Nguyen Amy, Li Tianqi, Traugot Conner, Paulsen Kimberly, Nelson Tiffany S, Xie Mingyi, Ma Zhe
Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, Florida, USA.
Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida, USA.
J Virol. 2025 Aug 13:e0026625. doi: 10.1128/jvi.00266-25.
The integrator complex (INT) is an essential regulator of RNA biogenesis across evolution. Most current findings describe INT's function in states of equilibrium, presenting a research gap in INT's role in dynamic states, such as in infections and cancers. Viruses hijack cellular RNA machinery to transcribe their genes and produce viral progeny, presenting a unique condition to investigate INT-dependent RNA regulation under perturbation. Kaposi's sarcoma-associated herpesvirus (KSHV) is an oncogenic DNA virus that causes two deadly cancers, Kaposi's sarcoma and primary effusion lymphoma. KSHV undergoes a highly regulated and robust transcription of viral genes upon lytic reactivation, providing a complex and dynamic system to investigate integrator-mediated viral/host RNA regulation. We find that integrator subunit 11 (INTS11), the enzymatic core of INT, is essential for KSHV lytic replication triggered by reactivation or primary infection. Further RNA-seq analyses revealed a dynamic and unique signature of human transcriptomes during each lytic stage, respectively. Although the knockdown of INTS11 resulted in selective upregulation and downregulation of certain human gene transcription, INTS11's loss globally repressed the KSHV transcriptome throughout KSHV lytic replication. This inhibited viral lytic gene expression, viral genome replication, and virion production. Integrator subunits 9 and 6 are also important for KSHV lytic replication. Mechanistically, ChIP-seq analysis showed that INTS11 is increasingly recruited to the KSHV genome with some unique binding patterns as the lytic cycle progresses, suggesting that KSHV hijacks INTS11 during lytic gene transcriptions. In all, our findings reveal the essential roles of the Integrator complex in KSHV lytic replication.IMPORTANCEThe integrator complex (INT) is essential for RNA metabolism and is fundamental to all organisms, but its function and regulation during viral infection are not well described. Kaposi's sarcoma-associated herpesvirus (KSHV) infection establishes lifelong infection and causes two deadly cancers; however, no vaccine is available. Using KSHV as a model, we found that integrator subunit 11 (INTS11), the enzymatic core of INT, is recruited to the KSHV genome under lytic phases and plays an essential role in facilitating global KSHV lytic mRNA transcription and viral production. This reveals the critical role of INT in viral infection, a common and inevitable event in human life.
整合酶复合体（INT）是进化过程中RNA生物合成的关键调节因子。目前大多数研究结果描述的是INT在平衡状态下的功能，在INT在动态状态（如感染和癌症）中的作用方面存在研究空白。病毒劫持细胞RNA机制来转录其基因并产生病毒后代，这为研究INT依赖性RNA在干扰下的调控提供了独特条件。卡波西肉瘤相关疱疹病毒（KSHV）是一种致癌DNA病毒，可导致两种致命癌症，即卡波西肉瘤和原发性渗出性淋巴瘤。KSHV在裂解再激活时会经历高度调控且强劲的病毒基因转录，为研究整合酶介导的病毒/宿主RNA调控提供了一个复杂而动态的系统。我们发现，整合酶亚基11（INTS11）作为INT的酶核心，对于由再激活或初次感染引发的KSHV裂解复制至关重要。进一步的RNA测序分析分别揭示了每个裂解阶段人类转录组的动态且独特的特征。虽然INTS11的敲低导致某些人类基因转录的选择性上调和下调，但INTS11的缺失在KSHV裂解复制过程中整体上抑制了KSHV转录组。这抑制了病毒裂解基因表达、病毒基因组复制和病毒粒子产生。整合酶亚基9和6对KSHV裂解复制也很重要。从机制上讲，染色质免疫沉淀测序分析表明，随着裂解周期的进展，INTS11以一些独特的结合模式越来越多地被招募到KSHV基因组中，这表明KSHV在裂解基因转录过程中劫持了INTS11。总之，我们的发现揭示了整合酶复合体在KSHV裂解复制中的重要作用。
整合酶复合体（INT）对RNA代谢至关重要，是所有生物体的基础，但它在病毒感染期间的功能和调控尚未得到充分描述。卡波西肉瘤相关疱疹病毒（KSHV）感染会建立终身感染并导致两种致命癌症；然而，目前尚无可用疫苗。以KSHV为模型，我们发现整合酶亚基11（INTS11）作为INT的酶核心，在裂解阶段被招募到KSHV基因组中，在促进KSHV整体裂解性mRNA转录和病毒产生方面发挥着重要作用。这揭示了INT在病毒感染中的关键作用，而病毒感染是人类生活中常见且不可避免的事件。
