Comparing transcriptomes of wild-type, hyperfilamentous, and hypofilamentous biofilms in S. cerevisiae
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ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE115657 | GEO | 2018/06/13
REPOSITORIES: GEO
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Project description:Cellular processes are subject to variability, or noise, yet mechanisms that promote cell-to-cell uniformity are poorly understood. We have identified such a role for Dig1, a redundant (with Dig2) MAPK-responsive inhibitor of the S. cerevisiae mating pathway transcription factor Ste12. Cells lacking Dig1, but not Dig2, exhibited increased variability in outputs of the mating pathway. dig1∆ mutants also displayed a Ste12-dependent defect in growth in the absence of mating pheromone and a quantitative defect in the process of mating, itself. In cells expressing two reporter genes driven by the same promoter, both intrinsic/uncorrelated and extrinsic/correlated noise were found to increase. Remarkably, the extrinsic noise phenotype in cells lacking Dig1 correlates with the aggregation of target genes: we observed subnuclear foci of Ste12 specifically in dig1∆ cells and, using a newly-developed method to immunoprecipitate a single locus from crosslinked chromatin, we found that Dig1 inhibits long-range interactions between Ste12 target genes in vivo. Dig1 may shield binding surfaces on Ste12 whose unmasking leads to inappropriate gene associations and increased gene expression noise. These studies reveal how investigations of variability modulation mechanisms can yield unexpected biological insights.
2010-12-15 | GSE17583 | GEO
Project description:Cellular processes are subject to variability, or noise, yet mechanisms that promote cell-to-cell uniformity are poorly understood. We have identified such a role for Dig1, a redundant (with Dig2) MAPK-responsive inhibitor of the S. cerevisiae mating pathway transcription factor Ste12. Cells lacking Dig1, but not Dig2, exhibited increased variability in outputs of the mating pathway. dig1∆ mutants also displayed a Ste12-dependent defect in growth in the absence of mating pheromone and a quantitative defect in the process of mating, itself. In cells expressing two reporter genes driven by the same promoter, both intrinsic/uncorrelated and extrinsic/correlated noise were found to increase. Remarkably, the extrinsic noise phenotype in cells lacking Dig1 correlates with the aggregation of target genes: we observed subnuclear foci of Ste12 specifically in dig1∆ cells and, using a newly-developed method to immunoprecipitate a single locus from crosslinked chromatin, we found that Dig1 inhibits long-range interactions between Ste12 target genes in vivo. Dig1 may shield binding surfaces on Ste12 whose unmasking leads to inappropriate gene associations and increased gene expression noise. These studies reveal how investigations of variability modulation mechanisms can yield unexpected biological insights. The FUS1 locus is tagged with an array of lac operators. Wild type and dig1∆ cells containing this tagged FUS1 locus and expressing a mCherry-LacI were grown up for ChIP-chip. The FUS1 locus was selectively immunoprecipitated using an anti-DsRed antibody.
2010-12-15 | E-GEOD-17583 | biostudies-arrayexpress
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
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. K. lactis Ste12-myc vs. untagged control under pheromone response condition with 3 technical replicates done on different days
2015-07-06 | E-GEOD-65792 | biostudies-arrayexpress
Project description:This model is from the article:
Positive roles for negative regulators in the mating response of yeast.
Houser JR, Ford E, Nagiec MJ, Errede B, Elston TC. Mol Syst Biol
2012 June 5;8:586 22669614
,
Abstract:
All cells must detect and respond to changes in their environment, often through changes in gene expression. The yeast pheromone pathway has been extensively characterized, and is an ideal system for studying transcriptional regulation. Here we combine computational and experimental approaches to study transcriptional regulation mediated by Ste12, the key transcription factor in the pheromone response. Our mathematical model is able to explain multiple counterintuitive experimental results and led to several novel findings. First, we found that the transcriptional repressors Dig1 and Dig2 positively affect transcription by stabilizing Ste12. This stabilization through protein-protein interactions creates a large pool of Ste12 that is rapidly activated following pheromone stimulation. Second, we found that protein degradation follows saturating kinetics, explaining the long half-life of Ste12 in mutants expressing elevated amounts of Ste12. Finally, our model reveals a novel mechanism for robust perfect adaptation through protein-protein interactions that enhance complex stability. This mechanism allows the transcriptional response to act on a shorter time scale than upstream pathway activity.
2005-01-01 | MODEL1204040000 | BioModels
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
Project description:The transcription regulators HMS1, RTG1, RTG3, ZCF21, LYS14 and LYS144 play roles in the proliferation of C. albicans in a mammalian host. Chromatin immunoprecipitation (ChIP) of HMS1-MYC, RTG1-MYC, RTG3-MYC, GFP-ZCF21, GFP-LYS14, GFP-LYS144 followed by array hybridization (Agilent) uncovered a network of target genes required for C. albicans to thrive in the host.
2012-10-02 | GSE41237 | GEO
Project description:In Saccharomyces cerevisiae, a heterochromatin-like chromatin structure called the silencing region is present at the telomere as a complex of Sir2, Sir3, and Sir4. Sir2 is a histone deacetylase, and Sir3 and Sir4 promote spreading of the silencing region at the telomere. Histone acetyltransferases restrict the silencing region. Here, we show that Spt3 and Spt8 block the spread of silencing regions. Spt3 and Spt8 are members of the Spt-Ada-Gcn5-acetyltransferase (SAGA) complex, which has histone acetyltransferase activity. Although both Spt3 and Spt8 interact with telomere-binding proteins (TBPs), Spt3 had a greater effect on genome-wide transcription. Mutant analysis showed that TBPs play an important role in boundary formation, in particular the interaction between Spt3 and TBPs.
2023-03-29 | GSE220290 | GEO
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 | GSE19635 | GEO
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