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，以适应并存活于持续变化的环境条件中。可变剪接（alternative splicing, AS）在植物胁迫响应中的调控动态与贡献机制尚未明确。本研究对低温胁迫下的时间序列拟南芥（Arabidopsis thaliana）样本开展RNA测序，明确了显著可变剪接事件的发生时间节点。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，转录与可变剪接活性同步出现峰值，且在整个低温胁迫过程中持续发生可变剪接事件。具体而言，数百个基因因低温胁迫下快速发生的可变剪接而出现表达变化，这类基因被称为“早期可变剪接（"early AS"）”基因；其中包含诸多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对微小温度变化具备快速响应能力与高度敏感性，这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”剪接调控基因对植物的耐寒性与低温驯化至关重要；本研究为第5个基因U2B"-LIKE"提供了实验佐证。这类剪接调控因子可能通过调控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的生理过程与存活响应。