GSE125950
Comparison of transcript profiles of acclimated and de-acclimated Arabidopsis plants to high light, cold and heat.
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. Overall design: Transcriptome profiling of pools from shoots of 14-d-old Arabidopsis plants treated with standard controls or acclimated and de-acclimated to high light, heat and cold for 4d. Illumina Sequencing protocols were applied to biologically independent triplicates, unless indicated otherwise.