Table S7 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 <i>lhycca1</i>, <i>prr7prr9</i>, <i>gi</i> and <i>toc1</i> 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研究均依托昼夜转录组变化，以阐明生物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及toc1四类生物钟突变体莲座叶，在昼末与夜末两个时间点开展比较分析。各突变体均会影响特定的基因与蛋白质组，这表明生物钟的调控具有模块性。此外，每一类生物钟突变体均拥有自身特有的动态波动转录组与蛋白质组谱，且该谱具有亚细胞区室特异性。绝大多数被检测的蛋白质水平与其对应转录本的变化并无显著关联。丰度存在协同变化的转录本与蛋白质，其富集的基因多为碳水化合物响应与低温响应基因。四类生物钟突变体的转录组变化，还会影响编码淀粉降解酶、转录因子与蛋白激酶的基因。本研究的全套转录组与蛋白质组数据集表明，未来开展系统驱动的生物钟研究，需采用多维度实验手段。本研究同时指出，仍需进一步阐明翻译后修饰与蛋白质降解在生物钟相关调控过程中的具体作用。