The chromatin landscape of Kaposi's sarcoma-associated herpesvirus

Abstract

Kaposi's sarcoma-associated herpesvirus is an oncogenic γ-herpesvirus that causes latent infection in humans. In cells, the viral genome adopts a highly organized chromatin structure, which is controlled by a wide variety of cellular and viral chromatin regulatory factors. In the past few years, interrogation of the chromatinized KSHV genome by whole genome-analyzing tools revealed that the complex chromatin landscape spanning the viral genome in infected cells has important regulatory roles during the viral life cycle. This review summarizes the most recent findings regarding the role of histone modifications, histone modifying enzymes, DNA methylation, microRNAs, non-coding RNAs and the nuclear organization of the KSHV epigenome in the regulation of latent and lytic viral gene expression programs as well as their connection to KSHV-associated pathogenesis.

Figure 1

Chromatin components and their effect on gene expression. (A) The basic unit of chromatin is the nucleosome, which consists of 147 bp DNA wrapped around histones H2A, H2B, H3 and H4. The N terminus of histones is subject to different posttranslational modifications; (B) The levels and types of histone marks are dynamically regulated by antagonistic histone modifying enzymes (writers and erasers). Histone marks are recognized and interpreted by specific nuclear proteins (readers), resulting in the recruitment of either repressor or activator transcription regulatory complexes onto the target promoters. Some examples of repressive and activating chromatin modifications are listed in the boxed text.

Figure 2

Chromatinization of the KSHV episome and the role of the latent KSHV protein, LANA. (A) The KSHV genome is linear and histone-free in the viral capsid and becomes a closed circular episome following de novo infection. Subsequently, the viral DNA is organized into a nucleosome structure and it persists in the nucleus as a non-integrated minichromosome; (B) LANA is a constitutively expressed gene that is encoded within the major latency-associated locus of the KSHV genome. LANA binds to terminal repeat (TR) region of the viral genome and tethers the viral genome to the host chromosome by interacting with histones or other components of the cellular chromatin such as Brd4, MeCP2…etc. LANA also binds to several sites within the viral genome and it is involved in the recruitment of the H3K9me1/2 histone demethylase JMJD1A and repression of lytic genes. The posttranslational modifications of LANA play a critical role in the association of LANA with the KSHV genome and also regulate its activity in transcription regulation. During latency, LANA in maintained in an arginine methylated state resulting in its binding to the KSHV genome. Upon HDAC inhibitor (HDACi) treatment, LANA gets acetylated, which leads to its dissociation from the KSHV genome and the concomitant induction of lytic genes.

Figure 3

The chromatin landscape of KSHV during latency. (A) Schematic of the KSHV genome and the genome-wide distribution of different histone marks along the viral genome. There are distinct chromatin domains on the viral episome, which are characterized by different histone modification patterns indicating the targeted recruitment of specific cellular chromatin modifying enzyme complexes to different sites of the viral genome. The cellular chromatin modifying factors associated with each histone mark are listed to the right. The position of the latency locus and examples of an IE gene (RTA), some early genes (viral interferon regulatory factors or vIRFs and the OriLytL-K7 locus) and L genes (ORF25 and ORF64) are indicated at the top; (B) The PRC2 complex co-localizes with H3K27me3-rich chromatin domains, while the binding of the H3K9me3 histone demethylase JMJD2A overlaps with the H3K4me3/acH3-enriched chromatin regions that have a low level of H3K9me3. PRC2 is involved in the inhibition of ORF50 (RTA) expression during latency.

Figure 4

Regulation of the RTA promoter during latency and reactivation. The H3K27me3 histone methyltransferase complex PRC2 as well as specific histone deacetylases (HDAC1, 5 and 7) are critical transcriptional repressors that are present on the RTA promoter during latency. The bivalent chromatin of the RTA promoter is indicated by the presence of both activating (H3K4me3 and acH3) and repressive (H3K27me3) histone marks. After reactivation RTA binds to its own promoter via CBF-1 (also called RBP-Jκ) and recruits several cellular transcription factors such as the Mediator, the ATP-dependent chromatin remodeling complex SWI/SNF2 and the histone acetyltransferase CBP. The induction of transcription is accompanied by the rapid recruitment of RNA polymerase II (RNAPII) and increased binding of Sp1 to the promoter. The KSHV non-coding PAN RNA can also interact with the RTA promoter and recruit the H3K4me3 histone methyltransferase MLL2 as well as the H3K27me3 histone demthylases UTX and JMJD3. The Sp1/3-binding sites play an important role in the HDAC inhibitor-mediated reactivation of the RTA promoter. While these sites contribute to the LANA-mediated repression of the RTA promoter during latency, they are also involved in recruitment of CBP, which can catalyze the hyperacetylation of histones on the viral promoter during reactivation.