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Wide-type, brm, clf, and brm clf mutant seedlings

ABSTRACT: Wide-type, brm, clf, and brm clf mutant seedlings

PROVIDER: PRJNA232492 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1057660.fastq.gz	Fastqsanger.gz
	SRR1057651.fastq.gz	Fastqsanger.gz
	SRR1057661.fastq.gz	Fastqsanger.gz
	SRR1057652.fastq.gz	Fastqsanger.gz
	SRR1057662.fastq.gz	Fastqsanger.gz

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Genome-wide profiling of trimethylated histone H3 lysine 27 (H3K27me3) in wide-type, brm, clf, and brm clf mutant seedlings

Project description:By using ChIP-seq, we found that loss of BRM activity in developing seedlings leads to ectopic and increased H3K27me3 deposition at several hundred genes, indicating the critical role of BRM in preventing the inappropriate deposition of this histone mark. Removal of CLF in brm mutant could partcially suppress the increased H3K27me3. Examination of H3K27me3 in 14-day-old wt, brm, clf, and brm clf seedlings. Two biological replicates for each one.

2015-03-09 | E-GEOD-53620 | biostudies-arrayexpress

Genome-wide profiling of trimethylated histone H3 lysine 27 (H3K27me3) in wide-type, brm, clf, and brm clf mutant seedlings

2015-03-09 | GSE53620 | GEO

Expression data from Col, brm-1, clf-29 and brm-1 clf-29 14-d-old seedlings

Project description:To understand how actions of the chromatin-remodeler BRAHMA (BRM) and Polycomb Group (PcG) proteins are coordinated during plant development, we performed a genome-wide profiling of trimethylated histone H3 lysine 27 (H3K27me3) in brm mutant seedlings by chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq). Increased H3K27me3 deposition at several hundred genes was observed in brm mutants and this increase was partially supressed upon removal of the CURLING LEAF (CLF) H3K27me3 methyltransferase. ChIP experiments demonstrated that BRM directly binds to a subset of genes and prevents the inappropriate association of PcG proteins at some of the loci. Together, these results indicate a crucial role of BRM in restricting the inappropriate activity of PcG protein complexes during plant development.

2015-03-09 | GSE53621 | GEO

Wide-type, brm, clf, and brm clf mutant seedlings

Project description:This SuperSeries is composed of the SubSeries listed below.

2015-03-09 | GSE53623 | GEO

Genome-wide profiling of trimethylated histone H3 lysine 27 (H3K27me3) in brm mutant seedlings and in wt seedlings

Project description:By using ChIP-seq, we found that loss of BRM activity in developing seedlings leads to ectopic and increased H3K27me3 deposition at several hundred genes, indicating the critical role of BRM in preventing the inappropriate deposition of this histone mark. Unexpectedly, BRM also facilitates PcG function at some PcG targets, suggesting the requirement for BRM in the deposition of this mark at certain PcG target genes. Examination of H3K27me3 in 14-day-old wt and brm seedlings. Two biological replicates for each one.

2014-03-01 | E-GEOD-47202 | biostudies-arrayexpress

Genome-wide profiling of trimethylated histone H3 lysine 27 (H3K27me3) in brm mutant seedlings and in wt seedlings

Project description:By using ChIP-seq, we found that loss of BRM activity in developing seedlings leads to ectopic and increased H3K27me3 deposition at several hundred genes, indicating the critical role of BRM in preventing the inappropriate deposition of this histone mark. Unexpectedly, BRM also facilitates PcG function at some PcG targets, suggesting the requirement for BRM in the deposition of this mark at certain PcG target genes.

2014-03-01 | GSE47202 | GEO

Arabidopsis thaliana seedlings: Wild type vs. sdg26, atx1, sdg25, clf, ldl1 ldl2 and combined mutants

Project description:Transcriptional profiling of 16-day-old seedlings of Arabidopsis wild type control and mutants is performed using AligentM-bM-^@M-^Ys Whole Arabidopsis Gene Expression Microarray (4x44K). Two-condition experiment, seedlings of wild type control vs. Mutant sdg25, sdg26, sdg25 sdg26, atx1, sdg26 atx1, clf, sdg26 clf, ldl1 ldl2, sdg25 ldl1 ldl2 or sdg26 ldl1 ldl2. Three biological replicates: 3 control, 3 each of the ten mutants, independently grown under 12h light/ 12h dark photoperiods and harvested.

2014-12-22 | E-GEOD-55167 | biostudies-arrayexpress

Transcription profiling of Arabidopsis brm-101 and syd-2 mutants 10 day old seedlings

Project description:Global analysis of gene expression in 10 day old brm-101 and syd-2 mutant seedlings compared to wild type Landsberg erecta seedlings. Experiment Overall Design: 3 genotypes (2 mutant, 1 wild type), 2 replicates each

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Polycomb mutant seedlings

Project description:We have identified a histone methyltransferase gene CURLY LEAF (CLF), which is required to repress a floral homeotic gene AGAMOUS (AG). CLF acts redundantly with a related gene SWINGER (SWN), so that clf swn double mutants have extreme, near lethal phenotypes in which expression of many target genes is disrupted. To understand better when and where these genes act, we propose to use a system for generating mosaic plants in which marked sectors of cells are created that gain or lose CLF (or other Pc-G) gene function in SWN+ and swn- mutant backgrounds. This will allow us to address questions such as whether the Pc-G genes are needed throughout development to silence their targets, whether they are needed once cell division has ceased, whether they can silence their targets once the targets have been activated, and whether genes that are epigenetically silenced by CLF are impervious to activating factors. Aim is to compare gene expression in wild-type and polycomb mutant seedlings. Comparison of bulked seedlings of four genotypes: wild-type (Columbia), clf-28, swn-7, clf-28 swn-7 double mutant. 8 samples were used in this experiment, 2 of each genotype. Tissue grown in tissue culture.

2010-04-28 | E-GEOD-20256 | biostudies-arrayexpress

Transcription profiling by array of Arabidopsis seedlings mutant for essp3 and brm

Project description:Synthesis and accumulation of seed storage proteins (SSPs) is an important aspect of the seed maturation program. Genes encoding SSPs are specifically and highly expressed in the seed during maturation. However, the mechanisms that repress the expression of these genes in leaf tissue are not well understood. To gain insight into the repression mechanisms, we have performed a transgenic screening for mutants that express SSPs in leaves. Here we show that mutations of BRAHMA (BRM), a SNF2 chromatin remodelling ATPase, cause the ectopic expression of a subset of SSPs and other embryogenesis related genes in leaf tissue. Consistent with the notion that such SNF2-like ATPases form protein complexes in vivo, we observed similar phenotypes for mutations of AtSWI3C, a BRM interacting partner, and BSH, a SNF5 homolog and essential SWI/SNF subunit. Further, we present chromatin immunoprecipitation evidence that BRM is recruited to the promoters of a number of embryogenesis genes including the 2S genes, which are expressed/elevated in brm leaves. Consistent with its role in nucleosome remodelling, BRM appears to control the chromatin structure of the At2S2 promoter. These results show that a BRM-containing chromatin remodelling ATPase complex is involved in the direct repression of SSPs in leaf tissue. A matrix comprising the signal intensity value of each gene per replicate hybridization and the averaged data of each gene generated from three replicate hybridizations of the wild type and mutant samples, respectively, is linked below as a supplementary file. Experiment Overall Design: Total RNA was isolated from three independent biological replicates of essp3 mutant and Wild type (Pro?CG:GUS)) respectively. Three ATH1 chips were used for the mutant and three for the wild type.

2009-02-07 | E-GEOD-11505 | biostudies-arrayexpress

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