Dissecting HSV-1-induced host shut-off at RNA level-猫眼课题宝

DOI：

10.1101/2020.05.20.106039

发表时间：

2020-05

期刊：

bioRxiv

影响因子：

通讯作者：

中科院分区：

其他

文献类型：

作者：

C. Friedel;Adam W. Whisnant;Lara Djakovic;Andrzej J. Rutkowski;Marie-Sophie Friedl;M. Kluge;J. Williamson;Somesh Sai;R. Vidal;S. Sauer;Thomas Hennig;B. Prusty;P. Lehner;N. Matheson;Florian Erhard;L. Dölken

单纯疱疹病毒1型（HSV-1）在裂解感染期间安装了一个深刻的宿主关闭。病毒体宿主关闭（vhs）蛋白通过以抑制起始依赖性方式有效地切割宿主和病毒mRNA在该过程中起关键作用。此外，病毒DNA复制的开始伴随着宿主基因组转录活性的快速下降。这两种机制都对感染细胞的RNA表达谱产生巨大影响。为了剖析它们的相对贡献并阐明在裂解性HSV-1感染的前8小时内的基因特异性宿主转录应答，我们在此采用了野生型（WT）和Δvhs感染的原代人成纤维细胞中的总RNA、新转录的（4sU标记的）RNA和染色质相关RNA的RNA-seq。在病毒进入后，vhs活性以每小时约30%的细胞mRNA的消除速率迅速稳定，直到感染后8小时。同时，宿主转录活性下降至10- 20%。虽然这两种现象的综合影响占主导地位的感染诱导的总RNA的变化，广泛的基因特异性转录调控染色质相关的RNA中观察到。这在WT HSV-1和其Δvhs突变体之间令人惊讶地一致，并且至少部分由胚胎转录因子DUX 4介导。此外，WT和Δvhs感染都诱导了一小部分基因的强烈转录上调。这些基因中的大多数在感染前表达很差或根本不表达，但已经在其启动子处被H3 K4 me 3组蛋白标记引发。最有趣的是，染色质相关RNA的分析揭示了至少150个细胞基因的vhs-核酸酶活性依赖性转录下调，特别是编码整合素粘附体和细胞外基质组分的许多基因。这伴随着vhs依赖性的蛋白质水平在8 h p.i.降低。for many许多of these genes基因.总之，我们的研究提供了一个全面的图片的分子机制，在第一个8小时的裂解HSV-1感染的细胞RNA代谢。HSV-1病毒体宿主关闭（vhs）蛋白以抑制依赖性方式有效切割宿主和病毒mRNA。在这项研究中，我们的模型和量化的变化VHS活动以及病毒诱导的全球损失的主机在生产HSV-1感染的转录活性。一般来说，HSV-1诱导的总RNA水平的改变被发现主要是由这两个全球性的过程，而不是基因特异性调控。与此相反，染色质相关的RNA描绘基因特异性的转录变化。这揭示了WT和Δvhs感染中高度一致的转录变化，证实DUX 4是HSV-1感染中的关键转录调节因子，并描述了整合素粘附体和细胞外基质的vhs依赖性转录下调。后者解释了先前归因于vhs介导的mRNA降解的一些基因特异性效应，并导致了8 h p.i.对于许多各自的基因。

Herpes simplex virus 1 (HSV-1) installs a profound host shut-off during lytic infection. The virion host shut-off (vhs) protein plays a key role in this process by efficiently cleaving both host and viral mRNAs in a translation-initiation-dependent manner. Furthermore, the onset of viral DNA replication is accompanied by a rapid decline in transcriptional activity of the host genome. Both mechanisms have tremendous impact on the RNA expression profile of the infected cells. To dissect their relative contributions and elucidate gene-specific host transcriptional responses throughout the first 8h of lytic HSV-1 infection, we here employed RNA-seq of total, newly transcribed (4sU-labelled) and chromatin-associated RNA in wild-type (WT) and Δvhs infection of primary human fibroblasts. Following virus entry, vhs activity rapidly plateaued at an elimination rate of around 30% of cellular mRNAs per hour until 8h p.i. In parallel, host transcriptional activity dropped down to 10-20%. While the combined effects of both phenomena dominated infection-induced changes in total RNA, extensive gene-specific transcriptional regulation was observable in chromatin-associated RNA. This was surprisingly concordant between WT HSV-1 and its Δvhs mutant and at least in parts mediated by the embryonic transcription factor DUX4. Furthermore, both WT and Δvhs infection induced strong transcriptional up-regulation of a small subset of genes. Most of these were either poorly or not at all expressed prior to infection but already primed by H3K4me3 histone marks at their promoters. Most interestingly, analysis of chromatin-associated RNA revealed vhs-nuclease-activity-dependent transcriptional down-regulation of at least 150 cellular genes, in particular of many genes encoding integrin adhesome and extracellular matrix components. This was accompanied by a vhs-dependent reduction in protein levels by 8h p.i. for many of these genes. In summary, our study provides a comprehensive picture of the molecular mechanisms that govern cellular RNA metabolism during the first 8h of lytic HSV-1 infection. Author Summary The HSV-1 virion host shut-off (vhs) protein efficiently cleaves both host and viral mRNAs in a translation-dependent manner. In this study, we model and quantify changes in vhs activity as well as the virus-induced global loss of host transcriptional activity during productive HSV-1 infection. In general, HSV-1-induced alterations in total RNA levels were found to be predominantly shaped by these two global processes rather than gene-specific regulation. In contrast, chromatin-associated RNA depicted gene-specific transcriptional changes. This revealed highly concordant transcriptional changes in WT and Δvhs infection, confirmed DUX4 as a key transcriptional regulator in HSV-1 infection and depicted vhs-dependent, transcriptional down-regulation of the integrin adhesome and extracellular matrix. The latter explained some of the gene-specific effects previously attributed to vhs-mediated mRNA degradation and resulted in a concordant loss in protein levels by 8h p.i. for many of the respective genes.

Dissecting HSV-1-induced host shut-off at RNA level

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