Table S4 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.生物钟（circadian clock）调控着支撑生长与存活的核心生理过程。截至目前，绝大多数植物生物钟相关研究均以昼夜转录组变化为研究基础，用以解析野生型（wild-type）植物中生物钟与可观测表型之间的分子联系。本研究整合了RNA测序（RNA-sequencing）与蛋白质质谱（protein mass spectrometry）数据，对终昼与终夜时刻的lhycca1、prr7prr9、gi及toc1生物钟突变体莲座叶开展了比较分析。各突变体均可影响特定的基因与蛋白质组，这提示生物钟调控具备模块化特征。进一步而言，每个生物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图谱。本次检测的绝大多数蛋白质水平，与其对应转录本的变化并不相关。丰度存在协同变化的转录本与蛋白质，显著富集于碳水化合物响应基因与低温响应基因中。四个生物钟突变体的转录组变化还会对编码淀粉降解酶、转录因子及蛋白激酶的基因产生影响。这份全面的转录组与蛋白质组数据集证实，未来开展系统性生物钟研究必须采用多维度实验手段。本研究同时表明，后续仍需进一步阐明翻译后修饰（post-translational modifications）与蛋白质降解（protein degradation）在生物钟相关调控过程中的具体作用。