Modulation of enhancer looping and differential gene targeting by Epstein-Barr virus transcription factors directs cellular reprogramming.
Modulation of enhancer looping and differential gene targeting by Epstein-Barr virus transcription factors directs cellular reprogramming.
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DOI：
10.1371/journal.ppat.1003636
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发表时间：
2013-09
期刊：
影响因子：
6.7
通讯作者：
West MJ
中科院分区：
文献类型：
--
作者：
McClellan MJ;Wood CD;Ojeniyi O;Cooper TJ;Kanhere A;Arvey A;Webb HM;Palermo RD;Harth-Hertle ML;Kempkes B;Jenner RG;West MJ
EB病毒（EBV）表观遗传学重编程B淋巴细胞，以驱动永生化和促进病毒持久性。宿主细胞转录主要通过EBV EBNA 2、3A、3B和3C的作用受到干扰，细胞基因通过未知机制被这些EBNA的特定组合解除调节。通过比较这些病毒转录因子与人类基因组的结合，我们发现25%的结合位点被EBNA 2和EBNA 3共享，并且主要位于增强子中。此外，80%的潜在EBNA 3A、3B或3C靶基因也被EBNA 2靶向，这暗示了EBNA 2和EBNA 3蛋白在细胞重编程中的广泛相互作用。研究邻近两个新靶点（WEE 1和CTBP 2）的共享增强子位点，我们发现EBNA 3蛋白通过调节增强子-启动子环的形成来抑制转录，以建立抑制性染色质枢纽或阻止活性枢纽的组装。Re-ChIP分析显示EBNA 2和3蛋白在共享位点不同时结合，而是竞争结合，从而调节增强子-启动子相互作用。在ADAM 28和ADAMDEC 1之间的EBNA 3-only基因间增强子位点，EBNA 3C也能够通过增强子-启动子环独立地指导两个基因的表观遗传抑制。值得注意的是，通过研究在WEE 1、CTBP 2、ITGAL（LFA-1 α链）、BCL 2L 11（Bim）和亚当斯上的共有或独特的EBNA 3结合位点，我们还发现不同的EBNA 3蛋白以基因和细胞类型特异性方式结合调控元件。结合谱与单个EBNA 3蛋白对这些基因表达的影响相关，为EBNA 3靶向不同的细胞基因组提供了分子基础。因此，我们的研究结果突出了基因组和细胞环境的影响，在确定特异性的基因失调的EBV和宿主细胞重编程通过病毒转录因子的增强子-启动子相互作用的调制提供了一个范例。EB病毒（EBV）与许多癌症有关。病毒感染B细胞并将其从短命细胞转化为永生细胞的能力是其促癌特性的关键。少数EBV转录因子是永生化所需的，并通过未知的机制解除细胞基因表达的调控来共同驱动细胞生长。我们已经证明，这些关键的转录因子中的四个通过长距离增强子元件靶向共同基因并调节它们与基因启动子的相互作用来协同发挥作用。具体来说，我们表明，基因阻遏的EBV EBNA 3蛋白家族可以通过调节增强子启动子循环介导。我们的研究结果还表明，EBNA 3蛋白的不同子集结合在不同的基因，这种差异结合可以在淋巴瘤细胞相比，在培养中永生化的细胞，表明细胞背景特异性基因调控可能是重要的淋巴瘤的发展。我们的研究结果表明，细胞基因可以通过调节增强子-启动子环与病毒转录因子结合的特异性，以基因和细胞类型特异性的方式控制细胞重编程，从而被致癌病毒解除调节。
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. Epstein-Barr virus (EBV) is associated with numerous cancers. The ability of the virus to infect B-cells and convert them from short-lived into immortal cells is the key to its cancer-promoting properties. A small number of EBV transcription factors are required for immortalization and act in concert to drive cell growth by deregulating the expression of cellular genes through largely unknown mechanisms. We have demonstrated that four of these key transcription factors function cooperatively by targeting common genes via long-range enhancer elements and modulating their looping interactions with gene promoters. Specifically we show that gene repression by the EBV EBNA 3 family of proteins can be mediated through the modulation of enhancer-promoter looping. Our results also reveal that different subsets of EBNA 3 proteins are bound at different genes and that this differential binding can vary in lymphoma cells compared to cells immortalized in culture, indicating that cell-background-specific gene regulation may be important in lymphoma development. Our results demonstrate how cellular genes can be deregulated by an oncogenic virus through modulation of enhancer-promoter looping with the specificity of binding by viral transcription factors controlling cellular reprogramming in a gene and cell-type specific manner.
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影响因子：
64.8
作者：
Heintzman, Nathaniel D.;Hon, Gary C.;Hawkins, R. David;Kheradpour, Pouya;Stark, Alexander;Harp, Lindsey F.;Ye, Zhen;Lee, Leonard K.;Stuart, Rhona K.;Ching, Christina W.;Ching, Keith A.;Antosiewicz-Bourget, Jessica E.;Liu, Hui;Zhang, Xinmin;Green, Roland D.;Lobanenkov, Victor V.;Stewart, Ron;Thomson, James A.;Crawford, Gregory E.;Kellis, Manolis;Ren, Bing
通讯作者：
Ren, Bing
影响因子：
5.4
作者：
Fuentes-Panan치, EM;Peng, RS;Ling, PD
通讯作者：
Ling, PD
影响因子：
6.7
作者：
Hertle ML;Popp C;Petermann S;Maier S;Kremmer E;Lang R;Mages J;Kempkes B
通讯作者：
Kempkes B
DOI：
10.1073/pnas.0910668107
发表时间：
2010-05-25
影响因子：
11.1
作者：
Ahmadiyeh, Nasim;Pomerantz, Mark M.;Freedman, Matthew L.
通讯作者：
Freedman, Matthew L.
影响因子：
5.4
作者：
Bain, M;Watson, RJ;Allday, MJ
通讯作者：
Allday, MJ