Systems biology analysis of herpes simplex virus 1 induced host shut-off

单纯疱疹病毒1诱导宿主关闭的系统生物学分析

• 批准号: 272269602
• 负责人: Professor Dr. Lars Dölken
• 金额: --
• 依托单位: Institut für Virologie und Immunbiologie
• 依托单位国家: 德国
• 项目类别: Research Grants
• 财政年份: 2015
• 资助国家: 德国
• 起止时间: 2014-12-31 至 2018-12-31
• 项目状态: 已结题
• 来源: https://gepris.dfg.de/gepris/projekt/272269602?language=en
• 关键词: Systems; biology; analysis; herpes; simplex

Herpes simplex virus 1 (HSV-1) is the causative agent of the common cold sores but also responsible for severe, life-threatening diseases including encephalitis, pneumonia, hepatitis and generalised skin infections. HSV-1 is a paradigm for virus-induced host shut-off exerted at RNA level. This is thought to be mediated by two viral proteins, namely the virus host shut-off protein (vhs) and ICP27. We employed two cutting-edge methodologies, i.e. 4sU-tagging of newly transcribed RNA and ribosome profiling, to study global changes in transcription and RNA processing as well as their impact on translation throughout the full course of infection. Unexpectedly, we found HSV-1 infection to trigger widespread disruption of transcription termination of cellular but not viral genes. This results in extensive transcription activity bypassing poly(A) sites, commonly extending for tens-of-thousands of nucleotides and into downstream genes. Read-in transcription explained the surprising observation that hundreds of cellular genes were transcriptionally induced but not translated. In contrast to previous reports, we found that HSV-1 does not install a general inhibition of splicing but rather only inhibits post-transcriptional but not co-transcriptional splicing. A manuscript on these fascinating findings is currently in revision with Nature. Work is ongoing to identify the responsible viral gene product. We now seek to study the role of vhs, ICP27 and disruption of transcription termination in HSV-1 induced host-shut-off. This will include the following three work packages:i) We will study co- and post-transcriptional RNA processing and nuclear export by analysing subcellular RNA fractions (total cytoplasmic, nuclear and chromatin-associated RNA).ii) We will detail the role of chromatin status, individual nucleosomes, alterations in DNA-binding proteins and the massive transcription of intergenic regions resulting from disrupted transcription termination in the modulation of cellular and viral gene expression using ATAC-seq (Assay for Transposase-Accessible Chromatin using Sequencing).iii) We will define the interaction of the two key viral proteins mediating HSV-1 host shut-off, namely ICP27 and vhs, with both cellular and viral RNAs at nucleotide resolution using PAR-CLIP (Photo-Activated Ribonucleotide-enhanced Cross-Linking ImmunoPrecipitation). Results obtained from this work will detail a fascinating new host-shut-off mechanism employed by an important human pathogen and establish HSV-1 as an interesting new model to study the molecular mechanisms coupling RNA synthesis, processing, export and translation in mammalian cells.

单纯疱疹病毒 1 (HSV-1) 是普通唇疱疹的病原体，但也会导致严重的危及生命的疾病，包括脑炎、肺炎、肝炎和全身皮肤感染。 HSV-1 是在 RNA 水平上实现病毒诱导宿主关闭的范例。这被认为是由两种病毒蛋白介导的，即病毒宿主关闭蛋白 (vhs) 和 ICP27。我们采用两种尖端方法，即新转录 RNA 的 4sU 标记和核糖体分析，来研究转录和 RNA 加工的整体变化及其在整个感染过程中对翻译的影响。出乎意料的是，我们发现 HSV-1 感染会引发细胞而非病毒基因转录终止的广泛破坏。这导致绕过聚腺苷酸位点的广泛转录活性，通常延伸数万个核苷酸并进入下游基因。读入转录解释了令人惊讶的观察结果：数百个细胞基因被转录诱导但不被翻译。与之前的报道相反，我们发现HSV-1并没有普遍抑制剪接，而是仅抑制转录后剪接，而不抑制共转录剪接。关于这些令人着迷的发现的手稿目前正在与《自然》杂志一起修订。鉴定相关病毒基因产物的工作正在进行中。我们现在寻求研究 vhs、ICP27 和转录终止破坏在 HSV-1 诱导的宿主关闭中的作用。这将包括以下三个工作包：i) 我们将通过分析亚细胞 RNA 组分（总细胞质、核和染色质相关 RNA）来研究共转录和转录后 RNA 加工和核输出。ii) 我们将详细介绍染色质状态、单个核小体、DNA 结合蛋白的改变以及因断裂而导致的基因间区域的大量转录的作用 使用 ATAC-seq（使用测序分析转座酶可及的染色质）调节细胞和病毒基因表达中的转录终止。iii) 我们将使用 PAR-CLIP（光激活）在核苷酸分辨率下定义介导 HSV-1 宿主关闭的两种关键病毒蛋白（即 ICP27 和 vhs）与细胞和病毒 RNA 的相互作用 核糖核苷酸增强交联免疫沉淀）。这项工作获得的结果将详细介绍一种重要的人类病原体所采用的一种令人着迷的新宿主关闭机制，并将 HSV-1 建立为一个有趣的新模型，用于研究哺乳动物细胞中 RNA 合成、加工、输出和翻译耦合的分子机制。

项目成果

Integrative functional genomics decodes herpes simplex virus 1

综合功能基因组学解码单纯疱疹病毒 1

• DOI: 10.1038/s41467-020-15992-5
• 发表时间: 2020
• 期刊: Nature Communications
• 影响因子: 16.6
• 作者: Whisnant;Adam W;Jürges;Christopher S;Hennig;Thomas;Emanuel;Prusty;Bhupesh;Rutkowski;Andrzej J;L'hernault;Djakovic;Göbel;Margarete;Döring;Kristina;Menegatti;Jennifer;Antrobus;Matheson;Nicholas J;Künzig
• 通讯作者: Künzig