Systems Biology of the Circadian Clock Output Network

描述(由申请人提供)： 生物钟是一种进化上保守的计时机制，通过调节有节奏的基因表达，协调生物体的生理和日常环境周期。由于人类生理和行为的几乎所有方面都与时钟有关，昼夜节律系统的异常与一系列疾病有关，包括影响高达40%的50岁以上成年人的代谢综合征。因此，了解哪些基因受时钟调控，以及这种调控的机制，对于理解时钟相关疾病是必要的。此外，时钟控制的转录本在昼夜节律周期的所有可能阶段达到顶峰；然而，我们缺乏对什么控制阶段的基本了解。为了开始了解昼夜节律输出基因网络，我们在粗枝脉孢菌中鉴定了核心时钟成分和转录因子(Tf)WCC的直接靶标，并发现在大约200个直接靶标中Tf过表达。在这些第一级转录因子中，ADV-1被证明具有强烈的节律性，在时钟控制的发育中存在缺陷，并与下游代谢网络密切相关。我们还发现，除了WCC外，还有几个第一层转录因子与Adv-1启动子结合，并且Adv-1反馈与这些相同TF的启动子结合。这些相同的转录因子还相互结合并潜在地共同调节，以及ADV-1的直接靶标。此外，我们对ADV-1的直接靶标的分析显示，参与发育、代谢和转录调控的基因丰富。总之，这些数据表明了一个复杂的调控网络，将WCC与ADV-1以及下游的发育和代谢基因联系起来。我们的数据还表明，这个网络的一个功能是产生不同的基因表达的时间动态，这对生物功能中的强劲节奏至关重要。通过将计算生物学和实验生物学相结合，我们将在我们的特定目标中直接测试这一想法。我们将确定上游网络如何塑造Adv-1(Aim1)的节律，以及Adv-1下游网络如何产生不同的基因表达时间模式(Aim 2)。我们将结合上游和下游网络模型来预测和验证哪些基因变化将选择性地改变由ADV-1节律控制的特定代谢途径的表达阶段(目标3)。因此，这项工作的一个主要成果是开发干预措施的令人兴奋的潜力，以减少时钟扰乱对人类疾病的严重影响，例如与倒班工作相关的代谢综合征。

DESCRIPTION (provided by applicant): The circadian clock is an evolutionarily conserved time-keeping mechanism that, through the regulation of rhythmic gene expression, coordinates the physiology of an organism with daily environmental cycles. Because virtually all aspects of human physiology and behavior are linked to the clock, abnormalities in the circadian system are associated with a wide range of diseases, including metabolic syndrome that affects up to 40% of adults over the age of 50. Thus, knowing what genes are regulated by the clock, and the mechanisms of this regulation, are necessary to understand clock-associated diseases. Furthermore, clock-controlled transcripts peak at all possible phases of the circadian cycle; however, we lack a basic understanding of what controls phase. To begin to understand the circadian output gene network, we identified the direct targets of the core clock component and transcription factor (TF) WCC in Neurospora crassa, and found an overrepresentation of TFs in the roughly 200 direct targets. Among these first tier TFs, ADV-1 was shown to be robustly rhythmic, defective in clock-controlled development, and closely linked to the downstream metabolic network. We also discovered that in addition to WCC, several first tier TFs bind to the adv-1 promoter, and that ADV-1 feeds back to bind to the promoters of these same TFs. These same TFs also bind and potentially co- regulate each other, and the direct targets of ADV-1. In addition, our analysis of the direct targets of ADV-1 revealed enrichment for genes involved in development, metabolism, and transcription control. Together, these data suggest a complex regulatory network linking WCC to ADV-1 and to downstream developmental and metabolic genes. Our data also suggest that one function of this network is to generate distinct temporal dynamics of gene expression critical to robust rhythms in biological functions. By combining computational and experimental biology, we will directly test this idea in our specific aims. We will determine how the upstream network sculpts the rhythms in ADV-1 (Aim1), and how the ADV-1 downstream network generates distinct temporal patterns of gene expression (Aim 2). We will combine the upstream and downstream network models to predict and validate which genetic changes will selectively alter the phase of expression of specific metabolic pathways that are rhythmically controlled by ADV-1 (Aim 3). As such, one major outcome of this work is the exciting potential to develop interventions to diminish the serious effects of disruption of the clock on human disease, such as metabolic syndrome associated with shift work.