GEO DataSets

(Submitter supplied) For the histone methylation analysis of undifferentiated and differentiated tissues a meristem enriched fraction and young leaves (up to 3 mm leaf blade length) were isolated from clavata3-9 plants. Clavata3-9 mutants harbour larger shoot apical meristems than wild type plants enabling the preparation of meristematic tissue by manual dissection. Samples from both tissues were used for expression and histone H3 lysine 27 trimethylation (H3K27me3) analysis. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL3371

4 Samples

Download data: GFF, PAIR, XLSX

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

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array; Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL6177 GPL3371

8 Samples

Download data: GFF, PAIR, TXT

(Submitter supplied) For the expression analysis of undifferentiated and differentiated tissues a meristem enriched fraction and young leaves (up to 3 mm leaf blade length) were isolated from clavata3-9 plants. Clavata3-9 mutants harbour larger shoot apical meristems than wild type plants enabling the preparation of meristematic tissue by manual dissection. Samples from both tissues were used for expression and histone H3 lysine 27 trimethylation (H3K27me3) analysis. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL6177

4 Samples

Download data: TXT, XLSX

(Submitter supplied) Callus formation is usually a necessary step in regenerating a new plant from detached plant tissues, and the nature of the callus is similar to that of the root meristem. In this study, we intended to address the molecular basis that directs different plant tissues to form the root-meristem-like callus. We found that leaves, but not roots, of the Polycomb group (PcG) double mutant curly leaf-50 swinger-1 lost the ability to form a callus. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

6 Samples

Download data: CEL

(Submitter supplied) In plants, multiple detached tissues are capable of forming a pluripotent cell mass, termed callus, when cultured with appropriate plant hormones. Recent studies demonstrated that callus resembles the tip of a root meristem, even if it is derived from aerial organs. However, the underlying mechanism that guides differentiated organs to form callus is unknown. Here we show that genome-wide reprogramming of histone H3 lysine 27 trimethylation (H3K27me3) is critical in callus formation. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL10977

2 Samples

Download data: BAR, CEL

(Submitter supplied) CHD3 proteins are ATP-dependent chromatin remodeling factors that are components of diverse multisubunit complexes that can either repress or activate gene expression. In plants, the CHD3 protein PICKLE (PKL) is necessary for repression of seed-specific genes during germination and promotes deposition of the repressive epigenetic mark trimethylation of histone H3 lysine 27 (H3K27me3). It is unknown, however, if PKL acts directly at H3K27me3-enriched loci. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

6 Samples

Download data: CEL

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

Organism:

Arabidopsis thaliana

Type:

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

Platform:

GPL13222

25 Samples

Download data: TXT

(Submitter supplied) BACKGROUND: Polycomb group complexes PRC1 and PRC2 repress gene expression at the chromatin level in eukaryotes. The classic recruitment model of Polycomb group complexes in which PRC2-mediated H3K27 trimethylation recruits PRC1 for H2A monoubiquitination was recently challenged by data showing that PRC1 activity can also recruit PRC2. However, the prevalence of these two mechanisms is unknown, especially in plants as H2AK121ub marks were examined at only a handful of Polycomb group targets. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13222

21 Samples

Download data: TXT

(Submitter supplied) BACKGROUND: Polycomb group complexes PRC1 and PRC2 repress gene expression at the chromatin level in eukaryotes. The classic recruitment model of Polycomb group complexes in which PRC2-mediated H3K27 trimethylation recruits PRC1 for H2A monoubiquitination was recently challenged by data showing that PRC1 activity can also recruit PRC2. However, the prevalence of these two mechanisms is unknown, especially in plants as H2AK121ub marks were examined at only a handful of Polycomb group targets. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

4 Samples

Download data: TXT

(Submitter supplied) H3K27me3 is a repressive chromatin mark of genes and is catalyzed by homologs of Enhancer of zeste [E(z)], a component of Polycomb-repressive complex 2 (PRC2), while DNA methylation that occurs in CG and non-CG (CHG and CHH, where H is A, C or T) contexts is a hallmark of transposon silencing in plants. However, relationship between H3K27me3 and DNA methylation in gene repression remains unclear. In addition, the mechanism of PRC2 recruitment to specific genes is not known in plants. more...

