Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

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


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.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

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.

Similar content being viewed by others


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

    Article  CAS  Google Scholar 

  2. Tong, A.H. et al. Global mapping of the yeast genetic interaction network. Science 303, 808–813 (2004).

    Article  CAS  Google Scholar 

  3. Pan, X. et al. A DNA integrity network in the yeast Saccharomyces cerevisiae. Cell 124, 1069–1081 (2006).

    Article  CAS  Google Scholar 

  4. Pan, X. et al. A robust toolkit for functional profiling of the yeast genome. Mol. Cell 16, 487–496 (2004).

    Article  CAS  Google Scholar 

  5. Kelley, R. & Ideker, T. Systematic interpretation of genetic interactions using protein networks. Nat. Biotechnol. 23, 561–566 (2005).

    Article  CAS  Google Scholar 

  6. 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 

  7. Collins, S.R. et al. Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map. Nature 446, 806–810 (2007).

    Article  CAS  Google Scholar 

  8. Collins, S.R., Schuldiner, M., Krogan, N.J. & Weissman, J.S. A strategy for extracting and analyzing large-scale quantitative epistatic interaction data. Genome Biol. 7, R63 (2006).

    Article  Google Scholar 

  9. Schuldiner, M., Collins, S.R., Weissman, J.S. & Krogan, N.J. Quantitative genetic analysis in Saccharomyces cerevisiae using epistatic miniarray profiles (E-MAPs) and its application to chromatin functions. Methods 40, 344–352 (2006).

    Article  CAS  Google Scholar 

  10. Sipiczki, M. Where does fission yeast sit on the tree of life? Genome Biol. 1, reviews1011.1–1011.4 (2000).

    Article  Google Scholar 

  11. Pluta, A.F., Mackay, A.M., Ainsztein, A.M., Goldberg, I.G. & Earnshaw, W.C. The centromere: hub of chromosomal activities. Science 270, 1591–1594 (1995).

    Article  CAS  Google Scholar 

  12. Grewal, S.I. & Jia, S. Heterochromatin revisited. Nat. Rev. Genet. 8, 35–46 (2007).

    Article  CAS  Google Scholar 

  13. Hentges, P., Van Driessche, B., Tafforeau, L., Vandenhaute, J. & Carr, A.M. Three novel antibiotic marker cassettes for gene disruption and marker switching in Schizosaccharomyces pombe. Yeast 22, 1013–1019 (2005).

    Article  CAS  Google Scholar 

  14. Ekwall, K. & Ruusala, T. Budding yeast CAN1 gene as a selection marker in fission yeast. Nucleic Acids Res. 19, 1150 (1991).

    Article  CAS  Google Scholar 

  15. Kaufer, N.F., Fried, H.M., Schwindinger, W.F., Jasin, M. & Warner, J.R. Cycloheximide resistance in yeast: the gene and its protein. Nucleic Acids Res. 11, 3123–3135 (1983).

    Article  CAS  Google Scholar 

  16. Ibrahim, M.A. & Coddington, A. Genetic studies on cycloheximide-resistant strains of Schizosaccharomyces pombe. Heredity 37, 179–191 (1976).

    Article  CAS  Google Scholar 

  17. Spahn, C.M. et al. Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation. EMBO J. 23, 1008–1019 (2004).

    Article  CAS  Google Scholar 

  18. Stevens, D.R., Atteia, A., Franzen, L.G. & Purton, S. Cycloheximide resistance conferred by novel mutations in ribosomal protein L41 of Chlamydomonas reinhardtii. Mol. Gen. Genet. 264, 790–795 (2001).

    Article  CAS  Google Scholar 

  19. Varma, A. & Kwon-Chung, K.J. Characterization of the L41 gene in Cryptococcus neoformans: its application as a selectable transformation marker for cycloheximide resistance. Yeast 16, 1397–1403 (2000).

    Article  CAS  Google Scholar 

  20. Kawai, S. et al. Drastic alteration of cycloheximide sensitivity by substitution of one amino acid in the L41 ribosomal protein of yeasts. J. Bacteriol. 174, 254–262 (1992).

    Article  CAS  Google Scholar 

  21. Tanaka, K., Davey, J., Imai, Y. & Yamamoto, M. Schizosaccharomyces pombe map3+ encodes the putative M-factor receptor. Mol. Cell. Biol. 13, 80–88 (1993).

    Article  CAS  Google Scholar 

  22. Styrkarsdottir, U., Egel, R. & Nielsen, O. The smt-0 mutation which abolishes mating-type switching in fission yeast is a deletion. Curr. Genet. 23, 184–186 (1993).

    Article  CAS  Google Scholar 

  23. Doe, C.L. & Whitby, M.C. The involvement of Srs2 in post-replication repair and homologous recombination in fission yeast. Nucleic Acids Res. 32, 1480–1491 (2004).

    Article  CAS  Google Scholar 

  24. Edwards, R.J., Bentley, N.J. & Carr, A.M.A. Rad3-Rad26 complex responds to DNA damage independently of other checkpoint proteins. Nat. Cell Biol. 1, 393–398 (1999).

    Article  CAS  Google Scholar 

  25. Torres, J.Z., Schnakenberg, S.L. & Zakian, V.A. Saccharomyces cerevisiae Rrm3p DNA helicase promotes genome integrity by preventing replication fork stalling: viability of rrm3 cells requires the intra-S-phase checkpoint and fork restart activities. Mol. Cell. Biol. 24, 3198–3212 (2004).

    Article  CAS  Google Scholar 

  26. Moreno, S., Klar, A. & Nurse, P. Molecular genetic analysis of fission yeast Schizosaccharomyces pombe. Methods Enzymol. 194, 795–823 (1991).

    Article  CAS  Google Scholar 

Download references


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.

Author information

Authors and Affiliations


Corresponding author

Correspondence to Nevan J Krogan.

Ethics declarations

Competing interests

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

Supplementary information

Supplementary Text and Figures

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

Rights and permissions

Reprints and permissions

About this article

Cite this article

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).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

This article is cited by


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing