DNA Methylation Enzymes and PRC1 Restrict B-cell Epstein-Barr Virus Oncoprotein Expression

To accomplish the remarkable task of lifelong infection, Epstein-Barr virus (EBV) switches between four viral genome latency and lytic programs to navigate the B-cell compartment and evade immune responses. The transforming program, comprised of highly immunogenic EBV nuclear antigen (EBNA) and Latent Membrane Proteins (LMP), is expressed in newly infected B-lymphocytes and in post-transplant lymphomas. Upon memory cell differentiation and in most EBV-associated Burkitt lymphomas (BL), all but one viral antigen are repressed for immunoevasion. To gain insights into epigenetic mechanisms that restrict immunogenic oncoprotein expression, a genome-scale CRISPR/Cas9 screen was performed in EBV+ BL cells. Here we show that the ubiquitin ligase UHRF1 and its DNA methyltransferase partner DNMT1 were critical for restriction of EBNA and LMP expression. All UHRF1 reader and writer domains were necessary for silencing, and DNMT3B was identified as an upstream viral genome CpG methylation initiator. Polycomb repressive complex I exerted a further layer of control over LMP expression, suggesting a second mechanism for latency program switching. UHRF1, DNMT1 and DNMT3B are upregulated in germinal center B-cells, the BL cell of origin, providing a molecular link between B-cell state and EBV latency program. These results suggest rational therapeutic targets to manipulate EBV oncoprotein expression.