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Genome-wide mapping of BES1 binding sites in Arabidopsis thaliana

ABSTRACT: Brassinosteroids (BRs) are important regulators for plant growth and development. BRs signal to control the activities of the BES1 and BZR1 family transcription factors. In order to further understand the mechanism by which BES1/BZR1 regulates downstream genes, we performed chromatin immunoprecipitation coupled with tiling arrays (ChIP-chip) to identify BES1 binding sites in the genome. By combining ChIP-chip data with gene expression microarray data, we are able to discover genes that are directly regulated by BES1 (i.e. BES1 target genes).

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE24684 | GEO | 2011/01/02

SECONDARY ACCESSION(S): PRJNA132371

REPOSITORIES: GEO

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Genome-wide mapping of BES1 binding sites in Arabidopsis thaliana

Project description:Brassinosteroids (BRs) are important regulators for plant growth and development. BRs signal to control the activities of the BES1 and BZR1 family transcription factors. In order to further understand the mechanism by which BES1/BZR1 regulates downstream genes, we performed chromatin immunoprecipitation coupled with tiling arrays (ChIP-chip) to identify BES1 binding sites in the genome. By combining ChIP-chip data with gene expression microarray data, we are able to discover genes that are directly regulated by BES1 (i.e. BES1 target genes). Chromatin from bes1-D Arabidopsis seedlings are immunoprecipitated by anti-BES1 antibody with anti-GFP antibody as control.

2011-01-02 | E-GEOD-24684 | biostudies-arrayexpress

Transcriptomic profiling of CRISPR/Cas9-generated mutant of Marchantial polymorpha BES1 transcription factor (Mpbes1)

Project description:Brassinosteroid hormones are essential for growth and development in seed plants. In Arabidopsis, transcriptional factors from the AtBES1 (BRI1-EMS-SUPPRESSOR1)/AtBZR1 (BRASSINAZOLE-RESISTANT 1) family, are main regulators of steroid phytohormone Brassinosteroids, which finely coordinate gene expression. While genome sequence analysis in Marchantia polymorpha failed to identify BR receptors homologues to the BRI1-family, a homologue of downstream BR-regulated BES1/BZR1 transcription factors is present. Here, we decipher the biological function of MpBES1 in liverwort. Mpbes1 knock out plants have impaired thallus development, pointing up the conservation of BES1 function in organ development. RNAseq analysis of Mpbes1 reveals a prominent deregulation of oxidation processes, responses to stress and carbohydrate metabolism. Furthermore, in the Arabidopsis orthologs of Mpbes1 deregulated genes, described targets of AtBES1/BZR1 are overrepresented, suggesting a major conservation in the signaling module. In conclusion, this study unravels the origin of BES1/BZR1 family of transcriptional factors in plant cell division.

2021-03-15 | GSE166913 | GEO

RAV1 and BES1 mutually inhibit each other’s expression and oppositely co-regulate the genes for growth and defense in Arabidopsis

Project description:RAV1 (RELATED TO ABI3/VP1) is a plant-specific B3 domain and AP2 domain-containing transcription factor and acts as a negative regulator of growth in many plant species. Expression of the RAV1 was down-regulated by BR, and through the large-scale transcriptome analyses its expression was previously shown to be targeted by BES1 and BZR1 that are critical transcription factors for BR-signaling process. Using the RAV1-overexpressing transgenic plants, here we showed that RAV1 overexpression reduced BR signaling capacity, resulting in the up-regulation of BR biosynthetic genes and down regulation of BES1 expression. Furthermore, we demonstrated that BES1, not BZR1, directly bound to the RAV1 promoter and repressed RAV1 expression, and vice versa, RAV1 also bound to the BES1 promoter and repressed BES1 expression. This mutual inhibition was specific to between RAV1 and BES1, because RAV1 showed binding activity to BZR1 promoter but did not repressed BZR1 expression. To validate this mutual inhibition of RAV1 and BES1, we generated transgenic bes1-D plants overexpressing RAV1 and observed that constitutively activated BR-signaling phenotypes in bes1-D were attenuated due to the repression of endogenous BES1 expression. To investigate transcriptomic expressional changes that are regulated by RAV1 and BES1, we performed RNA-sequencing analysis from RAV1-overexpressing transgenic plants and bes1-D mutant plant. We identified differentially expressed genes (DEGs) by RAV1 and BES1, respectively, as well as the genes that are oppositely co-regulated by RAV1 and BES1. And we found that RAV1 and BES1 regulate different transcriptome but co-regulate a specific set of genes that are responsible for the balance between growth and defense. Taken together, these results suggested that mutual inhibitory transcriptional activities of the RAV1 and BES1 provide fine regulatory mechanisms for plants growth and development mediated by BR signaling.

