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Yeast Barcoders: a chemogenomic application of a universal donor-strain collection carrying bar-code identifiers

Nature Methods volume 5, pages 719–725 (2008)Cite this article

Abstract

The ability to perform complex bioassays in parallel enables experiments that are otherwise impossible because of throughput and cost constraints. For example, highly parallel chemical-genetic screens using pooled collections of thousands of defined Saccharomyces cerevisiae gene deletion strains are feasible because each strain is bar-coded with unique DNA sequences. It is, however, time-consuming and expensive to individually bar-code individual strains. To provide a simple and general method of barcoding yeast collections, we built a set of donor strains, called Barcoders, with unique bar codes that can be systematically transferred to any S. cerevisiae collection. We applied this technology by generating a collection of bar-coded 'decreased abundance by mRNA perturbation' (DAmP) loss-of-function strains comprising 87.1% of all essential yeast genes. These experiments validate both the Barcoders and the DAmP strain collection as useful tools for genome-wide chemical-genetic assays.

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Figure 1: Strategy used to bar-code DAmP strains.
Figure 2: Growth rate of DAmP strains.
Figure 3: Drug sensitivity assay.
Figure 4: Genome-wide profiles of strain sensitivity to selected compounds.

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References

  1. Hensel, M. et al. Simultaneous identification of bacterial virulence genes by negative selection. Science 269, 400–403 (1995).

    Article  CAS  Google Scholar 

  2. Giaever, G. et al. Functional profiling of the Saccharomyces cerevisiae genome. Nature 418, 387–391 (2002).

    Article  CAS  Google Scholar 

  3. Winzeler, E.A. et al. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285, 901–906 (1999).

    Article  CAS  Google Scholar 

  4. Jo, W.J. et al. Identification of genes involved in the toxic response of Saccharomyces cerevisiae against iron and copper overload by parallel analysis of deletion mutants. Toxicol. Sci. 101, 140–151 (2008).

    Article  CAS  Google Scholar 

  5. Brass, A.L. et al. Identification of host proteins required for HIV infection through a functional genomic screen. Science 319, 921–926 (2008).

    Article  CAS  Google Scholar 

  6. Moffat, J. et al. A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen. Cell 124, 1283–1298 (2006).

    Article  CAS  Google Scholar 

  7. Mazurkiewicz, P., Tang, C.M., Boone, C. & Holden, D.W. Signature-tagged mutagenesis: barcoding mutants for genome-wide screens. Nat. Rev. Genet. 7, 929–939 (2006).

    Article  CAS  Google Scholar 

  8. Giaever, G. et al. Chemogenomic profiling: identifying the functional interactions of small molecules in yeast. Proc. Natl. Acad. Sci. USA 101, 793–798 (2004).

    Article  CAS  Google Scholar 

  9. Giaever, G. et al. Genomic profiling of drug sensitivities via induced haploinsufficiency. Nat. Genet. 21, 278–283 (1999).

    Article  CAS  Google Scholar 

  10. Lum, P.Y. et al. Discovering modes of action for therapeutic compounds using a genome-wide screen of yeast heterozygotes. Cell 116, 121–137 (2004).

    Article  CAS  Google Scholar 

  11. Shoemaker, D.D., Lashkari, D.A., Morris, D., Mittmann, M. & Davis, R.W. Quantitative phenotypic analysis of yeast deletion mutants using a highly parallel molecular bar-coding strategy. Nat. Genet. 14, 450–456 (1996).

    Article  CAS  Google Scholar 

  12. Hillenmeyer, M.E. et al. The chemical genomic portrait of yeast: uncovering a phenotype for all genes. Science 320, 362–365 (2008).

    Article  CAS  Google Scholar 

  13. Schuldiner, M. et al. Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile. Cell 123, 507–519 (2005).

    Article  CAS  Google Scholar 

  14. Muhlrad, D. & Parker, R. Aberrant mRNAs with extended 3′ UTRs are substrates for rapid degradation by mRNA surveillance. RNA 5, 1299–1307 (1999).

    Article  CAS  Google Scholar 

  15. Tong, A.H. et al. Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science 294, 2364–2368 (2001).

    Article  CAS  Google Scholar 

  16. Baganz, F., Hayes, A., Marren, D., Gardner, D.C. & Oliver, S.G. Suitability of replacement markers for functional analysis studies in Saccharomyces cerevisiae. Yeast 13, 1563–1573 (1997).

    Article  CAS  Google Scholar 

  17. Pierce, S.E., Davis, R.W., Nislow, C. & Giaever, G. Genome-wide analysis of barcoded Saccharomyces cerevisiae gene-deletion mutants in pooled cultures. Nat. Protoc. 2, 2958–2974 (2007).

