Table S8 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）调控着对于植物生长与生存至关重要的生理过程。迄今为止，绝大多数植物昼夜节律钟研究均依托昼夜节律性转录组（transcriptome）变化，以阐明野生型植物中昼夜节律钟与可观测表型之间的分子关联。本研究整合了RNA测序（RNA-sequencing）与蛋白质质谱（protein mass spectrometry）数据，对昼末与夜末时刻的lhycca1、prr7prr9、gi及toc1四种昼夜节律钟突变体莲座丛进行了比较分析。各突变体均会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化特征。此外，每种昼夜节律钟突变体均拥有各自专属的、对应亚细胞区室（subcellular compartments）的动态波动转录组与蛋白质组（proteome）图谱。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，显著富集于碳水化合物响应与低温响应基因中。四种昼夜节律钟突变体的转录组变化，还会影响编码淀粉降解酶、转录因子以及蛋白激酶的基因。这套全面的转录组与蛋白质组数据集表明，未来开展系统驱动的昼夜节律钟研究，需要采用多层面的实验方法。本研究同时证实，后续仍需开展更多工作以阐明翻译后修饰（post-translational modifications）与蛋白质降解（protein degradation）在节律相关过程调控中的作用。