Whole genome expression profiling of Arabidopsis thaliana Di19 mutant vis-à-vis wild-type
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE104975 | GEO | 2020/06/29
REPOSITORIES: GEO
Similar Datasets
Project description:Plants have evolved shoot elongation mechanisms to escape from diverse environmental stresses such as flooding and vegetative shade. The apparent similarity in growth responses suggests possible convergence of the signalling pathways. Shoot elongation is mediated by passive ethylene accumulating in flooded plant organs and by changes in light quality and quantity under vegetation shade. Here we study hypocotyl elongation as a proxy for shoot elongation and delineated Arabidopsis hypocotyl length kinetics in response to ethylene and shade. Based on these kinetics, we further investigated ethylene and shade-induced genome-wide gene expression changes in hypocotyls and cotyledons separately. Both treatments induced a more extensive transcriptome reconfiguration in the hypocotyls compared to the cotyledons. Bioinformatics analyses suggested contrasting regulation of growth promotion- and photosynthesis-related genes. These analyses also suggested an induction of auxin, brassinosteroid and gibberellin signatures and the involvement of several candidate regulators in the elongating hypocotyls. Pharmacological and mutant analyses confirmed the functional involvement of several of these candidate genes and physiological control points in regulating stress-escape responses to different environmental stimuli. We discuss how these signaling networks might be integrated and conclude that plants, when facing different stresses, utilise a conserved set of transcriptionally regulated genes to modulate and fine tune growth.
2016-06-10 | GSE83212 | GEO
Project description:Understanding how developmental and environmental signals are integrated to produce specific responses is one of the main challenges of modern biology. Hormones and, most importantly, interactions between different hormones serve as crucial regulators of plant growth and development, playing central roles in the coordination of internal developmental processes with the environment. Herein, a combination of physiological, genetic, cellular, and whole-genome expression profiling approaches has been employed to investigate the mechanisms of interaction between two key plant hormones, ethylene and auxin. Quantification of the morphological effects of ethylene and auxin in a variety of mutant backgrounds indicates that auxin biosynthesis, transport, signaling and response are required for the ethylene-induced growth inhibition in roots but not in hypocotyls. Analysis of the activation of early auxin and ethylene responses at cellular level, as well as of global changes in gene expression in the wild type versus auxin and ethylene mutants, suggests a simple mechanistic model for the interaction between these two hormones in roots. This model not only implies existence of several levels of interaction but also provides a likely explanation for the strong ethylene response defects observed in auxin mutants. Keywords: Genetic modification. Plant hormone response
2007-07-13 | GSE7432 | GEO
Project description:photomorphogenesis-Expression profile of DET1-1 mutant during photomorphogenesis
| PRJNA122067 | ENA
Project description:Understanding how developmental and environmental signals are integrated to produce specific responses is one of the main challenges of modern biology. Hormones and, most importantly, interactions between different hormones serve as crucial regulators of plant growth and development, playing central roles in the coordination of internal developmental processes with the environment. Herein, a combination of physiological, genetic, cellular, and whole-genome expression profiling approaches has been employed to investigate the mechanisms of interaction between two key plant hormones, ethylene and auxin. Quantification of the morphological effects of ethylene and auxin in a variety of mutant backgrounds indicates that auxin biosynthesis, transport, signaling and response are required for the ethylene-induced growth inhibition in roots but not in hypocotyls. Analysis of the activation of early auxin and ethylene responses at cellular level, as well as of global changes in gene expression in the wild type versus auxin and ethylene mutants, suggests a simple mechanistic model for the interaction between these two hormones in roots. This model not only implies existence of several levels of interaction but also provides a likely explanation for the strong ethylene response defects observed in auxin mutants. Experiment Overall Design: The effect of ethylene on gene expression in Col-0 (wild-type) and aux1-7 (an auxin resistant mutant) seedlings' roots was investigated. Hydrocarbon-free air was used as control for the ethylene treatment. Two biological replicates were examined. Experiment Overall Design: Similarly, the effect of auxin (IAA) on gene expression in Col (wild-type) and ein2-5 (an ethylene insensitive mutant) seedlings' roots was studied. Two biological replicates were employed.
