The Epstein-Barr Virus Enhancer Interaction Landscapes in Virus-Associated Cancer Cell Lines

Area of Science:

• Virology
• Epigenetics
• Cancer Biology

Background:

• Epstein-Barr virus (EBV) persists as chromatinized episomes in human cells.
• EBV episome 3D conformation varies with latency gene expression.
• EBV is linked to approximately 200,000 cancer cases annually.

Purpose of the Study:

• To investigate EBV episome 3D conformation and enhancer function in different EBV-associated cancer cell lines.
• To identify regulatory mechanisms of EBV gene expression.
• To explore novel strategies for controlling EBV gene expression in cancer.

Main Methods:

• Utilized Hi-C and chromatin immunoprecipitation (ChIP) assays, specifically H3K27ac HiChIP and ChIP-seq.
• Employed CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa) for enhancer perturbation.
• Analyzed EBV episome conformation in lymphoblastoid cell lines (LCLs), T/NK lymphoma cells, and primary effusion lymphoma (PEL) cells.

Main Results:

• Identified abundant genomic interactions and a strong enhancer near BILF2 in type III latency LCLs, regulating linked genes like BARF0 and BALF2.
• Discovered strong EBV enhancers and intragenomic interactions in type II latency T/NK lymphoma cells, with BILF2 enhancer regulating BARF1.
• Observed significantly fewer intragenomic interactions in type I latency PEL cells.

Conclusions:

• EBV episome 3D conformation and enhancer activity are distinct across different EBV latency types.
• The BILF2 enhancer plays a crucial role in regulating EBV gene expression in various cancer contexts.
• Findings provide insights into EBV gene regulation and suggest potential therapeutic targets for EBV-associated cancers.