- Email: [email protected]
Chromatin dynamics during herpes simplex virus-1 lytic infection
Biochimica et Biophysica Acta 1799 (2010) 223–227
Contents lists available at ScienceDirect
Biochimica et Biophysica Acta j o u r n a l h o m e p a g e : w w w. e l s e v i e r. c o m / l o c a t e / b b a g r m
Review
Chromatin dynamics during herpes simplex virus-1 lytic infection Brandon J. Placek, Shelley L. Berger ⁎ Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA Department of Biology and Genetics, University of Pennsylvania, Philadelphia, PA, USA
a r t i c l e
i n f o
Article history: Received 18 August 2009 Received in revised form 29 January 2010 Accepted 29 January 2010 Available online 6 February 2010 Keywords: HSV-1 Chromatin Histone variant Transcription
a b s t r a c t Herpes simplex virus type 1 is a DNA virus that can establish lytic infections in epithelial cells and latent infections in sensory neurons. Upon entry into the nucleus the genome of HSV-1 rapidly associates with histone proteins. Similar to the genomes of the cellular host, HSV-1 is subject to chromatin-based regulation of transcription and replication. However, unlike the host genome, nucleosomes appear to be underrepresented on the HSV genome. During lytic infection, when the genome is transcribed, the HSV-1 chromatin structure appears to be disorganized, and characterized by histone variant sub-types and posttranslational modifications representative of active chromatin. In contrast, during latency, when the majority of the viral genome is transcriptionally silent, the chromatin is compacted into a regularly repeating, compact heterochromatic structure. Here we discuss recent studies that underscore the importance of chromatin regulation during the lytic phase of the HSV-1 life-cycle. © 2010 Published by Elsevier B.V.
1. Introduction Within all eukaryotic cells the DNA is packaged into a nucleoprotein complex termed chromatin [1]. Chromatin consists of regularly spaced nucleosomes, which are composed of two molecules each of the four core histone proteins (H2A, H2B, H3 and H4), surrounded by two turns of the DNA helix [2]. Further compaction of the DNA is facilitated by the addition of the linker histone H1 and other nonhistone proteins. The chromatin structure creates a barrier to the cellular machinery which must gain access to the DNA for transcription, repair, recombination and replication. The importance of chromatin structure and its functional role in genome regulation is becoming increasingly clear [3]. Indeed, the cell has evolved numerous mechanisms to alter the chromatin structure, including post-translational modifications of the histones, incorporation of histone variants, and directly altering the composition and spacing of nucleosomes via the action of ATP-dependent chromatin remodeling enzymes. Herpes simplex virus type-1 (HSV-1) is a DNA virus which establishes lytic infections in epithelial cells and latent infections within neurons [4]. The life-cycle of HSV-1 begins with infection of an epithelial cell, in which the virus establishes a productive lytic infection. Newly made infectious virions released from the initial site of infection can infect the local sensory neurons, and within these neurons the virus can establish latency and recurrent infections.
⁎ Corresponding author. Department of Cell and Developmental Biology, University of Pennsylvania, 1051 BRBII/III, 421 Curie Boulevard, Philadelphia, PA 19104-6058, USA. E-mail address: [email protected] (S.L. Berger). 1874-9399/$ – see front matter © 2010 Published by Elsevier B.V. doi:10.1016/j.bbagrm.2010.01.012
Through mechanisms that are poorly understood, the latent virus can reactivate from neurons and infect the surrounding epithelial cells, thereby re-establishing a lytic infection. The viral DNA within the virion is devoid of histone proteins [5]. However, immediately after entering the host nucleus, the HSV-1 genome becomes associated with histones [6–8]. The role of chromatin in HSV-1 biology has recently been intensively investigated. This review focuses on our current understanding of mechanisms used by HSV-1 to both manage and exploit this chromatin barrier during lytic infection.
2. HSV-1 and chromatin during lytic infection Although it was previously thought that the HSV-1 genome is not significantly associated into a nucleosomal structure during lytic infection, newer evidence indicates that histones are deposited onto the viral DNA. Within the virion, the HSV-1 genome is apparently devoid of histone proteins [5,9,10]. During infection of an epithelial cell, the HSV-1 genome enters as a linear DNA. Upon entry into the nucleus the DNA is rapidly circularized [11–13] and nucleosomes are deposited onto the naked genome. The order of these events is not yet determined, e.g. whether chromatin begins to be assembled prior to circularization. This is an important question, because chromatin could hinder, or alternatively, could actually facilitate circularization. Interestingly, the structure of the newly established HSV-1 chromatin appears to be distinct from the cellular host chromatin structure [6]. The viral genome is relatively low in histone content relative to DNA, and the nucleosomes appear to be disordered rather than in a regularly repeating structure. Initial evidence that nucleosomes associate with the
224
B.J. Placek, S.L. Berger / Biochimica et Biophysica Acta 1799 (2010) 223–227
viral genome utilized the technique of partial micrococcal nuclease (MNase) digestion [8]. DNA associated within nucleosomes is protected from MNase digestion, whereas the linker DNA located between nucleosomes is readily digested. A partial MNase digestion of DNA that is compacted into an ordered chromatin structure results in a ladder of DNA fragments upon gel electrophoresis, which correspond to arrays of increasing numbers of nucleosomes (i.e. mono-, di- and trinucleosomes, etc.). A complete MNase digestion will result in digestion of all linker DNA and will yield only a single DNA band of ∼150 bp corresponding to DNA contained in the core nucleosome. The notable finding is that partial MNase digestion of nuclei from HSV-1 infected cells does not result in the expected ladder of DNA fragments, but instead results in a smear of HSV-1 DNA, suggesting that nucleosomes are not evenly distributed on the viral genome. However a complete MNase digestion yields a single DNA fragment, corresponding to the molecular weight of mononucleosomes. Because of this irregular spacing, it will be of great interest to determine the precise localization of nucleosomes over the HSV-1 genome, e.g. how nucleosomes are spaced over origins of replication compared to transcribed regions. This nucleosome mapping information will be enhanced by examining the structure during a time course of infection, to determine how the localization of nucleosomes may become altered as infection progresses. Indeed, to begin to provide location information, many studies have utilized chromatin immunoprecipitation (ChIP) approaches to define which regions of the HSV-1 genome are associated with nucleosomes [6,8,14]. These reports indicate that several genes in each of the HSV-1 gene classes (immediate-early, early and late) are associated with nucleosomes during lytic infection. However, it appears that nucleosomes are underrepresented on the viral genome when compared to the host genome, especially late in infection [5,6,15]. It is intriguing that the partial MNase digestion experiment indicates that only a portion of the viral genome is associated with nucleosomes, however ChIP mapping reveals that many HSV-1 genes are nucleosome-associated. It is clear that genome-wide mapping analysis of nucleosome positioning on the HSV-1 genome will shed light on this apparent contradiction, discussed further below. 3. Lytic gene promoters are associated with nucleosomes and these nucleosomes contain active chromatin marks The details of location of nucleosomes, and temporal changes, are yet to be determined. None-the-less, it is clear from the partial information available, that, in general, lytic gene promoters are associated with nucleosomes at least early (3–6 h p.i.) during infection [7]. The nucleosomes have also been analyzed for the presence of histone modifications. Post-translational modifications of the histone proteins such as methylation, acetylation, phosphorylation, ubiquitylation and sumoylation have been demonstrated to be an important regulatory mechanism [16]. For example, acetylation of lysine residues within the N-terminal tail of H3 is enriched at sites of active transcription. Methylation of histones is an intriguing modification because it has been demonstrated to be associated with both activation and repression of transcription. Methylation of H3K4 has been associated with active transcription where as H3K9 methylation is present in heterochromatin. Histone modifications present in the chromatin associated with the HSV-1 genome during lytic and latent infections have been the focus of numerous recent reports [6–8,17–20]. It has been well established that, during lytic infection, the HSV-1 genome is associated with nucleosomes containing “active” euchromatin marks (including H3K9/ K14 acetylation and H3K4 methylation) [7,8]. The question remains of how important these modifications are to the viral life-cycle. Physiological importance of these modifications was demonstrated [7], in part by use of a general inhibitor of protein methylation (MTA). MTA strongly reduced both transcription and replication of HSV-1. VP16 is an HSV-1-encoded virion protein, and is a
