Genome-wide genetic analysis of polyploidy in yeast

Abstract

Polyploidy, increased sets of chromosomes, occurs during development, cellular stress, disease and evolution. Despite its prevalence, little is known about the physiological alterations that accompany polyploidy. We previously described ‘ploidy-specific lethality’, where a gene deletion that is not lethal in haploid or diploid budding yeast causes lethality in triploids or tetraploids. Here we report a genome-wide screen to identify ploidy-specific lethal functions. Only 39 out of 3,740 mutations screened exhibited ploidy-specific lethality. Almost all of these mutations affect genomic stability by impairing homologous recombination, sister chromatid cohesion, or mitotic spindle function. We uncovered defects in wild-type tetraploids predicted by the screen, and identified mechanisms by which tetraploidization affects genomic stability. We show that tetraploids have a high incidence of syntelic/monopolar kinetochore attachments to the spindle pole. We suggest that this defect can be explained by mismatches in the ability to scale the size of the spindle pole body, spindle and kinetochores. Thus, geometric constraints may have profound effects on genome stability; the phenomenon described here may be relevant in a variety of biological contexts, including disease states such as cancer.

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Figure 1: A genome-wide strategy identifies a small subset of gene deletions/mutations that result in ploidy-specific lethality.
Figure 2: The gene expression profile of diploid MATa/α and tetraploid MATa/a/α/α is not significantly altered by increased ploidy.
Figure 3: Genome instability and requirement for homologous recombination in yeast tetraploids.
Figure 4: Tetraploids have increased syntelic attachments without compromised Ipl1/aurora B activity.
Figure 5: Scaling effects can explain the increase in syntelic/monopolar attachments observed in tetraploids.

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Acknowledgements

We are grateful to many colleagues from the yeast community for providing the reagents. We thank A. Amon, G. Fink, J. Haber, R. Rothstein, M. McLaughlin, M. Raschle and members of the Pellman laboratory for discussions; G. Fink, S. Elledge, J. Haber, A. Van Oudenaarden, M. McLaughlin, R. Rothstein and J. Walter for comments on the manuscript; C. Glavin for Supplementary Fig. 9; and M. Lenburg for guidance on the analysis of the expression profile data. D.P. was supported by an NIH grant and a gift from the G. Harold and Leila Y. Mathers Foundation. The Boulder Laboratory for 3D Electron Microscopy of Cells is supported by an NIH grant to J. R. McIntosh.

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Correspondence to David Pellman.

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Competing interests

The transcriptional profiling data are available at MIAMExpress database (http://www.ebi.ac.uk/miamexpress) under accession number E-MEXP-822. Reprints and permissions information is available at www.nature.com/reprints. The authors declare no competing financial interests.

Supplementary information

Supplementary Notes

This file provides detailed descriptions of the genome-wide strategy for tetraploid formation, the plasmid shuffle strategy for tetraploid formation, Nuf2-GFP fluorescence intensity measurements, high-voltage EM tomography of yeast and description and explanation of expression profiling analysis. This file also contains Supplementary Figures 1–9 and Supplementary Tables 1–3. (PDF 9627 kb)

Supplementary Data 1

Complete results of the genome-wide screen for genes specifically required in yeast tetraploid cells. (XLS 633 kb)

Supplementary Data 2

Complete results of the expression profiling. (XLS 1693 kb)

Supplementary Movie

3D reconstruction of a tetraploid forming spindle. (MOV 132380 kb)

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Storchová, Z., Breneman, A., Cande, J. et al. Genome-wide genetic analysis of polyploidy in yeast. Nature 443, 541–547 (2006). https://doi.org/10.1038/nature05178

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