Spontaneous duplications in diploid Saccharomyces cerevisiae cells

Schacherer, Joseph; Tourrette, Yves; Potier, Serge; Souciet, Jean-Luc; Montigny, Jacky de

doi:10.1016/j.dnarep.2007.04.006

Cited by 9 publications

(7 citation statements)

References 46 publications

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“…Unfortunately, haploid strains could not be generated from diploids carrying segmental deletions and nonreciprocal translocations. In fact, these rearrangements involve essential genes, which result in non-viable haploid strains [ 20 , 21 ]. Meiosis was therefore induced in the diploid mutant strains carrying an aneuploidy or a segmental duplication.…”

Section: Resultsmentioning

confidence: 99%

Ploidy influences cellular responses to gross chromosomal rearrangements in saccharomyces cerevisiae

et al. 2011

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BackgroundGross chromosomal rearrangements (GCRs) such as aneuploidy are key factors in genome evolution as well as being common features of human cancer. Their role in tumour initiation and progression has not yet been completely elucidated and the effects of additional chromosomes in cancer cells are still unknown. Most previous studies in which Saccharomyces cerevisiae has been used as a model for cancer cells have been carried out in the haploid context. To obtain new insights on the role of ploidy, the cellular effects of GCRs were compared between the haploid and diploid contexts.ResultsA total number of 21 haploid and diploid S. cerevisiae strains carrying various types of GCRs (aneuploidies, nonreciprocal translocations, segmental duplications and deletions) were studied with a view to determining the effects of ploidy on the cellular responses. Differences in colony and cell morphology as well as in the growth rates were observed between mutant and parental strains. These results suggest that cells are impaired physiologically in both contexts. We also investigated the variation in genomic expression in all the mutants. We observed that gene expression was significantly altered. The data obtained here clearly show that genes involved in energy metabolism, especially in the tricarboxylic acid cycle, are up-regulated in all these mutants. However, the genes involved in the composition of the ribosome or in RNA processing are down-regulated in diploids but up-regulated in haploids. Over-expression of genes involved in the regulation of the proteasome was found to occur only in haploid mutants.ConclusionThe present comparisons between the cellular responses of strains carrying GCRs in different ploidy contexts bring to light two main findings. First, GCRs induce a general stress response in all studied mutants, regardless of their ploidy. Secondly, the ploidy context plays a crucial role in maintaining the stoichiometric balance of the proteins: the translation rates decrease in diploid strains, whereas the excess protein synthesized is degraded in haploids by proteasome activity.

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Section: Resultsmentioning

confidence: 99%

Ploidy influences cellular responses to gross chromosomal rearrangements in saccharomyces cerevisiae

et al. 2011

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“…Tandem gene arrays are observed in all yeast genomes, albeit in different proportions (Despons et al 2011), and are generally not conserved between species. Segmental amplifications are frequently observed in experiments using S. cerevisiae (Koszul et al 2004; Schacherer et al 2007b; Araya et al 2010; Payen et al 2014; Thierry et al 2015, 2016) but leave few traces in natural yeast genomes, except in subtelomeric regions (Fairhead and Dujon 2006). …”

Section: What Did We Learn From Comparative Genomics Of Other Saccharmentioning

confidence: 99%

Genome Diversity and Evolution in the Budding Yeasts (Saccharomycotina)

2017

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Considerable progress in our understanding of yeast genomes and their evolution has been made over the last decade with the sequencing, analysis, and comparisons of numerous species, strains, or isolates of diverse origins. The role played by yeasts in natural environments as well as in artificial manufactures, combined with the importance of some species as model experimental systems sustained this effort. At the same time, their enormous evolutionary diversity (there are yeast species in every subphylum of Dikarya) sparked curiosity but necessitated further efforts to obtain appropriate reference genomes. Today, yeast genomes have been very informative about basic mechanisms of evolution, speciation, hybridization, domestication, as well as about the molecular machineries underlying them. They are also irreplaceable to investigate in detail the complex relationship between genotypes and phenotypes with both theoretical and practical implications. This review examines these questions at two distinct levels offered by the broad evolutionary range of yeasts: inside the best-studied Saccharomyces species complex, and across the entire and diversified subphylum of Saccharomycotina. While obviously revealing evolutionary histories at different scales, data converge to a remarkably coherent picture in which one can estimate the relative importance of intrinsic genome dynamics, including gene birth and loss, vs. horizontal genetic accidents in the making of populations. The facility with which novel yeast genomes can now be studied, combined with the already numerous available reference genomes, offer privileged perspectives to further examine these fundamental biological questions using yeasts both as eukaryotic models and as fungi of practical importance.

