On the rate of aneuploidy reversion in a wild yeast model

Aneuploidy, arising from gain or loss of chromosomes due to nondisjunction, is a special class of mutation. It can create significant phenotypic changes by altering abundance of hundreds of genes in a single event, providing material for adaptive evolution. But it can also incur large fitness costs relative to other types of mutations. Understanding mutational dynamics of aneuploidy is important for modeling its impact in nature, but aneuploidy rates are difficult to measure accurately. One challenge is that aneuploid karyotypes may revert back to euploidy, biasing forward mutation rate estimates - yet the rate of aneuploidy reversion is largely uncharacterized. Furthermore, current rate estimates are confounded because fitness differences between euploids and aneuploids are typically not accounted for in rate calculations. We developed a unique fluctuation assay in a wild-yeast model to measure the rate of extra-chromosome loss across three aneuploid chromosomes, while accounting for fitness differences between aneuploid and euploid cells. We show that incorporating fitness effects is essential to obtain accurate estimates of aneuploidy rates. Furthermore, the rate of extra-chromosome loss, separate from karyotype fitness differences, varies across chromosomes. We also measured rates in a strain lacking RNA-binding protein Ssd1, important for aneuploidy tolerance and implicated in chromosome segregation. We found no role for Ssd1 in the loss of native aneuploid chromosomes, although it did impact an engineered chromosome XV with a perturbed centromeric sequence. We discuss the impacts and challenges of modeling aneuploidy dynamics in real world situations. ARTICLE SUMMARYErrors in chromosome segregation can produce aneuploid cells with an abnormal number of chromosomes. Aneuploidy is not uncommon in wild populations of fungi and can underlie emergence of drug-resistant pathogens. But modeling the impact of aneuploidy on evolution has been challenging, because rates of aneuploidy emergence and reversion have been difficult to measure. This work used a novel fluctuation assay that incorporates euploid-aneuploid fitness differences to calculate rates of extra-chromosome loss in aneuploid Saccharomyces cerevisiae, across several chromosomes. The results present for the first time estimates of aneuploidy reversion ("back mutation") rates and implications for previously measured rates of aneuploidy.