We study the translational control of gene expression in order to learn how cells change the translation of specific genes and better understand the role of this regulation in the cell. Our research makes extensive use of genome-scale approaches and deep sequencing.

The translation of mRNA into protein is a central step in gene expression. Recent studies suggest that translation affects protein levels as much as transcription. Translational control acts in diverse processes from cellular stress responses to synaptic plasticity. However, there are many gaps in our knowledge of translational regulation. We cannot predict the expression level of an mRNA from its sequence. We do not have a general framework for understanding how RNA-binding proteins affect translation.

The first step in studying translational control is simply measuring it more accurately. I developed a ribosome profiling technique that allows precise and quantitative analysis of genome-wide in vivo translation. Ribosome profiling measures expression at the level of translation, opening new windows on in vivo translation. It also reports on the exact position of translating ribosomes. This allows us to annotate the actual protein-coding sequences in complicated genomes and transcriptomes.

Ribosome profiling also revealed extensive translation upstream of many genes. This unexpected translation points to the regulated use of alternate sites of initiation, including substantial initiation at non-AUG codons. We believe that start codon selection is an underappreciated point of control in gene expression. The use of alternate sites of initiation can produce functionally distinct protein isoforms as well as affect the amount of protein synthesized. This poses several questions that we want to address. We want to understand how the potential start sites in an mRNA affect its translation. We want to know how changes in the proteins involed in initiation interact with these different sites. Finally, we want to know the impact of this phenomenon--when does the cell change start codon usage, and what are the effects?