Translational contributions to tissue-specificity in rhythmic and constitutive gene expression

BACKGROUND: The daily gene expression oscillations that underlie mammalian circadian rhythms show striking differences between tissues and involve post-transcriptional regulation. Both aspects remain poorly understood. We have used ribosome profiling to explore the contribution of translation efficiency to temporal gene expression in kidney, and contrasted our findings with liver data available from the same mice. RESULTS: Rhythmic translation of constantly abundant mRNAs affects largely nonoverlapping transcript sets with distinct phase clustering in the two organs. Moreover, tissue differences in translation efficiency modulate the timing and amount of protein biosynthesis from rhythmic mRNAs, consistent with organ-specificity in clock output gene repertoires and rhythmicity parameters. Our comprehensive datasets provided insights into translational control beyond temporal regulation. Between tissues, many transcripts show differences in translation efficiency, which are, however, of markedly smaller scale than mRNA abundance differences. Tissue-specific changes in translation efficiency are associated with specific transcript features and, intriguingly, globally counteracted and compensated transcript abundance variations, leading to higher similarity at the level of protein biosynthesis between both tissues. CONCLUSIONS: We show that tissue-specificity in rhythmic gene expression extends to the translatome and contributes to define the identities, the phases and the expression levels of rhythmic protein biosynthesis. Moreover, translational compensation of transcript abundance divergence leads to overall higher similarity at the level of protein production across organs. The unique resources provided through our study will serve to address fundamental questions of post-transcriptional control and differential gene expression in vivo. A total of 48 mice were entrained under 12hours light:dark conditions for 2 weeks and also collected under 12hours light:dark. Mice were sacrificed every two hours during the 24 hours daily cycle. Two replicates per time point, each replicate is a pool of livers or kidneys from 2 animals.一、研究背景：支撑哺乳动物昼夜节律（circadian rhythms）的每日基因表达振荡在不同组织间存在显著差异，且该过程涉及转录后调控（post-transcriptional regulation）。目前对于这两方面的认知仍较为匮乏。本研究采用核糖体谱（ribosome profiling）技术，探究了肾脏中翻译效率对时序基因表达的调控作用，并将所得结果与同批次小鼠的肝脏数据进行了对比分析。 二、研究结果：持续丰度稳定的mRNA的节律性翻译，在两个器官中分别对应具有显著相位聚类特征的、基本无重叠的转录本集合。此外，不同组织间的翻译效率差异可调控节律性mRNA的蛋白质生物合成时序与产量，这与生物钟下游基因库及节律参数的器官特异性特征相符。本研究的综合数据集还为时序调控之外的翻译调控机制提供了新的研究视角。跨组织对比发现，大量转录本存在翻译效率差异，但该差异的幅度显著小于mRNA丰度差异。组织特异性的翻译效率变化与特定转录本特征相关；有趣的是，这类变化可在全局水平抵消并补偿转录本丰度的差异，最终使得两个组织在蛋白质生物合成层面的相似性显著提升。 三、研究结论：本研究证实，节律性基因表达的组织特异性可延伸至翻译组（translatome）层面，且有助于塑造节律性蛋白质生物合成的特征、时序与表达水平。此外，针对转录本丰度差异的翻译补偿机制，可使得跨器官的蛋白质合成整体相似性得以提升。本研究产生的独特研究资源，将为解答体内转录后调控与差异基因表达的核心科学问题提供支撑。 四、实验方案：本研究共纳入48只小鼠，将其在12小时光照:12小时黑暗的环境中同步饲养2周，并于相同光照周期下开展采样工作。在每日24小时的周期内，每2小时采集一次样本。每个时间点设置两个生物学重复，每个重复由2只小鼠的肝脏或肾脏组织混合而成。