Saccharomyces cerevisiae
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA261399 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1578450.fastq.gz | Fastqsanger.gz | |||
| SRR1578460.fastq.gz | Fastqsanger.gz | |||
| SRR1578470.fastq.gz | Fastqsanger.gz | |||
| SRR1578480.fastq.gz | Fastqsanger.gz | |||
| SRR1578451.fastq.gz | Fastqsanger.gz |
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Project description:Dosage compensation can buffer copy-number variation in wild yeast
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Project description:The aim of present study is to understand the impact of genetic engineering event, integration of ClCBH2 gene into yeast genome, as well as the subsequent biological process, such as expression and secretion of CBH2 protein. Further, the ‘dosage’ of genetic engineering event, the copy number inserted ClCBH2 gene, is also of particular interest. In parallel, the relationship between the copy number of ClCBH2 gene and the condition of yeast culture during CBH2 production, as well as the effect of these two factors towards yeast metabolism are investigated. Extensive transcriptomics analysis and comparison were conducted for three CBP yeast strains with different copy numbers of ClCBH2 gene, at two growth rates
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Project description:We show that aneuploidy is common in wild isolates of yeast, which are inherently tolerant to chromosome amplification and down-regulate expression at 40% of amplified genes. To dissect the mechanism of this dosage response, we generated isogenic strain panels in which diploid cells carried either two, three, or four copies of the affected chromosomes. Using a mixture of linear regression (MLR) model to classify genes, we find that expression is actively down regulated in proportion to increased gene copy at up to 30% of genes. Genes subject to dosage control are under higher expression constraint – but show elevated rates of gene amplification – in wild populations, suggesting that dosage compensation buffers copy number variation (CNV) at toxic genes
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Project description:Copy-number variants (CNVs) are large-scale amplifications or deletions of DNA that can drive rapid adaptive evolution and result in large-scale changes in gene expression. Whereas alterations in the copy number of one or more genes within a CNV can confer a selective advantage, other genes within a CNV can decrease fitness when their dosage is changed. Dosage compensation - in which the gene expression output from multiple gene copies is less than expected - is one means by which an organism can mitigate the fitness costs of deleterious gene amplification. Previous research has shown evidence for dosage compensation at both the transcriptional level and at the level of protein expression; however, the extent of compensation differs substantially between genes, strains, and studies. Here, we investigated sources of dosage compensation at multiple levels of gene expression regulation by defining the transcriptome, translatome and proteome of experimentally evolved yeast (Saccharomyces cerevisiae) strains containing adaptive CNVs.
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Project description:Aneuploidy, the state in which an organism’s genome contains one or more missing or additional chromosomes, often causes widespread genotypic and phenotypic effects. Most often, aneuploidies are deleterious; the most common examples in humans being Down’s syndrome (Trisomy 21) and Turner’s syndrome (monosomy X). However, aneuploidy is surprisingly common in wild yeast populations. In recent years, there has been debate as to whether yeast contain an innate dosage compensation response on the whole-genome level, or if these natural isolates are robust to aneuploidy without such a mechanism. In this study, we tested for differential gene expression in 20 aneuploid and 18 euploid lines of yeast from two previous mutation accumulation experiments, where selection was low and therefore aneuploidies arose spontaneously. We found no evidence for whole-chromosome dosage compensation in aneuploid yeast but did find some evidence for attenuation of expression on a gene-by-gene basis. We additionally found that aneuploidy has no effect on the expression of the rest of the genome (i.e. “trans” genes), and that very few mutually exclusive aneuploid lines shared differentially expressed genes. However, we found a small common differential expression response in the euploid lines, suggesting an effect of mutation accumulation on gene expression. Our findings contribute to our understanding of aneuploidy in yeast and support the hypothesis that there is no innate dosage compensation mechanism at the whole-chromosome level.
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Project description:The aim of present study is to understand the impact of genetic engineering event, integration of ClCBH2 gene into yeast genome, as well as the subsequent biological process, such as expression and secretion of CBH2 protein. Further, the ‘dosage’ of genetic engineering event, the copy number inserted ClCBH2 gene, is also of particular interest. In parallel, the relationship between the copy number of ClCBH2 gene and the condition of yeast culture during CBH2 production, as well as the effect of these two factors towards yeast metabolism are investigated. Extensive transcriptomics analysis and comparison were conducted for three CBP yeast strains with different copy numbers of ClCBH2 gene, at two growth rates A twenty-four array study using total RNA recovered from three CBP yeast strains with different copy numbers of ClCBH2 gene, at two growth rates
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2015-05-08 | E-GEOD-61532 | biostudies-arrayexpress
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