Comparison of transcript profiles of Arabidopsis WT and VPZ plants to fluctuating light and high light
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ABSTRACT:
PROVIDER: PRJNA566150 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10137300_1.fastq.gz | Fastqsanger.gz | |||
| SRR10137300_2.fastq.gz | Fastqsanger.gz | |||
| SRR10137301_1.fastq.gz | Fastqsanger.gz | |||
| SRR10137301_2.fastq.gz | Fastqsanger.gz | |||
| SRR10137302_1.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: Overexpression of VDE, ZEP and PsbS (VPZ) in plants confers enhanced dynamics of non-photochemical quenching of NPQ under FL light. VPZ overexpression in tobacco has been reported to increase plant biomass under fluctuating light. However, our work demonstrates that such strategy had no advantageous effect when asssayed in Arabidopsis thaliana. To investigate whether this observation is due to impairements in signaling pathways due to the expression of VPZ in Arabidopsis thaliana, transcriptome profiles of VPZ plants exposed to fluctuating light or high light were conducted. Methods: mRNA-Seq libraries were prepared from 21-d-old Col0 plants and VPZ lines #2 and #4 cultivated under standard control conditions and then exposed to fluctuating light or high light for 6h and 30 h. Standard Illumina protocols were used for mRNA-Seq sequencing. Triplicates for 3 independent plants were used. Adaptor sequences were removed with Trimmomatic and resulting reads mapped to the Arabidopsis genome (Araport11) with Tophat 2.1.1. Normalised counts reads were quantified with featureCounts to provide processed data files and differential expression analysis were conducted with the DEseq2 pipeline. Results: mRNA-Seq libraries contained app. 9 milion reads each. Transcript analysis for differential gene expression was conducted according to the Tophat/featureCounts/DESeq2 pipeline. To declare significant differences, a cut-off for absolute log2(FC) ≥ 1 compared to the initial timepoint (0h) and FDR ≤ 0.05 was applied. Significant transcripts exclusively found for Col0 and both VPZ lines in each time-point were considered for subsequent analysis. Accordingly, 528 and 415 transcripts (6h and 30h) were found for Col0, and 326 and 896 (6h and 30h) for the VPZ under control conditions. For FL, 490 and 591 transcripts qualified as specific (6h and 30h) for Col0 and 938 and 401 (6h and 30h) for VPZ. Strikingly, the amount of transcripts raised to 2847 and 2902 DEGs (6h and 30h) for Col0, whereas only 546 and 304 (6h and 30h) were detected for VPZ under HL. transcripts). Conclusions: the overexpression of VPZ in Arabidopsis leads to particular transcriptome response under fluctuating light related to changes in photosynthesis and response to abscisic acid, among all. However, Col0 displayed wider transcriptome responses than VPZ after exposure to high light .
2022-09-08 | GSE137650 | GEO
Project description:Plants experience dynamic light daily, with light conditions varying on a second-by-second basis. Little is understood about the mechanisms that allow plants to survive such variable conditions. Here, we have exposed Arabidopsis thaliana plants to naturally fluctuating light regimes alongside traditional square light regimes. The response was highly consistent across experiments, leading us to believe there is an epigenetic mechanism involved. We show significant alterations in DNA methylation between fluctuating light acclimated plants, and square light acclimated plants, demonstrating the frequency of fluctuations impacts the plant methylation. This was accompanied by significant changes in gene expression, some of which correlated with altered DNA methylation. Interestingly, several transposable elements which displayed differential methylation were found to be differentially expressed between light regimes. This data suggests DNA methylation may have a role in acclimation to natural light which may directly regulate gene expression and impact transposable element activation.
2025-09-02 | GSE261532 | GEO
Project description:Plants experience dynamic light daily, with light conditions varying on a second-by-second basis. Little is understood about the mechanisms that allow plants to survive such variable conditions. Here, we have exposed Arabidopsis thaliana plants to naturally fluctuating light regimes alongside traditional square light regimes. The response was highly consistent across experiments, leading us to believe there is an epigenetic mechanism involved. We show significant alterations in DNA methylation between fluctuating light acclimated plants, and square light acclimated plants, demonstrating the frequency of fluctuations impacts the plant methylation. This was accompanied by significant changes in gene expression, some of which correlated with altered DNA methylation. Interestingly, several transposable elements which displayed differential methylation were found to be differentially expressed between light regimes. This data suggests DNA methylation may have a role in acclimation to natural light which may directly regulate gene expression and impact transposable element activation.
