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ABSTRACT:
PROVIDER: PRJNA1040773 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Metabolomics of Arabidopsis photorespiration mutants under fluctuating light conditions
2023-04-26 | MSV000091798 | GNPS
Project description:Metabolomics of Arabidopsis photorespiration mutants under fluctuating light conditions
2023-04-26 | MSV000091798 | MassIVE
Project description:We identified 737 differentially expressed genes, including 430 upregulated genes and 307 downregulated genes, by calculating the gene FPKM in each sample and conducting differential gene analysis. Gene ontology analysis and KEGG pathway enrichment analysis suggested that blue light influenced visual perception, sensory perception of light stimulus, phototransduction, and JAK-STAT signaling pathways. Differential lncRNA, circRNA and miRNA analysis suggested that blue light exposure affected pathways for retinal cone cell development and phototransduction, among others.
2020-08-24 | GSE149549 | GEO
Project description:Transcriptional Response of Arabidopsis thaliana to Fluctuating Light
| PRJEB31094 | ENA
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:Adaptation of liver to the postprandial state requires coordinate regulation of protein synthesis and folding aligned with changes in lipid metabolism. Here we demonstrate that sensory food perception is sufficient to elicit early activation of hepatic mTOR-signaling, Xbp1-splicing, increased expression of ER-stress genes and phosphatidylcholine synthesis, which translate into a rapid morphological ER-remodeling. These responses overlap with those activated during refeeding, where they are maintained and constantly increase upon nutrient supply. Sensory food perception activates POMC-neurons in the hypothalamus, optogenetic activation of POMC-neurons activates hepatic mTOR-signaling and Xbp1-splicing and lack of MC4R-expression attenuates these responses to sensory food perception. Chemogenetic POMC-neuron activation promotes sympathetic nerve activity (SNA) subserving the liver, and norepinephrine evokes the same responses in hepatocytes in vitro and liver in vivo as observed upon sensory food perception. Collectively, our experiments unravel that sensory food perception coordinatly primes postprandrial liver ER adaption through a melanocortin-SNA-mTOR-Xbp1s-axis
2018-10-31 | GSE118973 | GEO
Project description:Olfaction is fundamental for survival but there is little known about the connection between smell perception and metabolism. In this study we implemented IGF1R knockout mice in the olfactory sensory neurons, by olfactory marker protetin (OMP) Cre specific recombination, and investigated metabolic parameters, smell perception and transcriptome sequencing. We could demonstrate that IGF1R knockout in the olfactory sensory neurons results in enhanced smell perception, insulin resistance under normal chow diet conditions and increased adiposity in mice fed control diet. Transcriptome analysis of the olfactory epithelium revealed differential expression of markers for mature and immature olfactory sensory neurons, being down-regulated and up- regulated respectively, pointing to differentiation-dependent changes that result in increased olfactory perception. Collectively, this study provides evidence that enhanced smell perception can result in insulin resistance and increased adiposity.
2017-05-22 | GSE85329 | GEO