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

ABSTRACT: 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

ORGANISM(S): Arabidopsis thaliana Arabidopsis

PROVIDER: GSE233416 | GEO | 2024/01/19

REPOSITORIES: GEO

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

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

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Effect of BRM on BR-regulated gene expression during growth and development in Arabidopsis

Project description:To clarify the genome-wide role of the BZR1-BAS complexes in BR-regulated transcriptional activation or repression processes, we conducted RNA-sequencing (RNA-seq) assay using Col, bzr1-1D, brm-1, and bzr1-1D brm-1 seedlings grown on the medium containing 2 ?M PPZ in the dark for five days.

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Brassinosteroid mutant (bzr1-1D and det2) analysis

Project description:Brassinosteroid (BR) homeostasis and signaling are crucial for normal growth and development of plants. BR signaling through cell-surface receptor kinases and intracellular components leads to dephosphorylation and accumulation of the nuclear protein BZR1. How BR signaling regulates gene expression, however, remains unknown. Here we show that BZR1 is a transcriptional repressor that has a previously unknown DNA binding domain and binds directly to the promoters of feedback-regulated BR biosynthetic genes. To identify additional BZR1-regulated genes and to understand the BR-regulated transcriptional pathways, we examined the effects of bzr1-1D and det2 mutations on the expression of BR-regulated genes by using the Arabidopsis full-genome oligo microarray (Affymetrix). Microarray analyses identified additional potential targets of BZR1 and illustrated, together with physiological studies, that BZR1 coordinates BR homeostasis and signaling by playing dual roles in regulating BR biosynthesis and downstream growth responses. Keywords: other

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Genome wide BZR1 binding site analysis in Arabidopsis

Project description:BR induces rapid dephosphorylation and nuclear localization of BZR1 through a cascade of signaling events thus regulates BR-responsive gene expression and plant development. We use chromatin-immunoprecipitation microarray (ChIP-chip) experiments identified about 2200 high confidence BZR1 binding sites, which includes all previous known binding regions. The binding sites are distributed throughout the genome but are rare in the centromere regions, which is similar to the distribution of expressed genes. The binding sites were substantially enriched in the 5’ and 3’ intergenic regions compared to the transcribed regions of genes. Combining with transcription profilling of BR regulated genes generated 953 BR regulated BZR1 targets.

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Overexpression of BEH2 regulates a much broader range of gene expression than BZR1

Project description:Based on the distinct phenotypes of BEH2-overexpressing plants, we compared the functional roles of BZR1 and BEH2. The BEH2 is a stronger transcriptional regulator of BR-responsive gene expression than BZR1. It appears that BEH2 also regulates gene expression in a BR-independent manner.

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Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses [RNA-seq]

Project description:Plant growth is coordinately regulated by environmental and hormonal signals. Brassinosteroid (BR) plays essential roles in growth regulation by light and temperature, but the interactions between BR and these environmental signals remain poorly understood at the molecular level. Here, we show that direct interaction between the dark- and heat-activated transcription factor phytochrome-interacting factor4 (PIF4) and the BR-activated transcription factor BZR1 integrates the hormonal and environmental signals. BZR1 and PIF4 interact with each other in vitro and in vivo, bind to nearly two thousand common target genes, and synergistically regulate many of these target genes, including the PRE family HLH factors required for promoting cell elongation. Genetic analysis indicates that BZR1 and PIFs are interdependent in promoting cell elongation in response to BR, darkness, or heat. These results show that the BZR1-PIF4 interaction controls a core transcription network, allowing plant growth co-regulation by the steroid and environmental signals.

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Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses [ChIP-seq]

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Transcription profiling of Arabidopsis Brassinosteroid mutant (bzr1-1D and det2) analysis

Project description:Brassinosteroid (BR) homeostasis and signaling are crucial for normal growth; and development of plants. BR signaling through cell-surface receptor; kinases and intracellular components leads to dephosphorylation and; accumulation of the nuclear protein BZR1. How BR signaling regulates gene; expression, however, remains unknown. Here we show that BZR1 is a; transcriptional repressor that has a previously unknown DNA binding domain; and binds directly to the promoters of feedback-regulated BR biosynthetic; genes. To identify additional BZR1-regulated genes and to understand the; BR-regulated transcriptional pathways, we examined the effects of bzr1-1D; and det2 mutations on the expression of BR-regulated genes by using the; Arabidopsis full-genome oligo microarray (Affymetrix). Microarray analyses; identified additional potential targets of BZR1 and illustrated, together; with physiological studies, that BZR1 coordinates BR homeostasis and; signaling by playing dual roles in regulating BR biosynthesis and downstream; growth responses.

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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

Expression data from dark-grown BR double mutant bzr1-1D;bri1-116, single mutant bri1-116, and wildtype

Project description:Molecular genetic analyses support a central role of BZR1 in Brassinosteroid (BR) regulation of plant development. The dominant bzr1-1D mutation, which stabilizes the BZR1 protein, completely suppresses the de-etiolated phenotype of the null bri1-116 mutant grown in the dark. Using microarray analysis, we identified genes differentially expressed in bri1-116 compared to wild type and genes differentially expressed in the bzr1-1D;bri1-116 double mutant compared to the bri1-116 single mutant. Consistent with the phenotypic suppression of bri1-116 by bzr1-1D, about 80% of the genes affected in bri1-116 were affected oppositely by bzr1-1D

2010-12-31 | GSE25134 | GEO

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