SG200 vs. SG200 delta-tup1
Ontology highlight
ABSTRACT:
ORGANISM(S): Ustilago maydis
SUBMITTER: Jose Ibeas
PROVIDER: E-GEOD-29591 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Plant pathogenic fungi cause massive crop losses and therefore, severe economic deficits. The smut Ustilago maydis, a ubiquitous pest of corn, is highly adapted to its host to parasitize on its organic carbon sources. Recently, we identified the U. maydis sucrose transporter Srt1 to be of crucial importance for biotrophic development. Here we report the identification of Hxt1, a further member of the U. maydis sugar transporter family, which is of importance for full fungal virulence. Hxt1 mainly utilizes the hexoses glucose, fructose and mannose, but with lower affinity also secondary carbon sources like galactose and xylose. Deletion of hxt1 in U. maydis reduces virulence and growth on hexoses, in contrast growth on the secondary carbon sources is enhanced. Expression analysis revealed that monosaccharide-dependent regulation of transcription is hampered in hxt1 deletion mutants, leading to the expression of genes involved in the metabolism of secondary sugars and in the initiation of pathogenicity. Thus, we propose that Hxt1 has a dual function as monosaccharide-transporter and -sensor. While Hxt1 aids the initiation of pathogenicity by sensing starvation conditions on the plant surface as a receptor, it feeds the fungus in planta as a transporter. To analyze expression changes of SG200 and SG200∆hxt1 both strains were grown in glutamine minimal array media supplemented with 1% glucose or 1 %xylose to an OD600 of 1.0 for 6 h, respectively. For each experiment two independent replicates were conducted.
2009-09-29 | E-GEOD-16634 | biostudies-arrayexpress
Project description:We use this array to determine genes under the control of the transcriptional regulator Tup1
2011-08-01 | GSE29591 | GEO
Project description:The budding yeast transcriptional corepressor Tup1-Ssn6 is a model for studying similar repressosome complexes in multicellular eukaryotes. Tup1-Ssn6 does not bind DNA directly, but is directed to individual promoters by one or more DNA-binding proteins, referred to as Tup1 recruiters. We determined the genomic distribution of Tup1 and Ssn6 by ChIP-chip and found that most loci bound by Tup1-Ssn6 could not be explained by co-occupancy with a known recruiting cofactor. Furthermore, we found that individual deletions of known Tup1 recruiters did not significantly alter Tup1 binding profile. These two observations suggest that Tup1 recruitment typically depends on multiple recruiting cofactors, and that new Tup1 recruiting proteins remain to be discovered. To identify new recruiting proteins we computationally screened for factors with binding patterns similar to the observed Tup1-Ssn6 genomic distribution. Four top candidates, Cin5, Skn7, Phd1, and Yap6, all known to be associated with stress response gene regulation, were experimentally confirmed to physically interact with Tup1 and/or Ssn6. Incorporating these new cofactors with previously characterized cofactors now accounts for the majority of Tup1 binding across the genome, and expands our understanding of the mechanism by which Tup1-Ssn6 is directed to its targets.
2011-03-01 | GSE26311 | GEO
Project description:The Tup1-Cyc8 corepressor complex of Saccharomyces cerevisiae is recruited to promoters by DNA-binding proteins to repress transcription of genes, including the a-specific mating type genes. We report here a tup1(S649F) mutant that displays mating irregularities similar to a tup1 null and an a-predominant growth defect. RNA-Seq and ChIP-Seq were used to analyze gene expression and Tup1 binding changes in mutant vs. wild-type in both a and a cells. Increased Tup1(S649F) binding tended to occur upstream of upregulated genes, whereas locations with decreased binding usually did not show changes in gene expression, suggesting this mutant not only loses corepressor function but also behaves as a coactivator. Based upon studies demonstrating a dual role of Tup1 in both repression and activation, we postulate that the coactivator function of Tup1(S649F) results from diminished interaction with repressor proteins, including a2. We also found that large changes in mating type-specific gene expression between a and a or between mutant and wild-type were not easily explained by the range of Tup1 binding levels within their promoters, as predicted by the classic model of a-specific gene repression by Tup1. Most surprisingly, we observed Tup1 binding upstream of the a-specific gene MFA2 and the a-specific gene MF(ALPHA)1 in cells in which each gene was expressed rather than repressed. These results, combined with identification of additional mating related genes upregulated in the tup1(S649F) a strain, illustrate that the role of Tup1 in distinguishing mating types in yeast appears to be both more comprehensive and more nuanced than previously appreciated.
2021-09-01 | GSE173721 | GEO
Project description:The Tup1-Cyc8 corepressor complex of Saccharomyces cerevisiae is recruited to promoters by DNA-binding proteins to repress transcription of genes, including the a-specific mating type genes. We report here a tup1(S649F) mutant that displays mating irregularities similar to a tup1 null and an a-predominant growth defect. RNA-Seq and ChIP-Seq were used to analyze gene expression and Tup1 binding changes in mutant vs. wild-type in both a and a cells. Increased Tup1(S649F) binding tended to occur upstream of upregulated genes, whereas locations with decreased binding usually did not show changes in gene expression, suggesting this mutant not only loses corepressor function but also behaves as a coactivator. Based upon studies demonstrating a dual role of Tup1 in both repression and activation, we postulate that the coactivator function of Tup1(S649F) results from diminished interaction with repressor proteins, including a2. We also found that large changes in mating type-specific gene expression between a and a or between mutant and wild-type were not easily explained by the range of Tup1 binding levels within their promoters, as predicted by the classic model of a-specific gene repression by Tup1. Most surprisingly, we observed Tup1 binding upstream of the a-specific gene MFA2 and the a-specific gene MF(ALPHA)1 in cells in which each gene was expressed rather than repressed. These results, combined with identification of additional mating related genes upregulated in the tup1(S649F) a strain, illustrate that the role of Tup1 in distinguishing mating types in yeast appears to be both more comprehensive and more nuanced than previously appreciated.
