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Systematic pathway analysis using high-resolution fitness profiling of combinatorial gene deletions

Nature Genetics volume 39, pages 199206 (2007) | Download Citation

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Abstract

Systematic genetic interaction studies have illuminated many cellular processes. Here we quantitatively examine genetic interactions among 26 Saccharomyces cerevisiae genes conferring resistance to the DNA-damaging agent methyl methanesulfonate (MMS), as determined by chemogenomic fitness profiling of pooled deletion strains. We constructed 650 double-deletion strains, corresponding to all pairings of these 26 deletions. The fitness of single- and double-deletion strains were measured in the presence and absence of MMS. Genetic interactions were defined by combining principles from both statistical and classical genetics. The resulting network predicts that the Mph1 helicase has a role in resolving homologous recombination–derived DNA intermediates that is similar to (but distinct from) that of the Sgs1 helicase. Our results emphasize the utility of small molecules and multifactorial deletion mutants in uncovering functional relationships and pathway order.

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Acknowledgements

We thank M. Evangelista and S. Pierce for critically reading the manuscript; and B. Andrews, C. Boone, J. Greenblatt, N. Krogan and J. Weissman for discussions. R.P.S. was supported by a postdoctoral fellowship from the Canadian Institutes of Health Research. F.P.R. was supported by grant R01 HG003224 from the National Institutes of Health National Human Genome Research Institute (NIH/NHGRI). This work was supported by a grant from the NHGRI awarded to R.W.D. and G.G.

Author information

Affiliations

  1. Department of Biochemistry, Stanford University, Stanford, California 94305, USA.

    • Robert P St Onge
    • , Julia Oh
    • , Michael Proctor
    • , Eula Fung
    •  & Ronald W Davis
  2. Biological Chemistry and Molecular Pharmacology Department, Harvard, Boston, Massachusetts 02115, USA.

    • Ramamurthy Mani
    •  & Frederick P Roth
  3. Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S3E1, Canada.

    • Corey Nislow
    •  & Guri Giaever
  4. Center for Cancer Systems Biology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, Massachusetts 02115, USA.

    • Frederick P Roth

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Contributions

R.P.St.O. was involved in every aspect of the study, from experimental design and performance to writing the manuscript. R.M. designed and executed algorithms and performed bioinformatic analysis. J.O. performed genetic experiments and growth curves. M.P. designed custom robotics and automation software. E.F. wrote software and performed database management. R.W.D. contributed intellectually throughout to experimental design and execution. C.N. helped design the experiments and write the manuscript. F.P.R. was involved in data analysis and manuscript preparation. G.G. was involved in every aspect of the study, including manuscript preparation.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Frederick P Roth or Guri Giaever.

Supplementary information

PDF files

  1. 1.

    Supplementary Fig. 1

    96-well growth assay for individual yeast deletion strains.

  2. 2.

    Supplementary Fig. 2

    Prediction of functional links by 'scaled epsilon'.

  3. 3.

    Supplementary Fig. 3

    Deletions in genes encoding members of the Shu complex suppress the synthetic lethality of rad54Δhpr5Δ.

  4. 4.

    Supplementary Fig. 4

    Deletions in HR and SHU genes rescue the MMS sensitivity of the mph1Δmus81Δ double deletion strain.

  5. 5.

    Supplementary Fig. 5

    Deletions in HR and SHU genes suppress the synthetic lethality of sgs1Δmms4Δ and sgs1Δmus81Δ double deletion mutants.

  6. 6.

    Supplementary Fig. 6

    Data aggregation identifies additional genetic interactions involving the SHU complex.

Excel files

  1. 1.

    Supplementary Table 1

    Chemogenic profiling of the homozygous diploid deletion collection with MMS.

  2. 2.

    Supplementary Table 2

    Genetic interaction results for 323 unique gene pairs in the presence of MMS.

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DOI

https://doi.org/10.1038/ng1948

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