School of Life Sciences, John Maynard-Smith Building, University of Sussex, Falmer, Brighton, United Kingdom.
PLoS Pathog. 2013 Sep;9(9):e1003636. doi: 10.1371/journal.ppat.1003636. Epub 2013 Sep 12.
Epstein-Barr virus (EBV) epigenetically reprogrammes B-lymphocytes to drive immortalization and facilitate viral persistence. Host-cell transcription is perturbed principally through the actions of EBV EBNA 2, 3A, 3B and 3C, with cellular genes deregulated by specific combinations of these EBNAs through unknown mechanisms. Comparing human genome binding by these viral transcription factors, we discovered that 25% of binding sites were shared by EBNA 2 and the EBNA 3s and were located predominantly in enhancers. Moreover, 80% of potential EBNA 3A, 3B or 3C target genes were also targeted by EBNA 2, implicating extensive interplay between EBNA 2 and 3 proteins in cellular reprogramming. Investigating shared enhancer sites neighbouring two new targets (WEE1 and CTBP2) we discovered that EBNA 3 proteins repress transcription by modulating enhancer-promoter loop formation to establish repressive chromatin hubs or prevent assembly of active hubs. Re-ChIP analysis revealed that EBNA 2 and 3 proteins do not bind simultaneously at shared sites but compete for binding thereby modulating enhancer-promoter interactions. At an EBNA 3-only intergenic enhancer site between ADAM28 and ADAMDEC1 EBNA 3C was also able to independently direct epigenetic repression of both genes through enhancer-promoter looping. Significantly, studying shared or unique EBNA 3 binding sites at WEE1, CTBP2, ITGAL (LFA-1 alpha chain), BCL2L11 (Bim) and the ADAMs, we also discovered that different sets of EBNA 3 proteins bind regulatory elements in a gene and cell-type specific manner. Binding profiles correlated with the effects of individual EBNA 3 proteins on the expression of these genes, providing a molecular basis for the targeting of different sets of cellular genes by the EBNA 3s. Our results therefore highlight the influence of the genomic and cellular context in determining the specificity of gene deregulation by EBV and provide a paradigm for host-cell reprogramming through modulation of enhancer-promoter interactions by viral transcription factors.
EB 病毒（EBV）通过表观遗传重编程 B 淋巴细胞来驱动永生化并促进病毒持续存在。宿主细胞转录主要通过 EBV EBNA2、3A、3B 和 3C 的作用受到干扰，通过这些 EBNA 以未知机制的特定组合，细胞基因被下调。通过比较这些病毒转录因子对人类基因组的结合，我们发现 25%的结合位点被 EBNA2 和 EBNA3s 共享，并且主要位于增强子中。此外，80%的潜在 EBNA3A、3B 或 3C 靶基因也被 EBNA2 靶向，这表明 EBNA2 和 3 蛋白在细胞重编程中存在广泛的相互作用。研究两个新靶标（WEE1 和 CTBP2）附近的共享增强子位点时，我们发现 EBNA3 蛋白通过调节增强子-启动子环形成来抑制转录，从而建立抑制性染色质中心或防止活性中心的组装。重新 ChIP 分析表明，EBNA2 和 3 蛋白不会同时结合共享位点，而是竞争结合，从而调节增强子-启动子相互作用。在 ADAM28 和 ADAMDEC1 之间的一个仅含 EBNA3 的基因间增强子位点上，EBNA3C 还能够通过增强子-启动子环形成独立地直接指导这两个基因的表观遗传抑制。重要的是，在 WEE1、CTBP2、ITGAL（LFA-1 alpha 链）、BCL2L11（Bim）和 ADAMs 上研究共享或独特的 EBNA3 结合位点时，我们还发现不同的 EBNA3 蛋白以基因和细胞类型特异性的方式结合调节元件。结合谱与单个 EBNA3 蛋白对这些基因表达的影响相关，为 EBNA3 对不同细胞基因的靶向提供了分子基础。因此，我们的结果强调了基因组和细胞环境在确定 EBV 基因失调特异性方面的影响，并为通过病毒转录因子调节增强子-启动子相互作用进行宿主细胞重编程提供了范例。
