Characterisation of the epidermal circadian transcriptome of mice with tissue-specific circadian clock activity [DD]

To preserve a state of health, mammals employ an integrated network of molecular oscillators to drive daily rhythms of tissue-specific homeostatic processes. Importantly, the output, structure and coherence of this network is compromised by physiological ageing, disease and lifestyle changes. Yet, the key signalling nodes in this network, their underlying mechanisms of communication, and potential for therapeutic intervention, remain undefined. To dissect this system, we construct a minimal clock network consisting of two communicating nodes: the peripheral epidermal clock and central brain clock. We show that communication between the brain and epidermal clocks is sufficient for wiDD-type core clock activity and specific homeostatic processes, but inputs from other clock nodes are essential for full daily physiology. Unexpectedly, we find evidence that the epidermal clock selectively suppresses or interprets systemic signals to ensure coherence of specific homeostatic processes, identifying an unrecognised gatekeeper role for peripheral clocks. Together, we introduce a novel approach for dissecting a tissues daily physiology, and in turn identify key signalling nodes required to maintain epidermal homeostasis. The circadian transcriptome of the skin epidermis was profiled for mice in which circadian clock activity was present only in the skin epidermis, only in the brain, only in the skin and brain, or all tissues. After a 1 week exposure to constant darkness, RNA-seq of epidermis samples were taken at four hour intervals throughout the day (four biological replicates per timepoint), and subsequently the algorithms JTK_CYCLE and BIOCYCLE were used to generate a consensus circadian transcriptome for each condition. In addition, the algorithm DryR was used to identify groups of genes with specific rhythmic parameters either shared or differing between the different conditions.为维持健康状态，哺乳动物借助一套整合的分子振荡器网络，驱动组织特异性稳态过程的每日节律。值得注意的是，该网络的输出特性、结构组成与协同协调性会因生理衰老、疾病及生活方式改变而受损。然而，该网络内的关键信号节点、其通信的底层机制，以及治疗干预的潜在潜力，至今尚未阐明。为解析这一系统，我们构建了一套包含两个通信节点的极简时钟网络：外周表皮时钟（peripheral epidermal clock）与中枢大脑时钟（central brain clock）。我们证实，大脑与表皮时钟间的通信足以维持wiDD型核心时钟活性与特定稳态过程，但来自其他时钟节点的输入对于完整的每日生理节律而言必不可少。出乎意料的是，我们发现表皮时钟可选择性抑制或解读系统性信号，以确保特定稳态过程的协调性，这一发现揭示了外周时钟此前未被认知的守门人（gatekeeper）功能。综上，我们提出了一种解析组织每日生理节律的全新方法，并借此明确了维持表皮稳态所需的关键信号节点。我们对四类小鼠的皮肤表皮开展了昼夜节律转录组（circadian transcriptome）分析：这些小鼠的昼夜节律时钟活性分别仅存在于皮肤表皮、仅存在于大脑、同时存在于皮肤与大脑，或是遍布所有组织。在持续黑暗环境中暴露1周后，我们每隔4小时采集一次表皮样本进行RNA测序（RNA-seq），每个时间点设置4个生物学重复（biological replicates）。随后，我们借助JTK_CYCLE与BIOCYCLE算法为每类实验条件生成了一致性昼夜节律转录组。此外，我们使用DryR算法来识别在不同实验条件间具有特定共享或差异化节律参数的基因簇。