GEO DataSets

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

Organism:

Populus trichocarpa

Type:

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

Platform:

GPL17415

24 Samples

Download data

(Submitter supplied) We report on the genome-wide distribution pattern of histone H3 lysine 9 acetylation (H3K9ac) and the pattern’s association with whole genome expression profiles in Populus trichocarpa subjected to soil-water depletion. We identified a set of drought responsive genes whose expression is directly regulated by differential modification of H3K9ac.

Organism:

Populus trichocarpa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17415

12 Samples

Download data: TXT

(Submitter supplied) To identify genes that are drought-responsive we conducted drought (soil water depletion) experiments on 3-month-old *P*. *trichocarpa *clonal plants. The plants undergo five different stages based on the appearance of their shoots and leaves during the drought experiments. Stage I: The shoot and leaves are green, and the leaves are well-spread. Stage II: The leaves are droopy. Stage III: The shoot is droopy, and the leaves are partially dry. more...

Organism:

Populus trichocarpa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17415

12 Samples

Download data: XLSX

(Submitter supplied) ChIP-seq was carried out with H3K4me3 antibody using Stem differentiating xylem from wild-type plants under drought conditions

Organism:

Populus trichocarpa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26322

12 Samples

Download data: BW, NARROWPEAK

(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) 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) Populus euphratica is a natural population grown in semirid areas. The molecular response of the poplar to drought maintain to be elucided, especially at global genome level. We used Affymetrix poplar genome genechip microarrays to analyze the full transcript expression underlying different drought intensities and identified significantly differently expressed genes during this process.

Organism:

Populus sp.; Populus euphratica

Type:

Expression profiling by array

Platform:

GPL4359

10 Samples

Download data: CEL

(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) Microarray experiments were performed on the roots and leaves samples seperately using custom based Nimblgen platform (12plex). This is a time-course study. The plants were grown in controlled growth chamber condiditons ambiient to soybean growth and development using a hydrophonics system. The tissues were harvested after 30days of growth in six time points- 0min, 30mins, 1hour, 2hours, 3hours and 5hours of dehydration.

Organism:

Glycine max

Type:

Expression profiling by array

Platform:

GPL17531

36 Samples

Download data: CALLS, PAIR

(Submitter supplied) Transcription regulation in pluripotent embryonic stem (ES) cells is a complex process that involves multitude of regulatory layers, one of which is post-translational modification of histones. Here we have investigated the genome-wide occurrence of two histone marks, acetylation of histone H3K9 and K14 (H3K9ac and H3K14ac), in mouse ES cells. We demonstrate genome-wide that H3K9ac and H3K14ac show very high correlation.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9185

4 Samples

Download data: BED, WIG

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

Organism:

Oryza sativa

Type:

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

Platform:

GPL19290

16 Samples

Download data: TXT

(Submitter supplied) Plant stress response and tolerance mechanisms are controlled by diverse genes. Transcription factors have been implicated in drought tolerance under drought stress conditions. Identification of target genes of such transcription factors could offer molecular regulatory networks by which the tolerance mechanisms orchestrated. Previously, we generated transgenic rice plants with 4 rice transcription factors OsNAC5, 6, 9, and 10 under the root-specific promoter RCc3 that were tolerant to drought stress with less loss of grain yield under drought conditions. more...

Organism:

Oryza sativa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19290

6 Samples

Download data: TXT

(Submitter supplied) To understand the molecular mechanisms of drought tolerance, we performed ChIP-Seq and RNA-Seq analyses to identify direct target genes of the OsNACs using the RCc3:MYC-OsNACs roots. A total of 475 binding loci of 4 OsNACs were identified by cross-referencing the binding occupancy of OsNACs at promoter regions and expression levels of corresponding genes. The binding loci are distributed on promoter regions of 391 target genes that were directly up-regulated by OsNACs in four RCc3:MYC-OsNAC transgenic roots. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19290

10 Samples

Download data: TXT

(Submitter supplied) We reported that ethylene specifically elevated acetylation of histone H3 at K14 and the non-canonical acetylation of histone H3 at K23,but not H3K9ac.Thus, we further performed Chip-sequencing of H3K9Ac, using chromatins isolated from 3-day old etiolated ein2-5 seedlings treated with ethylene or air gas.

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13222

6 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) Recognition of post-translational modifications on histones by epigenetic readers is a fundamental mechanism for the regulation of chromatin and transcription. Compared to the large number of readers that recognize histone methylation, only a few acetyllysine readers have been identified, including bromodomain, YEATS, and double plant homeodomain zinc finger (DPF). Here, we report the identification of a novel reader of histone H3, the ZZ-type zinc finger (ZZ) domain of ZZZ3, a subunit of the Ada-Two-A Containing (ATAC) histone acetyltransferase complex. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL11154

37 Samples

Download data: BW, TXT

(Submitter supplied) In this work, we detected lysinebutyrylation (Kbu) and crotonylation(Kcr) sites in rice histone proteins by mass spectrometry, and found both similar and specific acylation patterns compared with that in mammalian cells. Comparative analysis of genome-wide histone Kbu, Kcr, and H3K9ac in combination of RNA-sequencing revealed that a large number of rice genes are marked by both Kbu and Kcr, most of which overlap with H3K9ac and are active genes. more...

Organism:

Oryza sativa Japonica Group

Type:

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

Platform:

GPL13834

41 Samples

Download data: TXT, XLSX

(Submitter supplied) Although a conserved SAGA complex containing the histone acetyltransferase GCN5 is known to mediate histone acetylation and transcriptional activation in eukaryotes, how to maintain different levels of histone acetylation and transcription at the whole-genome level remains to be determined. Here, we identify and characterize a plant-specific GCN5-containing complex, which we term PAGA, in Arabidopsis thaliana and Oryzae sativa. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26208

21 Samples

Download data: TXT

(Submitter supplied) Although a conserved SAGA complex containing the histone acetyltransferase GCN5 is known to mediate histone acetylation and transcriptional activation in eukaryotes, how to maintain different levels of histone acetylation and transcription at the whole-genome level remains to be determined. Here, we identify and characterize a plant-specific GCN5-containing complex, which we term PAGA, in Arabidopsis thaliana and Oryzae sativa. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26208

12 Samples

Download data: BW

(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 high throughput sequencing

Platform:

GPL26208

81 Samples

Download data: BW

(Submitter supplied) Although the conserved histone acetyltransferase HAG1/GCN5-containing complex SAGA (Spt-Ada-Gcn5 acetyltransferase) has been extensively studied in plants, whether HAG1 forms a plant-specific complex is unknown. Here, we identified a plant-specific GCN5-containing complex, PAGA (plant-ADA2A-GCN5-acetyltransferase), in Arabidopsis thaliana; the complex consists of two conserved subunits (HAG1/GCN5 and ADA2A) and four plant-specific subunits (SPC, ING1, SDRL, and EAF6). more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26208

30 Samples

Download data: TXT