potent transcriptional activator of the immediate-early (IE) gene class [21]. The activation-domain of VP16 associates with and recruits a number of transcription factors and chromatin modifiers (histone acetyltransferases and ATP-dependent remodeling enzymes) to IE gene promoters [6]. VP16 also forms a complex with the protein host cell factor (HCF-1). HCF-1 has been identified as a component of several chromatin modifying complexes, including a Set1 methyltransferase complex [22]. The yeast orthologue of Set1 trimethylates H3K4 [23]. Indeed, small interfering RNA (siRNA) to reduce the level of Set1 specifically lowers the level of H3K4me3 on the viral genome and correlates with a reduction in HSV-1 transcription and replication [7]. However these effects on viral function are modest compared to MTA. There are several possible interpretations of this difference in level effect. First, MTA would inhibit methylation of all residues on histones associated with HSV-1, therefore it is possible that sites other than H3K4 are also methylated and may positively affect HSV-1 transcription. Second, Set1 was examined because it is associated with HCF-1 and can methylate H3K4, however, other histone methyltransferases methylate H3K4 as well. Therefore, one of these enzymes may have a redundant function with Set1 in terms of HSV-1 gene regulation, either on H3K4, or other histone methylation sites. It is noteworthy that a similar role of Set1 to methylate H3K4 was seen for the closely related herpesvirus varicella zoster virus [24], suggesting a conserved role for Set1 in the entire family of herpes viruses. A third possible explanation for the more dramatic effects of MTA is that methylation of lysines on other proteins that are required for HSV-1 transcription and replication may be lowered by MTA, and these non-histone proteins may be methylated by numerous SET domain enzymes [14]. These results lead to several general conclusions. The chromatin state of the HSV-1 genome affects the HSV-1 life-cycle, even during the initial phase of the acute infection. The chromatin is apparently a barrier to infection, because the virus itself has a positive role in recruiting chromatin-altering factors to manipulate the chromatin status. In the early stages of infection, the changes occur via interaction of HCF-1 with VP16 and subsequent recruitment of histone modifiers via VP16 action. It will be important to study other histone modifications present on the HSV-1 genome as well to fully understand how chromatin modifications and nucleosome remodeling regulate the biology of the virus. 4. Nucleosomes are underrepresented on the viral genome, especially late during infection Several studies have examined the level of histones during infection. A consistent result is that, by several hours post infection, the amount of histones relative to DNA present on the viral genome is low compared to the host genome [6,8,15]. Several possible mechanisms have been suggested for this observation. First, it may be that only a subset of viral genomes within the nucleus is associated with histones. In this case newly replicated viral genomes may be prevented from association into nucleosomes, and instead are immediately incorporated into a form to be encapsidated. A second possibility is that certain broad regions of the genome are associated with histones, such as transcribed regions, and other regions are reduced in association, such as origins of replication or repeat regions. However, this scenario seems unlikely, since both H3.3, the replication-independent form of H3, and H3.1, the replication-dependent form of H3 are incorporated during lytic infection (see below for extended discussion of this; [25]). A third possibility explaining the lower nucleosome occupancy of viral DNA compared to the host DNA, is that certain localized regions of the viral genome might be devoid or reduced in nucleosome content, such that gene promoters might contain reduced levels of nucleosomes while transcribed regions may contain nucleosome levels similar to the host genome. As mentioned above, VP16 recruits chromatin modulating enzymes and their protein complexes, including the histone acetyltransferases (HATs) p300 and CBP, as well
B.J. Placek, S.L. Berger / Biochimica et Biophysica Acta 1799 (2010) 223–227
as the ATP-dependent chromatin remodeling enzymes BRG1 and BRM [6]. Infection of cells with a virus lacking the activation-domain of VP16 shows reduced recruitment of these transcription factors to the IE gene promoters and correlates with an increase in the occupancy of histone H3 at these VP16-targeted sites [6]. The implication is that the activation-domain of VP16 recruits chromatin modifying enzymes to IE gene promoters to decrease nucleosome occupancy and therefore facilitate transcription. This latter idea is consistent with previous observations and models using genome-wide ChIP, first for the eukaryotic model, budding yeast S. cerevisiae, and subsequently for mammalian cells [26–29]. In both cases promoter regions are relatively low in nucleosomes relative to other genomic regions. The general idea, which apparently is also the case in the HSV-1 infecting genome, is that transcriptional activation involves activatordependent removal of nucleosomes from the promoter upstream of the start site of transcription. ICP0 is a second HSV-1 protein that has been implicated in depletion of nucleosomes on the HSV-1 genome. ICP0 is an IE gene product which is able to activate expression of the three HSV-1 gene classes [30–32]. In the case of ICP0, nucleosome depletion could have a different mechanistic basis: ICP0 interacts with the REST/Co-REST/ HDAC1 complex, leading to the dissociation of HDAC1 from the complex, which would indirectly permit increased acetylation of the viral chromatin [15,33,34]. However it should be noted that it is not clear how the increase in acetylation may lead to a decrease in nucleosome deposition. Specifically, cells infected with a wild-type HSV-1 show a decrease in the amount of H3 associated with the viral genome between 3 and 8 h p.i., however, cells infected with an ICP0 null virus did not show a decrease in H3 levels, strongly implicating ICP0 in facilitating removal of histones from the HSV-1 genome. The authors speculate that changes in nucleosome occupancy are a mechanism by which the virus is able to regulate its gene expression, again, consistent with models proposed for eukaryotes, as described above. Thus, during the earliest stages of infection, there appears to be a “standoff”, or competition between nucleosome assembly onto the HSV-1 genome, and VP16 and ICP0 action to prevent such assembly at the crucial early promoters that need to be immediately activated. The precise role for the loss of histones during infection remains unclear and further study is necessary to fully define the mechanism by which histones are lost or actively removed, and the mechanistic role that viral gene products may play. 5. The HSV-1 genome is associated with histone variants An additional mechanism to alter chromatin state is by incorporation of histone variants. Histone variants differ from canonical histones in amino acid composition, expression patterns and function within the context of chromatin. A particular histone variant, H3.3 is incorporated into the HSV-1 genome immediately after infection (Fig. 1) [25]. H3.3 is a variant of the canonical H3 histone, called H3.1, and although the amino acid composition of the two H3 variants is highly similar (in mammals they differ by only 4 amino acids), their functions in chromatin biology are quite distinct (for review, [35,36]). H3.1 is expressed during the S phase of the cell cycle, during DNA synthesis, and its incorporation is coupled to replication; in contrast, H3.3 is expressed throughout the cell cycle and its incorporation is replication-independent. Association with HSV-1 is consistent with this cycle: immediately following infection, before replication, the viral genome is incorporated into chromatin which predominately contains H3.3 [25]. In contrast, the incorporation of H3.1 is coupled to viral replication. Reduction of the histone H3.3 chaperone (HIRA) lowers incorporation of the H3.3 into the viral genome. This decrease in H3.3 leads to a significant reduction of both transcription and replication of HSV-1. In contrast, the incorporation of H3.1 differed greatly from H3.3; H3.1 was incorporated only during viral replica-
225
Fig. 1. Histone H3 variant association with the HSV-1 genome. Upon nuclear entry, the HSV-1 genome is packaged into nucleosomes which predominately contain the histone variant H3.3. Deposition of H3.3 by HIRA facilitates transcription of HSV-1. Replication of HSV-1 genome is associated with H3.1 deposition.