2008-06-15 | E-GEOD-7432 | biostudies-arrayexpress
Project description:Plants have evolved shoot elongation mechanisms to escape from diverse environmental stresses such as flooding and vegetative shade. The apparent similarity in growth responses suggests possible convergence of the signalling pathways. Shoot elongation is mediated by passive ethylene accumulating in flooded plant organs and by changes in light quality and quantity under vegetation shade. Here we study hypocotyl elongation as a proxy for shoot elongation and delineated Arabidopsis hypocotyl length kinetics in response to ethylene and shade. Based on these kinetics, we further investigated ethylene and shade-induced genome-wide gene expression changes in hypocotyls and cotyledons separately. Both treatments induced a more extensive transcriptome reconfiguration in the hypocotyls compared to the cotyledons. Bioinformatics analyses suggested contrasting regulation of growth promotion- and photosynthesis-related genes. These analyses also suggested an induction of auxin, brassinosteroid and gibberellin signatures and the involvement of several candidate regulators in the elongating hypocotyls. Pharmacological and mutant analyses confirmed the functional involvement of several of these candidate genes and physiological control points in regulating stress-escape responses to different environmental stimuli. We discuss how these signaling networks might be integrated and conclude that plants, when facing different stresses, utilise a conserved set of transcriptionally regulated genes to modulate and fine tune growth. 1 day old Arabidopsis seedlings were subjected to control, ethylene and shade conditions. Hypocotyl and cotyledon tissues were harvested at 1.5 h, 13.5 h and 25.5 h of treatment time respectively. Microarray hybridization was carried out with 3 biological replicates (collected over 3 independent experiments) of each sample using the Affymetrix Arabidopsis Gene 1.1 ST platform.
2016-06-10 | E-GEOD-83212 | biostudies-arrayexpress
Project description:Ethylene induced hyponastic growth in Arabidopsis thaliana F.F. Millenaar L.A.C.J. Voesenek and A.J.M. Peeters Our aim is to identify genes involved in the ethylene induced hyponastic growth. Upon submergence some plant species like Rumex palustris changes its leaf angle (hyponastic growth) and shows enhanced petiole elongation to reach the water surface. In Rumex palustris the hyponastic growth is initiated by an increased concentration of ethylene due to physical entrapment and ongoing ethylene biosynthesis. A proteomics, genomics and genetical approach to improve our understanding of above described flooding-induced responses are not feasible in Rumex palustris since genomic information about this species is limited. However it is possible to use the model plant Arabidopsis thaliana as a tool in flooding research. Natural accessions (Be0 Col Cvi Kas Ler Nd Rld Shah and Ws) show considerable genetic variation in hyponastic growth upon exposure to ethylene Col exhibiting the largest effect (maximum rate after 3 hours) and Ler no effect whatsoever. Using a computer controlled digital camera the hyponastic growth is measured in great detail. Next to ethylene addition also a transfer to low light causes hyponastic growth. This seems to be an ethylene independent pathway because etr1 and ctr1 showed hyponastic growth after transfer to low light. Ethylene and low light showed additive effects in Col. It is likely that ethylene induces more changes in gene expression than only the ones involved in hyponastic growth. By subtracting changes in the Ler expression profile from changes in the Col expression profile we expect to find why Col and Ler respond differently on ethylene by finding specific ethylene induced genes that are involved in hyponastic growth. The expression profile of Col following transfer to low light will be substracted from Col following ethylene addition to distinguish between genes that are involved in hyponastic growth but are not specific for ethylene induced hyponastic growth. There are strong indications in Rumex palustris that other hormones i.e. auxin ABAand GA are involved in the ethylene induced hyponastic growth. Currently mutants in ethylene auxin and ABA biosynthesis and/or signal transduction are screened for hyponastic growth. Preliminary results showed that also in Arabidopsis these other hormones are involved in ethylene induced hyponastic growth. Beside the mutant approach we also started a proteomics and a PCR based differential screen approach. Together with the proposed transcriptome analysis we hope to find new genes involved in ethylene induced hyponastic growth.
