The three-dimensional structure of the EBV genome plays a crucial role in regulating viral gene expression in EBVaGC [RNA-seq]

Epstein-Barr virus (EBV) establishes lifelong asymptomatic infection by replication of its chromatinized episomes with the host genome. EBV exhibits different latency-associated transcriptional repertoires, each with distinct three-dimensional structures. CTCF, Cohesin and PARP1 are involved in maintaining viral latency and establishing episome architecture. Epstein-Barr virus-associated gastric cancer (EBVaGC) represents 1.3% to 30.9% of all gastric cancers globally. EBV-positive gastric cancers exhibit an intermediate viral transcription profile known as "Latency II", expressing specific viral genes and noncoding RNAs. In this study, we investigated the impact of PARP1 inhibition on CTCF/Cohesin binding in Type II latency. We observed destabilization of the binding of both factors, leading to a disrupted three-dimensional architecture of the episomes and an altered viral gene expression. Despite sharing the same CTCF binding profile, Type I, II, and III latencies exhibit different 3D structures that correlate with variations in viral gene expression. Additionally, our analysis of H3K27ac-enriched interactions revealed differences between Type II latency episomes and a link to cellular transformation through docking of the EBV genome at specific sites of the Human genome, thus promoting oncogene expression. Overall, this work provides insights into the role of PARP1 in maintaining active latency and novel mechanisms of EBV-induced cellular transformation. Overall design: RNA sequencing of Human and EBV transcriptome in YCCEL1 and SNU719 cell lines

EB病毒（Epstein-Barr virus, EBV）可通过其染色质化附加体与宿主基因组同步复制，建立终身无症状感染。该病毒存在多种与潜伏感染相关的转录谱，每种转录谱均具有独特的三维结构。CCCTC结合因子（CTCF）、黏连蛋白（Cohesin）与多聚ADP核糖聚合酶1（PARP1）参与维持病毒潜伏状态，并构建附加体的三维结构。EB病毒相关胃癌（Epstein-Barr virus-associated gastric cancer, EBVaGC）在全球所有胃癌中占比为1.3%至30.9%。EB病毒阳性胃癌呈现一种被称为"Latency II"的中间型病毒转录谱，表达特定的病毒基因与非编码RNA。本研究探究了PARP1抑制对II型潜伏感染中CTCF/Cohesin结合的影响。研究团队观察到两种因子的结合稳定性下降，导致附加体的三维结构被破坏，同时病毒基因表达发生改变。尽管I型、II型与III型潜伏感染共享相同的CTCF结合谱，但三者的三维结构存在差异，且这种差异与病毒基因表达的变化相关。此外，本研究对富集组蛋白H3赖氨酸27乙酰化（H3K27ac）的相互作用进行分析后发现，II型潜伏感染的附加体存在差异，且EB病毒基因组可锚定在人类基因组的特定位点，从而与细胞转化相关，最终促进癌基因的表达。综上，本研究揭示了PARP1在维持病毒活跃潜伏状态中的作用，以及EB病毒诱导细胞转化的全新机制。实验整体设计：对YCCEL1与SNU719细胞系中的人类转录组及EB病毒转录组进行RNA测序。