An Atlas of the Epstein-Barr Virus Transcriptome and Epigenome Reveals Host-Virus Regulatory Interactions

Abstract

Epstein-Barr Virus (EBV), which is associated with multiple human tumors, persists as a minichromosome in the nucleus of B-lymphocytes and induces malignancies through incompletely understood mechanisms. Here, we present a large-scale functional genomic analysis of EBV. Our experimentally generated nucleosome positioning maps and viral protein binding data were integrated with over 700 publicly available high-throughput sequencing data sets for human lymphoblastoid cell lines mapped to the EBV genome. We found that viral lytic genes are coexpressed with cellular cancer-associated pathways, suggesting that the lytic cycle may play an unexpected role in virus-mediated oncogenesis. Host regulators of viral oncogene expression and chromosome structure were identified and validated, revealing a role for the B-cell-specific protein Pax5 in viral gene regulation and the cohesin complex in regulating higher order chromatin structure. Our findings provide a deeper understanding of latent viral persistence in oncogenesis and establish a valuable viral genomics resource for future exploration.

How virus persistence can initiate the tumorigenesis process

“…), or cells being in a particular phase of the cell cycle [42] , which could be a frequent event for rapidly replicating cells or a very infrequent event for slowly replicating cells, as for liver cells. Recent evidence reveals that in an EBV latency model lytic genes can be transcribed to considerable levels [43] , contrary to what had been thought previously. Similarly in Kaposi sarcoma virus associated tumors, subpopulations of cells express lytic gene products within a general latency setting [44] , suggesting the distinction between latency and lytic transcription is less clear cut than expected.…”

Epigenetic Deregulation of the LMP1/LMP2 Locus of Epstein-Barr Virus by Mutation of a Single CTCF-Cohesin Binding Site

“…We have previously found that this CTCF-cohesin site formed a DNA-loop interaction with OriP (38). We used chromosome conformation capture (3C) and shRNA depletion studies to show that cohesin is important for DNA long-range interactions and that this protein complex also contributes to LMP1 and LMP2A transcription efficiency.…”

“…In EBV, CTCF binds at several key regulatory regions, many of which are cooccupied by cohesin (38)(39)(40). In particular, CTCF and cohesin can bind to the LMP1 and LMP2A control region at a position within the first intron of LMP2A and the 3= untranslated region (3=UTR) of LMP1 (38) (Fig. 1A to C).…”

“…Cohesin is a multiprotein complex that can form a ring-like structure capable of stabilizing interactions between DNA molecules, which is important for both sister chromatid cohesion in mitosis and promoter-enhancer interactions in transcriptional regulation (34)(35)(36)(37). In EBV, CTCF binds at several key regulatory regions, many of which are cooccupied by cohesin (38)(39)(40). In particular, CTCF and cohesin can bind to the LMP1 and LMP2A control region at a position within the first intron of LMP2A and the 3= untranslated region (3=UTR) of LMP1 (38) (Fig.…”

Viral noncoding RNAs: more surprises

“…Given its nuclear location, we recently probed EBER2's association with chromatin (Lee et al 2015) using capture hybridization analysis of RNA targets (CHART), a technique similar to chromatin immunoprecipitation that allows RNA localization to specific sites on DNA (Simon et al 2011). EBER2 was found to bind to the so-called terminal repeats (TRs) of the EBV genome, overlapping previously identified binding sites for the cellular transcription factor paired box protein 5 (PAX5) (Arvey et al 2012). PAX5 is a well-characterized master regulator of B-lymphocyte development and function (Medvedovic et al 2011).…”