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Genome-wide analyses reveal the coordination between alternative splicing and DNA methylation for light response in plants

ABSTRACT: In this study, we investigated the possibility that light regulates alternative splicing (AS) through modulating DNA methylation of specific gene loci. The bisulfite sequencing data were extensively evaluated with AS pattern from mRNA sequencing of samples with the same light treatment.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE115838 | GEO | 2021/06/15

REPOSITORIES: GEO

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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 .

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Genome-wide analyses reveal the coordination between alternative splicing and DNA methylation for light response in plants

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