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，已适应并得以在持续变化的环境条件下存活。目前，可变剪接（alternative splicing, AS）在胁迫响应中的贡献动态尚不明确。本研究对低温胁迫下的拟南芥（Arabidopsis thaliana）植株进行时序RNA测序，明确了其显著可变剪接变化发生的时间节点。研究结果显示，植株存在大规模且快速的可变剪接响应：在温度降低的最初数小时内，转录活性与可变剪接活性同步出现峰值，且在整个低温胁迫期间持续发生可变剪接事件。尤为关键的是，数百个基因因低温响应下快速发生的可变剪接而出现表达变化，这类基因被称为“早期可变剪接基因”（early AS genes）；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响应速度以及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（thermo-plasticity）。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抗冻性与低温驯化至关重要；本研究为第5个基因——U2B"-LIKE——提供了相关证据支持。这类调控因子可能介导下游基因的可变剪接级联反应，与转录调控共同塑造转录组重编程过程，进而协同调控植物应对低温的生理响应与存活策略。