Project description:Gene expression is known to vary among individuals, and this variability can impact the phenotypic diversity observed in natural populations. While the transcriptome and proteome have been extensively studied, little is known about the translation process itself. Here, we therefore performed ribosome and transcriptomic profiling on a genetically and ecologically diverse subset of natural isolates of the Saccharomyces cerevisiae yeast. Interestingly, we found that the Euclidean distances between each profile and the expression fold changes in each pairwise isolate comparison were approximately 10% higher at the transcriptomic level. This observation clearly indicates that the transcriptional variation observed in the different isolates is buffered through a phenomenon known as post-transcriptional buffering at the translation level. Furthermore, this phenomenon seemed to have a specific signature by preferentially affecting essential genes as well as genes involved in complex-forming proteins, and low transcribed genes. We also explored the translation of the S. cerevisiae pangenome and found that the accessory genes related to introgression events displayed similar transcription and translation levels as the core genome. By contrast, genes acquired through horizontal gene transfer events tended to be less efficiently translated. Together, our results highlight both the extant and signature of the post- transcriptional buffering.

2024-02-01 | GSE173654 | 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

The transcriptional consequences of mutation and natural selection in Caenorhabditis elegans

Project description:This set of arrays contains all microarray experiments done involving comparisons among C. elegans natural isolates and mutation-accumulation lines. Abstract: The evolutionary importance of gene-expression divergence is unclear: some studies suggest that it is an important mechanism for evolution by natural selection, whereas others claim that most between-species regulatory changes are neutral or nearly neutral. We examined global transcriptional divergence patterns in a set of Caenorhabditis elegans mutation-accumulation lines and natural isolate lines to provide insights into the evolutionary importance of transcriptional variation and to discriminate between the forces of mutation and natural selection in shaping the evolution of gene expression. We detected the effects of selection on transcriptional divergence patterns and characterized them with respect to coexpressed gene sets, chromosomal clustering of expression changes and functional gene categories. We directly compared observed transcriptional variation patterns in the mutation-accumulation and natural isolate lines to a neutral model of transcriptome evolution to show that strong stabilizing selection dominates the evolution of transcriptional change for thousands of C. elegans expressed sequences. An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract. Computed

2006-01-31 | E-GEOD-4123 | biostudies-arrayexpress

Copy number variation in the genomes of twelve natural isolates of Caenorhabditis elegans

Project description:Background: Copy number variation is an important component of genetic variation in higher eukaryotes. The extent of natural copy number variation in C. elegans is unknown outside of 2 highly divergent wild isolates and the canonical N2 Bristol strain. Results: We have used array comparative genomic hybridization (aCGH) to detect copy number variation in the genomes of 12 natural isolates of Caenorhabditis elegans. Deletions relative to the canonical N2 strain are more common in these isolates than duplications, and indels are enriched in multigene families on the autosome arms. Among the strains in our study, the Hawaiian and Madeiran strains (CB4856 and JU258) carry the largest number of deletions, followed by the Vancouver strain (KR314). Overall we detected 510 different deletions affecting 1136 genes, or over 5% of the genes in the canonical N2 genome. The indels we identified had a median length of 2.7 kb. Since many deletions are found in multiple isolates, deletion loci were used as markers to derive an unrooted tree to estimate genetic relatedness among the strains. Conclusion: Copy number variation is extensive in C. elegans, affecting over 5% of the genes in the genome. The deletions we have detected in natural isolates of C. elegans contribute significantly to the number of deletion alleles available to researchers. The relationships between strains are complex and different regions of the genome possess different genealogies due to recombination throughout the natural history of the species, which may not be apparent in studies utilizing smaller numbers of genetic markers.

2009-12-17 | GSE19440 | GEO

Species-wide quantitative transcriptomes and proteomes reveal distinct genetic control of gene expression variation in yeast

Project description:Gene expression varies between individuals and corresponds to a key step linking genotypes to phenotypes. Regulation of transcript and protein abundances can affect the final phenotypes and has been related to many human diseases. However, our knowledge regarding the species-wide genetic control of protein abundance, including its dependency on transcript levels, is very limited. Here, we have determined quantitative proteomes of a large population of 942 diverse natural Saccharomyces cerevisiae yeast isolates. We found that mRNA and protein abundances are weakly correlated at the population gene level (r = 0.165). While the protein co-expression network recapitulates the major biological functions, differential expression patterns reveal proteomic signatures related to specific populations, mainly domesticated. Most importantly, comprehensive genetic association analyses highlight that genetic variants associated with variation in protein (pQTL) and transcript (eQTL) levels poorly overlap (3.6%), with mostly common local QTL. Our results demonstrate that transcriptome and proteome are clearly two distinct layers of regulation, governed by distinct genetic bases in natural populations, and therefore highlight the importance of integrating these different levels of gene expression to better understand the genotype-phenotype relationship. This submission contains the raw files for the wild isolates collection, the library used for the analysis and the corresponding DIA-NN report and associated files.

2024-04-30 | PXD044523 | Pride

Leveraging natural variation in the Saccharomyces cerevisiae stress response to understand lignocellulosic hydrolysate toxicity

Project description:Here, we explored natural variation in stress tolerance and in transcriptomic responses to synthetic hydrolysate, mimicking chemically pretreated plant material, to dissect the physiological effects hydrolysate components. Using six different Saccharomyces cerevisiae strains that together maximized phenotypic and genetic diversity, we explored transcriptomic differences between resistant and sensitive strains. We identified both common and strain-specific responses. Comparing responses of resistant and sensitive strains provided insights about primary cellular targets of hydrolysate toxins, implicating cell wall structure, protein and DNA stability, energy stores and redox balance. Importantly, we uncovered lower expression of thiamine genes while in the presence of toxins, which we argue are most likely an indirect effect that increases sensitivity. We also demonstrate synergistic interactions between the nutrient composition, osmolarity, pH, and classes of hydrolysate toxins. Together, this work provides a platform for further dissecting hydrolysate toxins and strain responses. RNA-seq and transcriptome analysis of six S. cerevisiae natural isolates having different resistant to lignocellulosic hydrolysate. Two biological replicate cell samples (collected on different days) were harvested for RNAseq analysis. Strains were grown in YPD, synthetic hydrolysate without toxins (SynH -HTs), and synthetic hydrolysate with toxins (SynH). Cells were grown for at least three generations to log phase (OD600 ~0.5) and collected by centrifugation.

2016-04-01 | E-GEOD-77505 | biostudies-arrayexpress

yeast wt-matA pool

Project description:Contains a collection of wildtype matA Saccharomyces cerevisiae strains for estimating the biological variation.

2012-11-14 | GSE42240 | GEO

The transcriptional consequences of mutation and natural selection in Caenorhabditis elegans

2006-02-01 | GSE4123 | GEO