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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Chromatin immunoprecipitation and RNA-seq analysis in purified quiescent yeast cells to identify the genomic RNA polymerase II and histone H3 methylation occupancy profiles and the transcriptome

ABSTRACT: A defining characteristic of quiescent cells is their low level of gene activity compared to growing cells. Using a yeast model for cellular quiescence, we compared the genome-wide profiles of multiple histone modifications between growing and quiescent cells, and correlated these profiles with the presence of RNA polymerase II and its transcripts. Quiescent cells retained several forms of histone methylation normally associated with transcriptionally active chromatin and had many transcripts in common with growing cells. Quiescent cells also contained high levels of RNA polymerase II, but only low levels of the canonical initiating and elongating forms of the polymerase. The data suggest that the transcript and histone methylation marks in quiescent cells were either inherited from growing cells or established early during the development of quiescence and then retained in this non-growing cell population. This might ensure that quiescent cells can rapidly adapt to a changing environment to resume growth. Immunoprecipitation experiments were carried out for Pol II, H3K36me3, H3K4me3, H3K79me3 and H3 separately using both Log-phase and Quiescent cells. Each ChIP-chip assay was conducted using a control (IN) and in all instances, at least one replicate experiment was performed.

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Mary Ann Osley

PROVIDER: E-GEOD-72802 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Chromatin immunoprecipitation and RNA-seq analysis in purified quiescent yeast cells to identify the genomic RNA polymerase II and histone H3 methylation occupancy profiles and the quiescent cell transcriptome.

Project description:A defining characteristic of quiescent cells is their low level of gene activity compared to growing cells. Using a yeast model for cellular quiescence, we compared the genome-wide profiles of multiple histone modifications between growing and quiescent cells, and correlated these profiles with the presence of RNA polymerase II and its transcripts. Quiescent cells retained several forms of histone methylation normally associated with transcriptionally active chromatin and had many transcripts in common with growing cells. Quiescent cells also contained high levels of RNA polymerase II, but only low levels of the canonical initiating and elongating forms of the polymerase. The data suggest that the transcript and histone methylation marks in quiescent cells were either inherited from growing cells or established early during the development of quiescence and then retained in this non-growing cell population. This might ensure that quiescent cells can rapidly adapt to a changing environment to resume growth. RNA-seq analysis was performed in yeast Log-phase cells and purified Quiescent yeast cells and the transcriptomes in each were compared. The RNA data was correlated with genomic RNA polymerase II and histone H3 methylation occupancy profiles in the log and quiescent cells.

2016-09-01 | E-GEOD-72650 | biostudies-arrayexpress

Histone 3 lysine 4 trimethylation (H3K4me3) ChIP in bas1 and ino4 mutants

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2015-08-21 | E-GEOD-67907 | biostudies-arrayexpress

Chip-seq analysis of hrpRSL and Lon in Pseudomonas syringas

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Molecular mechanisms of two-component system RhpRS regulating type III secretion system in Pseudomonas syringae

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2014-10-01 | E-GEOD-58533 | biostudies-arrayexpress

Genome-wide mapping of the binding sites of transcription factor Cst6p in Saccharomyces cerevisiae

Project description:The transcription factor Cst6p in Saccharomyces cerevisiae has been reported to play important roles in several biological processes. However, the genome-wide targets of Cst6p and the mechanisms for its physiological functions remain unknown. Here, we mapped the genome-wide binding sites of Cst6p with ChIP-exo at high resolution. Cst6p binds to the promoter regions of 59 genes with various biological functions when cells are grown on ethanol, but hardly binds to the genome on glucose. The growth deficiency of CST6 deletion mutant on ethanol is attributed to the markedly decreased expression of carbonic anhydrase gene NCE103, which is a direct target of Cst6p. The target genes of Cst6p have a large overlap with those of stress-responsive transcription factors, such as Sko1p and Skn7p. In addition, the CST6 deletion mutant growing on ethanol shows hypersensitivity to oxidative stress and ethanol stress, assigning Cst6p as a new member of the stress-responsive transcriptional regulatory network. These results show that genome-wide binding site mapping is able to provide new insights into the function of transcription factors, and highlight the highly connected and condition-dependent nature of the transcriptional regulatory network in S. cerevisiae. The binding sites of Cst6p when cells were grown in glucose or ethanol were measured in biological duplicates, so there are four samples in total.

2016-04-04 | E-GEOD-76154 | biostudies-arrayexpress

Map of DnaC localization in the presence or absence of PcrA (PcrA depletion)

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2014-03-10 | E-GEOD-54305 | biostudies-arrayexpress

Genome-wide identification of RNA polymerase, RpoD, and RpoS binding sites in Klebsiella pneumoniae MGH 78578

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2012-12-31 | E-GEOD-35927 | biostudies-arrayexpress

ORC precisely positions nucleosomes at origins of replication

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2010-03-19 | E-GEOD-16926 | biostudies-arrayexpress

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2014-08-04 | E-GEOD-57284 | biostudies-arrayexpress

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