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Analysis of gene expression controlled by light and brassinosteroids

ABSTRACT: 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. Total RNAs were isolated from four different genotypes: wild type, bri1-5, gul2-1/phyB-77, bri1-5 gul2-1 double mutant, and the RNAs were subjected to microarray analysis using Affymetrix GenChip arrays. Three biological replicates for each genotype resulted in 12 experiments.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Sunghwa Choe

PROVIDER: E-GEOD-46456 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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

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.

2017-02-08 | GSE87591 | GEO

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.

2020-07-25 | GSE101875 | GEO

E-GEOD-46456

Project description: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

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

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

2010-12-31 | GSE25134 | 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

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

Induced variation in BRASSINOSTEROID INSENSITIVE 1 (BRI1) confers a compact wheat architecture

Project description:The brassinosteroid (BR) plant hormones regulate numerous developmental processes, including those determining stem height, leaf angle, and grain size that have agronomic relevance in cereals. Indeed, barley (Hordeum vulgare) varieties containing uzu alleles that impair BR perception through mutations in the BR receptor BRASSINOSTEROID INSENSITIVE 1 (BRI1) exhibit a semi-dwarf growth habit and more upright leaves suitable for high-density planting. We used forward and reverse genetic approaches to develop novel BRI1 alleles in wheat (Triticum aestivum L.) and investigated their potential for crop improvement. The combination of ethyl methanesulfonate-induced mutations introducing premature stop codons in all three homoeologous TaBRI1 genes resulted in severe dwarfism, malformed leaves and sterility as observed in bri1 mutants in other species. Double mutants had reduced flag leaf angles (FLAs) conferring a more upright canopy but exhibited no differences in height or grain weight. In a forward genetics screen using a double mutant, we identified two BR-insensitive lines with reduced height and FLA that contained amino acid substitutions in conserved regions of BRI-A1. The less severe mutant had a 56% reduction in FLA and was 35% shorter than the wild-type although seed set, seed area and grain weights were also reduced. The most severe mutants contained elevated levels of bioactive BRs and increased expression of BR-biosynthesis genes consistent with reduced feedback suppression of biosynthesis. Our study gives a better understanding of BRI1 function in wheat and provides mutants that could potentially be explored for improving grain yields when sown at high density.

2024-08-14 | GSE274403 | GEO

Genetic Suppression of Plant Development and Chloroplast Biogenesis by SCO3 and PhyB Pathways

Project description:In this study we used genetic approaches and transcriptome profiling to unravel the complex interaction of different developmental pathways required for chloroplast development in plants. The recently described snowy cotyledon 3 (sco3) mutant as well as the Phytochrome B (phyb) mutant revealed, in the double mutant, a complex suppressive or additive genetically linked regulation of chloroplast development, flowering time and transcription regulation. Transcriptional profilling of mutants with aberrant chloroplast development: sco3, phyb and the double mutant sco3phyb.

2015-03-24 | GSE67168 | GEO

Phytochrome B photobodies are comprised of phytochrome B and its primary and secondary interacting proteins

Project description:Phytochrome B (phyB) is a plant photoreceptor that forms a membraneless organelle called a photobody. However, its constituents are not fully known. Here, we isolated phyB photobodies from Arabidopsis leaves using fluorescence-activated particle sorting and analyzed their components. We found that a photobody comprises ~1,500 phyB dimers along with other proteins that could be classified into two groups: The first includes proteins that directly interact with phyB and localize to the photobody when expressed in protoplasts, while the second includes proteins that interact with the first group proteins and require co-expression of a first-group protein to localize to the photobody. As an example of the second group, TOPLESS (TPL) interacts with PHOTOPERIODIC CONTROL OF HYPOCOTYL 1 (PCH1) and localizes to the photobody when co-expressed with PCH1. Mutations in TPL family members cause shortened hypocotyls under red light, demonstrating that the method identifies photobody components that regulate red light signaling. Together, our results support that phyB photobodies include not only phyB and its primary interacting proteins but also its secondary interacting proteins.

2023-04-03 | PXD040702 | Pride

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