E-GEOD-108912
Ontology highlight
ABSTRACT:
PROVIDER: E-GEOD-108912 | ExpressionAtlas | 2020-04-14
REPOSITORIES: ExpressionAtlas
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| E-GEOD-108912-analysis-methods.tsv | Tabular | |||
| E-GEOD-108912-analytics.tsv | Tabular | |||
| E-GEOD-108912-atlasExperimentSummary.Rdata | Rdata | |||
| E-GEOD-108912-configuration.xml | Xml | |||
| E-GEOD-108912-g1_g2-mvaPlot.png | Other |
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Project description:Ethylene-independent Promotion of Photomorphogenesis by Cytokinin Requires a Functional Cytokinin and Light Signaling Pathway.
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Project description:The transition of skotomorphogenesis to photomorphogenesis is induced by the perception of light and is characterized by the inhibition of hypocotyl elongation and opening of cotyledons. Although it is known that the plant hormone cytokinin, when applied in high concentrations, inhibits hypocotyl elongation in the dark-grown Arabidopsis plants, it is unclear to what extent this response is the result of cytokinin alone or cytokinin-induced ethylene production. We show that treatment of etiolated seedlings in presence of ethylene inhibitors (eg. AgNO3) or treatment of the ethylene-resistant mutant ein2, resulted in a significant inhibition of hypocotyl elongation. This indicates that cytokinin induced de-etiolation is largely independent of ethylene and suggests a close connection between the cytokinin two component system and the light singalling networks. We show that this cytokinin signal is mainly mediated through the cytokinin receptor ARIBIDOPSIS HISTIDIN KINASE 3 (AHK3) and the ARABIDOPSIS RESPONSE REGULATORS 1 (ARR1) in combination with ARR12. Interestingly, mutation of COP1, DET1 and CIN4/COP10 renders plants insensitive to cytokinin and these factors are indispensable for the transcriptional response during cytokinin induced de-etiolation which indicates that a functional light signaling pathway is essential for this cytokinin response. In addition, the cytokinin effect on hypocotyl elongation is highly dependent on the ambient light conditions where higher light intensities causes a switch in the response to CK from an inhibitor to a promoter of hypocotyl elongation.
2018-10-01 | GSE108912 | GEO
Project description:A ChIP-seq analysis revealed 378 targets of OsMADS29, which include genes involved in cytokinin metabolism and auxin signaling, carbohydrate metabolism, transporters and a large number of transcription factors, reflecting on its functional diversity. Chromatin Immunonoprecipitation of MADS29 using antiMADS29 antibody was done using rice 9 DAP seed tissue with total input chromatin and mock immunoprecipitated chromatin as controls
2013-12-31 | E-GEOD-42201 | biostudies-arrayexpress
Project description:A ChIP-seq analysis revealed 378 targets of OsMADS29, which include genes involved in cytokinin metabolism and auxin signaling, carbohydrate metabolism, transporters and a large number of transcription factors, reflecting on its functional diversity.
2013-12-31 | GSE42201 | GEO
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.
2015-01-01 | GSE62334 | GEO
Project description:Effect of the cytokinin BA on wt and arr1,10,12 mutant seedlings The type B Arabidopsis Response Regulators (ARRs) of Arabidopsis thaliana are transcription factors that act as positive regulators in the two-component cytokinin signaling pathway. We employed a mutant-based approach to perform a detailed characterization of the roles of ARR1, ARR10, and ARR12 in plant growth and development. The most pronounced phenotype was found in the arr1-3 arr10-5 arr12-1 triple loss-of-function mutant, which showed almost complete insensitivity to high levels of exogenously applied cytokinins. The triple mutant exhibited reduced stature due to decreased cell division in the shoot, enhanced seed size, increased sensitivity to light, altered chlorophyll and anthocyanin concentrations, and an aborted primary root with protoxylem but no metaxylem. Microarray analysis revealed that expression of the majority of cytokinin-regulated genes requires the function of ARR1, ARR10, and ARR12. Characterization of double mutants revealed differing contributions of the type B ARRs to mutant phenotypes. Our results support a model in which cytokinin regulates a wide array of downstream responses through the action of a multistep phosphorelay that culminates in transcriptional regulation by ARR1, ARR10, and ARR12. This data was originally made available through ArrayExpress under the accession number E-MEXP-1573.
2014-02-12 | GSE54870 | GEO
Project description:The phytohormone cytokinin plays a significant role in nearly all aspects of plant growth and development. Cytokinin signaling has primarily been studied in the dicot model Arabidopsis, with relatively little work done in monocots, which include rice (Oryza sativa) and other cereals of agronomic importance. The cytokinin signaling pathway is a phosphorelay comprised of the histidine kinase receptors (HKs), the authentic histidine phosphotransfer proteins (AHPs), and the type-B Response Regulators (ARRs). Two negative regulators of cytokinin signaling have been identified: the type-A ARRs, which are cytokinin primary response genes, and the pseudo histidine phosphotransfer proteins (PHPs), which lack the His residue required for phosphorelay. Here, we describe the role of the PHP genes from rice. Phylogenic analysis indicates that the PHPs are generally first found in the genomes of gymnosperms and that they arose independently in monocots and dicots. Consistent with this, the three rice PHPs fail to complement an Arabidopsis php mutant (ahp6). Disruption of the three PHPs results in a molecular phenotype consistent with these elements acting as negative regulators of basal cytokinin signaling, including the constitutive up-regulation of a number of type-A RR and cytokinin oxidase genes. The triple php mutant affects multiple aspects of rice growth and development, including shoot morphology, panicle architecture and seed fill. However, in contrast to Arabidopsis, disruption of the rice PHPs does not affect root vascular patterning, suggesting that while many aspects of key signaling networks are conserved between monocots and dicots, the molecular components regulating some processes are distinct.
2022-12-31 | GSE141408 | GEO
Project description:Phytohormones like ethylene and cytokinin are important regulators of plant growth and development. Perception of these hormones is accomplished by families of sensor histidine kinase-type receptors. Here, we identified the response regulator ARR2 as a signaling component functioning downstream of not only cytokinin receptors but also of the ethylene receptor ETR1. Transcriptome analyses suggest that ARR2 also participates in the regulation of several other signaling pathways. Further investigations indicate that hormone-initiated multi-step phosphorelais regulate the transcription factor activity of ARR2. The ETR1-dependent mechanism thereby creates a CTR1-independent ethylene signal transfer. From our data we propose that a two-component signaling network exists in higher plants that is predominantly responsible for fine-tuning and integration of a large number of signal transduction pathways.
2004-07-31 | E-MEXP-125 | biostudies-arrayexpress
Project description:We analyzed transcriptome-wide gene expression and AS changes in etiolated Arabidopsis seedlings exposed to red, blue, and white light. Our study revealed that different types of light signals trigger rapid AS responses of numerous genes, including splicing factors and other functional groups. Among these candidates was RRC1, which was previously shown to function in PHYB signaling. The light signaling phenotype of an rrc1 mutant could only be complemented with the splicing variant being up-regulated upon light exposure, indicating a self-reinforcing circuit. Finally, we provide evidence that light-regulated AS can occur in a phytochrome-independent manner and is closely intertwined with the plant’s energy status.
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