Epstein-Barr virus induces germinal center light zone chromatin architecture and promotes survival through enhancer looping at the BCL2A1 locus

Abstract

ABSTRACT Epstein-Barr virus (EBV) is a ubiquitous human virus that promotes B-cell activation and maturation through expression of latency proteins and non-coding RNAs. In this study, we provide evidence that EBV mimics the molecular phenotype of germinal center (GC) B cells. EBV infection of primary human B cells promotes their rapid proliferation and GC dark zone (DZ)-like gene expression profile. Following this transient hyperproliferative period, the activation of NF-κB target genes, including Bcl2a1 (BFL-1), simulates the transition from the DZ to the T-cell supported light zone (LZ). We previously characterized the regulatory landscape of EBV + B cells at the Bcl2a1 locus defining a key role for the viral EBV nuclear antigen (EBNA) 3A protein in promoting three-dimensional chromatin architecture correlated with BFL-1 expression. Here, we define the global chromatin accessibility of tonsillar B cells and find that naïve and memory B cells have highly similar accessibility profiles that differ substantially from those of DZ and LZ B cells. Notably, multiple regions within the Bcl2a1 locus are significantly more accessible in DZ and LZ versus naïve and memory subsets. However, we found that BFL-1 upregulation from DZ to LZ correlates with a significant increase in three-dimensional (3-D) chromatin association between accessible upstream enhancer regions and the BFL-1 transcriptional start site. These elements were critical for BFL-1 expression in lymphoblastoid cell lines (LCLs). Moreover, increased BFL-1 expression in LCLs protected against extrinsic apoptosis. Collectively, these results suggest a conserved mechanism underlying BFL-1 upregulation that promotes survival of both LZ and EBV + immortalized B cells. IMPORTANCE Epstein-Barr virus has evolved with its human host leading to an intimate relationship where infection of antibody-producing B cells mimics the process by which these cells normally recognize foreign antigens and become activated. Virtually everyone in the world is infected by adulthood and controls this virus pushing it into life-long latency. However, immune-suppressed individuals are at high risk for EBV+ cancers. Here, we isolated B cells from tonsils and compare the underlying molecular genetic differences between these cells and those infected with EBV. We find similar regulatory mechanism for expression of an important cellular protein that enables B cells to survive in lymphoid tissue. These findings link an underlying relationship at the molecular level between EBV-infected B cells in vitro with normally activated B cells in vivo . Our studies also characterize the role of a key viral control mechanism for B cell survival involved in long-term infection.