Decoding viral infection by ribosome profiling

Abstract

Ribosome profiling is an emerging technique that uses deep sequencing to monitor translation in live cells. Studies using ribosome profiling have already provided novel insights into the identities and amounts of the proteins being produced in cells, as well as novel insights into the mechanism of protein synthesis and translation regulation. Application of ribosome profiling to cells infected with human cytomegalovirus and Kaposi's sarcoma-associated herpesvirus revealed unanticipated complexity in the coding capacity of herpesviruses. Here, I discuss these results and how the application of ribosome profiling to cells infected with other viruses can reveal novel insights into the process of infection.

FIG 1

Ribosome profiling allows the identification of translated elements. Cells infected with a given virus are treated with cycloheximide and then lysed. After nuclease digestion, ribosome footprints are isolated and converted to deep-sequencing libraries. Reads are then mapped to the viral genome and allow mapping of translated ORFs in an unbiased quantitative manner.

FIG 2

Parallel RNA-seq and ribosome-profiling measurements provide a platform to calculate translation efficiency of expressed genes. By dividing the number of footprints by the number of mRNA reads at every time point during infection, one can accurately calculate the translation efficiency of every expressed gene.