Saccharomyces cerevisiae
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA284589 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Centromere-Like Regions in Budding Yeast
| PRJNA145663 | ENA
Project description:Determining the different sources of heritable variation underlying quantitative traits in nature is currently at the forefront of genetic studies. To this end, molecular profiling studies in S. cerevisiae have shown that individual gene expression levels are subject to genetic control and this variation can mediate genetic differences on phenotype. Thus, determining how natural variation influences allele specific expression (ASE) and ultimately complex traits represents a useful tool to determine the mechanisms leading to yeast niche adaptation. Here, in order to test the hypothesis that allele-specific expression differences between isolates contributes to the phenotypic diversity in natural populations, we evaluated ASE levels in a grid of six F1 hybrids from the cross of four representative founder strains from major lineages. Genome-wide and across hybrids we quantified ASE for 3,320 genes. We found evidence for abundant genome-wide expression differences between alleles, with levels ranging between 27% up to 61% of the evaluated genes, depending on the cross. We observed that ASE can be explained by allele-specific differences in transcription factor binding to cis-regulatory regions and differences in strain-specific trans-activation can be detected by taking advantage of the shared trans environment of F1 hybrids. Furthermore, modules of genes under cis-regulatory variation with related function are enriched within the different genetic backgrounds, supporting the premise of intraspecies directional regulatory selection in yeast. Finally, we were able to identify two genes, GDB1 and ASN1 exhibiting high expression levels in the Wine/European strain and underlying phenotypic differences for oenological phenotypes due to polymorphisms within non-coding regions, providing direct evidence of the importance of regulatory variation in natural trait diversity.
2016-05-21 | GSE69115 | GEO
Project description:Natural genetic variation in yeast longevity
| PRJNA161891 | ENA
Project description:Genomic analyses in budding yeast have helped to define the foundational principles of eukaryotic gene expression, but have systematically excluded specific classes of potential coding regions, including those with non-AUG start codons. Without methods to define coding regions empirically, the prevalence of these non-canonical coding regions has been impossible to assess. Here, we applied an experimental approach to globally annotate translation initiation sites in yeast and identified a class of 149 genes that encode N-terminally extended alternate protein isoforms that result from translation initiation at non-AUG codons upstream of the annotated AUG start codon. These alternate isoforms are produced in concert with canonical isoforms and are translated with a high degree of specificity, resulting from initiation at only a small subset of possible start codons in 5’ leader regions. Their translation is enriched during meiosis, and is induced by low eIF5A levels, which are observed in this context. These findings reveal widespread production of non-canonical protein isoforms and, more generally, show unexpected complexity to the rules by which the budding yeast genome is decoded.
2020-07-24 | GSE150375 | GEO
Project description:The molecular chaperone heat shock protein 90 (HSP90) is thought to buffer genetic variation uncoupling phenotypic outcome from individual genotypes. HSP90 thus acts as an evolutionary capacitor by facilitating an accumulation of natural genetic variation. The molecular mechanism underlying the buffering ability is unclear, and HSP90-contingent genetic variation maps both to coding and non-coding parts of the genome. Our genome-wide data indicate that a compromised chaperoning activity of HSP90 causes derepression of endogenous retroviruses (ERVs) in mouse somatic cells. This results in an upregulation of host genes located in the neighborhood of pre-existing ERVs insertion sites. We provide genetic and biochemical evidence that HSP90 cooperates with KAP1/ SETDB1 histone methyltranferase pathway to repress ERVs. Individual mouse strains have unique integration sites of ERVs in their genomes. Consequently distinct genes are responsive to HSP90 inhibitor in different mouse strains depending on the position of the genes vis-à-vis strain-specific ERV insertion sites. Since ERVs have been exapted to drive novel transcriptional networks during mammalian evolution, HSP90 may have acted as a capacitor by buffering variation caused by ERV in non-coding regions of the genome. Our studies provide the first molecular framework by which HSP90 can mitigate genetic variation in gene-regulatory regions affecting gene expression and phenotypes.
2017-01-30 | GSE87119 | GEO
Project description:Deciphering the genetic architecture of human cardiac disorders is of fundamental importance but their underlying complexity is a major hurdle. We investigated the natural variation of cardiac performance in the sequenced inbred lines of the Drosophila Genetic Reference Panel (DGRP). Genome Wide Associations Studies (GWAS) identified genetic networks associated with natural variation of cardiac traits which were used to gain insights as to the molecular and cellular processes affected. Non-coding variants that we identified were used to map potential regulatory non-coding regions, which in turn were employed to predict Transcription Factors (TFs) binding sites. Cognate TFs, many of which themselves bear polymorphisms associated with variations of cardiac performance, were also validated by heart specific knockdown. Additionally, we showed that the natural variations associated with variability in cardiac performance affect a set of genes overlapping those associated with average traits but through different variants in the same genes. Furthermore, we showed that phenotypic variability was also associated with natural variation of gene regulatory networks. More importantly, we documented correlations between genes associated with cardiac phenotypes in both flies and humans, which supports a conserved genetic architecture regulating adult cardiac function from arthropods to mammals. Specifically, roles for PAX9 and EGR2 in the regulation of the cardiac rhythm were established in both models, illustrating that the characteristics of natural variations in cardiac function identified in Drosophila can accelerate discovery in humans.
2022-11-23 | GSE217655 | GEO
Project description:Quantitative variation of epigenetic marks, such as histone modifications, can modify gene expression and eventually contribute to inter-individual phenotypic variation. Our goal is to investigate natural inter-individual variation of the epigenome in a quantitative manner. To probe the degree of natural epigenomic diversity in S. cerevisiae, we compared two unrelated wild strains using replicated Mnase-seq and ChIP-seq profiling at mononucleosomal resolution for H3K14 acetylation.
2015-07-22 | E-MTAB-2671 | biostudies-arrayexpress
Project description:In this study, we measured histone H3Lys4 trimethylation in budding yeast S. cerevisiae for wild type and cnc1Djhd2D yeast mutants. These experiments were performed for yeast cultured to mid-logarithmic phase in non-fermentable carbon.
2017-03-01 | GSE93641 | GEO
Project description:Genome-wide identification of Dal80- and Gat1-bound regions in budding yeast
| PRJNA341383 | ENA
Project description:Genome architecture in budding yeast
| PRJNA378800 | ENA