Karyotypic Determinants of Chromosome Instability in Aneuploid Budding Yeast Jin Zhu1., Norman Pavelka1,2., William D. Bradford1, Giulia Rancati1,3.*, Rong Li1,4* 1 Stowers Institute for Medical Research, Kansas City, Missouri, United States of America, 2 Singapore Immunology Network Agency of Science, Technology, and Research, Singapore, Singapore, 3 Institute of Medical Biology, Agency of Science, Technology, and Research, Singapore, Singapore, 4 Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, Kansas, United States of America Abstract Recent studies in cancer cells and budding yeast demonstrated that aneuploidy, the state of having abnormal chromosome numbers, correlates with elevated chromosome instability (CIN), i.e. the propensity of gaining and losing chromosomes at a high frequency. Here we have investigated ploidy- and chromosome-specific determinants underlying aneuploidy-induced CIN by observing karyotype dynamics in fully isogenic aneuploid yeast strains with ploidies between 1N and 2N obtained through a random meiotic process. The aneuploid strains exhibited various levels of whole-chromosome instability (i.e. chromosome gains and losses). CIN correlates with cellular ploidy in an unexpected way: cells with a chromosomal content close to the haploid state are significantly more stable than cells displaying an apparent ploidy between 1.5 and 2N. We propose that the capacity for accurate chromosome segregation by the mitotic system does not scale continuously with an increasing number of chromosomes, but may occur via discrete steps each time a full set of chromosomes is added to the genome. On top of such general ploidy-related effect, CIN is also associated with the presence of specific aneuploid chromosomes as well as dosage imbalance between specific chromosome pairs. Our findings potentially help reconcile the divide between gene-centric versus genome-centric theories in cancer evolution. Citation: Zhu J, Pavelka N, Bradford WD, Rancati G, Li R (2012) Karyotypic Determinants of Chromosome Instability in Aneuploid Budding Yeast. PLoS Genet 8(5): e1002719. doi:10.1371/journal.pgen.1002719 Editor: Beth A. Sullivan, Duke University, United States of America Received November 18, 2011; Accepted April 4, 2012; Published May 17, 2012 Copyright: 2012 Zhu et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was funded by the grant GM R01059964 to RL; GR and NP are currently supported by A*STAR Investigatorship awards. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: giulia.rancati@imb.a-star.edu.sg (GR); rli@stowers.org (RL) . These authors contributed equally to this work. Introduction The nature of the genetic changes driving cellular evolution has been a central issue in both adaptive evolution of unicellular organisms and somatic evolution of cancer cells. Phenotypic variation, acting as a substrate of Darwinian selection and as an origin of phenotypic innovation, can be driven by sequence-based mutations as well as copy number changes [1,2,3,4,5,6,7]. In cancer, the gene-centric theory posits that cancer progression is driven by sequence alterations in specific genes playing key roles in cell cycle control and genome stability, leading to malignant growth and accumulation of further genetic aberrations [8]. Under this perspective, aneuploidy is more likely to be an innocent byproduct than a driver of the evolutionary process leading towards malignant transformation. The chromosome theory, on the other hand, emphasizes the cytogenetic diversity in cancer and proposes that it is the abnormal chromosome copy numbers, or aneuploidy, rather than variation in specific gene sequences, that accounts for both the loss of growth control and the remarkable adaptability of tumor cell populations toward restrictive tissue environments or chemotherapy [9]. According to this theory, aneuploidy would lead to increased rates of various types of genomic instability, including chromosome instability (CIN), and therefore a continuous ability to generate new adaptive aneuploid genomes. This potential snowballing effect has been termed ‘‘genome chaos’’ and has been hypothesized to be at the basis of malignant transformation [9,10,11]. While the gene-centric theory of cancer is widely accepted, understanding the mechanisms by which aneuploidy could lead to CIN might reconcile the two theories. For example, is the increased CIN in an aneuploid genome a result of the abnormal chromosome numbers per se or of aneuploidy-driven alteration of the expression of specific genes? Whereas studying the contribution of aneuploidy to CIN in cancer cells is complicated by the fact that most cancer cells possess both numerous point mutations and other kinds of chromosome abnormalities [6,12,13], simple model organisms such as the yeast Saccharomyces cerevisiae represent valuable systems for assessing independent effects of individual types of genetic changes. Budding yeast cells are especially suitable for these types of studies because they tolerate aneuploidy relatively well [14,15], most likely because their relatively small haploid genome (,6,000 ORFs over ,12 million base pairs) is segmented into a relatively large number of chromosomes (N = 16). Several studies have shown that aneuploid yeast cells not only are characterized by phenotypic variation but also exhibit genome instability [15,16,17,18]. For example, two independent studies with congenic aneuploid strains obtained by sporulation of triploid or pentaploid yeast found that, while some of the aneuploid strains were relatively stable, the majority of the strains were chromo- somally unstable [15,17]. Another paper recently reported decreased artificial chromosome transmission fidelity and elevated mitotic recombination in a set of disomic yeast strains compared to PLoS Genetics | www.plosgenetics.org 1 May 2012 | Volume 8 | Issue 5 | e1002719