Use of Pleiotropy to Model Genetic Interactions in a Population
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE34787 | GEO | 2012/09/01
SECONDARY ACCESSION(S): PRJNA151043
REPOSITORIES: GEO
Similar Datasets
Project description:Microarray data to analyze differential biology underlying pheromone response and overall mating efficiency in a yeast population One or more samples per strain, collected after 3 hr exposure to alpha-factor at 1uM.
2012-09-01 | E-GEOD-34787 | biostudies-arrayexpress
Project description:Haploid budding yeast has two mating types, defined by the alleles of the MAT locus, MATa and MATα. Mating occurs when two haploid cells of opposite mating types signal to each other using reciprocal pheromones and receptors, polarize and grow towards each other, and eventually fuse to form a single diploid cell. The pheromones and receptors are necessary and sufficient to define a mating type, but other mating type-specific proteins make mating more efficient. We examined the role of these proteins by genetically engineering “transvestite” cells that swap the pheromone, pheromone receptor, and pheromone processing factors of one mating type for another. These cells can mate with each other, but their mating is inefficient. By characterizing their mating defects and examining their transcriptomes, we found Afb1 (a-factor barrier), a novel MATα-specific protein that interferes with a-factor, the pheromone secreted by MATa cells. We show that strong pheromone secretion is essential for efficient mating and that the weak mating of transvestites can be improved by boosting their pheromone production. Using synthetic biology, it is possible to characterize the factors that control efficiency in biological processes. In the case of budding yeast mating, selection for increased mating efficiency is likely to have continually boosted pheromone levels and the ability to discriminate between partners who make more (potentially fitter) and less (potentially less fit) pheromones. This sensitivity to which partner makes more pheromone comes at a cost: it means mating is not robust in situations where all potential partners make less pheromone.
2014-01-07 | GSE49372 | GEO
Project description:Haploid budding yeast has two mating types, defined by the alleles of the MAT locus, MATa and MATM-NM-1. Mating occurs when two haploid cells of opposite mating types signal to each other using reciprocal pheromones and receptors, polarize and grow towards each other, and eventually fuse to form a single diploid cell. The pheromones and receptors are necessary and sufficient to define a mating type, but other mating type-specific proteins make mating more efficient. We examined the role of these proteins by genetically engineering M-bM-^@M-^\transvestiteM-bM-^@M-^] cells that swap the pheromone, pheromone receptor, and pheromone processing factors of one mating type for another. These cells can mate with each other, but their mating is inefficient. By characterizing their mating defects and examining their transcriptomes, we found Afb1 (a-factor barrier), a novel MATM-NM-1-specific protein that interferes with a-factor, the pheromone secreted by MATa cells. We show that strong pheromone secretion is essential for efficient mating and that the weak mating of transvestites can be improved by boosting their pheromone production. Using synthetic biology, it is possible to characterize the factors that control efficiency in biological processes. In the case of budding yeast mating, selection for increased mating efficiency is likely to have continually boosted pheromone levels and the ability to discriminate between partners who make more (potentially fitter) and less (potentially less fit) pheromones. This sensitivity to which partner makes more pheromone comes at a cost: it means mating is not robust in situations where all potential partners make less pheromone. 4 conditions were analysed, each with 3 biological replicates. The conditions were unstimulated MATa cells in YPD. Stimulated MATa cells in YPD+10nM M-NM-1-factor. Unstimulated MATM-NM-1 cells in YPD. Stimulated MATM-NM-1 cells in YPD+10nM M-NM-1-factor.
2014-01-07 | E-GEOD-49372 | biostudies-arrayexpress
Project description:Systems-level genetic studies in humans and model systems increasingly involve both high-resolution genotyping and multi-dimensional quantitative phenotyping. We present a novel method to infer and interpret genetic interactions that exploits the complementary information in multiple phenotypes. We applied this approach to a population of yeast strains with randomly assorted perturbations of five genes involved in mating. We quantified pheromone response at the molecular level and overall mating efficiency. These phenotypes were jointly analyzed to derive a network of genetic interactions that mapped mating-pathway relationships. To determine the distinct biological processes driving the phenotypic complementarity, we analyzed patterns of gene expression to find that the pheromone response phenotype is specific to cellular fusion, whereas mating efficiency was a combined measure of cellular fusion, cell cycle arrest, and modifications in cellular metabolism. We applied our novel method to global gene expression patterns to derive an expression-specific interaction network and demonstrate applicability to global transcript data. Our approach provides a basis for interpretation of genetic interactions and the generation of specific hypotheses from populations assayed for multiple phenotypes.