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“…The types of duplications commonly observed can be classified into six groups: (1) interstitial segmental duplications in which the breakpoints are in repeated sequences in direct orientation (Koszul et al 2004;Libuda and Winston 2006;Payen et al 2008;McCulley and Petes 2010); (2) segmental duplications unassociated with repeats at the duplication breakpoints (Koszul et al 2004;Schacherer et al 2005Schacherer et al , 2007Payen et al 2008); (3) interstitial duplications in which the duplicated segments are in an inverted orientation (Moore et al 2000;Rattray et al 2005;Watanabe and Horiuchi 2005;Narayanan et al 2006); (4) terminal duplications of part of one chromosome Figure 1 General mechanisms for the generation of deletions and duplications. In this figure, chromosomes are shown as horizontal blue or red lines, DNA repeats as solid arrows, reporter genes as shaded arrows, and centromeres as circles.…”

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Gene Copy-Number Variation in Haploid and Diploid Strains of the Yeast Saccharomyces cerevisiae

et al. 2013

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The increasing ability to sequence and compare multiple individual genomes within a species has highlighted the fact that copy-number variation (CNV) is a substantial and underappreciated source of genetic diversity. Chromosome-scale mutations occur at rates orders of magnitude higher than base substitutions, yet our understanding of the mechanisms leading to CNVs has been lagging. We examined CNV in a region of chromosome 5 (chr5) in haploid and diploid strains of Saccharomyces cerevisiae. We optimized a CNV detection assay based on a reporter cassette containing the SFA1 and CUP1 genes that confer gene dosage-dependent tolerance to formaldehyde and copper, respectively. This optimized reporter allowed the selection of low-order gene amplification events, going from one copy to two copies in haploids and from two to three copies in diploids. In haploid strains, most events involved tandem segmental duplications mediated by nonallelic homologous recombination between flanking direct repeats, primarily Ty1 elements. In diploids, most events involved the formation of a recurrent nonreciprocal translocation between a chr5 Ty1 element and another Ty1 repeat on chr13. In addition to amplification events, a subset of clones displaying elevated resistance to formaldehyde had point mutations within the SFA1 coding sequence. These mutations were all dominant and are proposed to result in hyperactive forms of the formaldehyde dehydrogenase enzyme.A S a consequence of studies that utilize genomic microarrays and next-generation DNA sequencing, it has become clear that much of the natural genetic variation that exists between individuals is due to alterations in the number of copies of genes rather than differences in the nucleotide sequence (Girirajan et al. 2011;Veltman and Brunner 2012). It has been calculated that 8-25 kb of DNA are deleted or duplicated per generation in humans compared to about 100 bp of point mutations (Itsara et al. 2010). Although deletions and duplications vary in size from a few base pairs (for example, changes in the lengths of microsatellites) to many megabases (for example, changes in ploidy), Girirajan et al. (2011) define copy-number variants (CNVs) in humans as changes that vary in size between 50 bp and 1 Mb. While most CNV events have no obvious effect, a significant number are associated with human diseases including Charcot-Marie-Tooth syndrome, autosomal dominant leukodystrophy, Williams syndrome, several cancer predispositions, and autism-related and other neurodevelopmental disorders (Abrahams and Geschwind 2008;Girirajan et al. 2011;Krepischi et al. 2012;Malhotra and Sebat 2012;Sullivan et al. 2012). There is also strong evidence suggesting that CNVs played a significant role in human evolution (Iskow et al. 2012). Finally, multiple somatic CNV events are frequently observed in the altered karyotypes of cancer cells (Stratton et al. 2009).CNVs have also been widely observed in natural populations and have been studied in detail in model organisms. In the discussion below, w...

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Spontaneous duplications in diploid Saccharomyces cerevisiae cells

Cited by 9 publications

References 46 publications

Ploidy influences cellular responses to gross chromosomal rearrangements in saccharomyces cerevisiae

Ploidy influences cellular responses to gross chromosomal rearrangements in saccharomyces cerevisiae

Genome Diversity and Evolution in the Budding Yeasts (Saccharomycotina)

Gene Copy-Number Variation in Haploid and Diploid Strains of the Yeast Saccharomyces cerevisiae

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