E-GEOD-98045
Ontology highlight
ABSTRACT:
PROVIDER: E-GEOD-98045 | ExpressionAtlas | 2020-04-15
REPOSITORIES: ExpressionAtlas
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| E-GEOD-98045-analysis-methods.tsv | Tabular | |||
| E-GEOD-98045-analytics.tsv | Tabular | |||
| E-GEOD-98045-atlasExperimentSummary.Rdata | Rdata | |||
| E-GEOD-98045-configuration.xml | Xml | |||
| E-GEOD-98045-g2_g1-mvaPlot.png | Other |
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Project description:Micro RNAs (miRNAs) are a class of small endogenous RNAs conserved in eukaryotic organisms including plants. They suppress gene expression post-transcriptionally in many different biological processes. Previously, we reported salinity-induced changes in gene expression in transgenic Arabidopsis thaliana plants that constitutively expressed a pea abscisic acid-responsive (ABR17) gene. In the current study, we used a microarray to investigate the role of miRNA-mediated post-transcriptional gene regulation in these same transgenic plants in the presence and absence of salinity stress. We identified nine miRNAs that were significantly modulated due to ABR17 gene expression, and seven miRNAs that were modulated in response to salt stress. The target genes regulated by these miRNAs were identified using starBase (sRNA target Base) Degradome analysis and through 5' RNA Ligase Mediated-Rapid Amplification of cDNA Ends (RLM-RACE). Our findings revealed miRNA:mRNA interactions comprising regulatory networks of Auxin Response Factor (ARF), ARGONAUTE 1, (AGO1), Dicer-like proteins 1 (DCL1), Squamosa Promoter Binding (SPB), NAC, APETALA 2 (AP2), Nuclear Factor-Y (NFY), RNA binding proteins, Arabidopsis thaliana vacuolar phyrophosphate 1 (AVP1) and Pentatricopetide repeat (PPR) in ABR17 transgenic A. thaliana, which control physiological, biochemical and stress signalling cascades due to the imposition of salt stress. Our results are discussed within the context of the effect of the transgene, ABR17, and the roles miRNA expression may play in mediating plant responses to salinity.
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Project description:Arabidopsis thaliana Transcriptome under Salt Stress
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Project description:To analyze global changes in AS under salt stress, we obtained high-coverage (~200 times) RNA sequencing data from Arabidopsis thaliana seedlings that were treated with different concentrations of NaCl. Our study provided a comprehensive view of AS under salt stress and revealed novel insights into the potential roles of AS in plant response to salt stress.
2014-01-15 | E-MTAB-4286 | biostudies-arrayexpress
Project description:Plant homeodomain (PHD) finger proteins affect growth and development by regulating transcription and reading epigenetic modifications of histones, but their functions in abiotic stress responses remain largely unclear. Here we characterize seven Arabidopsis thaliana Alfin1-like PHD finger proteins (ALs) in the response to abiotic stresses. ALs localize to the nucleus and repress transcription. Except AL6, all the ALs bind to G-box element. Changes of the amino acids at positions 34 and 35 in AL6 cause the loss of G-box binding ability. Expression of the ALs responded differently to osmotic stress, salt, cold and abscisic acid treatments. AL5 was induced by multiple stresses, and AL5-overexpressing plants showed higher tolerance to salt, drought and freezing stress than Col-0. Also, al5 mutants showed reduced stress tolerance. ChIP-Seq assay helps find the direct targets of AL5.
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Project description:Biotic and abiotic stresses limit agricultural yields, and plants are often simultaneously exposed to multiple stresses. Combinations of stresses such as heat and drought or cold and high light intensity, have profound effects on crop performance and yeilds To analyze such responses, we initially compared transcriptome changes in ten Arabidopsis thaliana ecotypes using cold, heat, high light, salt and flagellin treatments as single stress factors or their double combinations. Arabidopsis thaliana plants of ecotypes (Col, Ler, C24, Cvi, Kas1, An1, Sha, Kyo2, Eri and Kond) were subjected to the following stress treatments: Salt, Cold, Heat, High Light (HL), Salt+Heat, Salt+HL, Cold+HL, Heat+HL, as well as FLG (Flagellin, flg22 peptide), Cold+FLG, Heat+FLG
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Project description:RNA sequencing of salinity tolerant Arabidopsis thaliana mutants expressing zinc finger artificial transcription factors (ZF-ATFs), with and without salt treatment (0 mM and 75 mM NaCl).
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Project description:Adaptive response to stress involves an extensive reprogramming of gene expression. Under stressful conditions, the induction of efficient changes in mRNA production is crucial for maximized plant survival. Transcription and pre-mRNA processing are two closely related steps in mRNA biogenesis, yet how they are controlled in plant stress response remains elusive. Here, we show that the Arabidopsis nuclear cap-binding complex (CBC) component CBP20 directly interacts with ELF7, a subunit of the transcription elongation factor RNA Pol II-associated factor 1 complex (PAF1c) to promote RNA Pol II transcription in plant response to salt stress. CBP20 and ELF7 co-regulate the expression of a large number of genes including those crucial for salt tolerance. Both CBP20 and ELF7 are required for enhanced RNA Pol II elongation at salt-activated genes. Though CBP20 also regulates intron splicing, this function is largely independent of ELF7. Our study reveals the function of an RNA processing regulator CBC in assisting efficient RNA Pol II transcription and pinpoints the complex roles of CBC on mRNA production in plant salt stress resistance.
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Project description:Plant homeodomain (PHD) finger proteins affect growth and development by regulating transcription and reading epigenetic modifications of histones, but their functions in abiotic stress responses remain largely unclear. Here we characterize seven Arabidopsis thaliana Alfin1-like PHD finger proteins (ALs) in the response to abiotic stresses. ALs localize to the nucleus and repress transcription. Except AL6, all the ALs bind to G-box element. Changes of the amino acids at positions 34 and 35 in AL6 cause the loss of G-box binding ability. Expression of the ALs responded differently to osmotic stress, salt, cold and abscisic acid treatments. AL5 was induced by multiple stresses, and AL5-overexpressing plants showed higher tolerance to salt, drought and freezing stress than Col-0. Also, al5 mutants showed reduced stress tolerance. ChIP-Seq assay helps find the direct targets of AL5. Polyclonal antibody of AL5 protein was used to perform ChIP experiment. Two samples were analyzed, AL5 OE sample and its knock out mutant. Data was analyzed as OE sample Vs mutant sample and help find targets of AL5 protein.
2014-04-12 | E-GEOD-56706 | biostudies-arrayexpress
Project description:Arabidopsis Col-0 seeds were germinated and grown for two weeks on Arabidopsis thaliana salt media (ATS, control) or ATS media supplemented 50, 75, 100 or 125 mM NaCl that imposes both an ionic and osmotic stress; or ATS media supplemented with iso-osmolar concentrations of sorbitol (100, 150, 200 or 250 mM) that imposes only an osmotic stress. The aim of the study was to identify genes involved in plant growth and adaptation to ionic stress compared to genes involved in growth and adaptation to osmotic stress conditions. To do this we identified lists of genes that are differentially expressed in plants grown in NaCl (A) and lists of genes differentially expressed in plants grown in sorbitol (B). We then compared these lists to find ionic/salt-specific genes that are only expressed in plants grown in NaCl and not in plants grown in sorbitol; and osmotic genes that are expressed both in plants grown in NaCl and in plants grown in sorbitol. Associated publication: Cackett et al. (2022) Salt-specific gene expression reveals elevated auxin levels in Arabidopsis thaliana plants grown under saline conditions, DOI: 10.3389/fpls.2022.804716
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