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Project description:Kar4 is a putative transcription factor essential for mating in the budding yeast Saccharomyces cerevisiae. Kar4 has been shown to function with Ste12, the master transcriptional regulator of the yeast mating pheromone response, to promote the transcription of a subset of Ste12 targets required for efficient mating. However, the mechanism by which Kar4 modulates Ste12 activity has remained uncertain. Here, we examine the effect of Kar4 on the mating pheromone response via ChIP-exo
2025-12-08 | GSE306667 | GEO
Project description:Kar4 is a putative transcription factor essential for mating in the budding yeast Saccharomyces cerevisiae. Kar4 has been shown to function with Ste12, the master transcriptional regulator of the yeast mating pheromone response, to promote the transcription of a subset of Ste12 targets required for efficient mating. However, the mechanism by which Kar4 modulates Ste12 activity has remained uncertain. Here, we examine the effect of Kar4 on the mating pheromone response at the levels of transcription (RNA-seq)
2025-12-08 | GSE306669 | GEO
Project description:In yeast, the mating pheromone α-factor triggers a signaling cascade in haploid "a" cells, leading to G1 cell cycle arrest, polarized growth ("shmoo" formation), cell wall remodeling, and ultimately cell fusion. While the physiological responses to α-factor are well established, a genome-wide analysis of transcriptional changes in response to α-factor has not been previously reported. Here, we performed RNA sequencing (RNA-seq) to profile gene expression changes in "a" mating type yeast cells treated with α-factor. We identified 957 differentially expressed genes (DEGs), including 448 upregulated and 509 downregulated genes. Gene ontology (GO) analysis revealed enrichment of upregulated genes in pheromone signaling, cell wall biogenesis, and cell shape regulation. In contrast, downregulated genes were mainly associated with cell cycle progression, chromatin remodeling, histone gene expression, and nucleosome organization. Our dataset validates known pheromone-responsive genes and identifies novel candidates potentially involved in mating responses. These findings provide a valuable resource for understanding how transcriptional regulation and chromatin dynamics are coordinated during pheromone signaling in yeast.
2025-12-31 | GSE303575 | GEO
Project description:Transcriptome changes associated with mating interactions were performed in order to identify signaling components and targets of pheromone response. Two monokaryons (S. commune 12-43 and 4-39), a dikaryon (W22 x 12-43), both semi-compatible mating interactions (Aon: W22 x 4-39; Bon, flat: W21 x 4-39), and different S. commune pheromone receptor recipient strains (Vbar2f, Vbar2t) were analyzed for that purpose. In addition, a S. commune strain showing the thin-phenotype (W22-thin) was investigated to figure out the role of Thn1 in mating.
2012-06-15 | GSE26401 | GEO
Project description:Gene expression in G1 stage of Yeast strain BY4741 treated with alpha -factor mating pheromone to investigate nucleosome plasticity
2014-03-01 | E-MTAB-2195 | biostudies-arrayexpress
Project description:The regulation of cell cycle progression in response to environmental cues is essential for cellular adaptation. In Saccharomyces cerevisiae, the BAR1 gene modulates sensitivity to the mating pheromone α-factor, which induces cell cycle arrest. Here we investigated the dynamic proteomic response in the bar1 deletion strain using a 27-plex experimental design with TMTproD isobaric labeling. Asynchronous bar1Δ cells were arrested with α-factor and then released from the pheromone arrest. We acquired three replicate protein abundance time-course profiles following pheromone (α-factor) washout, with samples collected at eight time points from 0 to 165 minutes post-washout. Using higher-order TMTpro sample multiplexing, we generated global temporal profiles of protein abundance associated with recovery from pheromone-induced arrest. Our findings identify specific proteins and pathways involved in cell cycle re-entry and in the attenuation of the pheromone signal, providing insights into the regulatory mechanisms of mating response in yeast. This study contributes significantly to dynamic proteomic analysis in cell cycle progression. We present a powerful approach for investigating complex cellular processes and showcase cell cycle progression following pheromone washout in yeast.
2025-11-24 | PXD059092 | Pride