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Submitted on December 4, 2003
Biochemistry, University of Washington, Seattle, WA 98195
Corresponding Author: dmorris{at}u.washington.edu
The transcriptome provides the database from which a cell assembles its collection of proteins. Translation of individual mRNA species into their encoded proteins is regulated, producing discrepancies between mRNA and protein levels. Using a new modeling approach to data analysis, a striking diversity is revealed in association of the transcriptome with the translational machinery. Each mRNA has its own pattern of ribosome loading, a circumstance that provides an extraordinary dynamic range of regulation, above and beyond actual transcript levels. Using this approach together with quantitative proteomics, we explored the immediate changes in gene expression in response to activation of a MAP kinase pathway in yeast by mating pheromone. Interestingly, of the 3874 modeled transcripts, 199 of these had at least 2-fold changes in translation efficiency after incubation with -factor, whereas 617 showed at least 2-fold changes solely in transcript level. These observations underscore that analysis of transcript level, albeit extremely important, is insufficient by itself to describe completely the phenotypes of cells under different conditions.
Revised on January 31, 2004
Accepted on February 6, 2004
Gene expression in yeast responding to mating pheromone: Analysis by high-resolution translation state analysis and quantitative proteomics
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