Characterisation of the epidermal diurnal transcriptome of mice with K14-Cre-driven Bmal1 knockout

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 wild-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 diurnal transcriptome of the skin epidermis was profiled for mice in which circadian clock activity was absent in the skin epidermis, but present in all other tissues. Profiling was undertaken by performing RNA-seq of epidermis samples taken at four hour intervals throughout the day (four biological replicates per timepoint). Subsequently, a comparison with gene expression rhythmicity in WT epidermis was performed using the DryR algorithm.为维持健康稳态，哺乳动物依托一套整合的分子振荡器网络，驱动组织特异性稳态过程的昼夜节律。尤为关键的是，该网络的输出特性、结构完整性与信号协调性，会因生理性衰老、疾病及生活方式改变而遭到破坏。然而，该网络中的核心信号节点、其潜在的通信机制，以及治疗干预的潜在可能性，至今仍未被阐明。 为解析该系统，我们构建了一套仅包含两个通信节点的极简时钟网络：外周表皮时钟与中枢大脑时钟。实验证实，大脑与表皮时钟之间的通信足以维持野生型核心时钟的活性，并支撑部分特异性稳态过程，但其余时钟节点的输入对于完整的昼夜生理功能而言不可或缺。 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循环信号，以保障特定稳态过程的协调性，由此揭示了外周时钟此前未被认知的守门人功能。 综上，我们提出了一种解析组织昼夜生理功能的全新研究方法，并借此确定了维持表皮稳态所需的关键信号节点。 我们针对皮肤表皮缺失昼夜节律时钟（circadian clock）活性、其余组织均保留该活性的小鼠，开展了其皮肤表皮昼夜转录组的谱分析。该分析通过每日每隔4小时采集表皮样本并进行RNA-seq完成，每个时间点设置4个生物学重复。随后，我们采用DryR算法，将该数据集与野生型（wild-type，WT）表皮的基因表达节律性进行了对比分析。