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Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe

A Corrigendum to this article was published on 07 December 2010

This article has been updated

Abstract

We report the construction and analysis of 4,836 heterozygous diploid deletion mutants covering 98.4% of the fission yeast genome providing a tool for studying eukaryotic biology. Comprehensive gene dispensability comparisons with budding yeast—the only other eukaryote for which a comprehensive knockout library exists—revealed that 83% of single-copy orthologs in the two yeasts had conserved dispensability. Gene dispensability differed for certain pathways between the two yeasts, including mitochondrial translation and cell cycle checkpoint control. We show that fission yeast has more essential genes than budding yeast and that essential genes are more likely than nonessential genes to be present in a single copy, to be broadly conserved and to contain introns. Growth fitness analyses determined sets of haploinsufficient and haploproficient genes for fission yeast, and comparisons with budding yeast identified specific ribosomal proteins and RNA polymerase subunits, which may act more generally to regulate eukaryotic cell growth.

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Figure 1: Deletion construction and gene dispensability.
Figure 2: Analysis of gene dispensability.
Figure 3: Comparative analysis of gene dispensability profiles of fission yeast.
Figure 4: Dispensability comparison of orthologous pairs from the two yeasts.
Figure 5: A comparison of the relative growth rates for the total set of heterozygous deletion diploids in fission yeast (4,334 genes) and budding yeast (5,921 genes).

Change history

  • 07 December 2010

    In the version of this article initially published, the address of one of the authors, Young-Joo Jang, was incorrect. The correct address is Laboratory of Cell Cycle & Signal Transduction, WCU Department of NanoBioMedical Science, Institute of Tissue Regeneration Engineering, Dankook University, Cheonan, Korea.The error has been corrected in the HTML and PDF versions of the article.

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Acknowledgements

We thank members of our laboratories for their participation in the construction and analysis of the deletion mutants, particularly H.-R. Hwang, H.-S. Ahn, Y.-D. Kim, S. Park, H.-J. Lee, J.-H. Ahn, Y.-S. Kil, S.-Y. Park, J.-H. Lim, J.-H. Song, Y.-K. Ryoo, J.-Y. Kim, M.-J. Oh, S. Kong, J. Ahn, N. Sun, N. Peat, R. Mandeville and J.-J. Li. We also thank J.-H. Roe and W.-K. Huh for reading this manuscript and for their insightful comments and O. Nielsen for his patience with the many requests for pON177. This work was supported by the intramural research program of KRIBB (Mission 2007), the Chemical Genomics Research Program and the 21st Century Frontier Research Program from the Ministry of Education, Science and Technology (MOEST) of Korea. This work was also supported by Bioneer Corp., The Wellcome Trust, Cancer Research UK, The Breast Cancer Research Foundation (BCRF) and The Rockefeller University.

Author information

Authors and Affiliations

Authors

Contributions

D.-U.K., J.H., H.-O.P., M.W., H.-S.Y., P.N. and K.-L.H. conceived the project; D.-U.K., J.H., D.K., V.W., M.W., T.D., M.N., G.P., S.H., L.J., S.-T.B., H.L., Y.S.S., M.L., L.K., K.-S.H., E.J.N., A.-R.L., Y.-J.J., K.-S.C., S.-J.C., J.-Y.P., Y.P., H.M.K., S.-K.P., H.B.K., H.-S.K., H.-M.P., K.K., K.S. and K.B.S. performed experiments and data analysis; D.K., H.-J.P., E.-J.K. and H.-M.P. performed primer design; D.K. and V.W. performed bioinformatics; D.-U.K., J.H., D.K., V.W., P.N. and K.-L.H. wrote the paper.

Corresponding author

Correspondence to Kwang-Lae Hoe.

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Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Tables 2–10,12–14,18 Supplementary Figs. 1–10 and Supplementary Methods (PDF 4821 kb)

Supplementary Table 1

The 4,836 deletion set in fission yeast and its genome dataset as a reference (4,914) (XLS 2317 kb)

Supplementary Table 11

Spreadsheet of 2,438 'one to one' orthologous pairs in fission yeast and budding yeast (for details, see attached Excel file) (XLS 572 kb)

Supplementary Table 15

Growth fitness data of S. pombe heterozygous deletion mutants in rich YE media (XLS 1347 kb)

Supplementary Table 16

List of slow growers from the two yeasts, whose relative fitness is less than 0.97 (XLS 260 kb)

Supplementary Table 17

List of haploinsufficient (lowest 3% ranked by RF) and haploproficient (highest 3% ranked by RF) genes from the two yeasts in rich media (XLS 217 kb)

Supplementary Data 1

All the primer set for the construction of deletion strains (XLS 3027 kb)

Supplementary Data 2

Mapping of the deletions (PDF 19502 kb)

Supplementary Data 3

Sequence of KanMX4 (PDF 231 kb)

Supplementary Data 4

Design of Affymertix custom GeneChip (XLS 1653 kb)

Supplementary Data 5

Microarray data set for growth profiling (ZIP 10612 kb)

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Kim, DU., Hayles, J., Kim, D. et al. Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe. Nat Biotechnol 28, 617–623 (2010). https://doi.org/10.1038/nbt.1628

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