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Genome-wide analysis of the BR response in msg2 and axr2

ABSTRACT: Although a wide range of interactions between BRs and auxin have been recognized, knowledge about the direct molecular mechanism of interaction between them in specific physiological processes is very limited. In this study we found that auxin resisitent mutant msg2/iaa19 and arf7 were also resisitant to the BR effect on morphogenensis of dark-grown Arabidosis seedlings. Moreover, BR signaling transcription factor BZR1 can directly bind to promoter regions of IAA19 and ARF7. Microarray analysis revealed that a number of gene transcripts showed reduced BR response in msg2 and the control mutant axr2, suggesting the crucial role of IAA19 in mediating BR effects. Taken together, our results suggested that BRs regulate morphogenesis of dark-grown seedling by employing auxin signaling components IAA19 and ARF7.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE33412 | GEO | 2012/12/16

SECONDARY ACCESSION(S): PRJNA148941

REPOSITORIES: GEO

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Genome-wide analysis of the BR response in msg2 and axr2

Project description:Although a wide range of interactions between BRs and auxin have been recognized, knowledge about the direct molecular mechanism of interaction between them in specific physiological processes is very limited. In this study we found that auxin resisitent mutant msg2/iaa19 and arf7 were also resisitant to the BR effect on morphogenensis of dark-grown Arabidosis seedlings. Moreover, BR signaling transcription factor BZR1 can directly bind to promoter regions of IAA19 and ARF7. Microarray analysis revealed that a number of gene transcripts showed reduced BR response in msg2 and the control mutant axr2, suggesting the crucial role of IAA19 in mediating BR effects. Taken together, our results suggested that BRs regulate morphogenesis of dark-grown seedling by employing auxin signaling components IAA19 and ARF7. Four-day-old seedlings of WT, msg2 and axr2 grown on MS medium in the absence or presence of 24-eBL (100 nM) were used. Total RNA extraction and ATH1 microarray(Affymetrix) experiments were performend according to manufacturerM-bM-^@M-^Ys protocols. Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0. All experiments including two biological replicates and the Pearson correlation coefficient was analyzed to check the replicate quality.

2012-12-16 | E-GEOD-33412 | biostudies-arrayexpress

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

2010-12-31 | GSE25134 | GEO

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.

2024-01-19 | GSE233415 | 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 BZR1 regulated genes were generated from comparing genes differentially expressed by bzr1-1D;bri1-116 and bri1-116. Genes affected by BRI1 were generated from comparing differentially expressed genes of bri1-116 and Col control. ANOVA was used to find genes whose expression was different between bzr1-1D;bri1-116 and bri1-116 or between bri1-116 and Col samples [see Supplementary file below].

2010-12-31 | E-GEOD-25134 | biostudies-arrayexpress

Interaction between gibberellins and brassinosteroids during etiolated growth in Arabidopsis.

Project description:The proper transition between the skotomorphogenic and photomorphogenic developmental programs is key for seedling survival and it is therefore tightly regulated. Besides light, which is the major cue that triggers this transition, several hormone pathways participate in this control, mainly antagonizing the light effect. Two of these hormones are gibberellins (GA) and brassinosteroids (BR). Both hormones promote the skotomorphogenesis and prevent photomorphogenesis, as evidenced by the partially de-etiolated phenotype caused by GA or BR deficiency, or by a blockage in the respective signaling pathways. We have previously shown that BR mediate GA activity in the control of this transition. For instance, treatment of dark-grown, GA-deficient seedlings with BRs was able to partially restore morphological phenotypes such as hypocotyl growth, and importantly to restore completely the molecular phenotype of CAB2 and RbcS gene expression. On the contrary, GA-treatment did not alter the same phenotypes in the BR deficient det2 mutant. Thus, the aim of this study was to investigate to what extent BRs mediate GA activity in dark-grown seedlings, and for that purpose we have the examined global changes in gene expression caused by treatment with GA and BRs in BR- and GA-deficient seedlings, respectively.

2012-08-02 | GSE32889 | GEO

Genome-Wide Analysis Revealed the Complex Regulatory Network of Brassinosteroid Effects in Photomorphogenesis

Project description:Light and brassinosteroids (BRs) have been proved to be crucial in regulating plant growth and development, however, the mechanism of how they synergistically function is still largely unknown. To explore the underlying mechanisms in photomorphogenesis, genome-wide analyses were carried out through examining the gene expressions of the dark-grown WT or BR biosynthesis-defective mutant det2 seedlings in presence of light stimuli, or exogenous Brassinolide (BL). Results showed that BR deficiency stimulates, while BL treatment suppresses, the expressions of light responsive genes and photomorphogenesis, revealing the negative effects of BR in photomorphogenesis. This is consistent with that genes involved in cell wall modification and cellular metabolism were specifically modulated by BL during dark-light transition, and altered expressions of genes related to energy utilization. Further analysis revealed that hormone biosynthesis and signaling related genes, especially those of auxin, were altered under BL treatment or light stimuli, indicating that BR may modulate photomorphogenesis through synergetic regulation with other hormones. Additionally, suppressed ubiquitin-cycle pathway during light-dark transition hinted the presence of a complicated network among light, hormone and protein degradation. The study provides the direct evidence of BR effects in photomorphogenesis and identified the genes involved in BR and light signaling pathway, which will help to elucidate the molecular mechanism of plant photomorphogenesis.

