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

ABSTRACT: 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.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Maciej Kotliński

PROVIDER: E-GEOD-26848 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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.

2013-03-08 | GSE26848 | GEO

Espression data of control and heat-stressed Arabidopsis WT, hd2c-3, brm-1 and brm-1 hd2c-3 plants

Project description:Studies in yeast and animals have revealed that histone deacetylases (HDACs) often act as components of multiprotein complexes, including chromatin remodeling complexes (CRCs). In our group, we found evidence for the interaction between Arabidopsis HD2C deacetylase and a BRM-containing SWI/SNF chromatin remodeling complex. Moreover, we revealed a novel function of HD2C as a regulator of the heat stress response. HD2C transcript levels were strongly induced in plants subjected to heat treatment and the expression of selected heat-responsive genes was up-regulated in heat-stressed hd2c mutant, suggesting that HD2C acts to down-regulate heat-activated genes. Microarray transcriptome analysis of brm and hd2c mutants identified a subset of commonly regulated heat-responsive genes, and the effect of the double brm hd2c mutation on the expression of these genes was non-additive. Moreover, heat treated hd2c, brm and brm hd2c mutants displayed similar rates of growth retardation. Taken together, our findings suggest that HD2C and BRM act in a common genetic pathway to regulate the Arabidopsis heat stress response. 3-week-old WT (Col-0), hd2c-3, brm-1 and brm-1 hd3c-3 plants were collected before and after 1 hour of heat (38Â°C) treatment. For each variant, three biological replicates with similar expression levels of selected marker genes, were chosen for microarray analysis.

2015-12-04 | E-GEOD-75646 | biostudies-arrayexpress

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

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

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

Espression data of control and heat-stressed Arabidopsis WT, hd2c-3, brm-1 and brm-1 hd2c-3 plants

2015-12-04 | GSE75646 | GEO

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

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

| PRJNA232492 | ENA

Arabidopsis thaliana

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

| PRJNA135969 | ENA

fly brm knockdown RNA-seq

Project description:Drosophila PBAP complex, a form of SWI/SNF class of complexes, played a important role in metamorphosis. We conducted next-generation sequencing (NGS) to analyse the expression profile in both control and Brm knockdown fly larvae.

2014-05-08 | E-MTAB-1966 | biostudies-arrayexpress

RNA-seq Analysis of 14-day-old WT, bcl7a(brip3), bcl7b(brip4), bcl7a bcl7b(brip3 brip4), bcl7a bcl7b brm-3(brip3 brip4 brm-3) and bcl7a bcl7b brm-1(brip3 brip4 brm-1) seedlings under short day condition

Project description:Purpose：Examination of global gene expression of 14-day-old WT, bcl7a(brip3), bcl7b(brip4), bcl7a bcl7b(brip3 brip4), bcl7a bcl7b brm-3(brip3 brip4 brm-3) and bcl7a bcl7b brm-1(brip3 brip4 brm-1) seedlings under short day condition. Methods: Total RNA was extracted from 14-day-old Arabidopsis seedlings under short-day conditions using TRIzol reagent (Invitrogen) following the manufacturer's instructions. RNAs from three biological replicates was sequenced. separately at Novogene, using Illumina Hiseq X-Ten (Sequencing method: Hiseq-PE150). The paired-end RNA-seq reads were quantified by Salmon(Patro et al., 2017) (v1.5.1) with parameters -k 31 and --type quasi. Salmon index was generated using AtRTD2.fa as the reference transcriptome. The gene quantification files of all samples were used as inputs (TPM values) for differential gene expression analysis by DESeq2(Love et al., 2014) v3.10. To analyze differential gene expression in all samples, we used “parametric” Fit type, “ratio” method for estimate Size Factors and Wald significance test function provided by DESeq2. Conclusions: Our study represents the first detailed analysis of bcl7a(brip3), bcl7b(brip4), bcl7a bcl7b(brip3 brip4), bcl7a bcl7b brm-3(brip3 brip4 brm-3) and bcl7a bcl7b brm-1(brip3 brip4 brm-1) transcriptomes, with biologic replicates, generated by RNA-seq technology.

2024-01-03 | GSE215151 | GEO

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