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Gene expression profile in yeast under physiological changes of stress adaptation and stress recovery

ABSTRACT: The data provide information expression profile in yeast for 5 different physioloigcal conditions during stress adpatation and stress recovery (normal growth, during stress adaptation, after stress adaptation, under stress recovery, after stress recovery) in yeast. The purpose of the study is to understand how histone acetyltransferase HATs (Gcn5) apply it is function in gene regulation by changing global or local histone acetylation level under different physiological conditions.

ORGANISM(S): Schizosaccharomyces pombe Saccharomyces cerevisiae

PROVIDER: GSE36599 | GEO | 2013/07/22

SECONDARY ACCESSION(S): PRJNA155639

REPOSITORIES: GEO

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Genome-wide enrichment of Gcn5 and H3K18/H4K16 acetylation under physiological change of stress adaptation and stress recovery

Project description:The data provide information of Gcn5 enrichment, H3K18 and H4K16 acetylation level and Histone H3 density for 5 different physioloigcal conditions during stress adpatation and stress recovery (normal growth, during stress adaptation, after stress adaptation, under stress recovery, after stress recovery) in yeast. The purpose of the study is to understand how histone acetyltransferase HATs (Gcn5) apply it is function in gene regulation by changing global or local histone acetylation level under different physiological conditions. Gcn5 enrichment, H3K18 and H4K16 acetylation level and Histone H3 density are mearured and compared to input signal for 5 different physioloigcal conditions (normal growth, during stress adaptation, after stress adaptation, under stress recovery, after stress recovery). Replicates are used.

2013-07-22 | E-GEOD-36600 | biostudies-arrayexpress

Gene expression profile in yeast under physiological changes of stress adaptation and stress recovery

Project description:The data provide information expression profile in yeast for 5 different physioloigcal conditions during stress adpatation and stress recovery (normal growth, during stress adaptation, after stress adaptation, under stress recovery, after stress recovery) in yeast. The purpose of the study is to understand how histone acetyltransferase HATs (Gcn5) apply it is function in gene regulation by changing global or local histone acetylation level under different physiological conditions. Gene expression levels measured for at 5 different time points of physiological changes under stress adaptation and stress recovery.

2013-07-22 | E-GEOD-36599 | biostudies-arrayexpress

Genome-wide enrichment of Gcn5 and H3K18/H4K16 acetylation under physiological change of stress adaptation and stress recovery

2013-07-22 | GSE36600 | GEO

Yeast under physiological changes of stress adaptation and stress recovery

Project description:Background Gcn5 belongs to a family of histone acetyltransferases (HATs) that regulate protein function by acetylation. Gcn5 plays several different roles in gene transcription throughout the genome but their characterisation by classical mutation approaches is hampered by the high degree of apparent functional redundancy between HAT proteins. Results Here we utilise the reduced redundancy associated with the transiently high levels of genomic reprogramming during stress adaptation as a complementary approach to understand the functions of redundant protein families like HATs. We show genome-wide evidence for two functionally distinct roles of Gcn5. First, Gcn5 transiently re-localises to the ORFs of long genes during stress adaptation. Taken together with earlier mechanistic studies, our data suggests that Gcn5 plays a genome- wide role in specifically increasing the transcriptional elongation of long genes, thus increasing the production efficiency of complete long transcripts. Second, we suggest that Gcn5 transiently interacts with histones close to the transcription start site of the many genes that it activates during stress adaptation by acetylation of histone H3K18, leading to histone depletion, probably as a result of nucleosome loss as has been described previously. Conclusions We show that stress adaptation can be used to elucidate the functions of otherwise redundant proteins, like Gcn5, in gene transcription. Further, we show that normalization of chromatin-associated protein levels in ChIP experiments in relation to the histone levels may provide a useful complement to standard approaches. In the present study analysis of data in this way provides an alternative explanation for previously indicated repressive role of Gcn5 in gene transcription. Keywords: Gcn5; Gene length; Transcription elongation; Histone acetyltransferase; Stress; Genome-wide association study

