Effects of ein2-1 mutation on the miRNA expression during callus formation after submergence
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ABSTRACT:
PROVIDER: PRJNA865692 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR20791120.fastq.gz | Fastqsanger.gz | |||
| SRR20791121.fastq.gz | Fastqsanger.gz | |||
| SRR20791122.fastq.gz | Fastqsanger.gz | |||
| SRR20791123.fastq.gz | Fastqsanger.gz | |||
| SRR20791124.fastq.gz | Fastqsanger.gz |
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Project description:Col-0 and ein2-1 seedlings were submerged for 1 hour and then leaf explants was incubated on CIM for 7 days. The upper half of the explants were harvested for the small RNA sequencing.
2022-08-06 | GSE210413 | GEO
Project description:General translational repression is predicted as a key process to reduce energy consumption under hypoxia. We have previously showed that mRNA loading onto polysome is reduced in Arabidopsis under submergence. Here, we showed that plant stress activated GCN2 (general control nonderepressible 2) can phosphorylate eIF2a (Eukaryotic Initiation Factor 2a) in Arabidopsis under submergence, and this process is reversible after desubmergence. Compared to the wild-type, the reduction in polysome loading during submergence was less severe in the gcn2 mutant. Transgenic lines overexpressing GCN2 had more ATP and conferred better tolerance under submergence, suggesting that GCN2 might modulate the dynamics of translation to adjust the energy homeostasis under hypoxia. Interestingly, GCN2-eIF2a signaling was activated by ethylene under submergence. However, GCN2 activity was not affected in ein2-5 and eil1ein3 under submergence, suggesting that GCN2 activity was regulated by noncanonical ethylene signaling. In addition, the polysome loading was retained in both ein2-5 and etr1-1 under submergence, implying that ethylene modulated the dynamic translation under submergence via EIN2 and GCN2. Notably, our NGS analysis also demonstrated that EIN2 and GCN2 regulated the translation of 23 core hypoxia genes as well as 53% translational repressed genes under submergence. On the other hand, EIN2 and GCN2 also affected the expression of genes involved in hypoxic response, ethylene response, biotic stress and negative regulation of cytokinin signaling. Taken together, these demonstrated that entrapped ethylene triggers GCN2 and EIN2 to ensure the translation of stress required proteins under submergence and also provide a step stone for future investigation how eukaryotic cells modulate the translation to response for the changeable environments.
2022-06-08 | GSE149414 | GEO
Project description:Transcriptional profiling of age-related change of callus formation capability in Arabidopsis hypocotyls Organogenesis in vitro consists of many aspects such as phytohormone perception, dedifferentiation of differentiated cell to acquire organogenic competence, and re-entry of quiescent cells into cell cycle. In this study, we established an in vitro experimental system to study the age-dependent callus formation capacity in Arabidopsis. Interestingly, mature (35- to 38-day-old) hypocotyl explants exhibited better callus-forming potential than that of juvenile (7- to 10-day-old), determined by callus growth rates. To explore genome-wide expression changes underlying the phenomenon of age-dependent callus formation, a transcriptome-based analysis was performed. Gene expression profiling indicated that age-dependent callus formation capacity was associated with changes in phytohormone (auxins, cytokinins, abscisic acid, brassinosteroids and gibberellins) homeostasis, epigenetic mechanism and the cell cycle regulation. Besides, we identified two groups of genes involved in age-dependent callus formation capacity: (1) positive regulatory and (2) negative regulatory categories, i.e. genes that were significantly up- or down-regulated during callus formation derived from mature explants, respectively. One gene encoding DNA-binding protein (VARIANT IN METHYLATION 1, VIM1) belonging to the positive regulatory category was selected for functional analysis and assessment of age-dependent callus formation capacity. Indeed, vim1 reduced the efficiency of callus formation in mature explants, but not in juvenile. The result suggests that VIM1 plays an important role in regulating age-dependent callus formation capacity. Taken together, the investigation will help to better understand the molecular regulatory mechanism of age-dependent callus formation. Comparison of young and mature Arabidopsis hypocotyls either with or without auxin treatment for 1 day
2011-06-19 | E-GEOD-27508 | biostudies-arrayexpress
Project description:Transcriptional profiling of age-related change of callus formation capability in Arabidopsis hypocotyls Organogenesis in vitro consists of many aspects such as phytohormone perception, dedifferentiation of differentiated cell to acquire organogenic competence, and re-entry of quiescent cells into cell cycle. In this study, we established an in vitro experimental system to study the age-dependent callus formation capacity in Arabidopsis. Interestingly, mature (35- to 38-day-old) hypocotyl explants exhibited better callus-forming potential than that of juvenile (7- to 10-day-old), determined by callus growth rates. To explore genome-wide expression changes underlying the phenomenon of age-dependent callus formation, a transcriptome-based analysis was performed. Gene expression profiling indicated that age-dependent callus formation capacity was associated with changes in phytohormone (auxins, cytokinins, abscisic acid, brassinosteroids and gibberellins) homeostasis, epigenetic mechanism and the cell cycle regulation. Besides, we identified two groups of genes involved in age-dependent callus formation capacity: (1) positive regulatory and (2) negative regulatory categories, i.e. genes that were significantly up- or down-regulated during callus formation derived from mature explants, respectively. One gene encoding DNA-binding protein (VARIANT IN METHYLATION 1, VIM1) belonging to the positive regulatory category was selected for functional analysis and assessment of age-dependent callus formation capacity. Indeed, vim1 reduced the efficiency of callus formation in mature explants, but not in juvenile. The result suggests that VIM1 plays an important role in regulating age-dependent callus formation capacity. Taken together, the investigation will help to better understand the molecular regulatory mechanism of age-dependent callus formation.
