The newest area of work in the lab utilizes the technique of ribosome profiling developed by Nick Ingolia and Jonathan Weissman. This technique involves chemical halting of translating ribosomes and degradation of all of the organism's mRNA, excepting the regions protected by the ribosome's "footprint." These protected fragments are sequenced through high-throughput methods and aligned to the genome to provide a global snapshot of the relative likelihood of a translating ribosomes being found on any given mRNA with nucleotide resolution.
This technique has been used to profile a variety of yeast knockout strains for proteins implicated in mRNA quality control and ribosome recycling. This technique is also being extended to investigate the role of many other factors of interest to the lab, to provide a global view of their effects on translation. We are also beginning to employ reporter constructs in conjunction with ribosome profiling to obtain additional information about the mechanisms of these factors.