Table S11 from Parallel analysis of Arabidopsis circadian clock mutants reveals different scales of transcriptome and proteome regulation

The circadian clock regulates physiological processes central to growth and survival. To date, most plant circadian clock studies have relied on diurnal transcriptome changes to elucidate molecular connections between the circadian clock and observable phenotypes in wild-type plants. Here, we have integrated RNA-sequencing and protein mass spectrometry data to comparatively analyse the lhycca1, prr7prr9, gi and toc1 circadian clock mutant rosette at the end of day and end of night. Each mutant affects specific sets of genes and proteins, suggesting that the circadian clock regulation is modular. Furthermore, each circadian clock mutant maintains its own dynamically fluctuating transcriptome and proteome profile specific to subcellular compartments. Most of the measured protein levels do not correlate with changes in their corresponding transcripts. Transcripts and proteins that have coordinated changes in abundance are enriched for carbohydrate- and cold-responsive genes. Transcriptome changes in all four circadian clock mutants also affect genes encoding starch degradation enzymes, transcription factors and protein kinases. The comprehensive transcriptome and proteome datasets demonstrate that future system-driven research of the circadian clock requires multi-level experimental approaches. Our work also shows that further work is needed to elucidate the roles of post-translational modifications and protein degradation in the regulation of clock-related processes.昼夜节律钟（circadian clock）调控着与植物生长和生存核心相关的生理过程。截至目前，绝大多数植物昼夜节律钟研究均依托昼夜节律下的转录组变化，以阐明昼夜节律钟与野生型植物可观测表型之间的分子关联。本研究整合RNA测序（RNA-sequencing）与蛋白质质谱（protein mass spectrometry）数据，对lhycca1、prr7prr9、gi、toc1四种昼夜节律钟突变体的莲座叶在昼末与夜末两个时间点开展比较分析。各突变体仅靶向影响特定的基因与蛋白质集合，这表明昼夜节律钟的调控具有模块性特征。此外，各昼夜节律钟突变体均拥有各自独特的、与亚细胞区室对应的动态波动转录组与蛋白质组特征谱。绝大多数检测到的蛋白质水平与其对应转录本的丰度变化并不相关。丰度发生协同变化的转录本与蛋白质，其富集功能主要为碳水化合物响应与低温响应基因。四种昼夜节律钟突变体的转录组变化均会影响编码淀粉降解酶、转录因子与蛋白质激酶的基因。本研究获得的全面转录组与蛋白质组数据集证实，未来以系统生物学为导向的昼夜节律钟研究需采用多维度实验策略。本研究同时指出，仍需进一步开展相关工作以阐明翻译后修饰与蛋白质降解在节律相关调控过程中的具体作用。