Data from: Rapid and dynamic alternative splicing impacts the Arabidopsis cold response transcriptome

Plants have adapted to tolerate and survive constantly changing environmental conditions by re-programming gene expression. The dynamics of the contribution of alternative splicing (AS) to stress responses are unknown. RNA-sequencing of a time-series of Arabidopsis thaliana plants exposed to cold determines the timing of significant AS changes. This shows a massive and rapid AS response with coincident waves of transcriptional and AS activity occurring in the first few hours of temperature reduction, and further AS throughout the cold. In particular, hundreds of genes showed changes in expression due to rapidly occurring AS in response to cold ("early AS" genes); these included numerous novel cold-responsive transcription factors and splicing factors/RNA-binding proteins regulated only by AS. The speed and sensitivity to small temperature changes of AS of some of these genes suggest that fine-tuning expression via AS pathways contributes to the thermo-plasticity of expression. Four "early AS" splicing regulatory genes have been shown previously to be required for freezing tolerance and acclimation; we provide evidence of a fifth gene, U2B"-LIKE. Such factors likely drive cascades of AS of downstream genes which alongside transcription modulate transcriptome reprogramming that together govern the physiological and survival responses of plants to low temperature.Supplemental Dataset 1Results of the analysis of differentially expressed, differentially alternatively spliced and differential transcript usage.Supplemental_Dataset_1.xlsxSupplemental_Dataset_2Gene lists of the up- and down-regulated DE genes in the different contrast groups.Supplemental_Dataset_3Summary of previous studies on wild-type Arabidopsis genome-wide cold response.Supplemental_Dataset_4Gene lists of known Arabidopsis cold-response genes in Supplemental Dataset 5.Supplemental_Dataset_5Novel genes differentially regulated by cold at the expression (DE) and/or alternative splicing level (DAS).Supplemental_Dataset_6Gene Ontology (GO) enrichment analysis of DE genes and DAS genes.Supplemental_Dataset_7Genes in DE and DTU heatmap clusters and Gene Ontology (GO) enrichment analysis of individual heatmap DE gene clusters.Supplemental_Dataset_8Gene lists and descriptions of DE and DAS genes organised by the time-point at which they first become significantly differentially expressed upon cold.Supplemental_Dataset_9DAS gene lists and descriptions organised by different ΔPS cut-off values.Supplemental_Dataset_10Isoform switch and AS events analyses of transcripts from DAS genes.Supplemental_Dataset_11List of Arabidopsis Transcription Factor and SF-RBP genes.Supplemental_Dataset_12Summary of TF and SF-RBP DE and DAS genes with the largest and most rapid changes in AS.Supplemental_Dataset_13Timing of significantly DE and DAS SF-RBP and TF genes in the first 12 h after onset of cold treatment (T9-T13).Supplemental_Dataset_14AS data for the u2b''-like HR RT-PCR analysis panel.Supplemental_Dataset_15Summary of RNA-seq data derived from Arabidopsis rosettes time-series cold response study.Supplemental_Dataset_16Transcript expression in the Arabidopsis cold responseSupplemental_Dataset_17Primers used in this study