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Natural variation in the consequences of gene overexpression during osmotic stress [BAR-Seq]

ABSTRACT: Natural variation in the consequences of gene overexpression during osmotic stress [BAR-Seq]

PROVIDER: PRJNA939234 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23632707.fastq.gz	Fastqsanger.gz
	SRR23632708.fastq.gz	Fastqsanger.gz
	SRR23632709.fastq.gz	Fastqsanger.gz
	SRR23632710.fastq.gz	Fastqsanger.gz
	SRR23632711.fastq.gz	Fastqsanger.gz

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Natural variation in the consequences of gene overexpression during osmotic stress

Project description:Natural variation in the consequences of gene overexpression during osmotic stress

| PRJNA939229 | ENA

Natural variation in the consequences of gene overexpression during osmotic stress [BAR-Seq]

Project description:Free-living cells live in fluctuating environments and must be able to respond rapidly in order to survive. Genetic background can influence how an individual responds to a changing environment, including stressful changes. Changes in gene copy number can influence stress tolerance and responses, presumably due to corresponding changes in gene expression. However, we recently showed that strains vary in their ability to tolerate gene copy number differences; how this influences variation in stress tolerance is relatively unknown. Here we measured the tolerance to gene overexpression (OE) in four different Saccharomyces cerevisiae strains, including wild isolates, when strains were grown under osmotic and ionic stress induced by sodium chloride (NaCl). OE genes that were deleterious to most strains under NaCl stress were enriched for translation processes, similar to the enrichments of deleterious genes in rich, non-stress medium. We found that the West African NCYC3290 strain and the North American YPS128 strain are more sensitive to NaCl stress than other strains. These strains showed the greatest number of sensitivities to gene OE compared to other strains. Although most genes were deleterious in these strains, subsets of genes are highly beneficial when OE during NaCl stress. Many of these highly beneficial genes are functionally related and point to underlying differences in strain physiology. This work illustrates how tolerance to gene overexpression is influenced by genotype-environment interactions.

2023-06-30 | GSE226247 | GEO

Natural variation in the consequences of gene overexpression during osmotic stress [RNA-Seq]

Project description:Natural variation in the consequences of gene overexpression during osmotic stress [RNA-Seq]

| PRJNA939230 | ENA

Natural variation in the consequences of gene overexpression during osmotic stress [RNA-Seq]

Project description:We used RNA-Seq to measure transcript abundance in 4 Saccharomyces cerevisiae strains (BY4743, BC187, NCYC3290, and YPS128) from a diverse range of genetic lineages when growing in rich media (YPD) with 0.7M NaCl to characterize differential expression across strains in response to osmotic and ionic stress.

2023-06-30 | GSE226246 | GEO

Natural Variation in the Fitness Consequences of Gene Amplification in Wild Saccharomyces cerevisiae Isolates [Bar-seq]

Project description:Natural Variation in the Fitness Consequences of Gene Amplification in Wild Saccharomyces cerevisiae Isolates [Bar-seq]

| PRJNA720134 | ENA

Natural Variation in the Fitness Consequences of Gene Amplification in Wild Saccharomyces cerevisiae Isolates [Bar-seq]

Project description:Genetic variation that underlies phenotypic differences provides the material on which evolutionary selection acts. Gene duplication/amplification is one type of genetic variation that can allow an organism to rapidly respond to environmental changes by increasing gene dosage. While the potential benefits afforded by gene amplification during evolution are well known, there is also a significant fitness cost to increasing gene dosage including resource shortages and burdening cellular systems. Although the evolutionary importance of gene duplication has long been appreciated, little is known about natural variation in the tolerance of duplication of specific genes. To investigate this question, we expressed the same high-copy gene overexpression (OE) library in a laboratory strain and 14 different wild S. cerevisiae isolates, together representing 4 lineages and several admixed strains, to explore the natural variation in tolerance to gene OE. Our results distinguish universal effects common to many studied strains versus strain-specific effects including broad-scale and gene-specific differences in the consequences of OE. These results raise important implications for the accessibility of evolutionary trajectories afforded by gene OE, depending on genetic background.

2021-04-07 | GSE171586 | GEO

Natural variation in the consequences of gene overexpression during osmotic stress

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-06-30 | GSE226248 | GEO

Natural Variation in the Fitness Consequences of Gene Amplification in Wild Saccharomyces cerevisiae Isolates

Project description:Natural Variation in the Fitness Consequences of Gene Amplification in Wild Saccharomyces cerevisiae Isolates

| PRJNA720133 | ENA

Wairau Bar

Project description:Wairau Bar human mitochondrial genome sequences

| PRJEB550 | ENA

Natural variation in the consequences of gene overexpression and its implications for evolutionary trajectories.

Project description:Copy number variation through gene or chromosome amplification provides a route for rapid phenotypic variation and supports the long-term evolution of gene functions. Although the evolutionary importance of copy-number variation is known, little is understood about how genetic background influences its tolerance. Here, we measured fitness costs of over 4000 overexpressed genes in 15 Saccharomyces cerevisiae strains representing different lineages, to explore natural variation in tolerating gene overexpression (OE). Strain-specific effects dominated the fitness costs of gene OE. We report global differences in the consequences of gene OE, independent of the amplified gene, as well as gene-specific effects that were dependent on the genetic background. Natural variation in the response to gene OE could be explained by several models, including strain-specific physiological differences, resource limitations, and regulatory sensitivities. This work provides new insight on how genetic background influences tolerance to gene amplification and the evolutionary trajectories accessible to different backgrounds.

| S-EPMC8352584 | biostudies-literature

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