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Article
Nature Methods - 5, 711 - 718 (2008)
Published online: 11 July 2008; | doi:10.1038/nmeth.1234

A comprehensive strategy enabling high-resolution functional analysis of the yeast genome

David K Breslow1, 2, 3, 4, 6, Dale M Cameron1, 2, 3, 6, Sean R Collins1, 2, 3, Maya Schuldiner1, 2, 3, Jacob Stewart-Ornstein1, 2, 3, Heather W Newman5, Sigurd Braun2, 5, Hiten D Madhani2, 5, Nevan J Krogan1, 2 & Jonathan S Weissman1, 2, 3

1  Department of Cellular and Molecular Pharmacology, University of California, San Francisco, 1700 4th Street, San Francisco, California 94158, USA.

2  The California Institute for Quantitative Biomedical Research, University of California, San Francisco, 1700 4th Street, San Francisco, California 94158, USA.

3  Howard Hughes Medical Institute, University of California, San Francisco, 1700 4th Street, San Francisco, California 94158, USA.

4  Graduate Program in Chemistry and Chemical Biology, University of California, San Francisco, 1700 4th Street, San Francisco, California 94158, USA.

5  Department of Biochemistry and Biophysics, University of California, San Francisco, 1700 4th Street, San Francisco, California 94158, USA.

6  These authors contributed equally to this work.

Correspondence should be addressed to Jonathan S Weissman weissman@cmp.ucsf.edu

Functional genomic studies in Saccharomyces cerevisiae have contributed enormously to our understanding of cellular processes. Their full potential, however, has been hampered by the limited availability of reagents to systematically study essential genes and the inability to quantify the small effects of most gene deletions on growth. Here we describe the construction of a library of hypomorphic alleles of essential genes and a high-throughput growth competition assay to measure fitness with unprecedented sensitivity. These tools dramatically increase the breadth and precision with which quantitative genetic analysis can be performed in yeast. We illustrate the value of these approaches by using genetic interactions to reveal new relationships between chromatin-modifying factors and to create a functional map of the proteasome. Finally, by measuring the fitness of strains in the yeast deletion library, we addressed an enigma regarding the apparent prevalence of gene dispensability and found that most genes do contribute to growth.

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Nature Methods
ISSN: 1548-7091
EISSN: 1548-7105
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