2021-09-01 | GSE173720 | GEO
Project description:Comparison between Ustilago maydis cells grown in axenic culture and U. maydis cells from plant tumors. Keywords: developmental stages U. maydis FB1 cells were grown in axenic culture; corn plants were infected with a mixture of strains FB1 and FB2, and tumors were harvested 13 days post infection. SAmples were taken from two biological replicates each.
2010-06-20 | E-GEOD-5804 | biostudies-arrayexpress
Project description:The clp1 gene is a b-regulated gene that is required for clamp formation during the biotrophic growth phase of U. maydis. Clp1 expression blocks b-dependent filament formation and cell cycle arrest if co-induced with the b-heterodimer. Strains AB33 (control) and UMS84 were grown for the times indicated in array medium containing 3 g/l nitrate and 1% arabinose for the induction of nar1P- (bE1/bW2) and crg1P- (clp1) controlled gene expression. Samples were taken from two biological replicates each.
2011-03-30 | E-GEOD-21119 | biostudies-arrayexpress
Project description:The yeast Ssn6-Tup1 complex regulates gene expression through a variety of mechanisms, including positioning of nucleosomes over promoters of some target genes to limit accessibility to the transcription machinery. To further define the functions of Ssn6-Tup1 in gene regulation and chromatin remodeling, we performed genome-wide profiling of changes in nucleosome organization and gene expression that occur upon loss of SSN6 or TUP1, and observed extensive nucleosome alterations in both promoters and gene bodies of derepressed genes. Our improved nucleosome profiling and analysis approaches revealed low-occupancy promoter nucleosomes (P nucleosomes) at locations previously defined as nucleosome-free regions. In the absence of SSN6 or TUP1, this P nucleosome is frequently lost, whereas nucleosomes are gained at -1 and +1 positions, accompanying up-regulation of downstream genes. Our analysis of public ChIP-seq data revealed that Ssn6 and Tup1 preferentially bind TATA-containing promoters, which are also enriched in genes derepressed upon loss of SSN6 or TUP1. These results suggest that stabilization of the P nucleosome on TATA-containing promoters may be a central feature of the repressive chromatin architecture created by the Ssn6-Tup1 corepressor, and that releasing the P nucleosome contributes to gene activation.
2012-10-10 | GSE37466 | GEO
Project description:The Tup1-Cyc8 complex in Saccharomyces cerevisiae was one of the first global co-repressors of gene transcription discovered. The model for Tup1-Cyc8 function proposes that Tup1p mediates the repression activity, whilst Cyc8p recruits the complex to target genes. However, despite years of study, a full understanding of the contribution of Tup1p and Cyc8p to complex function is lacking. We examined TUP1 and CYC8 single and double deletion mutants and show that CYC8 represses more genes than TUP1, and there are genes subject to (i) unique repression by TUP1 or CYC8, (ii) redundant repression by TUP1 and CYC8, and (iii) there are genes at which de-repression in a cyc8 mutant is dependent upon TUP1, and vice-versa. We also reveal that Tup1p and Cyc8p can make distinct contributions to commonly repressed genes possibly via specific interactions with histone deacetylases. Furthermore, we show that Tup1p and Cyc8p can be found independently of each other to negatively regulate gene transcription and can persist at active genes to negatively regulate on-going transcription. Together, these data suggest that Tup1p and Cyc8p can associate with inactive and active genes to mediate distinct negative and positive regulatory roles when functioning within, and possibly out with the complex.
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Project description:The yeast Ssn6-Tup1 complex regulates gene expression through a variety of mechanisms, including positioning of nucleosomes over promoters of some target genes to limit accessibility to the transcription machinery. To further define the functions of Ssn6-Tup1 in gene regulation and chromatin remodeling, we performed genome-wide profiling of changes in nucleosome organization and gene expression that occur upon loss of SSN6 or TUP1, and observed extensive nucleosome alterations in both promoters and gene bodies of derepressed genes. Our improved nucleosome profiling and analysis approaches revealed low-occupancy promoter nucleosomes (P nucleosomes) at locations previously defined as nucleosome-free regions. In the absence of SSN6 or TUP1, this P nucleosome is frequently lost, whereas nucleosomes are gained at -1 and +1 positions, accompanying up-regulation of downstream genes. Our analysis of public ChIP-seq data revealed that Ssn6 and Tup1 preferentially bind TATA-containing promoters, which are also enriched in genes derepressed upon loss of SSN6 or TUP1. These results suggest that stabilization of the P nucleosome on TATA-containing promoters may be a central feature of the repressive chromatin architecture created by the Ssn6-Tup1 corepressor, and that releasing the P nucleosome contributes to gene activation.
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