tion. Indeed, inhibition of viral replication with the potent replication inhibitor PAA, led to a reduction in the incorporation of H3.1. It will be interesting and informative to examine other histone variants that may regulate HSV-1 biology. One intriguing recent example is the histone variant H2AX function during the life-cycle of the murine gamma-herpesvirus 68 (γHSV68) [37]. During infection the virus must evade the host cell response, which aims to inhibit and eliminate the viral pathogen, typically through the interferon response or apoptosis. For viral genomes that recombine into the host nuclear genome, there is the additional issue of activation of the host DNA damage response pathway in the innate defense mechanism. Many viruses have been shown to activate the host DNA damage response machinery, this includes Epstein–Barr virus (EBV) [38], polyomavirus [39], SV40 [40] and HSV-1 [41–43] (for review, [44]). Phosphorylation of H2AX occurs in response to γHV68 infection and is dependent on the virally encoded orf36 kinase and enhanced by the host encoded, wellcharacterized kinase ATM [37]. Replication of γHV68 was impaired in cells lacking either H2AX or ATM. The mechanism underlying this intriguing H2AX effect on γHV68 replication remains unclear. HSV-1 infection may involve related mechanisms, since infection is known to elicit a DNA damage response and induces activation of ATM [41,42]. Viral replication is inhibited in cells deficient for ATM [41]. While the mechanism for how ATM activation directly affects HSV-1 replication is unknown, it has been speculated that DNA damage response pathway may be involved in either circularization of the genome or perhaps recombination of the genome during replication. We have observed H2AX phosphorylation in response to HSV-1 infection, and a requirement for H2AX in viral replication (B.P. and S.L. B., unpublished data). The mechanism by which H2AX facilitates replication is a focus of our current studies.
6. Perspective and future directions It is clear that immediately after introduction of the HSV-1 genome into the nucleus of the infected cell at least some of the genomes become associated with nucleosomes. These nucleosomes contain posttranslational modifications that are consistent with transcriptionallyactive euchromatin. In addition, gene products, such as VP16 and ICP0, interact with chromatin modifying complexes. This indicates that the
226
B.J. Placek, S.L. Berger / Biochimica et Biophysica Acta 1799 (2010) 223–227
Fig. 2. Histone modifications on lytic IE, E and L genes during HSV-1 infection lifecycle. A. During lytic infection nucleosomes contain modifications characteristic of transcriptionally active euchromatic genes, H3 acetylation and H3 K4 methylation. B. During latency the modifications switch to those characteristic of transcriptionally silent heterochromatin, H3 K9 and K27 methylation. C. Model proposing histone modifications during reactivation from latency, to convert the heterochromatic-like chromatin to euchromatin to allow viral transcription and replication. Presumably the virus utilizes a number of cellular chromatin remodeling factors and histone modifying enzymes to facilitate the transition from latency to productive infection.
chromatin state of the viral genome is important to the regulation of viral transcription and replication and that viral gene products are recruiting these chromatin modifying complexes to the genome. However, the underlying mechanisms that lead to histone deposition onto, and removal of histones from the viral genome are less clear. How histone localization and post-translational modifications affect viral processes such as transcription and replication is also an area of interrogation. While previous reports strongly implicate viral activators in chromatin dynamics, a recent report, in contrast, suggests that many transcriptional coactivators are not required for HSV-1 transcription [45]. As previously mentioned the activationdomain of VP16 recruits a number of transcriptional coactivators to the promoters of IE genes, such as the acetyltransferases p300 and CBP, and components of the SWI/SNF family chromatin remodeling complexes, human BRG1 and BRM. This recent report utilized siRNA to knockdown the expression of several coactivators (p300, CBP, BRM, BRG-1, PCAF and GCN5) and did not detect diminishment of IE gene expression. This is an intriguing report and the explanation for the strikingly contrasting effects of coactivators in the various studies will need to be reconciled. One possible explanation is that the coactivator associations that have been observed during acute infection may be highly relevant during reactivation of the viral genome from latency, and indeed may be crucial during this phase of the viral life-cycle (Fig. 2). In general, with respect to chromatin regulation, the roles of histone localization, histone modifications, nucleosome remodeling and histone variants in the life-cycle of HSV-1 are of enormous interest and are areas of future investigation. It will be fascinating to determine the range of mechanisms used by the virus to overcome host-cell generated chromatin barriers, and also in seeming contradiction, how the virus also incorporates histone dynamics into its normal life-cycle. Moreover, understanding how viruses interface with the host chromatin machinery will be instructive in revealing completely novel chromatin-based pathways. References [1] R.D. Kornberg, Y. Lorch, Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome, Cell 98 (1999) 285–294.
[2] K. Luger, A.W. Mader, R.K. Richmond, D.F. Sargent, T.J. Richmond, Crystal structure of the nucleosome core particle at 2.8 A resolution, Nature 389 (1997) 251–260. [3] T. Kouzarides, Chromatin modifications and their function, Cell 128 (2007) 693–705. [4] B. Roizman, D.M. Knipe, R.J. Whitley, in: D.M. Knipe, P.M. Howley (Eds.), Fields Virology5th edn, , 2007, pp. 2501–2602. [5] J. Oh, N.W. Fraser, Temporal association of the herpes simplex virus genome with histone proteins during a lytic infection, J. Virol. 82 (2008) 3530–3537. [6] F.J. Herrera, S.J. Triezenberg, VP16-dependent association of chromatin-modifying coactivators and underrepresentation of histones at immediate-early gene promoters during herpes simplex virus infection, J. Virol. 78 (2004) 9689–9696. [7] J. Huang, J.R. Kent, B. Placek, K.A. Whelan, C.M. Hollow, P.Y. Zeng, N.W. Fraser, S.L. Berger, Trimethylation of histone H3 lysine 4 by Set1 in the lytic infection of human herpes simplex virus 1, J. Virol. 80 (2006) 5740–5746. [8] J.R. Kent, P.Y. Zeng, D. Atanasiu, J. Gardner, N.W. Fraser, S.L. Berger, During lytic infection herpes simplex virus type 1 is associated with histones bearing modifications that correlate with active transcription, J. Virol. 78 (2004) 10178–10186. [9] W. Gibson, B. Roizman, Compartmentalization of spermine and spermidine in the herpes simplex virion, Proc. Natl. Acad. Sci. U. S. A. 68 (1971) 2818–2821. [10] P.F. Pignatti, E. Cassai, Analysis of herpes simplex virus nucleoprotein complexes extracted from infected cells, J. Virol. 