2003-08-22 | E-NASC-2 | biostudies-arrayexpress
Project description:SLR/IAA14-dependent auxin induced lateral root initiation
| PRJNA93267 | ENA
Project description:Ethylene and auxin interactions in the roots of Arabidopsis seedlings
| PRJNA97955 | ENA
Project description:We performed an analysis of transcriptomic responses to auxin within four distinct tissues of the Arabidopsis thaliana root. This high-resolution dataset shows how different cell types are predisposed to react to auxin with discrete transcriptional responses. The sensitivity provided by the analysis lies in the ability to detect cell-type specific responses diluted in organ-level analyses. This dataset provides a novel resource to examine how auxin, a widespread signal in plant development, influences differentiation and patterning in the plant through tissue-specific transcriptional regulation. To analyze the effect of auxin in separate spatial domains of the root, early transcriptional changes in response to auxin treatment were assayed by means of fluorescence activated cell sorting (FACS) and microarray analysis in four tissues of the Arabidopsis root (wild type Col-0). The samples covered inner and outer as well as proximal and distal cell populations; including the stele (reporter line pWOL::GFP), xylem-pole (xp) pericycle (enhancer trap line E3754), epidermis/lateral root cap (reporter line pWER::GFP) and columella (enhancer trap line PET111). One-week-old seedlings of the individual lines were treated with auxin (two hours, 5µM indole-3-acetic acid [IAA]) or mock treated, after which roots were harvested and cells were dissociated by cell wall digestion (1 hour; including 5uM IAA) . GFP-positive cells were sorted and used for microarray transcriptome analysis (as in Bargmann and Birnbaum, Plant Phys. 2010). For comparison, transcriptional responses to auxin were also assayed in intact (undigested) roots.
2013-08-06 | E-GEOD-35580 | biostudies-arrayexpress
Project description:The plant hormone auxin represents an important regulator of growth and development. Significant insight into the mechanisms of auxin action have been obtained from studies of auxin resistant mutants such as aux1 and axr3. The Arabidopsis axr4 mutant was identified in a screen for auxin resistant root growth. In addition to the root growth of axr4 being resistant to exogenous auxin, there is also a 50% reduction in the number of lateral roots that form. The double axr4/aux1 mutant shows an additive effect in reducing lateral root numbers to 10% of wild-type. Gaining further information about the potential interaction between AUX1 and AXR4 may provide important insight into auxin regulated plant growth. Mapping experiments have placed the AXR4 gene on the lower arm of chromosome 1 between the ch1 and le markers (Hobbie and Estelle 1995). However, the AXR4 gene remains to be cloned. Identifying the AXR4 gene will help in elucidating the function of the protein. A transcript analysis of axr4 mutant seedlings will be used in 2 ways. Firstly, the transcription level of genes in the locality of the axr4 map position will be examined to identify those which are absent or significantly reduced in axr4 compared to the Col0 control. If the lesion causing the axr4 mutation results in a highly unstable mRNA or abolishes transcription then the signal will be dramatically reduced. Potential candidate genes identified in this way will be further analysed using a combination of RT-PCR and sequencing to identify the AXR4 gene. Secondly, the transcriptomics data obtained from axr4 and Col0 will be compared to identify genes which show significant transcript level differences and therefore represent targets for either direct or indirect regulation by AXR4. Hobbie, L. and Estelle, M. (1995) The axr4 auxin-resistant mutants of Arabidopsis thaliana define a gene important for root gravitropism and lateral root initiation. Plant J. 7 211-220
2022-11-21 | E-NASC-39 | biostudies-arrayexpress