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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of Saccharomyces cerevisiae treated with enediynes compared to gamma radiation

ABSTRACT: We are investigating the transcriptional response of yeast to treatment with enediynes or gamma radiation, which generate different extents of double or single strand breaks in DNA. We used microarrays to detail the global programme of gene expression underlying the DNA damage response in yeast Experiment Overall Design: Yeast were grown to mid log phase and treated with enediynes or gamma radiation (in biological triplicate) resulting in similar extents of cell killing. The responses were compared to each other and we have deciphered a gene expression profile that is specific for double and single strand breaks in DNA.

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Rebecca Fry

PROVIDER: E-GEOD-5301 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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The DNA-damage signature in Saccharomyces cerevisiae is associated with single-strand breaks in DNA.

Fry Rebecca C RC DeMott Michael S MS Cosgrove Joseph P JP Begley Thomas J TJ Samson Leona D LD Dedon Peter C PC

BMC genomics 20061212

<h4>Background</h4>Upon exposure to agents that damage DNA, Saccharomyces cerevisiae undergo widespread reprogramming of gene expression. Such a vast response may be due not only to damage to DNA but also damage to proteins, RNA, and lipids. Here the transcriptional response of S. cerevisiae specifically induced by DNA damage was discerned by exposing S. cerevisiae to a panel of three "radiomimetic" enediyne antibiotics (calicheamicin gamma1I, esperamicin A1 and neocarzinostatin) that bind speci ...[more]

PMID: 17163986

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Expression data from yeast treated with enediynes compared to gamma radiation

Project description:We are investigating the transcriptional response of yeast to treatment with enediynes or gamma radiation, which generate different extents of double or single strand breaks in DNA. We used microarrays to detail the global programme of gene expression underlying the DNA damage response in yeast Keywords: dose

2006-10-16 | GSE5301 | GEO

Transcription profiling of S. cerevisiae with modulated expression of base excision repair players

Project description:We are investigating the transcriptional response of yeast to modulation of the expression of base excision repair players, these generate different dna lesions of abasic sites of strand breaks; We used microarrays to detail the global programme of gene expression underlying the DNA damage response in yeast Experiment Overall Design: Yeaststrains with different expression levels of players in base excision repair (in biological triplicate) were grown to mid log phase. The expression responses were compared to each other and we have deciphered a gene expression profile that is specific for DNA damage in yeast.

2008-06-16 | E-GEOD-9295 | biostudies-arrayexpress

Ribosome profiling upon glucose starvation in S. cerevisiae

Project description:A universal feature of the response to stress and nutrient limitation is transcriptional upregulation of genes encoding proteins important for survival. Interestingly, under many of these conditions overall protein synthesis levels are reduced, thereby dampening the stress response at the level of protein expression. For example, during glucose starvation in yeast, translation is rapidly and reversibly repressed, yet transcription of many stress- and glucose-repressed genes is increased. Using ribosome profiling and microscopy, we found that this transcriptionally upregulated gene set consists of two classes: (1) one producing mRNAs that are preferentially translated during glucose limitation and are diffusely localized in the cytoplasm – this class includes many heat shock protein mRNAs; and (2) another producing mRNAs that are poorly translated during glucose limitation, have high rates of translation initiation, and are concentrated in foci that co-localize with P bodies and stress granules – this class is enriched for glucose metabolism mRNAs. Remarkably, the information specifying differential localization and translation of these two classes of mRNAs is encoded in the promoter sequence – promoter responsiveness to heat shock factor (Hsf1) specifies diffuse cytoplasmic localization and preferential translation upon glucose starvation, whereas different promoter elements upstream of genes encoding poorly translated glucose metabolism mRNAs direct these mRNAs to RNA granules under glucose starvation. Thus, promoter sequences and transcription factor binding can influence not only mRNA levels, but also subcellular localization of mRNAs and the efficiency with which they are translated, enabling cells to tailor protein production to environmental conditions. Examination of mRNA translation in S. cerevisiae upon glucose starvation.

2014-07-28 | E-GEOD-56622 | biostudies-arrayexpress

Acetylation of histone H4 at lysine 44 facilitates meiotic recombination by creating accessible chromatin [Mnase-seq]

Project description:Meiotic recombination hotspots are associated with histone post-translational modifications and open chromatin. However, it remains unclear how histone modifications and chromatin structure directly regulate meiotic recombination. Here, we identify acetylation of histone H4 at Lys44 (H4K44ac) as a new histone modification, occurring on the nucleosomal lateral surface. We show that H4K44ac is specific to yeast sporulation, rising during yeast meiosis and displaying genome-wide enrichment at recombination hotspots in meiosis. The H4K44 residue is required for normal meiotic recombination, for normal levels of double strand breaks during meiosis, and for optimal sporulation. Non-modifiable substitution H4K44R results in reduced MNase digestion and decreased binding of recombination-associated proteins at hotspots. Our results show that H4K44ac creates an accessible chromatin environment for key proteins to facilitate meiotic recombination. Two samples, one WT MNase-seq and one MNase-seq from yeast with a lysine->arginine mutation at H4K44, no replicates Two replicates each of MNase-seq in WT and H4K44->R mutant yeast grown in YPD or YPA.

