Heat shock stimulates genomic instability and phenotypic variations in yeast
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE150711 | GEO | 2020/05/18
REPOSITORIES: GEO
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Project description:Heat shock stimulates genomic instability and phenotypic variations in yeast
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Project description:Yeast Saccharomyces cerevisiae has been widely used as a model system for studying physiological and pharmacological action of small-molecular drugs. Here, a heterozygous diploid S. cerevisiae strain QSS4 was generated to determine whether drugs could induce chromosomal instability by determining the frequency of mitotic recombination. In combination of a custom SNP microarray, the patterns of chromosomal instability induced by drugs could also be explored at a whole genome level in QSS4. Using this system, we found Zeocin (a member of bleomycin family) treatment resulted in hundreds-fold higher rate of genomic alterations, including aneuploidy, loss of heterozygosity (LOH), and chromosomal rearrangement.
2018-12-20 | GSE124107 | GEO
Project description:Yeast Saccharomyces cerevisiae has been widely used as a model system for studying genome instability. Here, a heterozygous diploid S. cerevisiae strain DZP2 was generated to determine the genomic alterations induced by DNA polymerase ε. The expression of POL2 was regulated by the GAL1 promoter. In combination of a custom SNP microarray, the patterns of chromosomal instability induced by low Pol ε could be explored at a whole genome level in DZP2. Using this system, we found hundreds-fold higher rate of genomic alterations, including aneuploidy, loss of heterozygosity (LOH), and chromosomal rearrangement. DNA polymerase ε (Pol ε) is one of the three replicative eukaryotic DNA polymerases. Pol ε deficiency leads to genomic instability and multiple human diseases. Here, we explored global genomic alterations in yeast strains with reduced expression of POL2, the gene that encodes the catalytic subunit of Pol ε. Using whole-genome SNP microarray and sequencing, we found that low levels of Pol ε elevated the rates of mitotic recombination and chromosomal aneuploidy by two orders of magnitude. Strikingly, low levels of Pol ε resulted in a contraction of the number of repeats in the rDNA cluster and reduced the length of telomeres. These short telomeres led to an elevated frequency of break-induced replication, resulting in terminal loss of heterozygosity. In addition, low levels of Pol ε increased the rate of single-base mutations by 13-fold by a Pol ζ-dependent pathway. Finally, the patterns of genomic alterations caused by low levels of Pol ε were different from those observed in strains with low levels of the other replicative DNA polymerases Pol α and Pol δ, providing further insights into the different roles of the B-family DNA polymerases in maintaining genomic stability.
2021-10-07 | GSE185365 | GEO
Project description:Yeast Saccharomyces cerevisiae has been widely used as a model system for studying genome instability. Here, a heterozygous diploid S. cerevisiae strain DZP2 was generated to determine the genomic alterations induced by DNA polymerase ε. The expression of POL2 was regulated by the GAL1 promoter. In combination of a custom SNP microarray, the patterns of chromosomal instability induced by low Pol ε could be explored at a whole genome level in DZP2. Using this system, we found hundreds-fold higher rate of genomic alterations, including aneuploidy, loss of heterozygosity (LOH), and chromosomal rearrangement. DNA polymerase ε (Pol ε) is one of the three replicative eukaryotic DNA polymerases. Pol ε deficiency leads to genomic instability and multiple human diseases. Here, we explored global genomic alterations in yeast strains with reduced expression of POL2, the gene that encodes the catalytic subunit of Pol ε. Using whole-genome SNP microarray and sequencing, we found that low levels of Pol ε elevated the rates of mitotic recombination and chromosomal aneuploidy by two orders of magnitude. Strikingly, low levels of Pol ε resulted in a contraction of the number of repeats in the rDNA cluster and reduced the length of telomeres. These short telomeres led to an elevated frequency of break-induced replication, resulting in terminal loss of heterozygosity. In addition, low levels of Pol ε increased the rate of single-base mutations by 13-fold by a Pol ζ-dependent pathway. Finally, the patterns of genomic alterations caused by low levels of Pol ε were different from those observed in strains with low levels of the other replicative DNA polymerases Pol α and Pol δ, providing further insights into the different roles of the B-family DNA polymerases in maintaining genomic stability.
2021-10-07 | GSE185364 | GEO
Project description:Oxidative stress is a common factor threatening genomic stability in almost all aerobic organisms. Using a yeast screening system, we measured the frequency of mitotic recombination was greatly elevated after H2O2 treatment. H2O2 was able to break chromatid directly in G1 synchronized cells and homologous recombination was induced to repair DNA double stand breaks at S/G2 phase. By whole genome SNP microarray and sequencing, the patterns of H2O2 induced loss of heterozygosity (LOH; gene conversion and crossover), chromosomal rearrangement, and aneuploidy changes were revealed. LOH events were the most common genomic alterations induced by H2O2 and were randomly distributed throughout the genome.
