressed marker, is observed on lytic genes, while enrichment of the transcriptionally active histone mark dimethyl H3 lysine 4 (diMe H3K4) decreases (24). Furthermore, once the virus has established latency, the LAT region is enriched in the transcriptionally active marks, acetylated histone H3 lysines 9 and 14 and ...

Like other alpha-herpesviruses, Herpes Simplex Virus Type 1 (HSV-1) possesses the ability to establish latency in sensory ganglia as a non-integrated, nucleosome-associated episome in the host cell nucleus. Transcription of the genome is limited to the Latency-Associated Transcript (LAT), while the lytic genes are maintained in a transcriptionally-repressed state. This partitioning of the genome into areas of active and inactive transcription suggests epigenetic control of HSV-1 latent gene expression.During latency viral transcription is not regulated by DNA methylation but likely by posttranslational histone modifications. The LAT region is the only region of the genome enriched in marks indicative of transcriptional permissiveness, specifically dimethyl H3 K4 and acetyl H3 K9, K14, while the lytic genes appear under-enriched in those same marks. In addition, facultative heterochromatin marks, specifically trimethyl H3 K27 and the histone variant macroH2A, are enriched on lytic genes during latency. The distinct epigenetic domains of the LAT and the lytic genes appear to be separated by chromatin insulators. Binding of CTCF, a protein that binds to all known vertebrate insulators, to sites within the HSV-1 genome likely prevents heterochromatic spreading and blocks enhancer activity. When the latent viral genome undergoes stress-induced reactivation, it is possible that CTCF binding and insulator function are abrogated, enabling lytic gene transcription to ensue.In this review we summarize our current understanding of latent HSV-1 epigenetic regulation as it pertains to infections in both the rabbit and mouse models. CTCF insulator function and regulation of histone tail modifications will be discussed. We will also present a current model of how the latent genome is carefully controlled at the epigenetic level and how stress-induced changes to it may trigger reactivation.

Histone modifications are important regulators of gene expression in all eukaryotes. In Plasmodium falciparum, these epigenetic marks regulate expression of genes involved in several aspects of host-parasite interactions, including antigenic variation. While the identities and genomic positions of many histone modifications have now been cataloged, how they are targeted to defined genomic regions remains poorly understood. For example, how variant antigen encoding loci (var) are targeted for deposition of unique histone marks is a mystery that continues to perplex the field. Here we describe the recruitment of an ortholog of the histone modifier SET2 to var genes through direct interactions with the C-terminal domain (CTD) of RNA polymerase II. In higher eukaryotes, SET2 is a histone methyltransferase recruited by RNA pol II during mRNA transcription; however, the ortholog in P. falciparum (PfSET2) has an atypical architecture and its role in regulating transcription is unknown. Here we show that PfSET2 binds to the unphosphorylated form of the CTD, a property inconsistent with its recruitment during mRNA synthesis. Further, we show that H3K36me3, the epigenetic mark deposited by PfSET2, is enriched at both active and silent var gene loci, providing additional evidence that its recruitment is not associated with mRNA production. Over-expression of a dominant negative form of PfSET2 designed to disrupt binding to RNA pol II induced rapid var gene expression switching, confirming both the importance of PfSET2 in var gene regulation and a role for RNA pol II in its recruitment. RNA pol II is known to transcribe non-coding RNAs from both active and silent var genes, providing a possible mechanism by which it could recruit PfSET2 to var loci. This work unifies previous reports of histone modifications, the production of ncRNAs, and the promoter activity of var introns into a mechanism that contributes to antigenic variation by malaria parasites.

Trigeminal ganglia (TG) from rabbits latently infected with either wild-type herpes simplex virus type 1 (HSV-1) or the latency-associated transcript (LAT) promoter deletion mutant 17⌬Pst were assessed for their viral chromatin profile and transcript abundance. The wild-type 17syn؉ genomes were more enriched in the transcriptionally permissive mark dimethyl H3 K4 than were the 17⌬Pst genomes at the 5 exon and ICP0 and ICP27 promoters. Reverse transcription-PCR analysis revealed significantly more ICP4, tk, and glycoprotein C lytic transcripts in 17syn؉ than in 17⌬Pst. These results suggest that, for efficient reactivation from latency in rabbits, the LAT is important for increased transcription of lytic genes during latency.During herpes simplex virus type 1 (HSV-1) latency in sensory neurons, there is an overall repression of transcription from the viral genome, with the exception of the latency-associated transcript (LAT) region. The latent genomes are maintained as nucleosome-associated episomes (4) that are not repressed through DNA methylation (6, 11). Rather, histone tail modifications appear to correspond with transcriptional permissiveness. Specifically, during latency in the mouse, the

To study the regulation of herpes simplex virus type 1 (HSV-1) latency-associated transcript (LAT) expression and processing in the absence of other cis and trans viral functions, a transgenic mouse containing the region encompassing the LAT promoter (LAP1) and the LAT 5 exon through the 2.0-kb intron was created. LAT expression was detectable by reverse transcriptase PCR (RT-PCR) in a number of tissues, including the dorsal root ganglia (DRG), trigeminal ganglia (TG), brain, skin, liver, and kidney. However, when the accumulation of the 2.0-kb LAT intron was analyzed at the cellular level by in situ hybridization, little or no detectable accumulation was observed in the brain, spinal cord, kidney, or foot, although the 2.0-kb LAT intron was detected at high levels (over 90% of neurons) in the DRG and TG. Northern blot analysis detected the stable 2.0-kb LAT intron only in the sensory ganglia. When relative amounts of the spliced and unspliced LAT within the brain, liver, kidney, spinal cord, TG, and DRG were analyzed by real-time RT-PCR, splicing of the 2.0-kb LAT intron was significantly more efficient in the sensory ganglia than in other tissues. Finally, infection of both transgenic mice and nontransgenic littermates with HSV-1 revealed no differences in lytic replication, establishment of latency, or reactivation, suggesting that expression of the LAT transgene in trans has no significant effect on those functions. Taken together, these data indicate that the regulation of expression and processing of LAT RNA within the mouse is highly cell-type specific and occurs in the absence of other viral cis-and trans-acting factors.Herpes simplex virus type 1 (HSV-1) latency has long been characterized by the accumulation of a single abundant RNA, the latency-associated transcript (LAT). From the 8.3-to 8.5-kb polyadenylated primary transcript, a very stable 2.0-kb intron, which can be readily detected in the nuclei of latently infected sensory neurons, is spliced (6,21,29,32). Further processing of the 2.0-kb intron can yield a 1.5-kb product in a subpopulation of neurons (20,31). In sensory ganglia, LAT expression seems to be tightly regulated; during the lytic infection, most neurons express either the LAT or lytic genes, not both (21). In addition, there is a sharp drop in the amount of LAT during reactivation (3, 30), with a decrease in transcriptional permissiveness of the LAT promoter occurring as early as 30 min postexplant (1). These observations, combined with genetic data describing LAT mutants as being defective in reactivation (2,10,13,16,24), have led to the model showing that the LAT RNA may play a role in transcriptional silencing of lytic genes during latency (2,7,15,36). Additionally, a cis element encompassing the promoter and enhancer (rcr) may regulate LAT expression to allow the establishment of latency and the occurrence of reactivation (1,14). Two central questions that have been difficult to address in vivo, however, are (i) how dependent the regulation of LAT transcription on other viral el...