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Transcription profiling by tiling array of Saccharomyces cerevisiae segregants spores obtained from a cross of the yeast strains S96 and YJM789.

ABSTRACT: Transcription profile in YPD media of 48 segregants spores obtained from a cross of the yeast strains S96 and YJM789. These spores are a subset of those published by Mancera et al, Nature, 2008. Two CEL files were mislabelled: eQTL_080822_spore_38B.CEL and eQTL_080826_spore_21C.CEL, actually spores 24A and 8D respectively. The correct spore IDs are in the sample annotation (under StrainOrLine).

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Charles Girardot

PROVIDER: E-TABM-845 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Environmentally persistent genetic associations with gene expression reveal pathways mediating genetic signals to phenotype

Project description:Unraveling the causal chain of biochemical events that link genotype to phenotype is critical for understanding the molecular basis of genetic diseases and for designing personalized drug therapies. To this end, using yeast as a model system, we carried out joint profiling of fitness and gene expression. Transcription profile includes 4 media (YPD (YPE, YPMalt, YPE and YPD_BPS) of ~35 segregants spores each media were obtained from a cross of the yeast strains S96 and YJM789. These spores are a subset of those published by Mancera et al, Nature, 2008. Sufficient cells were grown at 30 °C in media of interest to the mid log phase. After harvest, gene expression profiling were performed using tiling array as previous described (Xu et al, Nature, 2009). The expression level of each transcript was used as molecular trait for further investigation in the study. 1 CEL data files was mislabelled: 110427_09C_BPS_(Scerevisiae_tlg).CEL.gz, actually spores 09D. The correct spore IDs are in the sample annotation (under StrainOrLine or sample name).

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Genotyping of yeast spores to map meiotic crossovers and non-crossovers across the yeast genome

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Gene Expression of MATa yeast segregants (YJM789 X S96) after alpha factor treatment

Project description:In this study, we mapped for the first time differences in transcription binding among individuals and elucidated the genetic basis of such variation. Whole-genome Ste12 binding profiles were determined using ChIP-Seq in pheromone-treated cells of 43 segregants of a cross between two highly diverged yeast strains, YJM789 and S288c, as well as the parental lines. We identified extensive Ste12 binding variation among individuals and mapped underlying cis- and trans- acting loci responsible for such variation. We showed that the majority of TF binding variation is cis-linked and that many variations are associated with polymorphisms residing in the binding motifs of Ste12 as well as those of several known and proposed Ste12 cofactors. We also identified two trans factors, AMN1 and FLO8, that modulate Ste12 binding to promoters of more than 10 genes under Î±-factor treatment. Neither of these two genes was known to regulate Ste12 previously, and we suggest that they may be key mediators of gene activity and phenotypic diversity. Ste12 binding strongly correlates with gene expression for more than 200 genes, indicating that binding variation is functional. Many of the variable bound genes are involved in cell wall organization and biogenesis. Overall, we identified key regulators of molecular diversity among individuals and provide novel insights into mechanisms of gene regulation. We measured gene expression levels after 30 minutes treatment with alpha factor for 43 MATa segregants from a YJM789 X S96 cross, as well as MATa parental lines. We also measured the gene expression levels without alpha factor treatment for parental lines (S96, HS959) and SEG8 as controls.

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Global Analysis of the Meiotic Crossover Landscape

Project description:Using microarrays to genotype the parental origin of progeny resulting from a cross between S96 and YJM789 yeast strains, we mapped the distribution of crossovers that occurred during meiosis. Knowledge of the crossover distribution allowed us to assess changes in crossover control in wild type and mutant strains. The S96 strain is a S288 derivative and thus its DNA sequence has high homology to the oligo sequences used to create the S98 Affymetrix Gene chip. The YJM789 strain is ~ 0.6% divergent from S288. Keywords: wild type and mutant analysis

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Genome-wide Ste12-binding site mapping in MATa segregants of YJM789 x S96 cross