Organism:

Oryza sativa Japonica Group

Type:

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

Platforms:

GPL22250 GPL13834

7 Samples

Download data: TAR, TXT, WIG

(Submitter supplied) VAL1 and 2 recruit SWN to targets

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13222

6 Samples

Download data: BW, XLS

(Submitter supplied) The Polycomb repressive complex 2 (PRC2) catalyzes histone H3 Lys27 trimethylation (H3K27me3) to repress gene transcription in multicellular eukaryotes. Despite its importance in gene silencing and cellular differentiation, how PRC2 is recruited to target loci is still not fully understood. Here, we report genome-wide evidence for the recruitment of PRC2 by the transcriptional repressors VIVIPAROUS1/ABI3-LIKE1 (VAL1) and VAL2 in Arabidopsis thaliana. more...

Organism:

Arabidopsis thaliana

Type:

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

Platform:

GPL13222

12 Samples

Download data: TXT

(Submitter supplied) 14-day-old seedling of WT, val1, val2, and val1val2 were performed RNA-seq to analyzed their differential expression genes in Arabidopsis.

Organism:

Arabidopsis thaliana

Type:

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

Platform:

GPL21785

12 Samples

Download data: TXT

(Submitter supplied) Transcriptional profiling of 6-day-old seedlings of Arabidopsis wild type control and zrf1 mutants is performed using Agilent's Whole Arabidopsis Gene Expression Microarray (4x44K).

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL12621

8 Samples

Download data: TXT

(Submitter supplied) ChIP-seq was performed using anti-H3, anti-H3K27me3, and anti-H2A.Z antibodies in three-week-old WT, pkl-1, clf-28, and pie1-5 shoots using paired-end sequencing. Strand-specific RNA-seq was performed on RNA extracted from the same biological samples.

Organism:

Arabidopsis thaliana

Type:

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

Platform:

GPL17639

44 Samples

Download data: BIGWIG, TXT

(Submitter supplied) Using Western blot, we found the level of H3K27me3, but not H3K4me3, H3K9me2 and H3K36me3, was specifically reduced in the tor-es mutant. To gain a genome-wide view of the effects of TOR activity on H3K27me3 distribution, we performed quantitative chromatin immunoprecipitation with an exogenous reference genome (ChIP-Rx) followed by deep-sequencing. We find a global reduction of H3K27me3 occupancy in tor-es, whereas the H3K9me2 level was largely unaffected. more...

Organism:

Arabidopsis thaliana

Type:

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

Platform:

GPL26208

45 Samples

Download data: BW, NARROWPEAK, TXT

(Submitter supplied) SPLAYED (SYD) is a SWItch/Sucrose Non-Fermentable (SWI/SNF)-type chromatin remodeler identified in Arabidopsis thaliana (Arabidopsis). It is believed to play both redundant and differential roles with its closest homolog BRAHMA (BRM) in diverse plant growth and development processes. To better understand how SYD functions, we profiled the genome-wide occupancy of SYD and its impact on the global transcriptome and deposition of trimethylation of histone H3 on lysine 27 (H3K27me3). more...

Organism:

Arabidopsis thaliana

Type:

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

Platforms:

GPL21785 GPL17639

15 Samples

Download data: BW, TXT

(Submitter supplied) 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). more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL7639

6 Samples

Download data: CEL

(Submitter supplied) Histone modifications are essential for chromatin activity and play an important role in many biological processes. Trimethylation of histone H3K27 (H3K27me3) is a repressive modification established by Polycomb repressive complex 2 (PRC2). Although the presence of the histone H3 serine 28 phosphorylation (H3S28ph) modification at adjacent amino acid residues has both positive and negative effects on Polycomb silencing in mammals, little is known about the effect of H3S28ph on H3K27me3-mediated gene silencing in plants. more...

Organism:

Arabidopsis thaliana

Type:

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

Platform:

GPL26208

38 Samples

Download data: BEDGRAPH, TXT

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

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL1979

12 Samples

Download data: CEL