An Epigenetic Journey: Epstein-Barr Virus Transcribes Chromatinized and Subsequently Unchromatinized Templates during Its Lytic Cycle

Abstract

The Epstein-Barr virus (EBV) lytic phase, like those of all herpesviruses, proceeds via an orderly cascade that integrates DNA replication and gene expression. EBV early genes are expressed independently of viral DNA amplification, and several early gene products facilitate DNA amplification. On the other hand, EBV late genes are defined by their dependence on viral DNA replication for expression. Recently, a set of orthologous genes found in beta-and gammaherpesviruses have been determined to encode a viral preinitiation complex (vPIC) that mediates late gene expression. The EBV vPIC requires an origin of lytic replication in cis, implying that the vPIC mediates transcription from newly replicated DNA. In agreement with this implication, EBV late gene mRNAs localize to replication factories. Notably, these factories exclude canonical histones. In this review, we compare and contrast the mechanisms and epigenetics of EBV early and late gene expression. We summarize recent findings, propose a model explaining the dependence of EBV late gene expression on lytic DNA amplification, and suggest some directions for future study.with 5-ethynyl uridine (EU) in the early and late lytic phases, followed by enrichment for EU-labeled RNAs and RNA-seq to assay for viral and cellular genes that are being actively transcribed at different times during the lytic cycle. Similar experiments using ribosome profiling may yield valuable information about which mRNAs are being actively translated during the lytic phase. For example, Bencun et al. (88) used ribosome profiling on EBV-positive cells to show highly variable translation of EBV transcripts. However, only about 4 to 6% of the cells used in the assay were in the lytic phase. TheFIG 3 A model for EBV late gene expression. (A) Early during the lytic cycle, EBV genomes are unreplicated and still chromatinized. The immediate early proteins BZLF1 and BRLF1 can bind to the promoters of early genes (which are usually methylated) and, along with cellular TATA box-binding protein (TBP), recruit RNA polymerase II to transcribe early genes. (B) Later in the lytic phase, EBV genomes are amplified in replication factories, while cellular chromatin moves to the periphery of the nucleus. The amplified viral DNA is unmethylated and unchromatinized, which allows the viral preinitiation complex (vPIC), including the viral TBP BcRF1, to recruit RNA Pol II to late promoters and transcribe late genes.

Pharmacologic Activation of Lytic Epstein-Barr Virus Gene Expression without Virion Production

“…5 and 7). We note that the regulation of transcription of late proteins in gammaherpesvirus infection is complex and appears to reflect changes in histones, CpG methylation, and the formation of replication centers in productively infected cells, as recently reviewed (36). An important role for PERK in inhibiting the translation of viral proteins has been detailed in other systems (37).…”

Conserved CxnC motifs in Kaposi’s sarcoma-associated herpesvirus ORF66 are required for viral late gene expression and mediate its interaction with ORF34

“…We next tested whether ORF66 plays a role in replication of the viral genome. It is well established that late gene transcription is licensed by the initiation of viral genome replication (15-17). Although it has been previously reported that other vTA mutants do not exhibit a defect in viral genome replication (6, 8-10), we recently reported that mutations in ORF24 result in a ∼6-fold defect in viral genome replication (1).…”

Histone loaders CAF1 and HIRA restrict Epstein-Barr virus B-cell lytic reactivation

“…Multiple layers of epigenetic regulation enable EBV to establish latency in newly-infected B-cells, in which a small number of viral encoded proteins and viral non-coding RNAs reprogram infected cell metabolism, growth and survival pathways (7–9). Within 3 days of infection, quiescent B-cells are reprogramed to become rapidly growing lymphoblasts that divide as frequently as every 8 hours (10–13).…”

“…Plasma cell differentiation is a trigger for EBV lytic reactivation. Induction of two viral immediate early gene transcription factors, BZLF1 and BRLF1, induce nearly 30 early genes important for production of lytic genomes (10, 14, 15). How these newly synthesized EBV genomes evade chromatinization by host histone loaders, including the heterotrimeric Chromatin Assembly Factor 1 (CAF1) complex that delivers newly synthesized H3/H4 dimers to host replication forks, is only partially understood (16, 17).…”

“…How these newly synthesized EBV genomes evade chromatinization by host histone loaders, including the heterotrimeric Chromatin Assembly Factor 1 (CAF1) complex that delivers newly synthesized H3/H4 dimers to host replication forks, is only partially understood (16, 17). EBV late genes are subsequently induced and include factors required for virion assembly and spread (10). Retrograde signals support ongoing lytic replication through subversion of chromatin-based repressors (18).…”