Table S3 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）调控与生长及生存密切相关的生理过程。迄今为止，绝大多数植物生物钟相关研究均依托昼夜转录组（transcriptome）变化，以解析野生型植物中生物钟与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（mass spectrometry）数据，对昼末与夜末时刻的lhycca1、prr7prr9、gi、toc1四种生物钟突变体莲座叶开展比较分析。每种突变体均可影响特定的基因与蛋白质组（proteome），这表明生物钟的调控具备模块化特征。此外，每种生物钟突变体均拥有各自专属的、随亚细胞分区动态变化的转录组与蛋白质组特征。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无显著相关性。丰度变化协同一致的转录本与蛋白质，在碳水化合物响应及低温响应基因中显著富集。四种生物钟突变体的转录组变化还会影响编码淀粉降解酶、转录因子及蛋白质激酶的基因。本研究获取的完整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需采用多维度实验方法。本研究同时表明，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。