Application of ribosomal profiling to investigate established and novel translational control phenomena in viruses (360G-Wellcome-096976_Z_11_Z)

Historically, studies of gene expression have measured mRNA abundances rather than rates of protein synthesis. RNA expression profiling techniques, including microarray analysis, have revolutionized our ability to monitor the internal state of cells; however, mRNA and protein levels are often imperfectly correlated, and translational control can have a crucial role in modulating gene expression. In 2009, Ingolia and colleagues described ribosomeprofiling, a technique that provides global analysis of ribosomal footprints on mRNAs, providing new insights into translational control. Together with thelatest advances in deep-sequencing, ribosome profiling can provide a high resolution map of the location of translating and paused ribosomes on the transcriptome at any one time. Ribosomal profiling has since been used to study a variety of translational processes through the definition of ribosomalpause sites, inevitably revealing novel coding sequences. However, profiling is yet to be applied to the study of the regulation of virus gene expression. We will use ribosome profiling to investigate (1) ribosomal pausing at sites