2025-09-02 | GSE261531 | GEO
Project description:Plants in the natural environment experience continuous dynamic changes in light intensity. Here, we exposed Arabidopsis thaliana plants to naturally fluctuating light regimes alongside traditional square light regimes such as those often found in control environment growth chambers. The physiological response was highly consistent across experiments in sibling plants, indicating the possibility of an epigenetic mechanism, leading us to investigated differences in DNA methylation. Our results identified a large number of changes in DNA methylation patterns between fluctuating light acclimated plants and square light acclimated plants, demonstrating natural fluctuations in light impacts plant epigenetic mechanisms. Most importantly, there are more differences in DNA methylation patterns between different light pattern regimes than between different light intensities. These differences in DNA methylation were accompanied by significant changes in gene expression, some of which correlated with altered DNA methylation. One of these genes, MCCA, was found to significantly impact photosynthetic efficiency when knocked out. Thousands of transposable elements copies were differentially methylated between light regimes. Interestingly, up to 30% of these TEs are linked to nearby differentially expressed genes. Our data suggests DNA methylation plays a role in acclimation to natural light which may directly regulate gene expression and impact transposable element activation.
2025-09-01 | GSE261533 | GEO
Project description:Plants are subjected to perpetual fluctuations of light intensity and spectral composition in their natural growth environment, particularly due to movement of clouds and upper canopy leaves. Sudden exposure to intense light is accompanied by absorption of excess light energy, which results in an overload of photosynthetic electron transport chain and generation of reactive oxygen species in and around thylakoid membranes. To cope with this photooxidative stress and to prevent chronic photoinhibition under dynamically changing light intensities, plants have evolved various short- and long-term photoprotective mechanisms. We used quantitative mass spectrometry to investigate long-term acclimation of Arabidopsis thaliana leaf proteome to fluctuating light (FL) which induces photooxidative stress. After three days of FL exposure the proteomes of young and mature leaves were analyzed separately in the morning and at the end of day to examine possible interaction between FL acclimation and leaf development or time of day.
2020-01-30 | PXD015330 | Pride
Project description:Metabolomics of Arabidopsis photorespiration mutants under fluctuating light conditions
2023-04-26 | MSV000091798 | MassIVE
Project description:Transcriptional Response of Arabidopsis thaliana to Fluctuating Light
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Project description:Metabolomics of Arabidopsis photorespiration mutants under fluctuating light conditions
2023-04-26 | MSV000091798 | GNPS
Project description:Purpose: Acclimation referes to reversible responses that plants trigger under frequently and moderate changes in natural environments, mostly light intensity and temperature. To better understand acclimation in Arabidopsis thaliana, modulators and integrators for this process should be identified. To achieve this goal, a dynamic set-up was designed to systematically cultivate Arabidopsis plants under moderate high light, heat and cold and a multiple high-throughput strategy was conducted to monitor changes in transcriptome, proteome and metabolome. As part of this comprehensive characterisation, lncRNA-Seq has been carried out to investigate transcriptome changes and further integrated in conditional correlation networks. Methods: lncRNA-Seq libraries were prepared from 14-d-old plants cultivated under standard control conditions or acclimated to high light, cold or heat for 4 d and then de-acclimated under normal conditions for 4 additional days. Standard Illumina protocols were used for lncRNA-Seq sequencing. Unless some quality issue in libraries was detected, triplicates for 3 independent plants were used. Adaptor sequences were removed with Trimmomatic and resulting reads mapped to the Arabidopsis genome (Araport11) with Tophat 2.1.1. FPKM reads were quantified with Cufflinks to provide processed data files and differential expression analysis were conducted with featureCounts/DEseq2 pipeline. Results: lncRNA-Seq libraries contained 10 milion reads each. Transcript analysis for differential gene expression was conducted according to the Tophat/featureCounts/DESeq2 pipeline. To declare significant differences, a cut-off for absolute log2(FC) ≥ 1 compared to the corresponding control and FDR ≤ 0.05 was applied. Transcripts significantly different in at least one time-point were considered for subsequent analysis. Accordingly, high light treatments caused changes in 2683 transcripts, followed by 3470 under heat and 6882 under cold. Further data analysis revealed that more than 12% of all altered transcripts were commonly miss-regulated among the three treatments. From a dynamic point of view, transcriptional changes occurred from 3h to 4d of treatment in all treatments and tend to recover to the initial state after 2 and 4d of de-acclimation. Conclusions: the reversibility of the transcriptional changes during the recovery phase validated the conditions of our set-up to investigate acclimation. Moreover, the existance of a common fraction of transcripts that responded to the three conditions unveiled a central response to acclimation.
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2022-04-12 | PXD027929 |