Analysis of transcriptional and translational regulation during virus infection using RNA tagging and ribosomal profiling

使用 RNA 标签和核糖体分析分析病毒感染期间的转录和翻译调控

• 批准号: 263141430
• 负责人: Professorin Dr. Caroline Friedel
• 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: 2014
• 资助国家: 德国
• 起止时间: 2013-12-31 至 2019-12-31
• 项目状态: 已结题
• 来源: https://gepris.dfg.de/gepris/projekt/263141430?language=en
• 关键词: Analysis; transcriptional; translational; regulation; during

Two recent methodological advances using next-generation sequencing now allow studying real-time changes in transcriptional and translational regulation at nucleotide resolution: metabolic labeling of newly transcribed RNA (RNA tagging) and ribosome profiling. In collaboration with Dr. Lars Dölken at the University of Cambridge, who will perform the wet-lab experiments for the proposed project, we will use these two powerful techniques for modeling the temporal cascades of transcriptional and post-transcriptional regulation during the course of lytic herpesvirus infection. For this purpose, time course experiments of real-time regulatory activities in virus-infected cells will be obtained for two model herpesviruses, namely murine cytomegalovirus (MCMV) and herpes simplex virus 1 (HSV-1). The objective of this project will be the development of bioinformatics methods for analyzing these interesting data to obtain a model of transcriptional, translational and post-translational regulatory mechanisms and the complex interplay between these mechanisms during virus infection. The developed methods will integrate measurements of de novo transcription, mRNA abundances, translation and protein abundances obtained using RNA tagging, ribosome profiling and SILAC. In this way, we will investigate inhibition of transcription termination during the course of virus infection, characterize transcriptional and post-transcriptional regulation for individual genes, identify groups of co-regulated genes and characterize transcription factor- and miRNA-binding for these genes. This will also provide the first ever comprehensive transcriptome and proteome atlas of MCMV and HSV-1. Method development will be performed in close collaboration with experimentalists (Dr. Lars Dölken, Babraham Institute, Cambridge), who will also perform validation experiments for the hypotheses proposed by the bioinformatics methods.

新一代测序技术的两项最新进展允许在核苷酸分辨率上研究转录和翻译调控的实时变化：新转录RNA的代谢标记（RNA标记）和核糖体分析。在与剑桥大学Lars博士Dölken的合作中，我们将使用这两种强大的技术来模拟溶性疱疹病毒感染过程中转录和转录后调控的时间级联。Lars博士将为拟议的项目进行湿实验室实验。为此，我们将对小鼠巨细胞病毒（MCMV）和单纯疱疹病毒1型（HSV-1）两种模型疱疹病毒在病毒感染的细胞中进行实时调控活性的时程实验。该项目的目标是发展生物信息学方法来分析这些有趣的数据，以获得病毒感染过程中转录、翻译和翻译后调控机制的模型以及这些机制之间复杂的相互作用。开发的方法将整合使用RNA标记、核糖体分析和SILAC获得的从头转录、mRNA丰度、翻译和蛋白质丰度的测量。通过这种方式，我们将研究病毒感染过程中转录终止的抑制，表征单个基因的转录和转录后调控，鉴定共调控基因组，并表征这些基因的转录因子和mirna结合。这也将提供MCMV和HSV-1的第一个全面的转录组和蛋白质组图谱。方法开发将与实验人员（Lars博士Dölken， Babraham研究所，剑桥）密切合作，他们也将对生物信息学方法提出的假设进行验证实验。

项目成果

Watchdog 2.0: New developments for reusability, reproducibility, and workflow execution

• DOI: 10.1093/gigascience/giaa068
• 发表时间: 2020-06-01
• 期刊: GIGASCIENCE
• 影响因子: 9.2
• 作者: Kluge, Michael;Friedl, Marie-Sophie;Friedel, Caroline C.
• 通讯作者: Friedel, Caroline C.

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

• DOI: 10.1101/2020.05.20.106039
• 发表时间: 2020-05
• 期刊: bioRxiv
• 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