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Biphasic Euchromatin-to-Heterochromatin Transition on the KSHV Genome Following De Novo Infection

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      Abstract

      The establishment of latency is an essential step for the life-long persistent infection and pathogenesis of Kaposi's sarcoma-associated herpesvirus (KSHV). While the KSHV genome is chromatin-free in the virions, the viral DNA in latently infected cells has a chromatin structure with activating and repressive histone modifications that promote latent gene expression but suppress lytic gene expression. Here, we report a comprehensive epigenetic study of the recruitment of chromatin regulatory factors onto the KSHV genome during the pre-latency phase of KSHV infection. This demonstrates that the KSHV genome undergoes a biphasic chromatinization following de novo infection. Initially, a transcriptionally active chromatin (euchromatin), characterized by high levels of the H3K4me3 and acetylated H3K27 (H3K27ac) activating histone marks, was deposited on the viral episome and accompanied by the transient induction of a limited number of lytic genes. Interestingly, temporary expression of the RTA protein facilitated the increase of H3K4me3 and H3K27ac occupancy on the KSHV episome during de novo infection. Between 24–72 hours post-infection, as the levels of these activating histone marks declined on the KSHV genome, the levels of the repressive H3K27me3 and H2AK119ub histone marks increased concomitantly with the decline of lytic gene expression. Importantly, this transition to heterochromatin was dependent on both Polycomb Repressive Complex 1 and 2. In contrast, upon infection of human gingiva-derived epithelial cells, the KSHV genome underwent a transcription-active euchromatinization, resulting in efficient lytic gene expression. Our data demonstrate that the KSHV genome undergoes a temporally-ordered biphasic euchromatin-to-heterochromatin transition in endothelial cells, leading to latent infection, whereas KSHV preferentially adopts a transcriptionally active euchromatin in oral epithelial cells, resulting in lytic gene expression. Our results suggest that the differential epigenetic modification of the KSHV genome in distinct cell types is a potential determining factor for latent infection versus lytic replication of KSHV.

      Author Summary

      Although the KSHV genome is linear and chromatin-free in the virions, it circularizes and adopts a repressive chromatin structure in latently infected cells, inhibiting the majority of viral gene expression. In this study, we investigate the epigenetic regulatory mechanism of the pre-latency phase of KSHV infection. We found that upon de novo infection, the KSHV genome undergoes distinct chromatin states in a temporally ordered manner prior to the establishment of latency. Initially, the KSHV genome carried a transcriptionally permissive chromatin structure to allow expression of a subset of viral lytic genes. Subsequently, cellular Polycomb Repressive Complex 1 (PRC1) and PRC2 were recruited to the KSHV genome, resulting in the deposition of repressive histone marks onto the viral chromatin and the accumulation of heterochromatin structures, both of which were critical for the establishment of viral latency. In contrast to the biphasic chromatinization and genome-wide inhibition of lytic genes observed in de novo-infected SLK and TIME cells, KSHV adopts a transcriptionally permissive chromatin form in human gingiva-derived epithelial cells, resulting in prolonged and robust lytic gene expression. Thus, our results suggest that the differential epigenetic modification of the KSHV genome in distinct cell types is a potential determining factor for latent infection versus lytic replication of KSHV.

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      Most cited references 42

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      Identification of herpesvirus-like DNA sequences in AIDS-associated Kaposi's sarcoma.

      Representational difference analysis was used to isolate unique sequences present in more than 90 percent of Kaposi's sarcoma (KS) tissues obtained from patients with acquired immunodeficiency syndrome (AIDS). These sequences were not present in tissue DNA from non-AIDS patients, but were present in 15 percent of non-KS tissue DNA samples from AIDS patients. The sequences are homologous to, but distinct from, capsid and tegument protein genes of the Gammaherpesvirinae, herpesvirus saimiri and Epstein-Barr virus. These KS-associated herpesvirus-like (KSHV) sequences appear to define a new human herpesvirus.
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        FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin.

        DNA segments that actively regulate transcription in vivo are typically characterized by eviction of nucleosomes from chromatin and are experimentally identified by their hypersensitivity to nucleases. Here we demonstrate a simple procedure for the isolation of nucleosome-depleted DNA from human chromatin, termed FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements). To perform FAIRE, chromatin is crosslinked with formaldehyde in vivo, sheared by sonication, and phenol-chloroform extracted. The DNA recovered in the aqueous phase is fluorescently labeled and hybridized to a DNA microarray. FAIRE performed in human cells strongly enriches DNA coincident with the location of DNaseI hypersensitive sites, transcriptional start sites, and active promoters. Evidence for cell-type-specific patterns of FAIRE enrichment is also presented. FAIRE has utility as a positive selection for genomic regions associated with regulatory activity, including regions traditionally detected by nuclease hypersensitivity assays.
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          PCGF homologs, CBX proteins, and RYBP define functionally distinct PRC1 family complexes.

          The heterogeneous nature of mammalian PRC1 complexes has hindered our understanding of their biological functions. Here, we present a comprehensive proteomic and genomic analysis that uncovered six major groups of PRC1 complexes, each containing a distinct PCGF subunit, a RING1A/B ubiquitin ligase, and a unique set of associated polypeptides. These PRC1 complexes differ in their genomic localization, and only a small subset colocalize with H3K27me3. Further biochemical dissection revealed that the six PCGF-RING1A/B combinations form multiple complexes through association with RYBP or its homolog YAF2, which prevents the incorporation of other canonical PRC1 subunits, such as CBX, PHC, and SCM. Although both RYBP/YAF2- and CBX/PHC/SCM-containing complexes compact chromatin, only RYBP stimulates the activity of RING1B toward H2AK119ub1, suggesting a central role in PRC1 function. Knockdown of RYBP in embryonic stem cells compromised their ability to form embryoid bodies, likely because of defects in cell proliferation and maintenance of H2AK119ub1 levels. Copyright © 2012 Elsevier Inc. All rights reserved.
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            Author and article information

            Affiliations
            [1 ]Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
            [2 ]Department of Dermatology, University of California Davis School of Medicine, University of California Davis Comprehensive Cancer Center, Sacramento, California, United States of America
            [3 ]Department of Biological Chemistry and Molecular Medicine, University of California Davis School of Medicine, University of California Davis Comprehensive Cancer Center, Sacramento, California, United States of America
            University of North Carolina at Chapel Hill, United States of America
            Author notes

            The authors have declared that no competing interests exist.

            Conceived and designed the experiments: ZT JUJ. Performed the experiments: ZT CT. Analyzed the data: ZT JUJ. Contributed reagents/materials/analysis tools: ZT KB HRL YI CT HJK. Wrote the paper: ZT KB JUJ.

            Contributors
            Role: Editor
            Journal
            PLoS Pathog
            PLoS Pathog
            plos
            plospath
            PLoS Pathogens
            Public Library of Science (San Francisco, USA )
            1553-7366
            1553-7374
            December 2013
            December 2013
            19 December 2013
            : 9
            : 12
            24367262 3868514 PPATHOGENS-D-13-01942 10.1371/journal.ppat.1003813

            This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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            Pages: 14
            Funding
            This work was partly supported by DE023926, CA082057, CA31363, CA115284, CA180779, AI105809, AI073099, Hastings Foundation, and Fletcher Jones Foundation (JUJ) and CA14779 (YI). The UC Davis Comprehensive Cancer Center Genomics Shared Resource is supported by Cancer Center Support Grant P30 CA093373 (R.W. dV.W.) from the NCI. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
            Categories
            Research Article

            Infectious disease & Microbiology

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