The Epigenetic Landscape of Latent Kaposi Sarcoma-Associated Herpesvirus Genomes

Abstract

Herpesvirus latency is generally thought to be governed by epigenetic modifications, but the dynamics of viral chromatin at early timepoints of latent infection are poorly understood. Here, we report a comprehensive spatial and temporal analysis of DNA methylation and histone modifications during latent infection with Kaposi Sarcoma-associated herpesvirus (KSHV), the etiologic agent of Kaposi Sarcoma and primary effusion lymphoma (PEL). By use of high resolution tiling microarrays in conjunction with immunoprecipitation of methylated DNA (MeDIP) or modified histones (chromatin IP, ChIP), our study revealed highly distinct landscapes of epigenetic modifications associated with latent KSHV infection in several tumor-derived cell lines as well as de novo infected endothelial cells. We find that KSHV genomes are subject to profound methylation at CpG dinucleotides, leading to the establishment of characteristic global DNA methylation patterns. However, such patterns evolve slowly and thus are unlikely to control early latency. In contrast, we observed that latency-specific histone modification patterns were rapidly established upon a de novo infection. Our analysis furthermore demonstrates that such patterns are not characterized by the absence of activating histone modifications, as H3K9/K14-ac and H3K4-me3 marks were prominently detected at several loci, including the promoter of the lytic cycle transactivator Rta. While these regions were furthermore largely devoid of the constitutive heterochromatin marker H3K9-me3, we observed rapid and widespread deposition of H3K27-me3 across latent KSHV genomes, a bivalent modification which is able to repress transcription in spite of the simultaneous presence of activating marks. Our findings suggest that the modification patterns identified here induce a poised state of repression during viral latency, which can be rapidly reversed once the lytic cycle is induced.

Kaposi's Sarcoma-Associated Herpesvirus Utilizes and Manipulates RNA N 6 -Adenosine Methylation To Promote Lytic Replication

“…Previous studies suggested that the switch of KSHV from latency to productive lytic replication is primarily controlled at the viral chromatin level through histone and DNA modifications (58)(59)(60)(61)(62)(63)(64)(65). In this study, we demonstrate that most KSHV-encoded mRNAs undergo posttranscriptional m 6 A modification.…”

The H3K27me3 demethylase, KDM6B, is induced by Epstein–Barr virus and over-expressed in Hodgkin's Lymphoma

“…However, the ectopic expression of KDM6B in cell lines infected with another gamma herpes virus, Kaposi's sarcoma-associated herpesvirus is followed by the upregulation of the viral gene ORF50. ORF50, which orchestrates the expression of lytic genes leading to viral amplification is a homolog of the EBV transactivator, BRLF1 (Rta) (Gu¨nther and Grundhoff, 2010). These observations suggest that in gamma herpesviruses, the latent/lytic switch may be dependent not only on the dynamics of DNA methylation on early viral promoters, but also on changes in the distribution of the H3K27me3 mark.…”

Pathogenetic Influences of Human Herpesvirus 8 (HHV-8) in Prostate Cancer Progression

“…Since suppression of RTA expression is due to tri-methylation of H3K27 at the RTA promoter (147,148), the presence of transcripts for RTA and other lytic genes represents evidence of histone demethylation on the viral genome, which allows RTA transcription. To confirm this, we used lysates from NaB-treated LNCaPv219-FBS cells and measured the expression of EZH2, SUZ12 and H3K27me3 by Western blot.…”

“…Chen and co-workers showed that steroid hormone signaling and expression of hormonally-regulated genes requires ligand-bound hormone receptors to complex with histone acetylases, which acetylate histones located at gene promoter regions and enable hormone receptors to access and transcribe target genes (184). It has been observed that chromatin remodeling, specifically histone acetylation of the RTA promoter is required for the induction of viral reactivation (147,148,185,186).…”

“…[187][188][189][190] Herpesvirus -etiological agent for Kaposi's sarcoma (KS), tumor of endothelial and lymphatic origin 101 ERG expression critical for lineage specific differentiation of endothelial cells, angiogenesis and expression of endothelial markers [187][188][189][190] KS lesions composed of "spindle cells," express endothelial and lymphatic markers; virus induces expression of numerous proangiogenic proteins 130 TMPRSS2-ERG gene fusion most prevalent genetic mutation in prostate cancer 27,28 transforms epithelial cells in part by activating MAP kinases 191,192 Virus-encoded proteins activate numerous host cell signaling pathways critical to KS development 130 Oncogenic fusion induces NF-κB activation and inflammation through TLR4 signaling 199 HHV-8 strong inducer of inflammation; activation of NF-κB critical in KS pathology [111][112][113] TMPRSS2-ERG mediates epigenetic regulation through EZH2 140 Viral latency maintained by EZH2 147,148 TMPRSS2-ERG induces epithelialmesenchymal transition [196][197][198] Induces epithelial-mesenchymal transition 149,150 epithelial dedifferentiation and the loss of expression of prostate-defining genes, such as PSA (194,195). This ERG-induced epithelial dedifferentiation occurs as the result of ERG activating EZH2-mediated epigenetic modifications (140).…”