Department of Dermatology, School of Medicine, University of California Davis (UC Davis), Sacramento, California, USA.
Lifescience Division, Lifematics, Osaka, Japan.
J Virol. 2022 Jul 27;96(14):e0056522. doi: 10.1128/jvi.00565-22. Epub 2022 Jul 11.
Eukaryotic genomes are structurally organized via the formation of multiple loops that create gene expression regulatory units called topologically associating domains (TADs). Here we revealed the KSHV TAD structure at 500 bp resolution and constructed a 3D KSHV genomic structural model with 2 kb binning. The latent KSHV genome formed very similar genomic architectures in three different naturally infected PEL cell lines and in an experimentally infected epithelial cell line. The majority of the TAD boundaries were occupied by structural maintenance of chromosomes (SMC1) cohesin complex and CCCTC-binding factor (CTCF), and the KSHV transactivator was recruited to those sites during reactivation. Triggering KSHV gene expression decreased prewired genomic loops within the regulatory unit, while contacts extending outside of regulatory borders increased, leading to formation of a larger regulatory unit with a shift from repressive to active compartments (B to A). The 3D genomic structural model proposes that the immediate early promoter region is localized on the periphery of the 3D viral genome during latency, while highly inducible noncoding RNA regions moved toward the inner space of the structure, resembling the configuration of a "bird cage" during reactivation. The compartment-like properties of viral episomal chromatin structure and its reorganization during the transition from latency may help facilitate viral gene transcription. The 3D architecture of chromatin allows for efficient arrangement, expression, and replication of genetic material. The genomes of all organisms studied to date have been found to be organized through some form of tiered domain structures. However, the architectural framework of the genomes of large double-stranded DNA viruses such as the herpesvirus family has not been reported. Prior studies with Kaposi's sarcoma-associated herpesvirus (KSHV) have indicated that the viral chromatin shares many biological properties exhibited by the host cell genome, essentially behaving as a mini human chromosome. Thus, we hypothesized that the KSHV genome may be organized in a similar manner. In this report, we describe the domain structure of the latent and lytic KSHV genome at 500 bp resolution and present a 3D genomic structural model for KSHV under each condition. These results add new insights into the complex regulation of the viral life cycle.
真核生物基因组通过形成多个环来进行结构组织，这些环创建了称为拓扑关联域（TAD）的基因表达调控单元。在这里，我们以 500bp 的分辨率揭示了 KSHV 的 TAD 结构，并构建了具有 2kb -bin 的 3D KSHV 基因组结构模型。潜伏的 KSHV 基因组在三种不同的天然感染的 PEL 细胞系和一种实验感染的上皮细胞系中形成了非常相似的基因组结构。大多数 TAD 边界被染色体结构维持（SMC1）黏合复合物和 CCCTC 结合因子（CTCF）占据，并且在再激活过程中，KSHV 反式激活因子被募集到这些位点。触发 KSHV 基因表达降低了调节单元内预先布线的基因组环，而延伸到调节边界之外的接触增加，导致形成更大的调节单元，从抑制区到活跃区（B 到 A）转变。3D 基因组结构模型表明，在潜伏期间，立即早期启动子区域定位于 3D 病毒基因组的外围，而高度诱导的非编码 RNA 区域向结构的内部空间移动，类似于再激活期间的“鸟笼”配置。病毒游离染色质结构的隔室样特性及其在潜伏到再激活过渡过程中的重新组织可能有助于促进病毒基因转录。染色质的 3D 结构允许对遗传物质进行有效的排列、表达和复制。迄今为止研究的所有生物体的基因组都被发现通过某种形式的分层结构域进行组织。然而，尚未报道疱疹病毒家族等双链 DNA 病毒基因组的架构框架。先前对卡波西肉瘤相关疱疹病毒（KSHV）的研究表明，病毒染色质具有宿主细胞基因组表现出的许多生物学特性，本质上表现为小型人类染色体。因此，我们假设 KSHV 基因组可能以类似的方式进行组织。在本报告中，我们以 500bp 的分辨率描述了潜伏和裂解 KSHV 基因组的结构域结构，并在每种条件下呈现了 KSHV 的 3D 基因组结构模型。这些结果为病毒生命周期的复杂调控增添了新的见解。