36 (1980) 816–828. [11] D.A. Garber, S.M. Beverley, D.M. Coen, Demonstration of circularization of herpes simplex virus DNA following infection using pulsed field gel electrophoresis, Virology 197 (1993) 459–462. [12] K.L. Poffenberger, B. Roizman, A noninverting genome of a viable herpes simplex virus 1: presence of head-to-tail linkages in packaged genomes and requirements for circularization after infection, J. Virol. 53 (1985) 587–595. [13] B.L. Strang, N.D. Stow, Circularization of the herpes simplex virus type 1 genome upon lytic infection, J. Virol. 79 (2005) 12487–12494. [14] J. Huang, S.L. Berger, The emerging field of dynamic lysine methylation of nonhistone proteins, Curr. Opin. Genet. Dev. 18 (2008) 152–158. [15] A.R. Cliffe, D.M. Knipe, Herpes simplex virus ICP0 promotes both histone removal and acetylation on viral DNA during lytic infection, J. Virol. 82 (2008) 12030–12038. [16] S.L. Berger, The complex language of chromatin regulation during transcription, Nature 447 (2007) 407–412. [17] J.L. Arthur, C.G. Scarpini, V. Connor, R.H. Lachmann, A.M. Tolkovsky, S. Efstathiou, Herpes simplex virus type 1 promoter activity during latency establishment, maintenance, and reactivation in primary dorsal root neurons in vitro, J. Virol. 75 (2001) 3885–3895. [18] N.J. Kubat, A.L. Amelio, N.V. Giordani, D.C. Bloom, The herpes simplex virus type 1 latency-associated transcript (LAT) enhancer/rcr is hyperacetylated during latency independently of LAT transcription, J. Virol. 78 (2004) 12508–12518. [19] N.J. Kubat, R.K. Tran, P. McAnany, D.C. Bloom, Specific histone tail modification and not DNA methylation is a determinant of herpes simplex virus type 1 latent gene expression, J. Virol. 78 (2004) 1139–1149. [20] Q.Y. Wang, C. Zhou, K.E. Johnson, R.C. Colgrove, D.M. Coen, D.M. Knipe, Herpesviral latency-associated transcript gene promotes assembly of heterochromatin on viral lytic-gene promoters in latent infection, Proc. Natl. Acad .Sci. U. S. A. 102 (2005) 16055–16059. [21] J.P. Weir, Regulation of herpes simplex virus gene expression, Gene 271 (2001) 117–130. [22] J. Wysocka, M.P. Myers, C.D. Laherty, R.N. Eisenman, W. Herr, Human Sin3 deacetylase and trithorax-related Set1/Ash2 histone H3-K4 methyltransferase are tethered together selectively by the cell-proliferation factor HCF-1, Genes Dev. 17 (2003) 896–911. [23] P.L. Nagy, J. Griesenbeck, R.D. Kornberg, M.L. Cleary, A trithorax-group complex purified from Saccharomyces cerevisiae is required for methylation of histone H3, Proc. Natl. Acad. Sci. U. S. A. 99 (2002) 90–94. [24] A. Narayanan, W.T. Ruyechan, T.M. Kristie, The coactivator host cell factor-1 mediates Set1 and MLL1 H3K4 trimethylation at herpesvirus immediate early promoters for initiation of infection, Proc. Natl. Acad. Sci. U. S. A. 104 (2007) 10835–10840. [25] B.J. Placek, J. Huang, J.R. Kent, J. Dorsey, L. Rice, N.W. Fraser, S.L. Berger, The histone variant H3.3 regulates gene expression during lytic infection with herpes simplex virus type 1, J. Virol. 83 (2009) 1416–1421. [26] N.D. Heintzman, R.K. Stuart, G. Hon, Y. Fu, C.W. Ching, R.D. Hawkins, L.O. Barrera, S. Van Calcar, C. Qu, K.A. Ching, W. Wang, Z. Weng, R.D. Green, G.E. Crawford, B. Ren, Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome, Nat. Genet. 39 (2007) 311–318. [27] W. Lee, D. Tillo, N. Bray, R.H. Morse, R.W. Davis, T.R. Hughes, C. Nislow, A highresolution atlas of nucleosome occupancy in yeast, Nat. Genet. 39 (2007) 1235–1244. [28] F. Ozsolak, J.S. Song, X.S. Liu, D.E. Fisher, High-throughput mapping of the chromatin structure of human promoters, Nat. Biotechnol. 25 (2007) 244–248. [29] D.K. Pokholok, C.T. Harbison, S. Levine, M. Cole, N.M. Hannett, T.I. Lee, G.W. Bell, K. Walker, P.A. Rolfe, E. Herbolsheimer, J. Zeitlinger, F. Lewitter, D.K. Gifford, R.A. Young, Genome-wide map of nucleosome acetylation and methylation in yeast, Cell 122 (2005) 517–527. [30] W. Cai, P.A. Schaffer, Herpes simplex virus type 1 ICP0 regulates expression of immediate-early, early, and late genes in productively infected cells, J. Virol. 66 (1992) 2904–2915. [31] J. Chen, S. Silverstein, Herpes simplex viruses with mutations in the gene encoding ICP0 are defective in gene expression, J. Virol. 66 (1992) 2916–2927. [32] R. Jordan, P.A. Schaffer, Activation of gene expression by herpes simplex virus type 1 ICP0 occurs at the level of mRNA synthesis, J. Virol. 71 (1997) 6850–6862. [33] H. Gu, Y. Liang, G. Mandel, B. Roizman, Components of the REST/CoREST/histone deacetylase repressor complex are disrupted, modified, and translocated in HSV1-infected cells, Proc. Natl. Acad. Sci. U. S. A. 102 (2005) 7571–7576.
B.J. Placek, S.L. Berger / Biochimica et Biophysica Acta 1799 (2010) 223–227 [34] H. Gu, B. Roizman, Herpes simplex virus-infected cell protein 0 blocks the silencing of viral DNA by dissociating histone deacetylases from the CoREST-REST complex, Proc. Natl. Acad. Sci. U. S. A. 104 (2007) 17134–17139. [35] S.B. Hake, C.D. Allis, Histone H3 variants and their potential role in indexing mammalian genomes: the “H3 barcode hypothesis”, Proc. Natl. Acad. Sci. U. S. A. 103 (2006) 6428–6435. [36] K. Sarma, D. Reinberg, Histone variants meet their match, Nat. Rev. Mol. Cell Biol. 6 (2005) 139–149. [37] V.L. Tarakanova, V. Leung-Pineda, S. Hwang, C.W. Yang, K. Matatall, M. Basson, R. Sun, H. Piwnica-Worms, B.P. Sleckman, H.W.t. Virgin, Gammaherpesvirus kinase actively initiates a DNA damage response by inducing phosphorylation of H2AX to foster viral replication, Cell Host Microbe 1 (2007) 275–286. [38] A. Kudoh, M. Fujita, L. Zhang, N. Shirata, T. Daikoku, Y. Sugaya, H. Isomura, Y. Nishiyama, T. Tsurumi, Epstein–Barr virus lytic replication elicits ATM checkpoint signal transduction while providing an S-phase-like cellular environment, J. Biol. Chem. 280 (2005) 8156–8163. [39] J. Dahl, J. You, T.L. Benjamin, Induction and utilization of an ATM signaling pathway by polyomavirus, J. Virol. 79 (2005) 13007–13017.
227
[40] Y. Shi, G.E. Dodson, S. Shaikh, K. Rundell, R.S. Tibbetts, Ataxia-telangiectasiamutated (ATM) is a T-antigen kinase that controls SV40 viral replication in vivo, J. Biol. Chem. 280 (2005) 40195–40200. [41] C.E. Lilley, C.T. Carson, A.R. Muotri, F.H. Gage, M.D. Weitzman, DNA repair proteins affect the lifecycle of herpes simplex virus 1, Proc. Natl. Acad. Sci. U. S. A. 102 (2005) 5844–5849. [42] N. Shirata, A. Kudoh, T. Daikoku, Y. Tatsumi, M. Fujita, T. Kiyono, Y. Sugaya, H. Isomura, K. Ishizaki, T. Tsurumi, Activation of ataxia telangiectasia-mutated DNA damage checkpoint signal transduction elicited by herpes simplex virus infection, J. Biol. Chem. 280 (2005) 30336–30341. [43] D.E. Wilkinson, S.K. Weller, Recruitment of cellular recombination and repair proteins to sites of herpes simplex virus type 1 DNA replication is dependent on the composition of viral proteins within prereplicative sites and correlates with the induction of the DNA damage response, J. Virol. 78 (2004) 4783–4796. [44] C.E. Lilley, R.A. Schwartz, M.D. Weitzman, Using or abusing: viruses and the cellular DNA damage response, Trends Microbiol. 15 (2007) 119–126. [45] S.B. Kutluay, S.L. DeVos, J.E. Klomp, S.J. Triezenberg, Transcriptional coactivators are not required for herpes simplex virus type 1 immediate-early gene expression in vitro, J. Virol. 83 (2009) 3436–3449.
