Tian Simon Zhongyuan, Yang Yang, Ning Duo, Yu Ting, Gao Tong, Deng Yuqing, Fang Ke, Xu Yewen, Jing Kai, Huang Guangyu, Chen Gengzhan, Yin Pengfei, Li Yiming, Zeng Fuxing, Tian Ruilin, Zheng Meizhen
Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China.
Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China.
EMBO J. 2025 May 27. doi: 10.1038/s44318-025-00466-5.
The three-dimensional (3D) chromatin structure of Epstein-Barr virus (EBV) within host cells and the underlying mechanisms of chromatin interaction and gene regulation, particularly those involving EBV's noncoding RNAs (ncRNAs), have remained incompletely characterized. In this study, we employed state-of-the-art techniques of 3D genome mapping, including protein-associated chromatin interaction analysis with paired-end tag sequencing (ChIA-PET), RNA-associated chromatin interaction technique (RDD), and super-resolution microscopy, to delineate the spatial architecture of EBV in human lymphoblastoid cells. We systematically analyzed EBV-to-EBV (E-E), EBV-to-host (E-H), and host-to-host (H-H) interactions linked to host proteins and EBV RNAs. Our findings reveal that EBV utilizes host CCCTC-binding factor (CTCF) and RNA polymerase II (RNAPII) to form distinct chromatin contact domains (CCDs) and RNAPII-associated interaction domains (RAIDs). The anchors of these chromatin domains serve as platforms for extensive interactions with host chromatin, thus modulating host gene expression. Notably, EBV ncRNAs, especially Epstein-Barr-encoded RNAs (EBERs), target and interact with less accessible regions of host chromatin to repress a subset of genes via the inhibition of RNAPII-associated chromatin loops. This process involves the cofactor nucleolin (NCL) and its RNA recognition motifs, and depletion of either NCL or EBERs alters expression of genes crucial for host infection control, immune response, and cell cycle regulation. These findings unveil a sophisticated interplay between EBV and host chromatin.
爱泼斯坦-巴尔病毒（EBV）在宿主细胞内的三维（3D）染色质结构以及染色质相互作用和基因调控的潜在机制，特别是那些涉及EBV非编码RNA（ncRNA）的机制，仍未得到充分表征。在本研究中，我们采用了最先进的3D基因组图谱技术，包括用于蛋白质相关染色质相互作用分析的双末端标签测序（ChIA-PET）、RNA相关染色质相互作用技术（RDD）和超分辨率显微镜，以描绘EBV在人淋巴母细胞中的空间结构。我们系统地分析了与宿主蛋白和EBV RNA相关的EBV与EBV（E-E）、EBV与宿主（E-H）以及宿主与宿主（H-H）之间的相互作用。我们的研究结果表明，EBV利用宿主CCCTC结合因子（CTCF）和RNA聚合酶II（RNAPII）形成不同的染色质接触结构域（CCD）和RNAPII相关相互作用结构域（RAID）。这些染色质结构域的锚定物作为与宿主染色质广泛相互作用的平台，从而调节宿主基因表达。值得注意的是，EBV ncRNA，特别是爱泼斯坦-巴尔编码RNA（EBER），靶向宿主染色质中较难接近的区域并与其相互作用，通过抑制与RNAPII相关的染色质环来抑制一部分基因。这个过程涉及辅因子核仁素（NCL）及其RNA识别基序，NCL或EBER的缺失会改变对宿主感染控制、免疫反应和细胞周期调控至关重要的基因的表达。这些发现揭示了EBV与宿主染色质之间复杂的相互作用。
