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The association between gene expression and whole genome histone H3K4 mono-, di, and trimethylation

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

OTHER RELATED OMICS DATASETS IN: PRJNA109137E-GEOD-11538PRJNA106165PRJNA109153

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE11658 | GEO | 2010/12/07

SECONDARY ACCESSION(S): PRJNA106165

REPOSITORIES: GEO

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The association between gene expression and whole genome histone H3K4 mono-, di, and trimethylation: expression data

Project description:These microarrays are part of a study where a comparison was made between the change in transcription and H3K4 mono-, di-, and tri-methylation levels (via ChIP-seq) in the Arabidopsis thaliana genome when plants are subjected to water deficit stress. Water deficit stress causes a large number of genes to change their transcript levels, which provided a large set of genes to examine for corresponding chromatine changes. Keywords: stress response Arabidopsis thaliana RNA was isolated from control (watered) and treatment (water-deficit) samples for analysis on microarrays with three biological reps.

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The association between gene expression and whole genome histone H3K4 mono-, di, and trimethylation: expression data

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The association between gene expression and whole genome histone H3K4 mono-, di, and trimethylation: ChIP-seq data

Project description:These ChIP-seq data files are part of a study where a comparison was made between the change in transcription and H3K4 mono-, di-, and tri-methylation levels in the Arabidopsis thaliana genome when plants are subjected to water deficit stress. Keywords: stress response, histone modification

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Genome-wide Analysis of Mono-, Di- and Trimethylation of Histone H3 Lysine 4 in Arabidopsis thaliana

Project description:Background. Post-translational modifications of histones play important roles in regulating transcription by modulating the structural properties of the chromatin. In plants, methylation of histone H3 lysine4 (H3K4me) is associated with genes and required for normal plant development. Results. We have characterized the genome-wide distribution patterns of mono-, di- and trimethylation of H3K4 (H3K4me1, H3K4me2 and H3K4me3, respectively) in Arabidopsis thaliana using chromatin immunoprecipitation and high-resolution whole-genome tiling microarrays (ChIP-chip). All three types of H3K4me are found to be almost exclusively genic, and two thirds of Arabidopsis genes contain at least one type of H3K4me in seedlings. H3K4me2 and H3K4me3 accumulate predominantly in promoters and 5’ genic regions, whereas H3K4me1 is distributed within transcribed regions. In addition, H3K4me3-containing genes are highly expressed with low levels of tissue specificity, but H3K4me1 or H3K4me2 may not be directly involved in transcriptional activation. Furthermore, a genome-wide preferential co-localization of H3K4me3 and H3K27me3 found in mammals does not appear to exist in plants, but H3K4me2 and H3K27me3 co-localize at a higher-than-expected frequency. Finally, the relationship between H3K4me and DNA methylation was explored by comparing the genome-wide distribution patterns of H3K4me1, H3K4me2 and H3K4me3 in wild type plants and the met1 DNA methyltransferase mutant. Conclusions. H3K4me plays widespread roles in regulating gene expression in plants. Although many aspects of the mechanisms and functions of H3K4me appear to be conserved among all three kingdoms, we observed significant differences in the relationship between H3K4me and transcription or other epigenetic pathways in plants and mammals.

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Histone H3R2 symmetric dimethylation and histone H3K4 trimethylation are tightly correlated in eukaryotic genomes.

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Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis.

Project description: Not available