The three-dimensional structure of the EBV genome plays a crucial role in regulating viral gene expression in EBVaGC [ChIP-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: Chromatin Immunoprecipitation DNA-sequencing of histones H3K4me1 and H3K27ac

爱泼斯坦-巴尔病毒（Epstein-Barr virus, EBV）可通过其染色质化游离基因（episome）与宿主基因组同步复制，建立终身无症状感染。EBV存在多种与潜伏感染相关的转录谱，每种转录谱对应独特的三维空间结构。CCCTC结合因子（CTCF）、黏连蛋白复合体（Cohesin）与多聚ADP核糖聚合酶1（PARP1）参与维持病毒潜伏状态并塑造游离基因的三维架构。全球范围内，EB病毒相关胃癌（Epstein-Barr virus-associated gastric cancer, EBVaGC）占所有胃癌病例的1.3%至30.9%。EB病毒阳性胃癌呈现一种被称为"II型潜伏（Latency II）"的中间型病毒转录谱，表达特定病毒基因与非编码RNA。本研究探讨了PARP1抑制对II型潜伏状态下CTCF/Cohesin结合的影响。研究团队观察到这两种因子的结合稳定性下降，导致游离基因的三维结构被破坏，同时病毒基因表达谱发生改变。尽管I型、II型与III型潜伏状态拥有相同的CTCF结合谱，但三者呈现不同的三维结构，且这些结构与病毒基因表达的差异密切相关。此外，针对富集H3K27ac（组蛋白H3赖氨酸27乙酰化）的染色质相互作用的分析显示，II型潜伏状态的游离基因存在特征差异，且EB病毒基因组通过锚定至人类基因组特定位点，与细胞转化存在关联，进而促进癌基因的表达。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EBV诱导细胞转化的全新机制。实验整体设计：针对组蛋白H3K4me1与H3K27ac的染色质免疫沉淀DNA测序。