2017-11-21 | GSE107178 | GEO
Project description:Oxidative stress is a common factor threating genomic stability in almost all aerobic organisms. Using a yeast screening system, we measured the frequency of mitotic recombination was greatly elevated after H2O2 treatment. H2O2 was able to break chromatid directly in G1 synchronized cells and homologous recombination was induced to repair DNA double stand breaks at S/G2 phase. By whole genome SNP microarray and sequencing, the patterns of H2O2 induced loss of heterozygosity (LOH; gene conversion and crossover), chromosomal rearrangement, and aneuploidy changes were revealed. LOH events were the most common genomic alterations induced by H2O2 and were randomly distributed throughout the genome.
2017-11-15 | GSE106816 | GEO
Project description:Voit2003 - Trehalose Cycle
This model is described in the article:
Biochemical and genomic
regulation of the trehalose cycle in yeast: review of
observations and canonical model analysis.
Voit EO.
J. Theor. Biol. 2003 Jul; 223(1):
55-78
Abstract:
The physiological hallmark of heat-shock response in yeast
is a rapid, enormous increase in the concentration of
trehalose. Normally found in growing yeast cells and other
organisms only as traces, trehalose becomes a crucial protector
of proteins and membranes against a variety of stresses,
including heat, cold, starvation, desiccation, osmotic or
oxidative stress, and exposure to toxicants. Trehalose is
produced from glucose 6-phosphate and uridine diphosphate
glucose in a two-step process, and recycled to glucose by
trehalases. Even though the trehalose cycle consists of only a
few metabolites and enzymatic steps, its regulatory structure
and operation are surprisingly complex. The article begins with
a review of experimental observations on the regulation of the
trehalose cycle in yeast and proposes a canonical model for its
analysis. The first part of this analysis demonstrates the
benefits of the various regulatory features by means of
controlled comparisons with models of otherwise equivalent
pathways lacking these features. The second part elucidates the
significance of the expression pattern of the trehalose cycle
genes in response to heat shock. Interestingly, the genes
contributing to trehalose formation are up-regulated to very
different degrees, and even the trehalose degrading trehalases
show drastically increased activity during heat-shock response.
Again using the method of controlled comparisons, the model
provides rationale for the observed pattern of gene expression
and reveals benefits of the counterintuitive trehalase
up-regulation.
To
induce a heat shock, set the parameter heat_shock from 0 to 1. This
changes the parameter values of X8 to X19 from 1 to the values
given in table 3 of the original publication.
As
this is an S-systems model, it does not contain any reactions
encoded in SBML.
This model is hosted on
BioModels Database
and identified by:
BIOMD0000000266.
To cite BioModels Database, please use:
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To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
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Public Domain Dedication for more information.
2010-07-20 | BIOMD0000000266 | BioModels
Project description:Furfural is a key inhibitor in S. cerevisiae fermentation causing serious economic loss. To understand the toxic mechanisms of furfural-induced genomic instability and phenotypic evolution, we mapped chromosomal alterations in 21 furfural-treated yeast strains by whole genome SNP microarrays at a resolution about 1kb.
2017-10-13 | GSE104879 | GEO
Project description:Mutants of the Mnn1 gene are hyper-sensitive to several stresses and display increased genome instability when subjected to conditions, such as heat shock, generally regarded as non-genotoxic. We describe a role for Menin as a global regulator of heat shock gene expression and critical factor in the maintenance of genome integrity 2-colour microarray design using 36 microarrays testing shock vs non shock in Drosophila melanogaster. Using a test of loss-of-heterozygosity, we show that Drosophila strains lacking a functional Mnn1 gene or expressing a Mnn1 dsRNAi are characterized by increased genome instability in response to short, repeated but non-lethal heat shock or hypoxia treatments. The same was true for strains lacking all Hsp70 genes.
2010-10-25 | E-GEOD-20497 | biostudies-arrayexpress
Project description:Microarray time courses followed the response of 5 yeast strains to heat shock. Expression variation due to genetic, environmental, and genotype-by-environment interactions were identified. Keywords: Timecourse and single timepoint expression studies of stress response in yeast The genomic expression response to heat shock was measured in 5 different yeast strains over the course of 2 hours. Basal expression at 25C was also compared in 4 non-lab strains to the S288c refernce. All experiments were done in duplicate, for a total of 68 Samples.
2010-05-18 | E-GEOD-15147 | biostudies-arrayexpress