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High-throughput genetic interaction mapping in the fission yeast Schizosaccharomyces pombe

Nature Methods volume 4, pages 861–866 (2007)Cite this article

Abstract

Epistasis analysis, which reports on the extent to which the function of one gene depends on the presence of a second, is a powerful tool for studying the functional organization of the cell. Systematic genome-wide studies of epistasis, however, have been limited, with the majority of data being collected in the budding yeast, Saccharomyces cerevisiae. Here we present two 'pombe epistasis mapper' strategies, PEM-1 and PEM-2, which allow for high-throughput double mutant generation in the fission yeast, S. pombe. These approaches take advantage of a previously undescribed, recessive, cycloheximide-resistance mutation. Both systems can be used for genome-wide screens or for the generation of high-density, quantitative epistatic miniarray profiles (E-MAPs). Since S. cerevisiae and S. pombe are evolutionary distant, this methodology will provide insight into conserved biological pathways that are present in S. pombe, but not S. cerevisiae, and will enable a comprehensive analysis of the conservation of genetic interaction networks.

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Figure 1: A flowchart representing a genetic cross leading to a homogenous population of haploid double mutants.
Figure 2: Two alternative strategies for systematic double mutant construction.
Figure 3: Validation of the PEM-1 and PEM-2 strategies.

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Acknowledgements

We thank A. Carr and O. Nielsen (pON177; University of Copenhagen) for providing reagents; S. Forsburg (FY1524 strain; University of Southern California) and K. Ekwall for reagents and discussion; C.J. Ingles, G. Cagney and D. Fiedler for critical reading of the manuscript and M. Shales for help with figures. J.S.W. is funded by the Howard Hughes Medical Institute, N.J.K. used funds from a Sandler Family Fellowship and A.R. was funded by a Howard Hughes Medical Institute postdoctoral fellowship. The work was also supported by funds from the California Institute of Quantitative Biology.

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Authors and Affiliations

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

    Assen Roguev, Marianna Wiren, Jonathan S Weissman & Nevan J Krogan

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

    Assen Roguev, Marianna Wiren, Jonathan S Weissman & Nevan J Krogan

  3. Department of Biosciences Novum, Department of Natural Sciences, Karolinska Institutet, University College Sodertorn, Huddinge, S-141 04, Sweden

    Marianna Wiren

  4. Howard Hughes Medical Institute, University of California, San Francisco, 94158, California, USA

    Jonathan S Weissman

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  1. Assen Roguev
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Correspondence to Nevan J Krogan.

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The authors plan on submitting a patent application for the genetic strategy described in this manuscript.

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Supplementary Figures 1–7, Supplementary Table 1, Supplementary Protocols 1–2 (PDF 235 kb)

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Roguev, A., Wiren, M., Weissman, J. et al. High-throughput genetic interaction mapping in the fission yeast Schizosaccharomyces pombe. Nat Methods 4, 861–866 (2007). https://doi.org/10.1038/nmeth1098

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