Contents lists available at ScienceDirect
Biochimica et Biophysica Acta j o u r n a l h o m e p a g e : w w w. e l s e v i e r. c o m / l o c a t e / b b a g r m
Review
Chromatin dynamics during herpes simplex virus-1 lytic infection Brandon J. Placek, Shelley L. Berger ⁎ Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA Department of Biology and Genetics, University of Pennsylvania, Philadelphia, PA, USA
a r t i c l e
i n f o
Article history: Received 18 August 2009 Received in revised form 29 January 2010 Accepted 29 January 2010 Available online 6 February 2010 Keywords: HSV-1 Chromatin Histone variant Transcription
a b s t r a c t Herpes simplex virus type 1 is a DNA virus that can establish lytic infections in epithelial cells and latent infections in sensory neurons. Upon entry into the nucleus the genome of HSV-1 rapidly associates with histone proteins. Similar to the genomes of the cellular host, HSV-1 is subject to chromatin-based regulation of transcription and replication. However, unlike the host genome, nucleosomes appear to be underrepresented on the HSV genome. During lytic infection, when the genome is transcribed, the HSV-1 chromatin structure appears to be disorganized, and characterized by histone variant sub-types and posttranslational modifications representative of active chromatin. In contrast, during latency, when the majority of the viral genome is transcriptionally silent, the chromatin is compacted into a regularly repeating, compact heterochromatic structure. Here we discuss recent studies that underscore the importance of chromatin regulation during the lytic phase of the HSV-1 life-cycle. © 2010 Published by Elsevier B.V.
1. Introduction Within all eukaryotic cells the DNA is packaged into a nucleoprotein complex termed chromatin [1]. Chromatin consists of regularly spaced nucleosomes, which are composed of two molecules each of the four core histone proteins (H2A, H2B, H3 and H4), surrounded by two turns of the DNA helix [2]. Further compaction of the DNA is facilitated by the addition of the linker histone H1 and other nonhistone proteins. The chromatin structure creates a barrier to the cellular machinery which must gain access to the DNA for transcription, repair, recombination and replication. The importance of chromatin structure and its functional role in genome regulation is becoming increasingly clear [3]. Indeed, the cell has evolved numerous mechanisms to alter the chromatin structure, including post-translational modifications of the histones, incorporation of histone variants, and directly altering the composition and spacing of nucleosomes via the action of ATP-dependent chromatin remodeling enzymes. Herpes simplex virus type-1 (HSV-1) is a DNA virus which establishes lytic infections in epithelial cells and latent infections within neurons [4]. The life-cycle of HSV-1 begins with infection of an epithelial cell, in which the virus establishes a productive lytic infection. Newly made infectious virions released from the initial site of infection can infect the local sensory neurons, and within these neurons the virus can establish latency and recurrent infections.
⁎ Corresponding author. Department of Cell and Developmental Biology, University of Pennsylvania, 1051 BRBII/III, 421 Curie Boulevard, Philadelphia, PA 19104-6058, USA. E-mail address: [email protected] (S.L. Berger). 1874-9399/$ – see front matter © 2010 Published by Elsevier B.V. doi:10.1016/j.bbagrm.2010.01.012
Through mechanisms that are poorly understood, the latent virus can reactivate from neurons and infect the surrounding epithelial cells, thereby re-establishing a lytic infection. The viral DNA within the virion is devoid of histone proteins [5]. However, immediately after entering the host nucleus, the HSV-1 genome becomes associated with histones [6–8]. The role of chromatin in HSV-1 biology has recently been intensively investigated. This review focuses on our current understanding of mechanisms used by HSV-1 to both manage and exploit this chromatin barrier during lytic infection.
2. HSV-1 and chromatin during lytic infection Although it was previously thought that the HSV-1 genome is not significantly associated into a nucleosomal structure during lytic infection, newer evidence indicates that histones are deposited onto the viral DNA. Within the virion, the HSV-1 genome is apparently devoid of histone proteins [5,9,10]. During infection of an epithelial cell, the HSV-1 genome enters as a linear DNA. Upon entry into the nucleus the DNA is rapidly circularized [11–13] and nucleosomes are deposited onto the naked genome. The order of these events is not yet determined, e.g. whether chromatin begins to be assembled prior to circularization. This is an important question, because chromatin could hinder, or alternatively, could actually facilitate circularization. Interestingly, the structure of the newly established HSV-1 chromatin appears to be distinct from the cellular host chromatin structure [6]. The viral genome is relatively low in histone content relative to DNA, and the nucleosomes appear to be disordered rather than in a regularly repeating structure. Initial evidence that nucleosomes associate with the
224
B.J. Placek, S.L. Berger / Biochimica et Biophysica Acta 1799 (2010) 223–227
viral genome utilized the technique of partial micrococcal nuclease (MNase) digestion [8]. DNA associated within nucleosomes is protected from MNase digestion, whereas the linker DNA located between nucleosomes is readily digested. A partial MNase digestion of DNA that is compacted into an ordered chromatin structure results in a ladder of DNA fragments upon gel electrophoresis, which correspond to arrays of increasing numbers of nucleosomes (i.e. mono-, di- and trinucleosomes, etc.). A complete MNase digestion will result in digestion of all linker DNA and will yield only a single DNA band of ∼150 bp corresponding to DNA contained in the core nucleosome. The notable finding is that partial MNase digestion of nuclei from HSV-1 infected cells does not result in the expected ladder of DNA fragments, but instead results in a smear of HSV-1 DNA, suggesting that nucleosomes are not evenly distributed on the viral genome. However a complete MNase digestion yields a single DNA fragment, corresponding to the molecular weight of mononucleosomes. Because of this irregular spacing, it will be of great interest to determine the precise localization of nucleosomes over the HSV-1 genome, e.g. how nucleosomes are spaced over origins of replication compared to transcribed regions. This nucleosome mapping information will be enhanced by examining the structure during a time course of infection, to determine how the localization of nucleosomes may become altered as infection progresses. Indeed, to begin to provide location information, many studies have utilized chromatin immunoprecipitation (ChIP) approaches to define which regions of the HSV-1 genome are associated with nucleosomes [6,8,14]. These reports indicate that several genes in each of the HSV-1 gene classes (immediate-early, early and late) are associated with nucleosomes during lytic infection. However, it appears that nucleosomes are underrepresented on the viral genome when compared to the host genome, especially late in infection [5,6,15]. It is intriguing that the partial MNase digestion experiment indicates that only a portion of the viral genome is associated with nucleosomes, however ChIP mapping reveals that many HSV-1 genes are nucleosome-associated. It is clear that genome-wide mapping analysis of nucleosome positioning on the HSV-1 genome will shed light on this apparent contradiction, discussed further below. 3. Lytic gene promoters are associated with nucleosomes and these nucleosomes contain active chromatin marks The details of location of nucleosomes, and temporal changes, are yet to be determined. None-the-less, it is clear from the partial information available, that, in general, lytic gene promoters are associated with nucleosomes at least early (3–6 h p.i.) during infection [7]. The nucleosomes have also been analyzed for the presence of histone modifications. Post-translational modifications of the histone proteins such as methylation, acetylation, phosphorylation, ubiquitylation and sumoylation have been demonstrated to be an important regulatory mechanism [16]. For example, acetylation of lysine residues within the N-terminal tail of H3 is enriched at sites of active transcription. Methylation of histones is an intriguing modification because it has been demonstrated to be associated with both activation and repression of transcription. Methylation of H3K4 has been associated with active transcription where as H3K9 methylation is present in heterochromatin. Histone modifications present in the chromatin associated with the HSV-1 genome during lytic and latent infections have been the focus of numerous recent reports [6–8,17–20]. It has been well established that, during lytic infection, the HSV-1 genome is associated with nucleosomes containing “active” euchromatin marks (including H3K9/ K14 acetylation and H3K4 methylation) [7,8]. The question remains of how important these modifications are to the viral life-cycle. Physiological importance of these modifications was demonstrated [7], in part by use of a general inhibitor of protein methylation (MTA). MTA strongly reduced both transcription and replication of HSV-1. VP16 is an HSV-1-encoded virion protein, and is a
