Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptional profiling of yeast transcription factor deletion strains (rox1, xbp1 or phd1) and wild-type strains in response to hydrogen peroxide or butanol

ABSTRACT: The goal of this study was to determine the effect of transcription factor deletions on the expression of subtelomeric genes in the presence of environmental stimuli. This study is a component of a larger study, which identified that environment-responsive transcription factors bind proto-silencer elements and regulate subtelomeric silencing. Subtelomeric chromatin is subject to evolutionarily conserved complex epigenetic regulation and is implicated in numerous aspects of cellular function including formation of heterochromatin, regulation of different stress response pathways, and control of lifespan. Subtelomeric DNA is characterized by the presence of specific repeated segments that serve to propagate silencing activities or to protect chromosomal regions from spreading epigenetic control. Here, using condition-specific genome wide chromatin immunoprecipitation and expression data, we show that multiple environment-responsive yeast transcription factors act as silencing factors when conditionally associated with subtelomeric proto-silencing regions called X elements. In this context, some factors control the propagation of silencing toward centromeres in response to stimuli affecting stress responses and metabolism, whereas others influence boundaries of silencing, regulating telomere-proximal genes in Y’ elements. These data suggest a fundamental mechanism to coordinate telomere biology related to aging and adaptation with cellular environment and the activities of other cellular processes. Each experiment was performed with two biological and two technical replicates of each condition resulting in a total of four replicates. Each experiment includes two replicates in each labeling orientation (two replicates of Cy3/Cy5 and two replicates of Cy5/Cy3 (test sample/reference sample)). There are two replicates per array.

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Jennifer Smith

PROVIDER: E-GEOD-21926 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Subtelomeric chromatin is subject to evolutionarily conserved complex epigenetic regulation and is implicated in numerous aspects of cellular function including formation of heterochromatin, regulation of different stress response pathways, and control of lifespan. Subtelomeric DNA is characterized by the presence of specific repeated segments that serve to propagate silencing activities or to protect chromosomal regions from spreading epigenetic control. Using condition-specific genome wide chromatin immunoprecipitation and expression data, we show that several yeast transcription factors regulate subtelomeric silencing in response to various environmental stimuli through conditional association with proto-silencing regions called X elements. In this context, some factors control the propagation of silencing toward centromeres in response to stimuli affecting stress responses and metabolism, whereas others appear to influence boundaries of silencing, regulating telomere-proximal genes in Y’ elements. The factors implicated here have previously been shown to control adjacent genes at intrachromosomal positions, suggesting dual functionality of the factors and a possible mechanism of coordinating intrachromosomal gene expression with subtelomeric silencing. These data suggest a fundamental mechanism to coordinate telomere biology related to aging and adaptation with cellular environment and the activities of other cellular processes. These are Chip-CHIP data for myc tagged Oaf1p transcription factor from S. cerevisiae grown in the presence or absence of the fatty acid oleate. ChIP-CHIP analysis was performed to determine the genomic distribution of Oaf1p transcription factor in the BY4742 yeast strain after growth in 0.1% glucose, or in the presence of the fatty acid oleate. Three biological replicates for each growth condition (in the presence of low glucose or 5 h after a shift to medium containing oleate as a carbon source). ChIP samples were amplified by PCR, labelled and hybridized to 50-mer tiling arrays covering both strands of the entire yeast genome at a 64 bp resolution.

Dataset Information

Transcriptional profiling of yeast transcription factor deletion strains (rox1, xbp1 or phd1) and wild-type strains in response to hydrogen peroxide or butanol

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