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.

植物通过重编程基因表达，已适应并存活于持续变化的环境条件之中。可变剪接（alternative splicing, AS）对植物胁迫响应的贡献动态目前仍不明晰。本研究对低温暴露下的拟南芥（Arabidopsis thaliana）进行时序转录组测序（RNA-sequencing），明确了显著可变剪接事件发生的时间节点。分析结果显示，植物在温度降低的最初数小时内即出现大规模且快速的可变剪接响应，伴随转录活性与可变剪接活性的同步波动，且在整个低温胁迫过程中持续发生可变剪接事件。尤为关键的是，百余个基因因低温诱导下快速发生的可变剪接而出现表达变化，此类基因被称为"早期可变剪接基因（early AS genes）"；其中包含大量仅通过可变剪接调控的新型低温响应转录因子与剪接因子/RNA结合蛋白。部分此类基因的可变剪接响应速度与对微小温度变化的敏感性表明，通过可变剪接通路对基因表达进行精细调控，有助于实现基因表达的温度可塑性。此前已有研究证实，4个"早期可变剪接剪接调控基因"参与植物的耐寒性与低温驯化过程；本研究新增证据表明第5个基因——U2B"-LIKE同样具备此类功能。这类调控因子可能通过触发下游基因的可变剪接级联反应，结合转录调控共同介导转录组重编程，进而协同调控植物应对低温胁迫的生理过程与存活应答。