Epigenetic crossroads of the Epstein-Barr virus B-cell relationship

Abstract

Epstein-Barr virus (EBV) is a gamma-herpesvirus that establishes lifelong infection in the majority of people worldwide. EBV uses epigenetic reprogramming to switch between multiple latency states in order to colonize the memory B-cell compartment and to then periodically undergo lytic reactivation upon plasma cell differentiation. This review focuses on recent advances in the understanding of epigenetic mechanisms that EBV uses to control its lifecycle and to subvert the growth and survival pathways that underly EBV-driven B-cell differentiation versus B-cell growth transformation, a hallmark of the first human tumor virus. These include the formation of viral super enhancers that drive expression of key host dependency factors, evasion of tumor suppressor responses, prevention of plasmablast differentiation, and regulation of the B-cell lytic switch.

Figure 1.. Methylation-dependent expressional changes of the EBV genome during latency progression.

Recent evidence suggests EBV latency begins with a pre-latent stage, in which lytic inducers Zta and Rta, along with the vIL-10 homolog BCRF1 and vBCL2 homologs BHRF1 and BALF1 are expressed and enhance transition into viral latency. Upon accumulation of EBNA2 and EBNA-LP, expression from the viral Cp and LMPp promoters is enhanced, leading to induction of all type III latency genes. Repressive methylation of Cp blocks EBNA2 an 3 expression in latency II, where Qp drives EBNA1 and LMPp drives LMP1/2A co-expression. Once repressive methylation is accrued on LMPp, the quiescent latency I is reached, where only EBNA 1 and viral ncRNAs are expressed.

Figure 2.. Epigenetic mechanisms affecting the EBV latent-lytic switch.

(A) Schematic diagram depicting repressive methylation (green circles) accrual on the EBV genome by cellular DNA methyltransferases (DMNTs), resulting in latency I. Shown also are selected treatments that can induce lytic gene expression. (B) TET2 conversion of viral genome methylated Z-response element (ZRE) 5’cytosine residues (5mC) into 5’ hydroxymethylation (5’hmC) precludes Zta binding and transactivation. 5’hmC does not affect Rta binding, but surprisingly enhances Rta-mediated activation. (C) PI3K pathway activation stimulates EBV lytic reactivation from latency I. Multiple lytic reactivation stimuli activate PI3K to upregulate Blimp1 and downmodulate Ikaros.

Figure 3.. Epigenetic silencing of PRDM1 in lymphoblastoid B-cells.

Shown are LCL ChIP-seq tracks at the Blimp1-encoding PRDM1 locus for the host transcription factors BATF and IRF4 (blue), EBV EBNA3A (yellow) and EBNA3C (green) and the histone epigenetic mark histone 3 lysine 27 acetyl (H3K27ac, red). A schematic diagram of the PRDM1 gene body is shown at bottom.

Overview Figure. Key epigenetic mechanisms regulating EBV and B-cell gene expression.

Upon B-cell infection, the EBV genome rapidly becomes chromatinized to establish latency. During latency III, EBV superenhancers, comprised of four EBNA and five NF-kB transcription factor subunts target key host growth and survival genes, including IRF4. EBNA2-superenhancers. Separately, EBNA3A, 3C and polycomb proteins block expression of tumor suppressors, including PRDM1 (which encodes Blimp1) and BCL2L11 (which encodes BIM). BATF and IRF4 occupy composite AP1-interferon sites and may anchor EBNA3/polycomb complexes. As B-cells transit through the germinal center and differentiate into memory cells, progressive methylation restricts EBV latency gene expression, whereas the TET2 demethylase promotes latency III. Inducing agents trigger PI3K activation and de-repression of the master plasma cell differentiation regulator Blimp to trigger EBV lytic reactivation.