Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA269009 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1687075.fastq.gz | Fastqsanger.gz | |||
| SRR1687076.fastq.gz | Fastqsanger.gz | |||
| SRR1687077.fastq.gz | Fastqsanger.gz | |||
| SRR1687078.fastq.gz | Fastqsanger.gz |
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Project description:Secondary metabolites are involved in the plant stress response. Among these are scopolin and its active form scopoletin, which are coumarin derivatives associated with reactive oxygen species scavenging and pathogen defence. Here we show that in Arabidopsis thaliana, scopolin accumulation can be induced in the root by osmotic stress and in the leaf by low temperature stress. A genetic screen for altered scopolin levels in Arabidopsis thaliana identified a mutant compromised for scopolin accumulation in response to stress; the lesion was present in a homologue of THO1, the product of which contributes to the THO/TREX complex. The THO/TREX complex contributes to RNA silencing, supposedly by trafficking precursors of small RNAs. Mutants carrying defective THO and RDR6 genes were impaired with respect to scopolin accumulation in response to stress, suggesting a mechanism based on RNA silencing like the transacting small interfering RNA pathway which requires THO/TREX and RDR6 function.
2018-02-05 | MTBLS389 | MetaboLights
Project description:SPLICING FACTOR FOR PHYTOCHROME SIGNALING promotes photomorphogenesis by regulating alternative splicing in Arabidopsis
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Project description:cea10-03_cyclocitral - analysis of arabidopsis transcriptome in response to b-cyclocitral treatment - Is beta--cyclocitral a bioactive molecule involved in stress response? - Analysis of Arabidopsis transcriptome in response to b-cyclocitral treatment.
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Project description:The shoots and roots of a plant respond differently to osmotic stress, as they have distinct functions and anatomical structures. Under conditions of high solute concentration, such as in saline soils or drought, water uptake by the roots is reduced, resulting in cellular dehydration. In this study, we performed transcriptional profiling of roots of Arabidopsis under osmotic stress conditions such as high salinity and drought using mRNA-Seq for the assessment of gene expression changes in roots of Arabidopsis. mRNA-Seq analysis showed that many differentially expressed genes showed differential expressions under both salt stress and drought stress conditions in roots and were distinct from aerial parts. We confirmed 68 transcription factor genes which is involved in osmotic stress signal transduction in roots and are connected tightly. Interestingly, well-known ABA-dependent and/or -independent osmotic stress-responsive genes were less increased in roots, indicating that osmotic stress response in roots might be regulated by stress pathways other than well-known pathways. We identified 26 osmotic stress-responsive genes, which have alternative splicing variant isoforms, showed distinct expression in roots under osmotic stress conditions from the mRNA-Seq analysis. Quantitative RT-PCR confirmed that alternative splicing variants, such as ANNAT4, MAGL6, TRM19, and CAD9, have differential expressions in roots under osmotic stress conditions, indicating that alternative splicing is an important regulatory mechanism in osmotic stress response in roots. Taken together, our study suggest that many transcription factor families are involved in osmotic stress response in roots and tightly connected each other. In addition, alternative splicing and function of alternative splicing variant isoforms are also important in osmotic stress response in roots. To understand the alternative splicing mechanism in roots, further study is necessary.
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Project description:We examined the changes in gene expression in Arabidopsis thaliana grown under arsenate stress. The transcriptional profiling reveals antioxidant activity and repression of the phosphate starvation response. Keywords: dual label, stress response
2008-02-08 | GSE10425 | GEO
Project description:In all living organisms, regulation of gene expression is fundamental for survival and adaptation. Gene expression can be modulated at various steps, including at the level of RNA processing. During the last few years, the importance of alternative splicing of mRNAs in controlling plant development and stress responses were emerged and highlighted its importance. Recently, an other type of alternative splicing has been reported which leads to the generation of circular RNAs (circRNAs), a novel class on endogenous noncoding RNAs. Several functions of circular RNAs have been proven or proposed, including functioning as microRNA or RNA-binding protein decoys, playing regulatory roles in gene expression or affecting transcriptional control via special RNA-RNA interactions. Despite the widening knowledge of circRNAs and their functional aspects in the animal kingdom, relatively little is known about circRNAs in plants. In order to detect and classify circRNAs in Arabidopsis thaliana, we created a workflow that includes generation of Illumina libraries enriched for circRNAs and a comparison of biocomputational tools developed for detecting endogenous circular RNAs in other species. With the power of high-throughput sequencing and evaluation of algorithms, high-fidelity candidates were subjected for an analysis of their functional role in plant development and stress-related responses, especially regarding the role of splicing, including alternative splicing events, splice site preference and strength variances and transcript composition and to comprehend the role of RNA processing in stress response. Here we present an approach combining bioinformatic tools and molecular techniques to investigate the adaptability of detection methods of circRNAs from other species to plant circular RNAs, and based on our high-fidelity results identify and understand the characteristics of circRNAs in Arabidopsis thaliana.
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Project description:Alternative splicing plays a major role in expanding the potential informational content of eukaryotic genomes. It is an important post-transcriptional regulatory mechanism that can increase protein diversity and affect mRNA stability. Cold stress, which adversely affects plants growth and development, regulates the transcription and splicing of plants splicing factors. This affects the pre-mRNA processing of many genes. To identify cold regulated alternative splicing we applied Affymetrix Arabidopsis tiling arrays to survey the transcriptome under cold treatment conditions.
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Project description:SICKLE is a novel factor involved in miRNA biogenesis and is important for development and stress tolerance of Arabidopsis
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