Yeast Gene Ontology by Phenotypic Profiling

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DESCRIPTION (provided by applicant): Research over the past 20 years has demonstrated that in Baker's yeast, S. cerevisiae, the basic cellular processes, and the proteins that carry them out, have strong similarities to those in human cells. This provides an important means of identifying the function of human proteins by their homologies, interacting partners, or similarities of function with the gene products of S. cerevisiae as well as other model organisms. However, despite the fact that Baker's yeast was the first eukaryote to be fully sequenced some eight years ago, there are still some 30% of the genes of this model organism whose function is unknown. The goal of this proposal is to identify the function of a large number of these uncharacterized genes by performing a genome-wide screen of the sensitivities to 250 carefully chosen treatments of strains with individual deletion of all non-essential genes, coupled with sophisticated analyses of the phenotypic profiles. Our phenotypic profiling technique involves hybridization of the PCR-amplified 20-nucleotide "barcodes" that identify each deletion strain, to high-density oligonucleotide arrays. The resulting phenotypic profile to any treatment is a continuum of sensitivity that allows more accurate comparative analyses of phenotypic profiles to the treatments than the common procedure of "binning" phenotypes into sensitive, normal, and resistant. We have demonstrated with some 50 different treatments that hierarchical clustering of the phenotypic profiles is a powerful method of clustering the genes by similarity of functional pathways . We propose to create for the biological community a resource that will allow individual investigators to interrogate our data for hypotheses as to the function of specific genes and, in addition, allow members of the community to suggest new treatments to aid in assigning function to individual genes. In addition to providing the phenotypic profiling data and analyses to the community, we will focus on new genes identified in DMA repair and chromatin remodeling and assess the extent to which these genes are involved in maintaining genome stability.