Functional profiling of the Saccharomyces cerevisiae genome

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Abstract

Determining the effect of gene deletion is a fundamental approach to understanding gene function. Conventional genetic screens exhibit biases, and genes contributing to a phenotype are often missed. We systematically constructed a nearly complete collection of gene-deletion mutants (96% of annotated open reading frames, or ORFs) of the yeast Saccharomyces cerevisiae. DNA sequences dubbed ‘molecular bar codes’ uniquely identify each strain, enabling their growth to be analysed in parallel and the fitness contribution of each gene to be quantitatively assessed by hybridization to high-density oligonucleotide arrays. We show that previously known and new genes are necessary for optimal growth under six well-studied conditions: high salt, sorbitol, galactose, pH 8, minimal medium and nystatin treatment. Less than 7% of genes that exhibit a significant increase in messenger RNA expression are also required for optimal growth in four of the tested conditions. Our results validate the yeast gene-deletion collection as a valuable resource for functional genomics.

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Figure 1: The KanMX deletion cassette module.
Figure 2: Growth of deletion strains exhibiting reduced fitness in galactose medium.
Figure 3: Clustering of genes required for growth in conditions of high osmolarity.
Figure 4: Comparison of expression and fitness profiling data.
Figure 5: The seven phenotypic categories of deletion mutant morphologies.

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Acknowledgements

We thank I. Bastiaens, J. Howard Dees, R. Diaz, F. Dietrich, K. Freidel, N. Liebundguth, C. Rebischong, R. Schiavon, J. Schneider, T. Verhoeven and R. Wysoki for technical assistance. G.G. thanks C. Nislow for critical readings of the manuscript. This work was primarily supported by grants from the European Commission and the National Human Genome Research Institute (USA), the Medical Research Council of Canada, and the Swiss Office for Science.

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Correspondence to Ronald W. Davis.

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