2015-12-07 | E-GEOD-59004 | biostudies-arrayexpress

Comparison of gene regulation by Gcn5 under KCl stress in S. cerevisiae and S. pombe

Project description:This is parallel comparison of gene regulation by Gcn5 in evolutionarily divergent yeasts S. pombe and S. cerevisiae. Our study showed Gcn5 is required for a similar spectrum of stress responses in both organisms, including the response to KCl. This DNA microarray studies is to find conserved or diverged gene regulation pattern under KCl stress condition in the two yeasts. There are 6 subsets in total, 3 subsets in each evolutionarily divergent yeasts including the following: 1 gcn5 mutant compared to wt under rich medium without treatment, 2 gcn5 mutant compared to wild type both under KCl treatment, 3 wild type strains under KCl treatment compared to wild type without treatment. Keywords: stress response, Gcn5, Comparative genomics, Transcriptional co-activator Gene expression profiling experiment in which gene expression in logarithmically growing cultures of test groups was compared to that of the control groups in rich medium at 25C. There are 6 subsets in total, 3 subsets in each yeast including the following: 1 gcn5 mutant compared to wt under rich medium without treatment, 2 gcn5 mutant compared to wild type both under KCl treatment, 3 wild type strains under KCl treatment compared to wild type without treatment. RNA was extracted and subjected to cDNA expression profiling analysis using the established protocols (Xue et al, 2004). Independent RNA preparations were used to hybridize to microarray slides with dye swap. Data normalized with 'Lowess' per chip per spot normalization.

2010-06-24 | E-GEOD-5218 | biostudies-arrayexpress

Effect of acadesine and overexpression of the karyopherin Kap123 on nuclear abundance of yeast proteins

Project description:Based on genetic and affinity chromatography experiments, the karyopherin Kap123 was identified as an important player in the cellular response to the drug acadesine (AICAR, 5′-phosphoribosyl-5-amino-4-imidazole carboxamide). Since Kap123 mediates nuclear import of multiple proteins we hypothesized that AICAR could affect nuclear trafficking. The effect of acadesine (AICAR) on nuclear trafficking was assayed by comparing protein composition of enriched nuclear extracts from yeast treated or not with AICAR by label-free quantitative analysis. Total protein extracts from the same cultures were also assayed by quantitative mass spectrometry. A parallel analysis was performed on yeast cells grown in the presence of AICAR and overexpressing or not Kap123 to identify those proteins that are enriched in the nuclear fraction when Kap123 was overexpressed.

2018-11-23 | PXD007779 | Pride

Yeast genomic expression patterns in response to zymolyase treatment

Project description:The evaluation of zymolyase treatment using yeast gene expression comparison analysis. The yeast BY4743 strain was used for this study. Yeast cells were treated with Zymolyase (final conc. 300 U/ml), and incubated at 37 degree for ten minutes. Digestion process was not provided for control sample. Total RNA was isolated with commercial kit (FastRNA Pro Red kit, Q-Biogene), and amplified RNA (aRNA) was synthesized with 3'IVT Express kit (Affymetrix). All samples were hybridized with Gene Chip (Yeast Genome 2.0 Array, Affymetrix), then each array chip was scanned by GeneChip Sanner 3000 (Affymetrix). Yeast were treated with zymolyase or left untreated. The only difference in conditions between the treated and untreated samples was the enzymatic digestion process. The conditioned samples were normalized with three replicates.

2013-03-21 | E-GEOD-36955 | biostudies-arrayexpress

Expression data from oxidant treated yeast

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2010-12-30 | E-GEOD-19213 | biostudies-arrayexpress

Transcription profiling by array of yeast cultured in the presence of dendritic cells

Project description:In order to establish the optimal conditions to study expression of genes of S. cerevisiae upon interaction with dendritic cells, Saccaromyces cerevisiae cells were cultured in presence of dendritic cells for 4 hours.<br>Dendritic cells were then treated with zymolase, the yeast cells recovered and lysed. RNA from lysed yeast cells was used for a transcription profiling analysis on Agilent arrays comparing internalized yeast with control yeast.

2010-12-01 | E-MEXP-2679 | biostudies-arrayexpress

Genome-wide Ifh1p occupancy at the OX growth phase and RC quiescent phase of the yeast metabolic cycle

Project description:We found ribosomal transcription factor Ifh1p is dynamically acetylated and phosphorylated in response to nutrient cues. ChIP-seq data revealed dynamic binding to ribosomal genes (RP) during the OX growth phase of the yeast metabolic cycle (YMC) when RP genes are highly induced, and weaker binding in the RC quiescent-like phase. Besides RP genes, our ChIP-seq data also reveals binding of Ifh1p to non-RP genes such as translation factors and metabolic genes. Examination of Ifh1p binding over two timepoints of the YMC (OX, RC) using Input as the control.

2013-07-05 | E-GEOD-39147 | biostudies-arrayexpress

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