Department of Biochemistry and Molecular Biology, University of Iowa, Iowa City, IA 52242, USA.
Departments of Internal Medicine and Epidemiology, University of Iowa and Iowa City Veterans Affairs Health Care System, Iowa City, IA 52242, USA.
Viruses. 2022 Apr 9;14(4):779. doi: 10.3390/v14040779.
How human cytomegalovirus (HCMV) infection impacts the transcription of the host genome remains incompletely understood. Here, we examine the global consequences of infection of primary human foreskin fibroblasts (HFFs) on transcription by RNA polymerase I, II, and III over the course of a lytic infection using PRO-Seq. The expected rapid induction of innate immune response genes is observed with specific subsets of genes exhibiting dissimilar expression kinetics. We find minimal effects on Pol II initiation, but increased rates of the release of paused Pol II into productive elongation are detected by 24 h postinfection and pronounced at late times postinfection. Pol I transcription increases during infection and we provide evidence for a potential Pol I elongation control mechanism. Pol III transcription of tRNA genes is dramatically altered, with many induced and some repressed. All effects are partially dependent on viral genome replication, suggesting a link to viral mRNA levels and/or a viral early-late or late gene product. Changes in tRNA transcription are connected to distinct alterations in the chromatin state around tRNA genes, which were probed with high-resolution DFF-ChIP. Additionally, evidence is provided that the Pol III PIC stably contacts an upstream -1 nucleosome. Finally, we compared and contrasted our HCMV data with results from published experiments with HSV-1, EBV, KSHV, and MHV68. We report disparate effects on Pol II transcription and potentially similar effects on Pol III transcription.
人巨细胞病毒（HCMV）感染如何影响宿主基因组的转录仍不完全清楚。在这里，我们使用 PRO-Seq 研究了在裂解感染过程中，人原代包皮成纤维细胞（HFF）感染对 RNA 聚合酶 I、II 和 III 转录的全局影响。可以观察到预期的先天免疫反应基因的快速诱导，而特定亚类的基因表现出不同的表达动力学。我们发现对 Pol II 起始的影响最小，但在感染后 24 小时检测到被暂停的 Pol II 释放到活跃延伸的速度增加，并在感染后期明显增加。Pol I 转录在感染过程中增加，我们提供了潜在的 Pol I 延伸控制机制的证据。tRNA 基因的 Pol III 转录发生显著改变，许多基因被诱导，一些基因被抑制。所有影响部分依赖于病毒基因组复制，这表明与病毒 mRNA 水平和/或病毒早期-晚期或晚期基因产物有关。tRNA 转录的变化与 tRNA 基因周围染色质状态的明显改变有关，这一点通过高分辨率 DFF-ChIP 进行了探测。此外，还提供了证据表明 Pol III PIC 可稳定接触到 -1 核小体。最后，我们将 HCMV 的数据与已发表的 HSV-1、EBV、KSHV 和 MHV68 实验的结果进行了比较和对比。我们报告了对 Pol II 转录的不同影响，以及对 Pol III 转录的潜在相似影响。