2011-06-19 | GSE27508 | GEO
Project description:Wounding is a primary trigger of organ regeneration but how wound stress reactivates cell proliferation and promotes cellular reprogramming remains elusive. In this study we combined the transcriptome analysis with quantitative hormonal analysis to investigate how wounding induces callus formation in Arabidopsis thaliana. Our time-course RNA-seq analysis revealed that wounding induces dynamic transcriptional changes that can be categorized into five clusters with distinct temporal patterns. Gene ontology analyses uncovered that wounding modifies the expression of hormone biosynthesis and response genes, and quantitative analysis of endogenous plant hormones revealed accumulation of cytokinin prior to callus formation. Mutants defective in cytokinin synthesis and signalling display reduced efficiency in callus formation, indicating that de novo synthesis of cytokinin has major contribution in wound-induced callus formation. We further demonstrate that type-A ARABIDOPSIS RESPONSE REGULATOR (ARR)-mediated cytokinin signalling regulates the expression of CYCLIN D3;1 (CYCD3;1) and mutations in CYCD3;1 and its homologs CYCD3;2-3 cause defects in callus formation. Our transcriptome data, in addition, showed that wounding activates multiple developmental regulators, and we found novel roles of ETHYLENE RESPONSE FACTOR 115 (ERF115) and PLETHORA3 (PLT3), PLT5, PLT7 in wound-induced callus formation. Together, this study provides novel mechanistic insights into how wounding reactivates cell proliferation during callus formation.
2017-10-01 | GSE101422 | GEO
Project description:Plants can regenerate from a variety of tissues on culturing in appropriate media. However, the metabolic shifts involved in callus formation and shoot regeneration are largely unknown. The metabolic profiles of callus generated from tomato (Solanum lycopersicum) cotyledons and that of shoot regenerated from callus were compared with the pct1-2 mutant that exhibits enhanced polar auxin transport and the shr mutant that exhibits elevated nitric oxide levels. The transformation from cotyledon to callus involved a major shift in metabolite profiles with denser metabolic networks in the callus. In contrast, the transformation from callus to shoot involved minor changes in the networks. The metabolic networks in pct1-2 and shr mutants were distinct from wild type and were rewired with shifts in endogenous hormones and metabolite interactions. The callus formation was accompanied by a reduction in the levels of metabolites involved in cell wall lignification and cellular immunity. On the contrary, the levels of monoamines were upregulated in the callus and regenerated shoot. The callus formation and shoot regeneration were accompanied by an increase in salicylic acid in wild type and mutants. The transformation to the callus and also to the shoot downregulated LST8 and upregulated TOR transcript levels indicating a putative linkage between metabolic shift and TOR signalling pathway. The network analysis indicates that shift in metabolite profiles during callus formation and shoot regeneration is governed by a complex interaction between metabolites and endogenous hormones.
2018-06-29 | MTBLS447 | MetaboLights
Project description:Plant regeneration could be achieved via formation of a pluripotent cell mass termed callus, nature of which is a group of fast-dividing root primordium cells. However, mechanisms that strictly control the stem cell fate transition in regeneration of callus remain elusive. Here we show that the Arabidopsis ISWI type chromatin remodelers specifically promote the second-step cell fate transition from root founder cells to root primordium cells in the leaf-to-callus transition.
2014-05-15 | GSE57145 | GEO
Project description:Plant regeneration could be achieved via formation of a pluripotent cell mass termed callus, nature of which is a group of fast-dividing root primordium cells. However, mechanisms that strictly control the stem cell fate transition in regeneration of callus remain elusive. Here we show that the Arabidopsis ISWI type chromatin remodelers specifically promote the second-step cell fate transition from root founder cells to root primordium cells in the leaf-to-callus transition. Leaf explants cultured in CIM from Col-0 or chr11-1 chr17-1 at time 0 and 8 days after culture (8 DAC) were used for RNA preparation. Microarray was performed using the AffymetrixGeneChip system. Three independent experiments were performed.
2014-05-15 | E-GEOD-57145 | biostudies-arrayexpress
Project description:Ethylene modulates the dynamics of translation via GCN2 and EIN2 in Arabidopsis under submergence
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Project description:Auxin and cytokinin can regulate callus formation from developed plant organs and shoot regeneration from callus. The regulation of dedifferentiation and regeneration of plant cells by auxin and cytokinin stimulation was considered to be caused by the regulation of reprograming of callus cells, but the hypothesis had been argued still in now. Although elucidation of the regulatory mechanisms of callus formation and shoot regeneration has helped advance plant biotechnology research, many plant species are intractable to transformation because of difficulties with callus regulation. In this study, we identified the compound Fipexide (FPX) as a useful regulatory compound through chemical biology-based screening. Compared with the activity of auxin and cytokinin, FPX showed higher efficiency as a chemical inducer in callus formation, shoot regeneration, and Agrobacterium infection. In regards to morphology, the cellular organization of FPX-induced callus differed from that produced under auxin/cytokinin conditions. According to a microarray analysis, the expressions of approximately 971 genes were two-fold up-regulated by FPX treatment for 2 days. Among these genes, 598 genes were also induced by auxin/cytokinin, while 373 genes, including metabolic regulation-related genes, were specifically expressed only under FPX treatment. FPX can promote callus formations in rice, poplar, and several vegetables. FPX should be a useful tool to reveal unknown mechanisms of plant development and to increase the number of transgenic plant species.
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