Changes in mRNA Stability Associated with Cold Stress in Arabidopsis Cells. Arabidopsis thaliana

Control of mRNA half-life is a powerful strategy to adjust individual mRNA levels to various stress conditions, because the mRNA degradation rate controls not only the steady-state mRNA level but also the transition speed of mRNA levels. Here, we analyzed mRNA half-life changes in response to cold stress in Arabidopsis cells using genome-wide analysis, in which mRNA half-life measurements and transcriptome analysis were combined. Half-lives of average transcripts were determined to be elongated under cold conditions. Taking this general shift into account, we identified more than a thousand transcripts that were classified as relatively stabilized or relatively destabilized. The relatively stabilized class was predominantly observed in functional categories that included various regulators involved in transcriptional, post-transcriptional and post-translational processes. On the other hand, the relatively destabilized class was enriched in categories related to stress and hormonal response proteins, supporting the idea that rapid decay of mRNA is advanta- geous for swift responses to stress. In addition, pentatricopeptide repeat, cyclin-like F-box and Myb transcription factor protein families were significantly over-represented in the relatively destabilized class. The global analysis presented here demonstrates not only the importance of mRNA turn-over control in the cold stress response but also several structural characteristics that might be important in the control of mRNA stability. Overall design: To demonstrate the importance of mRNA stability control in cold stress response, we investigated global changes in mRNA half-lives in response to cold treatment by micaroarray using Arabidopsis suspension cell cultures (T87 cells). Control cells were collected prior to transcriptional inhibitor (cordycepin) treatment (0 h), and 1 and 3 h after the start of cordycepin treatment. For cold-treated cells, 6 h samples were also used for microarray analyses. The experiments were performed with triplicate sets for each time point.

调控mRNA半衰期（mRNA half-life）是调整单个mRNA水平以适配各类胁迫环境的高效策略，因为mRNA降解速率不仅决定稳态mRNA水平，同时还调控mRNA水平的变化速率。本研究通过结合mRNA半衰期检测与转录组分析的全基因组分析方法，解析了拟南芥（Arabidopsis）细胞响应低温胁迫时的mRNA半衰期变化。结果显示，低温条件下平均转录本的半衰期显著延长。结合这一整体变化趋势，我们共鉴定出千余个转录本，可分为相对稳定与相对不稳定两类。相对稳定的转录本主要富集于涉及转录、转录后及翻译后调控的各类功能类别中。与之相反，相对不稳定的转录本则富集于与胁迫及激素响应蛋白相关的功能类别，这一结果支持"mRNA快速降解利于胁迫快速响应"的观点。此外，五肽重复序列（pentatricopeptide repeat）、类细胞周期蛋白F-box以及Myb转录因子蛋白家族在相对不稳定的转录本类别中显著富集。本研究的全基因组分析不仅揭示了mRNA周转调控在低温胁迫响应中的重要性，同时也鉴定出若干可能参与mRNA稳定性调控的结构特征。实验设计概述：为验证mRNA稳定性调控在低温胁迫响应中的重要性，本研究以拟南芥悬浮培养细胞（T87细胞）为材料，通过基因芯片（microarray）技术分析低温处理后mRNA半衰期的全局变化。对照组细胞分别在转录抑制剂虫草素（cordycepin）处理前（0小时）、处理开始后1小时及3小时收集；低温处理组细胞则额外收集了处理6小时的样本用于基因芯片分析。所有实验均设置三次生物学重复。