Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE53621 | GEO | 2015/03/09

SECONDARY ACCESSION(S): PRJNA232494

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

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

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

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

Project description:Wide-type, brm, clf, and brm clf mutant seedlings

| PRJNA232492 | ENA

Expression data from Arabidopsis wt and ga1-3, brm-1, ga1-3/brm-1 mutants

Project description:Arabidopsis brm plants depleted in a SWI/SNF-type ATPase BRM have decreased level of endogenous gibberellins and a phenotype that in many respects resembles the phenotype of mutants with repressed GA signaling or biosynthesis, like ga1-3. ga1-3/brm double mutant showed several additive and synergistic effects. To examine whether the phenotypic traits of brm, ga1-3 and ga1-3/brm lines are reflected at the gene expression level, we compared the expression profiles of brm, ga1-3, ga1-3/brm and wild-type plants using microarray analysis. Microarray analysis was performed on total RNA isolated from shoots of 18-d-old wt, brm, ga1-3, and ga1-3/brm seedlings. Three biological replicates were examined for each genotype. Plants were grown simultaneously under the same conditions.

2013-03-08 | E-GEOD-26848 | biostudies-arrayexpress

H3K27 tri-methyltransferases CLF and SWN redundantly buffer ABA-induced senescence

Project description:The phytohormone abscisic acid (ABA) induces senescence and facilitates nutrient reuse, which are essential for increasing stress tolerance. Senescence controls plant aging and is closely associated with crop yield and quality. It is a complicated process finely tuned by multiple layers of control. A significant proportion of ABA-responsive genes and cis-elements are targeted by H3K27me3 modification that is mediated by Polycomb group proteins (PcGs); however, the interplay between the major epigenetic machinery and the central stress hormone is poorly understood. Both pathways influence the transcription of thousands of genes, and the dynamic and quantitative epigenomic and transcriptomic changes cannot be characterized with high confidence. This issue is further complicated by the redundant roles of PcG components. This article revealed an intriguing mechanism of the interplay between ABA and PcG in regulating plant senescence, based on the integration of genetic evidence and quantitative comparison of epigenomic data derived from a purpose-developed computational model. We observed that >30% of ABA-induced genes are up-regulated in a double mutant of H3K27me3 methyltransferases CLF and SWN; and the double mutant, but not single-gene mutants, is hyper-sensitive to ABA treatment. Importantly, ABA-triggered H3K27me3 reduction preferentially occurred in regions around senescence-associated genes (SAGs), which are redundantly repressed by CLF and SWN in normal conditions. Furthermore, we revealed that the presence of H3K27me3 surrounding SAGs does not block ABA-induced SAG expression, but rather limits the extent of the induction, thereby preventing an over-sensitive response within a dynamic environment. These findings may serve as a paradigm for the crosstalk between the rapid-effect of phytohormone and the long-term effect of epigenetic machinery in regulating plant environmental responses through modulations of the senescence process.

2018-12-14 | GSE98301 | 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 SWI/SNF chromatin remodeler BRAHMA (BRM) and BRM Interacting Protein 1/2 (BRIP1/2) in Arabidopsis

Project description:SWI/SNF chromatin remodeling complexes control gene expression by regulating chromatin structure. However, the full subunit composition of SWI/SNF complexes in plants remains unclear. Here we show that BRAHMA Interacting Protein 1 (BRIP1) and BRIP2 in Arabidopsis thaliana are core subunits of plant SWI/SNF complexes. BRIP1 and 2 are two homolog proteins. brip1 brip2 double mutants exhibit developmental phenotypes and a transcriptome strikingly similar to those of BRAHMA (BRM) mutants. Genetic interaction tests indicated that BRIP1 and 2 act together with BRM to regulate gene expression. Furthermore, BRIP1 and 2 physically interact with BRM-containing SWI/SNF complexes, and extensively co-localize with BRM at endogenous genes. Loss-of-brip1brip2 results in decreased BRM occupancy at almost all BRM target genes and substantially reduced subunits incorporation into the BRM-containing SWI/SNF complexes. Together, our work identifies new core subunits of BRM-containing SWI/SNF complexes in plants, and uncovers the essential role of these subunits in regulating the integrity (assembly) of SWI/SNF complexes in plants.

2020-06-21 | GSE142621 | GEO

Genome-wide profiling of BRAHMA (BRM), BZR1, H3K4me3, H3K27me3, and H4K5ac with indicated growth conditions

Project description:To investigate the effect of BR deficiency on BRM occupancy in the genome. Effect of BR on chromatin accessibility during growth and development in Arabidopsis Examination the occupancy of BRM, BZR1, H3K4me3, H3K27me3, and H4K5ac with indicated growth conditions

2024-01-19 | GSE233416 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data