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E-GEOD-46456

ABSTRACT: Transcription profiling by array of Arabidopsis wild type, brassinosteroid insensitive1 mutant (bri1-5), long-hypocotyl mutant phytochrome B (gul2-1/phyB-77), and bri1-5 gul2-1 double mutant to study gene expression controlled by light and brassinosteroids

PROVIDER: E-GEOD-46456 | ExpressionAtlas | 2015-04-14

REPOSITORIES: ExpressionAtlas

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			Action	DRS
	E-GEOD-46456-analysis-methods.tsv	Tabular
	E-GEOD-46456-atlasExperimentSummary.Rdata	Rdata
	E-GEOD-46456-configuration.xml	Xml
	E-GEOD-46456-percentile-ranks.tsv	Tabular
	E-GEOD-46456.condensed-sdrf.tsv	Tabular

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Analysis of gene expression controlled by light and brassinosteroids

Project description:Plant photomorphogenesis and skotomorphogenesis depend on interplay of various plant hormones. Brassinosteroids (BRs) play crucial roles during hypocotyl establishment both in the light and darkness. Arabidopsis brassinosteroid insensitive1 (bri1-5) is a partial loss-of-function mutant, and the short-hypocotyl phenotype of bri1-5 is greatly suppressed by a long-hypocotyl mutant phytochrome B (pbyB-77) at the double mutant for the two in the light conditions to display additive phenotypes of both. To identify the genes responsible for this genetic interaction, we employed microarray analysis with the RNAs prepared from wild type, bri1-5, phyB-77, and bri1-5 phyB-77 double mutant. Microarray analysis supported the notion that PHYB acts upstream of BRs.

2014-07-01 | GSE46456 | GEO

Analysis of gene expression controlled by light and brassinosteroids

2014-07-01 | E-GEOD-46456 | biostudies-arrayexpress

Expression data from epidermis specific phytochrome B or global phytochrome B line comparing to phyB-9 mutant.

Project description:Seedling hypocotyls display negative gravitropism in the dark but agravitropism in the light. The Arabidopsis thaliana pif quadruple mutant (pifQ), which lacks four PHYTOCHROME-INTERACTING FACTORS (PIFs), is agravitropic in the dark. Endodermis-specific expression of PIF1 rescues gravitropism in pifQ mutant seedlings. Since phytochromes induce light responses by inhibiting PIFs and the COP1-SPA ubiquitin E3 ligase complex in the nucleus, we asked whether phyB can cell autonomously inhibit hypocotyl negative gravitropism in the endodermis. We found that while epidermis-specific expression of PHYB rescues hypocotyl negative gravitropism and all other phyB mutant phenotypes, endodermis-specific expression of PHYB does not. Epidermal phyB induces the phosphorylation and degradation of endodermal PIFs in response to red light. This induces a global gene expression pattern similar to that induced by red light treatment of seedlings expressing PHYB under the control of its own endogenous promoter. Our results imply that epidermal phyB generates an unidentified mobile signal that travels to the endodermis where it promotes PIF degradation and inhibits hypocotyl negative gravitropism.

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Analyses of phyB-regulated genes by RNA-seq

Project description:The phytochrome family consists of five numbers (phyA-phyE) in Arabidopsis, of which phyB is the best characterized and shown to play a major role in mediating red light inhibition of hypocotyl elongation. In order to reveal the molecular basis for phyB-mediated red light signaling to promote photomorphogenesis, we analyzed the gene expression profile of red light-grown WT and phyB mutant seedlings by high throughput sequencing.

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Genome-wide expression analysis of bri1-5 and its suppressors brs1-1D, bak1-1D, bri1-1D

Project description:bri1-5 is a weak mutant of Brassinosteroid Insensitive 1 (BRI1). Suppressors by activation tagging bri1-1D, brs1-1D and bak1-1D can recover bri1-5 phenotype. We use microarray to investigate which pathways or functional categories have been transcriptionally regulated by bri1-1D, brs1-1D and bak1-1D. Whole seedlings from wild-type (WS2), bri1-5, bri1-5/brs1-1D, bri1-5/bak1-1D, bri1-5/bri1-1D. Three biological replicates for each genotype.

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

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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

Genome-wide expression analysis of bri1-5 and its suppressors brs1-1D, bak1-1D, bri1-1D

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The Arabidopsis Zinc Finger Protein 3 integrates ABA and light signaling in seed germination and plant development

Project description:ZFP3, a nuclear C2H2 zinc finger protein acts as a negative regulator of ABA- suppressed germination. Regulated over-expression of ZFP3 and closely related ZFP1, ZFP4, ZFP6 and ZFP7 confers ABA insensitivity to seed germination while the zfp3,zfp4 double mutant displays enhanced ABA susceptibility. Reduced expression of a large set of ABA-induced genes such as RAB18 and transcription factors ABI3, ABI4, ABI5 and RGL2 in ZFP3ox seedling suggests that ZFP3 indeed negatively regulates ABA signaling. Analysis of ZFP3ox plants revealed multiple phenotypic alterations such as semidwarf growth habit, defects in fertility and enhanced sensitivity of hypocotyl elongation to red but not to far-red or blue light. Analysis of genetic interactions with phytochrome and abi mutants suggested that ZFP3 amplifies red light signals perceived by photoreceptors other than phyB, and controlled by ABI5 downstream of ZFP3. Comparison of ZFP3 overexpressing and wild type Arabidopsis seedlings

2014-01-01 | E-GEOD-48661 | biostudies-arrayexpress

Genome-wide identification of microRNAs and their targets involved in the phyB-mediated light signaling pathway in rice

Project description:Phytochrome B (phyB), one member of phytochrome family in rice, plays important roles in regulating a range of developmental processes, and stress responses. However, little information about the mechanism involved in phyB-mediated light signaling pathway has been reported in rice. Another, it has been well-known that microRNAs (miRNAs) perform important roles in plant development and stress responses. Thus it is intriguing to explore the role of miRNAs in phyB-mediated light signaling pathway in rice. In this study, comparative high-throughput sequencing and degradome analysis were adopted to identify candidate miRNAs and their targets that participate in phyB-mediated light signaling pathway. A total of 838 known miRNAs, 663 novel miRNAs and 1,957 target genes were identified from wild-type (WT) and phyB mutant. Among them, 135 miRNAs showed differential expression, suggesting that the expressions of these miRNAs are under the control of phyB. In addition, 32 out of the 135 differentially expressed miRNAs were detected to slice 70 genes in rice genome. Analysis of these target genes showed that members of various transcription factor families constitute the largest proportion, indicating miRNAs are probably involved in phyB-mediated light signaling pathway mainly via regulating the expression of transcription factors. This study presented a comprehensive expression analysis of miRNAs and their targets that might be involved in phyB-mediated light signaling pathway for the first time. The results provide new clues for functional characterization of miRNAs in phyB-mediated light signaling pathway, which would be helpful in comprehensively uncovering molecular mechanism of phytochrome-mediated photomorphogenesis and stress responses in plant. Examination of miRNA profiles in wild type (WT) and phyB mutant at four-leaf stage by deep sequencing using Illumina Hiseq2500.

2015-01-01 | E-GEOD-62334 | biostudies-arrayexpress

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