potent transcriptional activator of the immediate-early (IE) gene class [21]. The activation-domain of VP16 associates with and recruits a number of transcription factors and chromatin modifiers (histone acetyltransferases and ATP-dependent remodeling enzymes) to IE gene promoters [6]. VP16 also forms a complex with the protein host cell factor (HCF-1). HCF-1 has been identified as a component of several chromatin modifying complexes, including a Set1 methyltransferase complex [22]. The yeast orthologue of Set1 trimethylates H3K4 [23]. Indeed, small interfering RNA (siRNA) to reduce the level of Set1 specifically lowers the level of H3K4me3 on the viral genome and correlates with a reduction in HSV-1 transcription and replication [7]. However these effects on viral function are modest compared to MTA. There are several possible interpretations of this difference in level effect. First, MTA would inhibit methylation of all residues on histones associated with HSV-1, therefore it is possible that sites other than H3K4 are also methylated and may positively affect HSV-1 transcription. Second, Set1 was examined because it is associated with HCF-1 and can methylate H3K4, however, other histone methyltransferases methylate H3K4 as well. Therefore, one of these enzymes may have a redundant function with Set1 in terms of HSV-1 gene regulation, either on H3K4, or other histone methylation sites. It is noteworthy that a similar role of Set1 to methylate H3K4 was seen for the closely related herpesvirus varicella zoster virus [24], suggesting a conserved role for Set1 in the entire family of herpes viruses. A third possible explanation for the more dramatic effects of MTA is that methylation of lysines on other proteins that are required for HSV-1 transcription and replication may be lowered by MTA, and these non-histone proteins may be methylated by numerous SET domain enzymes [14]. These results lead to several general conclusions. The chromatin state of the HSV-1 genome affects the HSV-1 life-cycle, even during the initial phase of the acute infection. The chromatin is apparently a barrier to infection, because the virus itself has a positive role in recruiting chromatin-altering factors to manipulate the chromatin status. In the early stages of infection, the changes occur via interaction of HCF-1 with VP16 and subsequent recruitment of histone modifiers via VP16 action. It will be important to study other histone modifications present on the HSV-1 genome as well to fully understand how chromatin modifications and nucleosome remodeling regulate the biology of the virus. 4. Nucleosomes are underrepresented on the viral genome, especially late during infection Several studies have examined the level of histones during infection. A consistent result is that, by several hours post infection, the amount of histones relative to DNA present on the viral genome is low compared to the host genome [6,8,15]. Several possible mechanisms have been suggested for this observation. First, it may be that only a subset of viral genomes within the nucleus is associated with histones. In this case newly replicated viral genomes may be prevented from association into nucleosomes, and instead are immediately incorporated into a form to be encapsidated. A second possibility is that certain broad regions of the genome are associated with histones, such as transcribed regions, and other regions are reduced in association, such as origins of replication or repeat regions. However, this scenario seems unlikely, since both H3.3, the replication-independent form of H3, and H3.1, the replication-dependent form of H3 are incorporated during lytic infection (see below for extended discussion of this; [25]). A third possibility explaining the lower nucleosome occupancy of viral DNA compared to the host DNA, is that certain localized regions of the viral genome might be devoid or reduced in nucleosome content, such that gene promoters might contain reduced levels of nucleosomes while transcribed regions may contain nucleosome levels similar to the host genome. As mentioned above, VP16 recruits chromatin modulating enzymes and their protein complexes, including the histone acetyltransferases (HATs) p300 and CBP, as well
B.J. Placek, S.L. Berger / Biochimica et Biophysica Acta 1799 (2010) 223–227
as the ATP-dependent chromatin remodeling enzymes BRG1 and BRM [6]. Infection of cells with a virus lacking the activation-domain of VP16 shows reduced recruitment of these transcription factors to the IE gene promoters and correlates with an increase in the occupancy of histone H3 at these VP16-targeted sites [6]. The implication is that the activation-domain of VP16 recruits chromatin modifying enzymes to IE gene promoters to decrease nucleosome occupancy and therefore facilitate transcription. This latter idea is consistent with previous observations and models using genome-wide ChIP, first for the eukaryotic model, budding yeast S. cerevisiae, and subsequently for mammalian cells [26–29]. In both cases promoter regions are relatively low in nucleosomes relative to other genomic regions. The general idea, which apparently is also the case in the HSV-1 infecting genome, is that transcriptional activation involves activatordependent removal of nucleosomes from the promoter upstream of the start site of transcription. ICP0 is a second HSV-1 protein that has been implicated in depletion of nucleosomes on the HSV-1 genome. ICP0 is an IE gene product which is able to activate expression of the three HSV-1 gene classes [30–32]. In the case of ICP0, nucleosome depletion could have a different mechanistic basis: ICP0 interacts with the REST/Co-REST/ HDAC1 complex, leading to the dissociation of HDAC1 from the complex, which would indirectly permit increased acetylation of the viral chromatin [15,33,34]. However it should be noted that it is not clear how the increase in acetylation may lead to a decrease in nucleosome deposition. Specifically, cells infected with a wild-type HSV-1 show a decrease in the amount of H3 associated with the viral genome between 3 and 8 h p.i., however, cells infected with an ICP0 null virus did not show a decrease in H3 levels, strongly implicating ICP0 in facilitating removal of histones from the HSV-1 genome. The authors speculate that changes in nucleosome occupancy are a mechanism by which the virus is able to regulate its gene expression, again, consistent with models proposed for eukaryotes, as described above. Thus, during the earliest stages of infection, there appears to be a “standoff”, or competition between nucleosome assembly onto the HSV-1 genome, and VP16 and ICP0 action to prevent such assembly at the crucial early promoters that need to be immediately activated. The precise role for the loss of histones during infection remains unclear and further study is necessary to fully define the mechanism by which histones are lost or actively removed, and the mechanistic role that viral gene products may play. 5. The HSV-1 genome is associated with histone variants An additional mechanism to alter chromatin state is by incorporation of histone variants. Histone variants differ from canonical histones in amino acid composition, expression patterns and function within the context of chromatin. A particular histone variant, H3.3 is incorporated into the HSV-1 genome immediately after infection (Fig. 1) [25]. H3.3 is a variant of the canonical H3 histone, called H3.1, and although the amino acid composition of the two H3 variants is highly similar (in mammals they differ by only 4 amino acids), their functions in chromatin biology are quite distinct (for review, [35,36]). H3.1 is expressed during the S phase of the cell cycle, during DNA synthesis, and its incorporation is coupled to replication; in contrast, H3.3 is expressed throughout the cell cycle and its incorporation is replication-independent. Association with HSV-1 is consistent with this cycle: immediately following infection, before replication, the viral genome is incorporated into chromatin which predominately contains H3.3 [25]. In contrast, the incorporation of H3.1 is coupled to viral replication. Reduction of the histone H3.3 chaperone (HIRA) lowers incorporation of the H3.3 into the viral genome. This decrease in H3.3 leads to a significant reduction of both transcription and replication of HSV-1. In contrast, the incorporation of H3.1 differed greatly from H3.3; H3.1 was incorporated only during viral replica-
225
Fig. 1. Histone H3 variant association with the HSV-1 genome. Upon nuclear entry, the HSV-1 genome is packaged into nucleosomes which predominately contain the histone variant H3.3. Deposition of H3.3 by HIRA facilitates transcription of HSV-1. Replication of HSV-1 genome is associated with H3.1 deposition.
