Deep sequencing of ribosomal footprints for studying genome-wide mRNA translation in plants

Ribosome footprinting measures mRNA translation via deep sequencing of ribosome-protected mRNA fragments (footprints). Ribosome footprinting has been successfully applied to various model systems, including yeast, human, mouse, and worm; and it has been demonstrated that the technology is capable to produce global translation measurements with up to a single-codon resolution. Here we present our first experiences with a footprinting experiment that probes ethylene-induced translational changes in the reference plant Arabidopsis thaliana. The goal of our project is to develop genomic tools for the qualitative and quantitative characterization of the plant translatome. We hope ribosome footprinting will allow researchers to correlate precisely mRNA features with translation efficiency, and open the way to investigate globally the mechanism of protein synthesis and its regulation at an unprecedented level of detail.