GEO DataSets

(Submitter supplied) In eukaryotic cells, DNA is tightly packed in the nucleus in chromatin which has histones as its main protein component. Histones are subject to a large number of distinct post-translational modifications, whose sequential or combinatorial action affects genome function. Here, we report the identification of acetylation at lysine 36 in histone H3 (H3K36ac) as a modification in Arabidopsis thaliana. H3K36ac was found to be an evolutionary conserved modification in seed plants. It is highly enriched in euchromatin and very low in heterochromatin. Genome-wide ChIP-seq experiments revealed that H3K36ac is generally found at the 5’ end of genes. Independently of gene length, H3K36ac covers about 500 bp, about two to three nucleosomes, immediately downstream of the transcriptional start. H3K36ac overlaps with H3K4me3 and the H2A.Z histone variant. The histone acetyl transferase GCN5 and the histone deacetylase HDA19 are required for normal steady state levels of H3K36ac in plants. There is negative crosstalk between H3K36ac and H3K36me3, mediated by the histone methyl transferase SDG8 and GCN5. H3K36ac levels are associated with transcriptional activity but show no linear relation. Instead, H3K36ac is a binary indicator of transcription

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13222

29 Samples

Download data: BW

(Submitter supplied) Histone lysine (K) acetylation is a major mechanism by which cells regulate the structure and function of chromatin, and new sites of acetylation continue to be discovered. Here we identify and characterize histone H3K36 acetylation (H3K36ac). By mass spectrometric analysis of H3 purified from Tetrahymena thermophila and S. cerevisiae (yeast), we find that H3K36 is acetylated in addition to being methylated. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL4075

16 Samples

Download data: GPR

(Submitter supplied) ChIP-chip experiments were done to analyze the global distribution of H3K36Ac in yeast Keywords: ChIP-chip

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL4075

3 Samples

Download data: GPR

(Submitter supplied) ChIP-chip experiments were done to analyze the global distribution of H3K36Ac in yeast Keywords: ChIP-chip

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL4075

3 Samples

Download data: GPR

(Submitter supplied) ChIP-chip experiments were done to analyze the global distribution of H3K36Ac or H3K9K14Ac in yeast compared to H3 distribution Keywords: ChIP-chip

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL4075

4 Samples

Download data: GPR

(Submitter supplied) ChIP-chip experiments were done to analyze the global distribution of H3K9K14Ac in yeast Keywords: ChIP-chip

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL4075

3 Samples

Download data: GPR

(Submitter supplied) ChIP-chip experiments were done to analyze the global distribution of H3K36Ac in yeast Keywords: ChIP-chip

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL4075

3 Samples

Download data: GPR

(Submitter supplied) In plants, genome stability is maintained during DNA replication by the H3K27 methyltransferases ATXR5 and ATXR6, which catalyze the deposition of H3K27me1 on the replication-dependent H3.1 variant. Loss of H3.1K27me1 in atxr5 atxr6 mutants leads to heterochromatin defects, including transcriptional de-repression and genomic instability, but the molecular mechanisms involved remain largely unknown. In this study, we identified the conserved histone acetyltransferase GCN5 as a mediator of transcriptional de-repression and genomic instability in the absence of H3.1K27me1. GCN5 is part of a SAGA-like complex in plants and requires ADA2b and CHR6 to mediate the heterochromatic defects of atxr5 atxr6 mutants. Our results show that GCN5 acetylates multiple lysine residues on H3.1 variants, but that H3.1K27 and H3.1K36 play key roles in inducing genomic instability in the absence of H3.1K27me1. Overall, this work reveals a key molecular role for H3.1K27me1 in maintaining genome stability by preventing GCN5-dependent histone acetylation in plants.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26208

32 Samples

Download data: BW, TAB

(Submitter supplied) Histone lysine crotonylation (Kcr) is a newly discovered post-translational modification (PTM) existing in mammalian. To assess relevance in histone Kcr and genome, we performed on genomic localization analysis of histone Kcr by ChIP-seq analysis.