tion. Indeed, inhibition of viral replication with the potent replication inhibitor PAA, led to a reduction in the incorporation of H3.1. It will be interesting and informative to examine other histone variants that may regulate HSV-1 biology. One intriguing recent example is the histone variant H2AX function during the life-cycle of the murine gamma-herpesvirus 68 (γHSV68) [37]. During infection the virus must evade the host cell response, which aims to inhibit and eliminate the viral pathogen, typically through the interferon response or apoptosis. For viral genomes that recombine into the host nuclear genome, there is the additional issue of activation of the host DNA damage response pathway in the innate defense mechanism. Many viruses have been shown to activate the host DNA damage response machinery, this includes Epstein–Barr virus (EBV) [38], polyomavirus [39], SV40 [40] and HSV-1 [41–43] (for review, [44]). Phosphorylation of H2AX occurs in response to γHV68 infection and is dependent on the virally encoded orf36 kinase and enhanced by the host encoded, wellcharacterized kinase ATM [37]. Replication of γHV68 was impaired in cells lacking either H2AX or ATM. The mechanism underlying this intriguing H2AX effect on γHV68 replication remains unclear. HSV-1 infection may involve related mechanisms, since infection is known to elicit a DNA damage response and induces activation of ATM [41,42]. Viral replication is inhibited in cells deficient for ATM [41]. While the mechanism for how ATM activation directly affects HSV-1 replication is unknown, it has been speculated that DNA damage response pathway may be involved in either circularization of the genome or perhaps recombination of the genome during replication. We have observed H2AX phosphorylation in response to HSV-1 infection, and a requirement for H2AX in viral replication (B.P. and S.L. B., unpublished data). The mechanism by which H2AX facilitates replication is a focus of our current studies.
6. Perspective and future directions It is clear that immediately after introduction of the HSV-1 genome into the nucleus of the infected cell at least some of the genomes become associated with nucleosomes. These nucleosomes contain posttranslational modifications that are consistent with transcriptionallyactive euchromatin. In addition, gene products, such as VP16 and ICP0, interact with chromatin modifying complexes. This indicates that the
226
B.J. Placek, S.L. Berger / Biochimica et Biophysica Acta 1799 (2010) 223–227
Fig. 2. Histone modifications on lytic IE, E and L genes during HSV-1 infection lifecycle. A. During lytic infection nucleosomes contain modifications characteristic of transcriptionally active euchromatic genes, H3 acetylation and H3 K4 methylation. B. During latency the modifications switch to those characteristic of transcriptionally silent heterochromatin, H3 K9 and K27 methylation. C. Model proposing histone modifications during reactivation from latency, to convert the heterochromatic-like chromatin to euchromatin to allow viral transcription and replication. Presumably the virus utilizes a number of cellular chromatin remodeling factors and histone modifying enzymes to facilitate the transition from latency to productive infection.
chromatin state of the viral genome is important to the regulation of viral transcription and replication and that viral gene products are recruiting these chromatin modifying complexes to the genome. However, the underlying mechanisms that lead to histone deposition onto, and removal of histones from the viral genome are less clear. How histone localization and post-translational modifications affect viral processes such as transcription and replication is also an area of interrogation. While previous reports strongly implicate viral activators in chromatin dynamics, a recent report, in contrast, suggests that many transcriptional coactivators are not required for HSV-1 transcription [45]. As previously mentioned the activationdomain of VP16 recruits a number of transcriptional coactivators to the promoters of IE genes, such as the acetyltransferases p300 and CBP, and components of the SWI/SNF family chromatin remodeling complexes, human BRG1 and BRM. This recent report utilized siRNA to knockdown the expression of several coactivators (p300, CBP, BRM, BRG-1, PCAF and GCN5) and did not detect diminishment of IE gene expression. This is an intriguing report and the explanation for the strikingly contrasting effects of coactivators in the various studies will need to be reconciled. One possible explanation is that the coactivator associations that have been observed during acute infection may be highly relevant during reactivation of the viral genome from latency, and indeed may be crucial during this phase of the viral life-cycle (Fig. 2). In general, with respect to chromatin regulation, the roles of histone localization, histone modifications, nucleosome remodeling and histone variants in the life-cycle of HSV-1 are of enormous interest and are areas of future investigation. It will be fascinating to determine the range of mechanisms used by the virus to overcome host-cell generated chromatin barriers, and also in seeming contradiction, how the virus also incorporates histone dynamics into its normal life-cycle. Moreover, understanding how viruses interface with the host chromatin machinery will be instructive in revealing completely novel chromatin-based pathways. References [1] R.D. Kornberg, Y. Lorch, Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome, Cell 98 (1999) 285–294.
[2] K. Luger, A.W. Mader, R.K. Richmond, D.F. Sargent, T.J. Richmond, Crystal structure of the nucleosome core particle at 2.8 A resolution, Nature 389 (1997) 251–260. [3] T. Kouzarides, Chromatin modifications and their function, Cell 128 (2007) 693–705. [4] B. Roizman, D.M. Knipe, R.J. Whitley, in: D.M. Knipe, P.M. Howley (Eds.), Fields Virology5th edn, , 2007, pp. 2501–2602. [5] J. Oh, N.W. Fraser, Temporal association of the herpes simplex virus genome with histone proteins during a lytic infection, J. Virol. 82 (2008) 3530–3537. [6] F.J. Herrera, S.J. Triezenberg, VP16-dependent association of chromatin-modifying coactivators and underrepresentation of histones at immediate-early gene promoters during herpes simplex virus infection, J. Virol. 78 (2004) 9689–9696. [7] J. Huang, J.R. Kent, B. Placek, K.A. Whelan, C.M. Hollow, P.Y. Zeng, N.W. Fraser, S.L. Berger, Trimethylation of histone H3 lysine 4 by Set1 in the lytic infection of human herpes simplex virus 1, J. Virol. 80 (2006) 5740–5746. [8] J.R. Kent, P.Y. Zeng, D. Atanasiu, J. Gardner, N.W. Fraser, S.L. Berger, During lytic infection herpes simplex virus type 1 is associated with histones bearing modifications that correlate with active transcription, J. Virol. 78 (2004) 10178–10186. [9] W. Gibson, B. Roizman, Compartmentalization of spermine and spermidine in the herpes simplex virion, Proc. Natl. Acad. Sci. U. S. A. 68 (1971) 2818–2821. [10] P.F. Pignatti, E. Cassai, Analysis of herpes simplex virus nucleoprotein complexes extracted from infected cells, J. Virol. 