Epstein–Barr virus: a master epigenetic manipulator

Highlights

• EBV encodes viral epigenetic effectors that alter viral and host epigenomes.

• EBV-induced epigenetic changes to the host epigenome have oncogenic consequences.

• Epigenetic changes can maintain phenotypes in latency or after viral genome loss.

• EBV epigenetic changes provide a framework for viral ‘hit-and-run’ oncogenesis.

Like all herpesviruses, the ability of Epstein–Barr virus (EBV) to establish life-long persistent infections is related to a biphasic viral lifecycle that involves latency and reactivation/lytic replication. Memory B cells serve as the EBV latency compartment where silencing of viral gene expression allows maintenance of the viral genome, avoidance of immune surveillance, and life-long carriage. Upon viral reactivation, viral gene expression is induced for replication, progeny virion production, and viral spread. EBV uses the host epigenetic machinery to regulate its distinct viral gene expression states. However, epigenetic manipulation by EBV affects the host epigenome by reprogramming cells in ways that leave long-lasting, oncogenic phenotypes. Such virally-induced epigenetic alterations are evident in EBV-associated cancers.

Introduction

Epstein–Barr virus (EBV) is a herpesvirus that infects greater than 90% of adults worldwide [1, 2]. EBV is shed and transmitted in saliva infecting B cells and epithelial cells in the oral cavity [3, 4, 5, 6, 7]. Memory B cells provide the lifelong site for EBV latency and persistence. EBV can infect memory B cells directly or can navigate naïve B cells through their differentiation program to become memory B cells [8, 9]. Viral latency is guided by promoter silencing and promoter switching, which results in an increasingly restricted viral gene expression program as B cells differentiate [10]. In naïve B cells, EBV latency III (the growth program) is observed with the expression of EBV nuclear antigens (EBNA) 1, EBNA2, EBNA3A, EBNA3B, EBNA3C, EBNA-LP, latent membrane protein (LMP) 1, LMP2A, LMP2B, and viral noncoding RNAs: EBV encoded RNAs (EBER) 1, EBER2 and the BamHI A rightward transcripts (BARTs). Germinal B cells show expression of EBNA1, LMP1, LMP2A, and noncoding RNAs, known as latency II (the default program). In memory B cells, latent genes are restricted to EBNA1, LMP2A, and noncoding RNAs, referred as latency I. Terminal differentiation of memory B cells into antibody producing plasma cells signals EBV reactivation into the productive phase of the viral lifecycle [11, 12]. Epithelial cells support the productive phase of the viral lifecycle, with EBV replicating in the uppermost differentiated layers of the stratified epithelium [4, 5, 13, 14, 15]. Latent epithelial cell infections have been detected in basal tonsillar epithelial cells, but the nature of such latent infections is not well understood [16^••].

The distinct viral gene expression states adopted by EBV throughout the viral lifecycle are epigenetically regulated [17]. Epigenetic modifications stably propagate gene expression patterns in a heritable manner without affecting the DNA sequence. Epigenetic modifications involve DNA methylation where a methyl group is added to the C-5 position of cytosine residues, usually in the context of a CpG dinucleotide and post-translational modifications (acetylation, phosphorylation, ubiquitination, and ADP-ribosylation) on lysine or arginine residues in the tail region of the core histones [18, 19]. Such epigenetic marks alter the accessibility and recruitment of transcription factors and transcription machinery to chromatin. The regulatory proteins (chromatin readers, writers, and erasers) involved in epigenetic maintenance and reprogramming include DNA methyltransferases (DNMTs), methyl-CpG-binding proteins, histone modifying enzymes, and chromatin remodeling factors. Formation of higher order chromatin structures and gene looping also contribute to the regulation of epigenetic gene expression states. Such epigenetic states are reversible and can be altered by environmental factors (including viruses) in ways that have long-lasting detrimental effects on phenotype.