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E-GEOD-4135

ABSTRACT: Transcription profiling of S. cerevisiae wild type and amino-terminal mutant histone H3 and H4 strains

OTHER RELATED OMICS DATASETS IN: PRJNA95017

PROVIDER: E-GEOD-4135 | ExpressionAtlas | 2015-10-12

REPOSITORIES: ExpressionAtlas

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			Action	DRS
	E-GEOD-4135-analysis-methods.tsv	Tabular
	E-GEOD-4135-atlasExperimentSummary.Rdata	Rdata
	E-GEOD-4135-configuration.xml	Xml
	E-GEOD-4135-percentile-ranks.tsv	Tabular
	E-GEOD-4135.condensed-sdrf.tsv	Tabular

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Testing the effect of histone native chemical ligation on protein binding to di-nucleosomes

Project description:Here we examined whether histones H3 and H4 produced using native chemical ligation reaction affect protein binding to di-nucleosomes. To test this we performed a set of affinity purification pull-downs using di-nucleosomes containing the following histones H3 and H4: 1. unmodified ligated histone H3 and recombinant wild type histone H4 (unmod. H3), 2. recombinant wild type histone H3 and ligated unmodified histone H4 (unmod. H4) 3. ligated unmodified histones H3 and H4 (unmod. H3&H4). 4. recombinant wild type histones H3 and H4 (WT) Each pull-down was performed in three replicates. Co-purified proteins were quantified using label-free MS. Note that ligated histones H3 and H4 contain T32C or I29C single amino acid substitutions, respectively, that are introduced by the native chemical ligation procedure. In addition, ligated histone H4 is N-terminally acetylated to mimic its naturally blocked N-terminus.

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Control pull-downs testing the effect of histone native chemical ligation on protein binding to di-nucleosomes

Project description:Here we examined whether histones H3 and H4 produced using native chemical ligation reaction affect protein binding to di-nucleosomes. To test this we performed a set of affinity purification pull-downs using di-nucleosomes containing the following histones H3 and H4: 1. ligated unmodified histone H3 and recombinant wild type histone H4 (unmod. H3), 2. recombinant wild type histone H3 and ligated unmodified histone H4 (unmod. H4) 3. ligated unmodified histones H3 and H4 (unmod. H3&H4). 4. recombinant wild type histones H3 and H4 (WT) Each pull-down was performed in three replicates. Co-purified proteins were quantified using label-free MS. Note that ligated histones H3 and H4 contain T32C or I29C single amino acid substitutions, respectively, that are introduced by the native chemical ligation procedure. In addition, ligated histone H4 is N-terminally acetylated to mimic its naturally blocked N-terminus.

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Wild type yeast and H3del(1-28) and H4del(2-26) yeast grown in complete synthetic media

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Project description:Yeast lacking the H3 or H4 amino termini, and corresponding wild type strains, were grown in synthetic media. These conditions induce Gcn4-activated transcription. Experiment Overall Design: Three replicates of the H4del(2-26) and corresponding wild type strains, and four replicates of the H3del(1-28) and corresponding wild type strains, were performed. Note the strains are congenic, but differ in whether the histones were present on TRP1 marked (H4) or LEU2 marked (H3) plasmids. Samples were analysed using Affymetrix S98 microarrays.

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Project description:Total RNA samples from three replicate cultures of wild type and mutant yeast strains was isolated and expression profile done using Affymetrix arrays. Comparsion between the samples indicate how mutation in a single amino acid residue in histone H4 (H4R45H) affects gene expression in yeast. Such a mutation in histone H4 is known to generate a specific class of mutants called SWI/SNF independent (SIN) mutants, and the mutants were identified by their ability to carry out transcription in the absence of yeast chromatin remodeling complex SWI/SNF. SIN mutations are known to affect higher order chromatin structure and the comparative expression profile would help identification of genes which get affected by such altered chromatin landscape. Experiment Overall Design: Comparison of genes whose mRNA levels are affected in histone H4R45H mutant yeast strains compared to wild type yeast strain WY139. This comparison reveals how subtle change in a single amino acid residue in core domain of histone H4 affects gene expression profile in yeast.

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Comparison of yeast (Saccharomyces cerevisiae) strain with histone H4 R45 mutated to H with wild type yeast strain WY139

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