2013-07-22 | GSE36601 | GEO

Genome-wide localization of Gcn5 under normal and stress conditions in S. cerevisiae and S. pombe

Project description:Here we studied genome-wide localization of Gcn5 under normal and KCl stress conditions in both yeast species. We found that in Saccharomyces cerevisiae, the enrichment of Gcn5 on genes changes from a relatively even distribution between coding region and intergenic region in the absence of stress, to a predominant localization in gene coding regions under stress conditions. This altered pattern changes are at global level indicates an important role of Gcn5 in modifying chromatin structure for stress adaptation in S. cerevisiae. The altered pattern changes are not observed in Saccharomyces pombe suggesting the different regulatory mechinery between two yeast speices. The related data series is GSE5218, where we have compared the gene regulation of Gcn5 at expression level in S. cerevisiae and S. pombe.

2010-03-01 | GSE16514 | GEO

Gene expression of Arabidopsis leaves under heat stress and during recovery

2015-05-27 | GSE63128 | GEO

Specific acetylase-deacetylase balance controls stress adaptation by modulating global histone H3K14 acetylation.

Project description:Histone acetylation and deacetylation is important for gene regulation. The histone acetyltransferase, Gcn5, is a known activator of transcriptional initiation that is recruited to gene promoters. Here we map genome-wide levels of Gcn5 occupancy and histone H3K14ac at high resolution. Gcn5 is predominantly localized to coding regions of highly transcribed genes where it antagonistically collaborates with the class II histone deacetylase, Clr3, to regulate histone H3K14ac levels. Regulation of histone H3k14ac levels is critical for regulation of many genes during stress adaptation. Our findings suggest a novel role for Gcn5 during transcriptional elongation in addition to its known role in transcriptional initiation. The data in this series showed Gcn5 occupancy and H3K14 acetylation levels in wild type, gcn5- and gcn5-/clr3- cells under KCl stress condition. Related expression data are GSE5227 and GSE13817 Keywords: Chip-chip

2009-08-01 | GSE13790 | GEO

Gene expression of Arabidopsis leaves under heat stress and during recovery

Project description:To understand plant adaptation to heat stress, gene expression profiles of Arabidopsis leaves under heat stress, during recovery and control condition were obtained using microarray. Microarray data listed responsible candidate genes for glycerolipid metabolism. Arabidopsis thaliana ecotype Columbia (Col-0) seeds were surface-sterilised and sown on an agar-solidified Murashige and Skoog medium. Plants were grown at 22ºC under a 16-h-light/8-h-dark cycle. Vegetative plants were subjected to high temperature for a day, then continued to be grown under normal condition for a day.

2015-05-27 | E-GEOD-63128 | biostudies-arrayexpress

Deletion of Clr3 restores expression of a subset of genes in gcn5- mutant cells

Project description:Histone acetylation and deacetylation is important for gene regulation. The histone acetyltransferase, Gcn5, is a known activator of transcriptional initiation that is recruited to gene promoters. Here we map genome-wide levels of Gcn5 occupancy and histone H3K14ac at high resolution. Gcn5 is predominantly localized to coding regions of highly transcribed genes where it antagonistically collaborates with the class II histone deacetylase, Clr3, to regulate histone H3K14ac levels. Regulation of histone H3k14ac levels is critical for regulation of many genes during stress adaptation. Our findings suggest a novel role for Gcn5 during transcriptional elongation in addition to its known role in transcriptional initiation. The related data for this are GSE13790 and GSE5227 Data showed expression pattern of gcn5- vs gcn5-clr3- and clr3- vs wild type under KCl stress in S. pombe. Two biological replicates are used with dye-swap labeling.

2010-06-24 | E-GEOD-13817 | biostudies-arrayexpress

Transcription profiling of yeast recovery after hydrogen peroxide stress

Project description:Yeast cells response during recovery after hydrogen peroxide stress. Comparison of yeast cells treated with 1.5mM hydrogen peroxide for 30 min with cells allowed to recover for 60 min

2006-01-28 | E-MEXP-326 | biostudies-arrayexpress

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