Comparison between WT and bes1 in an in vitro tissue culture system, VISUAL
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PROVIDER: PRJNA433158 | ENA |
REPOSITORIES: ENA
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Project description:We have previously established an in vitro tissue culture system (named VISUAL; Kondo et al., 2016), in which xylem and phloem differentiation can be induced with Arabidopsis thaliana cotyledons To compare gene expression profiles between WT and bes1 during vascular development, we performed GeneChip analysis using VISUAL.
2018-02-07 | GSE110199 | GEO
Project description:We established a novel in vitro tissue culture system (named VISUAL), in which xylem and phloem differentiation can be induced with Arabidopsis thaliana cotyledons To compare gene expression profiles between WT and apl during vascular development, we performed GeneChip analysis using VISUAL.
2016-05-25 | GSE80026 | GEO
Project description:We established a novel in vitro tissue culture system (named VISUAL-CC), in which phloem companion cell (CC) differentiation can be induced with Arabidopsis thaliana cotyledons. To compare gene expression profiles between VISUAL and VISUAL-CC, we conducted GeneChip analysis using two different in vitro cultures. CC-S means a sample that strongly induces CC differentiation. CC-M means a sample that moderately induces CC differentiation. V means a VISUAL sample, that does not induce CC differentiation at all.
2020-03-31 | GSE141037 | GEO
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
Project description:We established a novel in vitro tissue culture system (named VISUAL), in which xylem and phloem differentiation can be induced with Arabidopsis thaliana cotyledons To isolate phloem-specific genes in VISUAL, we performed GeneChip analysis after cell-sorting experiments with SEOR1pro::SEOR1-YFP.
2016-05-25 | GSE80027 | GEO
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.
2016-08-05 | GSE85211 | GEO
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
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).
2011-01-02 | GSE24684 | GEO
Project description:Comparison among samples subjected to a novel in vitro tissue culture system, VISUAL-CC
| PRJNA591818 | ENA
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