Project description:In this study, we mapped for the first time differences in transcription binding among individuals and elucidated the genetic basis of such variation. Whole-genome Ste12 binding profiles were determined using ChIP-Seq in pheromone-treated cells of 43 segregants of a cross between two highly diverged yeast strains, YJM789 and S288c as well as the parental lines. We identified extensive Ste12 binding variation among individuals and mapped underlying cis- and trans- acting loci responsible for such variation. We showed that the majority of TF binding variation is cis-linked and that many variations are associated with polymorphisms residing in the binding motifs of Ste12 as well as those of several known and proposed Ste12 cofactors. We also identified two trans factors, AMN1 and FLO8, that modulate Ste12 binding to promoters of more than 10 genes under Î±-factor treatment. Neither of these two genes was known to regulate Ste12 previously, and we suggest that they may be key mediators of gene activity and phenotypic diversity. Ste12 binding strongly correlates with gene expression for more than 200 genes indicating that binding variation is functional. Many of the variable bound genes are involved in cell wall organization and biogenesis. Overall, we identified key regulators of molecular diversity among individuals and provide novel insights into mechanisms of gene regulation. Two ChIP-Seq experiments and one Input DNA-Seq experiment for the yeast strains S96, HS959 and 43 MATa segregants were performed under alpha factor treatment conditions; an additional replicate was also performed for some of the strains. One ChIP-Seq experiment for each parental strain was performed without alpha factor treatment, and one ChIP-Seq experiment for each of the 24 deletion strains was performed under alpha factor treatment.

2010-02-18 | E-GEOD-19635 | biostudies-arrayexpress

Saccharomyces cerevisiae

Project description:Gene Expression of MATa yeast segregants (YJM789 X S96) after alpha factor treatment

| PRJNA123987 | ENA

Saccharomyces cerevisiae

Project description:Genome-wide Ste12-binding site mapping in MATa segregants of YJM789 x S96 cross

| PRJNA123989 | ENA

Genotyping by array of yeast to map post-meiotic segregation across the yeast genome

Project description:To map post-meiotic segregation (PMS) across the yeast genome, we genotyped the two cells resulting from the first mitotic division of the four spores of 4 tetrads of a YJM789/S96 Saccharomyces cerevisiae hybrid strain. Sporulation was induced, tetrads were dissected, spores let to germinate and the two cells coming from the first mitotic division of each spore were finally dissected. DNA from each of the eight cells in each tetrad was extracted from independent overnight cultures in rich medium and hybridized to microarrays, one array per cell. Each hybridization was used to genotype the corresponding cell and genetic differences between the two cells from the same spore revealed PMS. Therefore there are 32 hybridization files, 2 per spore and 8 per tetrad.

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Saccharomyces cerevisiae S96 X YJM789

Project description:Saccharomyces cerevisiae S96 X YJM789 Genome sequencing

| PRJNA217883 | ENA

Gene Expression of MATa yeast segregants (YJM789 X S96) after alpha factor treatment

Project description:In this study, we mapped for the first time differences in transcription binding among individuals and elucidated the genetic basis of such variation. Whole-genome Ste12 binding profiles were determined using ChIP-Seq in pheromone-treated cells of 43 segregants of a cross between two highly diverged yeast strains, YJM789 and S288c, as well as the parental lines. We identified extensive Ste12 binding variation among individuals and mapped underlying cis- and trans- acting loci responsible for such variation. We showed that the majority of TF binding variation is cis-linked and that many variations are associated with polymorphisms residing in the binding motifs of Ste12 as well as those of several known and proposed Ste12 cofactors. We also identified two trans factors, AMN1 and FLO8, that modulate Ste12 binding to promoters of more than 10 genes under α-factor treatment. Neither of these two genes was known to regulate Ste12 previously, and we suggest that they may be key mediators of gene activity and phenotypic diversity. Ste12 binding strongly correlates with gene expression for more than 200 genes, indicating that binding variation is functional. Many of the variable bound genes are involved in cell wall organization and biogenesis. Overall, we identified key regulators of molecular diversity among individuals and provide novel insights into mechanisms of gene regulation.

2010-02-18 | GSE19634 | GEO

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