Epigenetic Regulation of Kaposi's Sarcoma-Associated Herpesvirus Latency

Abstract

Kaposi's sarcoma-associated herpesvirus (KSHV) is an oncogenic γ-herpesvirus that infects humans and exhibits a biphasic life cycle consisting of latent and lytic phases. Following entry into host cells, the KSHV genome undergoes circularization and chromatinization into an extrachromosomal episome ultimately leading to the establishment of latency. The KSHV episome is organized into distinct chromatin domains marked by variations in repressive or activating epigenetic modifications, including DNA methylation, histone methylation, and histone acetylation. Thus, the development of KSHV latency is believed to be governed by epigenetic regulation. In the past decade, interrogation of the KSHV epitome by genome-wide approaches has revealed a complex epigenetic mark landscape across KSHV genome and has uncovered the important regulatory roles of epigenetic modifications in governing the development of KSHV latency. Here, we highlight many of the findings regarding the role of DNA methylation, histone modification, post-translational modification (PTM) of chromatin remodeling proteins, the contribution of long non-coding RNAs (lncRNAs) in regulating KSHV latency development, and the role of higher-order episomal chromatin architecture in the maintenance of latency and the latent-to-lytic switch.

Keywords: DNA methylation; Kaposi’s sarcoma-associated herpesvirus (KSHV); epigenetic; histone modification; long non-coding RNAs (lncRNAs); post-translational modification (PTM).

FIGURE 1

Summary of epigenetic modulation of the latent KSHV genome. The research group (gr) associated with each publication is listed. (A) Mutual exclusive localization of histone activation (H3K4me3 and H3-ac) and repressive (H3K27me3 and H3K9me3) marks. The PRC2 complex binds and catalyzes H3K27me3. (B) Biphasic euchromatin-to-heterochromatin transition following KSHV infection with initial K-Rta-mediated deposit of active histone marks (H3K4me3 and H3K27-ac). One to three days post-infection (dpi), active histone marks decline and a sequential deposit of H3K27me3 by PRC2, recruitment of PRC1, and deposit of H2AK119-Ub by PRC1. The sequential recruitment of modifying complexes converges to increase repressive histone marks (H3K27me3 and H2AK119-Ub). (C) LANA mediated recruitment of histone-modifying enzymes and deposition of corresponding histone marks. (i) LANA recruits PRC2 that potentially increase H3K27me3. (ii) LANA associates with H3K4 methyltransferase hSET1. (iii) LANA associates with H3K9me1/2 histone demethylase KDM3A. (iv) PRMT1-directed methylation of LANA increases its chromatin binding. (D) ZIC2 contributes to tethering of PRC2 on the KSHV genome, thus maintaining H3K27me3. (E) PRC1 involvement in maintaining nucleosomes on the latent KSHV genome. (F) Widespread presence of both active marks (H3K4me3 and H3K9/K14-ac) and repressive marks (H3K27me3) across the latent KSHV genome. (G) Direct binding of KDM2B to CpG islands recruits PRC1.1 on the latent KSHV genome. (H) KDM2B rapidly binds to the incoming viral DNA and limits the enrichment of activating histone marks on the RTA promoter favoring the downregulation of RTA expression. This early event occurs prior to the polycomb protein-regulated heterochromatin formation on the viral genome. Summary: Following de novo infection, KSHV K-Rta initiates the acquisition of the active histone marks H3K4me3 and H3K27-ac on the KSHV genome. After LANA is expressed, it mediates the increase of the repressive mark H3K27me3 and the active mark H3K4me3. H3K27me3 consequently recruits PRC1 and increases H2AK119-Ub on the KSHV genome. The cellular protein KDM2B may also help recruit PRCs to the KSHV genome.

FIGURE 2

Episome Conformational Control of Latency. The figure depicts the region on the KSHV genome where chromatin contacts implicated in the maintenance of latency and the latent to lytic switch reside. Upper panel: The latency control locus contacts the lytic control region via a CTCF-dependent genomic loop during latency. CTCF sites in the latency control region are clustered within the first intron of ORF73. This looping mechanism permits latent gene expression while early lytic gene expression (i.e., K-Rta) is repressed. Lower panel: Opening of the cohesin ring during lytic reactivation results in loss of the genomic loop and facilitates RNA polymerase II (Pol II) activation at the early lytic locus resulting in K-Rta expression and induction of the lytic phase. The figure depicts RAD21 cohesin complex component (Rad21) cleavage as the initiating factor resulting in opening of the ring with subsequent loss of looping contacts. SMC, structural maintenance of chromosome proteins. CTCF, CCCTC-binding factor.