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

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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.