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

ABSTRACT: 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.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE19635 | GEO | 2010/02/18

SECONDARY ACCESSION(S): PRJNA123989

REPOSITORIES: GEO

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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

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

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.

2010-05-14 | E-GEOD-19634 | biostudies-arrayexpress

Binding and regulation of transcription by yeast Ste12 variants to drive mating and invasion phenotypes

Project description:Here, we examine how six single amino acid variants in the DNA-binding domain of Ste12 – a yeast transcription factor regulating mating and invasion – alter Ste12 genome binding, motif recognition and gene expression to yield markedly different phenotypes. Using a combination of the calling card method, RNA sequencing , we find that variants with dissimilar binding and expression profiles can converge onto similar cellular behaviors.

2020-01-30 | GSE141713 | GEO

Functions of STE12 in Trichoderma reesei

Project description:We investigated the function of the transcription factor STE12 and found an involvement in gene expression and growth in light and darkness

2023-11-02 | GSE222127 | GEO

K. lactis Ste12-myc ChIP-Seq in pheromone-responding a cells

Project description:The purpose of this experiment was to determine the genes directly regulated by Ste12 in K. lactis. The experiment was performed in a cells to determine if the a-specific genes were bound by Ste12. Ste12 was tagged with c-myc and was immunoprecipitated with a c-myc antibody. Cells were starved in SD media lacking phosphate for 2 hours, then treated with 10µg/mL K. lactis alpha factor for 2 hours before harvesting. A control untagged strain was processed in parallel. The experiment was repeated 3 times, and sequenced on an Illumina HiSeq 2500.

2015-07-06 | GSE65792 | GEO

K. lactis Ste12-myc ChIP-Seq in pheromone-responding a cells

2015-07-06 | E-GEOD-65792 | biostudies-arrayexpress

Transcription profiling of S. cerevisiae haploid Sigma1278b strains expressing different combinations and variants of TEC1 and STE12

Project description:We determined and classified Tec1-regulated genes in haploid strains of the Sigma1278b genetic background under vegetative growth conditions. For this purpose, we measured transcriptional profiles of five different haploid MATa yeast strains of the following relevant genotypes: (53 = YHUM1694) TEC1 STE12; (64 = YHUM1700) tec1? STE12; (66 = YHUM1701) tec1? ste12?; (10 = YHUM1676) (P)URA3-TEC1 ste12?; (42 = YHUM1642) (P)URA3-TEC1 1-280-STE12 1-688 tec1? ste12?. All strains were grown in duplicate in SC medium lacking leucine and histidine at 30 degree C to an optical density of 1.0 before extraction of total RNA and transcriptional profiling.

2010-05-22 | E-MEXP-2207 | biostudies-arrayexpress

Genome-wide expression profiling of nematode-trapping fungus Arthrobotrys oligospora ku70 and ste12 strains upon nematode exposure

Project description:We report the transcriptomic comparisions between ku70 control and ste12 mutant strains in nematode-trapping fungus Arthrobotrys oligospora when induced with nematodes. Fungal Ste12 transcription factor and the upstream MAPK cascade are highly conserved and plays a role in host sensing and pathogenesis in various fungal pathogens. Identification of Ste12-dependent in A. oligospora may provide further insights into the molecular mechanisms of nematode-sensing and trap morphogenesis. The reference assemly used for remapping is A. oligospora TWF154 (GenBank assembly accession: GCA_004768765.1)

2020-10-24 | GSE159974 | GEO

Saccharomyces cerevisiae

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

| PRJNA123989 | ENA