2023-05-01 | GSE202679 | GEO

Proteomic analyses of brassinosteroids mutants in response to salt stress in Arabidopsis

Project description:Salt stress is a major environmental factor limiting plant growth and development. Previous studies have indicated that the steroidal hormones—brassinosteroids (BRs) are important regulators of plant responses to salt stress. We found that bes1-D, a gain-of-function mutant of the BR-regulated transcriptional factor BES1 (AT1G19350) in Arabidopsis showed better salt tolerance than the wild-type plant (Col-0). Label-free based LC-MS/MS and proteomic analyses were performed to investigate protein expression in bes1-D and wild-type in response to salt stress.

2023-02-22 | PXD036880 | Pride

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

Analysis of BES1-PIF4 interdependency in gene expression

Project description:BES1 transcription factor is a master regulator of brassinosteroid signalling. Part of BES1 activity as a transcription factor is brought about upon dimerization with light-responsive PIF4 transcription factor. To analyse BES1-dependent transcriptional cascade, and to which extent BES1 requires PIF4/PIF5 for target gene regulation, we performed microarray analysis of the following phenotypes: Col-0, bes1-D, pif4pif5 and bes1-D;pif4pif5 in dark grown seedlings. Col-0, bes1-D, pif4pif5 and bes1-D;pif4pif5 5-days seedlings grown in the dark were used for RNA extraction. 3 independent biological samples were collected for each genoptye.

2016-08-05 | E-GEOD-85211 | biostudies-arrayexpress

Analysis of BES1-PIF4 interdependency in gene expression

2016-08-05 | GSE85211 | GEO

BAF1 and Brassinosteroid related mutant in Arabidopsis

Project description:Brassinosteroids (BRs) regulate plant growth, development and stress responses by activating the core transcription factor BRI1-EMS-SUPPRESSOR1 (BES1). The E3 Ubiquitin ligase(s) that modify BES1 for autophagy-mediated degradation remain to be fully defined. In this study, we identified an F-box family E3 ubiquitin ligase termed BES1-ASSOCIATED F-BOX1 (BAF1). BAF1 interacts with and ubiquitinates BES1. Accordingly, BES1 stability and protein levels were reduced in BAF1 overexpression plants but increased in a baf1 loss-of-function mutant and in BAF1-DF (BAF1 with F-box deleted, dominant-negative form) overexpression lines. Selective autophagy of BES1, but not bulk autophagy, was significantly compromised in the baf1 mutant under sucrose starvation. BES1 degradation mediated by BAF1 could be blocked through autophagy but not proteasome inhibitors, suggesting that BAF1 mediates BES1 degradation largely through autophagy. baf1 and BAF1-DF overexpression plants had increased BR-regulated growth but were sensitive to long-term sucrose starvation, while BAF1 overexpression plants had decreased BR-regulated growth but were highly tolerant of sucrose starvation. Our results not only established BAF1 as a novel E3 ubiquitin ligase that targets BES1 for degradation through selective autophagy pathway, but also revealed a mechanism for plants to reduce growth during sucrose starvation by targeting this central growth regulator.

2022-08-01 | GSE155219 | GEO

24-epibrassinolide regulates the expression of miRNAs in Arabidopsis thaliana

Project description:Brassinosteroids (BRs) are endogenous plant hormones and essential for normal plant growth and development. MicroRNAs (miRNAs) of Arabidopsis thaliana are involved in mediating cell proliferation in leaves, stress tolerance, and root development. The specifics of BRs mechanisms involving miRNAs are unknown. To explore the role of miRNAs in BR-mediated pathways, we analyzed differences in miRNA profiles between control (mock solution) and 24-epibrassinolide (EBR) treatments from customized miRNA microarrays.

2016-03-25 | GSE46377 | GEO

Transcriptomic profiling of Arabidopsis hypocotyls of brl3 mutants and tissue-specific overexpressors under elevated temperatures

Project description:Climate change is having a drastic impact on global agriculture. Indeed stress factors such as elevated temperature, drought and rising atmospheric CO2 reduce arable land surface, crop cultivation and yield and overall sustainable food production on earth. However, plants possess immense innate adaptive plasticity and a more in-depth understanding of the underlying molecular mechanisms is crucial to strategize for sustaining populations under worsening climate change. Brassinosteroids (BRs) are constitutive plant growth regulators that also control plant adaptation to abiotic stress. Downstream components of the BR biosynthetic pathway, BES1/BZR1 play central role in thermomorphogenesis, but involvement of the BR receptors is not well understood. Here, we show that the BRL3 receptor is essential for plant adaptation to warmer environment. The brl3 mutants lack thermal responsiveness and the BRL3 overexpression causes hyper-thermomorphogenesis response. BRL3 activates canonical BRI1 pathway upon elevated temperature. Further, phloem-specific expression of BRL3 completely rescues the growth adaptation defects of the brl3 mutant. This ability of BRL3 represents a previously unknown thermoresponsive mechanism specifically from phloem and uncouples the roles of BR receptors in generic growth vs adaptation to changing climate conditions.

2021-12-06 | GSE190107 | GEO

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