Organism:

Oryza sativa Japonica Group

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18525

4 Samples

Download data: TXT

(Submitter supplied) Histone acetylation is involved in the regulation of gene expression in plants and eukaryotes. Histone deacetylases (HDACs) are enzymes that catalyze the removal of acetyl groups from histones, which is associated with the repression of gene expression. To study the role of histone acetylation in the regulation of gene expression during seed germination, trichostatin A (TSA), a specific inhibitor of histone deacetylase, was used to treat imbibing Arabidopsis thaliana seeds. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platforms:

GPL198 GPL71

7 Samples

Download data

(Submitter supplied) Histone acetylation is involved in the regulation of gene expression in plants and eukaryotes. Histone deacetylases (HDACs) are enzymes that catalyze the removal of acetyl groups from histones, which is associated with the repression of gene expression. To study the role of histone acetylation in the regulation of gene expression during seed germination, trichostatin A (TSA), a specific inhibitor of histone deacetylase, was used to treat imbibing Arabidopsis thaliana seeds. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

3 Samples

Download data

(Submitter supplied) Histone acetylation is involved in the regulation of gene expression in plants and eukaryotes. Histone deacetylases (HDACs) are enzymes that catalyze the removal of acetyl groups from histones, which is associated with the repression of gene expression. To study the role of histone acetylation in the regulation of gene expression during seed germination, trichostatin A (TSA), a specific inhibitor of histone deacetylase, was used to treat imbibing Arabidopsis thaliana seeds. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Dataset:

GDS2559

Platform:

GPL71

4 Samples

Download data

Analysis of seeds imbibed for 3 days in the presence of trichostatin A, a specific inhibitor of histone deacetylase. Results provide insight into the role of histone acetylation in the regulation of gene expression during seed germination.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array, count, 2 agent sets

Platform:

GPL71

Series:

GSE3783

4 Samples

Download data

(Submitter supplied) We generated genome-wide high-resolution maps of H4K16ac and H3K23ac in Arabidopsis thaliana and Oryza sativa.

Organism:

Arabidopsis thaliana; Oryza sativa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL13160 GPL13222

5 Samples

Download data: BW

(Submitter supplied) The modification of histones by acetyl groups has a key role in the regulation of chromatin structure and transcription. The Arabidopsis thaliana histone acetyltransferase GCN5 regulates histone modifications as part of the Spt-Ada-Gcn5 Acetyltransferase (SAGA) transcriptional coactivator complex. GCN5 was previously shown to acetylate lysine 14 of histone 3 (H3K14ac) in the promoter regions of its target genes; however, its binding did not systematically correlate with gene activation and the mechanism by which GCN5 controls transcription thus remained unclear. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19580

16 Samples

Download data: BED, BIGWIG

(Submitter supplied) Amino-terminal tails of histones are targets for diverse post-translational modifications whose combinatorial action may constitute a code that will be read and interpreted by cellular proteins to define particular transcriptional states. Here, we describe monomethylation of histone H3 lysine 23 (H3K23me1) as a novel histone modification in plants. H3K23me1 is an evolutionary conserved mark in diverse flowering plant species. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13222

12 Samples

Download data: BW

(Submitter supplied) We analysed genome-wide histone H3 lysine 4 trimethylation and histone H3 lysine 9 acetylation, two modifications typically associated with active genes, in meristematic cells at the base and expanding cells in the maturing zone of the maize (Zea mays) leaf. These data were compared to transcript levels of associated genes. Our data revealed that for individual genes fold-changes in histone modification and transcript abundance were much better correlated than absolute intensities. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17628 GPL15463

6 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by array

Platforms:

GPL9062 GPL198

12 Samples

Download data: CEL, TAR, XLS

(Submitter supplied) 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

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9062

6 Samples

Download data: TAR, XLS

(Submitter supplied) 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. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

6 Samples

Download data: CEL