    Article  CAS  Google Scholar 

  18. Pierce, S.E. et al. A unique and universal molecular barcode array. Nat. Methods 3, 601–603 (2006).

    Article  CAS  Google Scholar 

  19. Dwight, S.S. et al. Saccharomyces genome database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res. 30, 69–72 (2002).

    Article  CAS  Google Scholar 

  20. Deutschbauer, A.M. et al. Mechanisms of haploinsufficiency revealed by genome-wide profiling in yeast. Genetics 169, 1915–1925 (2005).

    Article  CAS  Google Scholar 

  21. St Onge, R.P. et al. Systematic pathway analysis using high-resolution fitness profiling of combinatorial gene deletions. Nat. Genet. 39, 199–206 (2007).

    Article  CAS  Google Scholar 

  22. Lee, W. et al. Genome-wide requirements for resistance to functionally distinct DNA-damaging agents. PLoS Genet. 1, e24 (2005).

    Article  Google Scholar 

  23. Gadsden, M.H., McIntosh, E.M., Game, J.C., Wilson, P.J. & Haynes, R.H. dUTP pyrophosphatase is an essential enzyme in Saccharomyces cerevisiae. EMBO J. 12, 4425–4431 (1993).

    Article  CAS  Google Scholar 

  24. Game, J.C. Yeast cell-cycle mutant cdc21 is a temperature-sensitive thymidylate auxotroph. Mol. Gen. Genet. 146, 313–315 (1976).

    Article  CAS  Google Scholar 

  25. Hardman, J.G., Limbird, L.E. & Gilman, A.G. (eds.) Goodman and Gilman's The Pharmacological Basis of Therapeutics 10th edn. (McGraw-Hill, New York, 2001).

    Google Scholar 

  26. Scherf, U. et al. A gene expression database for the molecular pharmacology of cancer. Nat. Genet. 24, 236–244 (2000).

    Article  CAS  Google Scholar 

  27. Ross-Macdonald, P. et al. Large-scale analysis of the yeast genome by transposon tagging and gene disruption. Nature 402, 413–418 (1999).

    Article  CAS  Google Scholar 

  28. Mnaimneh, S. et al. Exploration of essential gene functions via titrable promoter alleles. Cell 118, 31–44 (2004).

    Article  CAS  Google Scholar 

  29. Sopko, R. et al. Mapping pathways and phenotypes by systematic gene overexpression. Mol. Cell 21, 319–330 (2006).

    Article  CAS  Google Scholar 

  30. Uetz, P. et al. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403, 623–627 (2000).

    Article  CAS  Google Scholar 

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Acknowledgements

We thank J. Horecka, N. Berbenetz and M. Urbanus for comments on the manuscript. This work is supported by grants from the US National Institute of Health and Canadian Institutes of Health Research to G.G. (MOP-81340) and to C.N. (MOP-84305), and from Genome Canada (to C.B. and B.J.A.).

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Authors and Affiliations

  1. Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, M5S 3E1, Ontario, Canada

    Zhun Yan, Michael Costanzo, Lawrence E Heisler, Brenda J Andrews, Charles Boone, Guri Giaever & Corey Nislow

  2. Department of Pharmaceutical Sciences, University of Toronto, 144 College Street, Toronto, M5S 3M2, Ontario, Canada

    Zhun Yan & Guri Giaever

  3. Department of Molecular Genetics, University of Toronto, King's College Circle, M5S 1A8, Ontario, Canada

    Michael Costanzo, Lawrence E Heisler, Brenda J Andrews, Charles Boone, Guri Giaever & Corey Nislow

  4. Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, M5G 1L6, Ontario, Canada

    Michael Costanzo, Brenda J Andrews, Charles Boone & Corey Nislow

  5. University of Calgary, School of Medicine, 2500 University Dr. NW, Calgary, T2N 1N4, Alberta, Canada

    Jadine Paw

  6. Prognosys Biosciences, Inc., 505 Coast Blvd. S., Ste. 302, San Diego, 92037, California, USA

    Fiona Kaper

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  1. Zhun Yan
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Contributions

Z.Y. performed all bar-coding experiments and analysis and wrote this paper. M.C., B.J.A., J.P. and C.B. designed and created the original DAmP collection. L.E.H. did the data analysis. F.K. sequenced all bar codes. G.G. and C.N. designed the study, analyzed the data and wrote the paper.

Corresponding author

Correspondence to Corey Nislow.

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Competing interests

F.K. is employed by Prognosys Biosciences, Inc.

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Supplementary Figure 1, Supplementary Tables 1–5, Supplementary Methods (PDF 530 kb)

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Yan, Z., Costanzo, M., Heisler, L. et al. Yeast Barcoders: a chemogenomic application of a universal donor-strain collection carrying bar-code identifiers. Nat Methods 5, 719–725 (2008). https://doi.org/10.1038/nmeth.1231

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