36 (1980) 816–828. [11] D.A. Garber, S.M. Beverley, D.M. Coen, Demonstration of circularization of herpes simplex virus DNA following infection using pulsed field gel electrophoresis, Virology 197 (1993) 459–462. [12] K.L. Poffenberger, B. Roizman, A noninverting genome of a viable herpes simplex virus 1: presence of head-to-tail linkages in packaged genomes and requirements for circularization after infection, J. Virol. 53 (1985) 587–595. [13] B.L. Strang, N.D. Stow, Circularization of the herpes simplex virus type 1 genome upon lytic infection, J. Virol. 79 (2005) 12487–12494. [14] J. Huang, S.L. Berger, The emerging field of dynamic lysine methylation of nonhistone proteins, Curr. Opin. Genet. Dev. 18 (2008) 152–158. [15] A.R. Cliffe, D.M. Knipe, Herpes simplex virus ICP0 promotes both histone removal and acetylation on viral DNA during lytic infection, J. Virol. 82 (2008) 12030–12038. [16] S.L. Berger, The complex language of chromatin regulation during transcription, Nature 447 (2007) 407–412. [17] J.L. Arthur, C.G. Scarpini, V. Connor, R.H. Lachmann, A.M. Tolkovsky, S. Efstathiou, Herpes simplex virus type 1 promoter activity during latency establishment, maintenance, and reactivation in primary dorsal root neurons in vitro, J. Virol. 75 (2001) 3885–3895. [18] N.J. Kubat, A.L. Amelio, N.V. Giordani, D.C. Bloom, The herpes simplex virus type 1 latency-associated transcript (LAT) enhancer/rcr is hyperacetylated during latency independently of LAT transcription, J. Virol. 78 (2004) 12508–12518. [19] N.J. Kubat, R.K. Tran, P. McAnany, D.C. Bloom, Specific histone tail modification and not DNA methylation is a determinant of herpes simplex virus type 1 latent gene expression, J. Virol. 78 (2004) 1139–1149. [20] Q.Y. Wang, C. Zhou, K.E. Johnson, R.C. Colgrove, D.M. Coen, D.M. Knipe, Herpesviral latency-associated transcript gene promotes assembly of heterochromatin on viral lytic-gene promoters in latent infection, Proc. Natl. Acad .Sci. U. S. A. 102 (2005) 16055–16059. [21] J.P. Weir, Regulation of herpes simplex virus gene expression, Gene 271 (2001) 117–130. [22] J. Wysocka, M.P. Myers, C.D. Laherty, R.N. Eisenman, W. Herr, Human Sin3 deacetylase and trithorax-related Set1/Ash2 histone H3-K4 methyltransferase are tethered together selectively by the cell-proliferation factor HCF-1, Genes Dev. 17 (2003) 896–911. [23] P.L. Nagy, J. Griesenbeck, R.D. Kornberg, M.L. Cleary, A trithorax-group complex purified from Saccharomyces cerevisiae is required for methylation of histone H3, Proc. Natl. Acad. Sci. U. S. A. 99 (2002) 90–94. [24] A. Narayanan, W.T. Ruyechan, T.M. Kristie, The coactivator host cell factor-1 mediates Set1 and MLL1 H3K4 trimethylation at herpesvirus immediate early promoters for initiation of infection, Proc. Natl. Acad. Sci. U. S. A. 104 (2007) 10835–10840. [25] B.J. Placek, J. Huang, J.R. Kent, J. Dorsey, L. Rice, N.W. Fraser, S.L. Berger, The histone variant H3.3 regulates gene expression during lytic infection with herpes simplex virus type 1, J. Virol. 83 (2009) 1416–1421. [26] N.D. Heintzman, R.K. Stuart, G. Hon, Y. Fu, C.W. Ching, R.D. Hawkins, L.O. Barrera, S. Van Calcar, C. Qu, K.A. Ching, W. Wang, Z. Weng, R.D. Green, G.E. Crawford, B. Ren, Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome, Nat. Genet. 39 (2007) 311–318. [27] W. Lee, D. Tillo, N. Bray, R.H. Morse, R.W. Davis, T.R. Hughes, C. Nislow, A highresolution atlas of nucleosome occupancy in yeast, Nat. Genet. 39 (2007) 1235–1244. [28] F. Ozsolak, J.S. Song, X.S. Liu, D.E. Fisher, High-throughput mapping of the chromatin structure of human promoters, Nat. Biotechnol. 25 (2007) 244–248. [29] D.K. Pokholok, C.T. Harbison, S. Levine, M. Cole, N.M. Hannett, T.I. Lee, G.W. Bell, K. Walker, P.A. Rolfe, E. Herbolsheimer, J. Zeitlinger, F. Lewitter, D.K. Gifford, R.A. Young, Genome-wide map of nucleosome acetylation and methylation in yeast, Cell 122 (2005) 517–527. [30] W. Cai, P.A. Schaffer, Herpes simplex virus type 1 ICP0 regulates expression of immediate-early, early, and late genes in productively infected cells, J. Virol. 66 (1992) 2904–2915. [31] J. Chen, S. Silverstein, Herpes simplex viruses with mutations in the gene encoding ICP0 are defective in gene expression, J. Virol. 66 (1992) 2916–2927. [32] R. Jordan, P.A. Schaffer, Activation of gene expression by herpes simplex virus type 1 ICP0 occurs at the level of mRNA synthesis, J. Virol. 71 (1997) 6850–6862. [33] H. Gu, Y. Liang, G. Mandel, B. Roizman, Components of the REST/CoREST/histone deacetylase repressor complex are disrupted, modified, and translocated in HSV1-infected cells, Proc. Natl. Acad. Sci. U. S. A. 102 (2005) 7571–7576.
B.J. Placek, S.L. Berger / Biochimica et Biophysica Acta 1799 (2010) 223–227 [34] H. Gu, B. Roizman, Herpes simplex virus-infected cell protein 0 blocks the silencing of viral DNA by dissociating histone deacetylases from the CoREST-REST complex, Proc. Natl. Acad. Sci. U. S. A. 104 (2007) 17134–17139. [35] S.B. Hake, C.D. Allis, Histone H3 variants and their potential role in indexing mammalian genomes: the “H3 barcode hypothesis”, Proc. Natl. Acad. Sci. U. S. A. 103 (2006) 6428–6435. [36] K. Sarma, D. Reinberg, Histone variants meet their match, Nat. Rev. Mol. Cell Biol. 6 (2005) 139–149. [37] V.L. Tarakanova, V. Leung-Pineda, S. Hwang, C.W. Yang, K. Matatall, M. Basson, R. Sun, H. Piwnica-Worms, B.P. Sleckman, H.W.t. Virgin, Gammaherpesvirus kinase actively initiates a DNA damage response by inducing phosphorylation of H2AX to foster viral replication, Cell Host Microbe 1 (2007) 275–286. [38] A. Kudoh, M. Fujita, L. Zhang, N. Shirata, T. Daikoku, Y. Sugaya, H. Isomura, Y. Nishiyama, T. Tsurumi, Epstein–Barr virus lytic replication elicits ATM checkpoint signal transduction while providing an S-phase-like cellular environment, J. Biol. Chem. 280 (2005) 8156–8163. [39] J. Dahl, J. You, T.L. Benjamin, Induction and utilization of an ATM signaling pathway by polyomavirus, J. Virol. 79 (2005) 13007–13017.
227
[40] Y. Shi, G.E. Dodson, S. Shaikh, K. Rundell, R.S. Tibbetts, Ataxia-telangiectasiamutated (ATM) is a T-antigen kinase that controls SV40 viral replication in vivo, J. Biol. Chem. 280 (2005) 40195–40200. [41] C.E. Lilley, C.T. Carson, A.R. Muotri, F.H. Gage, M.D. Weitzman, DNA repair proteins affect the lifecycle of herpes simplex virus 1, Proc. Natl. Acad. Sci. U. S. A. 102 (2005) 5844–5849. [42] N. Shirata, A. Kudoh, T. Daikoku, Y. Tatsumi, M. Fujita, T. Kiyono, Y. Sugaya, H. Isomura, K. Ishizaki, T. Tsurumi, Activation of ataxia telangiectasia-mutated DNA damage checkpoint signal transduction elicited by herpes simplex virus infection, J. Biol. Chem. 280 (2005) 30336–30341. [43] D.E. Wilkinson, S.K. Weller, Recruitment of cellular recombination and repair proteins to sites of herpes simplex virus type 1 DNA replication is dependent on the composition of viral proteins within prereplicative sites and correlates with the induction of the DNA damage response, J. Virol. 78 (2004) 4783–4796. [44] C.E. Lilley, R.A. Schwartz, M.D. Weitzman, Using or abusing: viruses and the cellular DNA damage response, Trends Microbiol. 15 (2007) 119–126. [45] S.B. Kutluay, S.L. DeVos, J.E. Klomp, S.J. Triezenberg, Transcriptional coactivators are not required for herpes simplex virus type 1 immediate-early gene expression in vitro, J. Virol. 83 (2009) 3436–3449.