2010-02-10 | GSE14788 | GEO

Antagonistic Regulation of Abscisic Acid Inhibited Root Growth By Brassinosteroid is Partially Mediated by BRASSINAZOLE RESISTENT 1 suppressed ABSCISIC ACID INSENSITIVE 5 expression

Project description:Plant hormone brassinosteroids (BRs) and abscisic acids (ABA) antagonistically regulate many aspects of plant growth and responses. This study analyzes the molecular mechanisms by which regulate the crosstalk between BR and ABA signaling.Various BR deficient and gain-of-function signaling mutants were used to analyze their responses to ABA inhibited primary root growth. RNA sequencing was performed to identify the ABA regulated root genes that are also regulated by BR signaling components.Our result demonstrated that BR signaling negative regulates plant ABA response, and the crosstalk is mediated by BIN2 and BZR1. RNA sequencing has identified subsets of ABA responsive root genes that were regulated by BIN2 and/or BZR1. ChIP-qPCR and EMSA assays showed that BZR1 could bind directly with several G-box cis-elements on ABI5 promoter, suppress the expression of ABI5 and makes plant insensitive to ABA.These data demonstrated that ABI5 is a BZR1 direct targeted gene. Regulation of ABI5 expression by BZR1 plays important roles in regulating the crosstalk between BR and ABA signaling pathways.

2018-11-24 | GSE75377 | GEO

Hydrogen peroxide positively regulates brassinosteroid signaling through oxidation of the BRASSINAZOLE-RESISTANT1 transcription factor

Project description:Hydrogen peroxide (H2O2) is an important signaling molecule in plant developmental processes and stress responses. However, whether H2O2-mediated signaling can crosstalk with plant hormone signaling is largely unclear. Here, we show that H2O2 induces oxidation of the BRASSINAZOLE-RESISTANT1 (BZR1) transcription factor, which functions as a master regulator of Brassinosteroid (BR) signaling. Oxidative modification enhances BZR1 transcriptional activity by promoting its interaction with regulators of auxin- and light-signaling, including AUXIN RESPONSE FACTOR6 (ARF6) and PHYTOCHROME INTERACTING FACTOR4 (PIF4). Genome-wide analysis shows that H2O2-dependent regulation of BZR1 activity plays a major role in modifying gene expression related to several BR-mediated biological processes. Furthermore, we show that the thioredoxin TRXh5 can interact with, and catalyze reduction of, BZR1. We conclude that reversible oxidation of BZR1 connects H2O2- and thioredoxin-mediated redox signaling to BR signaling to regulate plant development

2018-03-21 | GSE110488 | GEO

Transcriptomic and ChIP-Seq analyses reveal an important role for the ABI4 during BR response in Arabidopsis

Project description:Brassinosteroids (BRs) are growth-promoting steroid hormones in plants. BRs affect plant growth by regulating panels of downstream genes. Much effort has been made to establish BR-regulated gene expression networks, but these published expression networks poorly overlap. To address this, here we build an optimal BR-regulated gene expression network. 7- and 24-day-old seedlings of constitutive photomorphogenesis and dwarfism (cpd) mutant and bri1-701 (brassinosteroid-insensitive 1) brl1 (BRI1-like receptor genes 1) brl3 (BRI1-like receptor genes 3) triple mutant seedlings were treated with brassinolide (BL), and RNA sequencing (RNA-seq) was used to detect differentially expressed genes (DEGs). By this approach, we generated a transcriptomic database of 4498 DEGs and identified 110 transcription factors specifically respond to BR at different stage. Moreover, we found that among the identified BR-responsive transcription factors, ABSCISIC ACID-INSENSlTIVE4 (ABI4), an ethylene response factor (ERF) transcription factor, inhibits BR-regulated growth. Compared to wild-type plants, the abi4-102 mutant was less sensitive to brassinazole (BRZ) and more sensitive to BR. Next, we performed a chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) assay and found that ABI4 directly binds to the BAK1 (BRI1 Associated receptor Kinase 1) promoter and inhibits transcription. These results provide new insights into BR-responsive gene functions in regulating plant growth at different stages and may serve as a basis for predicting gene function, selecting candidate genes, and improving the understanding of BR regulatory pathways.

2023-06-17 | GSE152690 | GEO

Spatiotemporal brassinosteroid signaling and antagonism with auxin control Arabidopsis root growth.

Project description:Analysis of brassinosteroid (BR) and auxin effects on gene expression in Arabidopsis roots. Our genomic results indicate that BR and auxin induce largely opposite gene expression responses in primary roots. RNA-Seq for 7-day-old Arabidopsis Col-0, dwf4, bri1-116, and bri1-116;bzr1-1D roots grown on regular medium and treated with brassinolide, auxin or mock solution for 4 hr.

2015-04-30 | E-GEOD-52966 | biostudies-arrayexpress

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