Systems Biology of the Circadian Clock Output Network

昼夜节律时钟输出网络的系统生物学

• 批准号: 8838960
• 负责人: Deborah Bell-Pedersen
• 金额: $ 40.44万
• 依托单位: TEXAS A&M UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-01-15 至 2018-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8838960
• 关键词: Adult; Affect; Age; Amino Acids; Asexual Reproduction; Back; Behavior; Binding; Biochemical Pathway; Biological Models; Biological Process; Biology; Carbon; ChIP-seq; Circadian Rhythms; Complex; Computer Simulation; Computing Methodologies; Data; Development; Disease; Eukaryota; Feedback; Feeds; Gene Expression; Gene Expression Profile; Gene Targeting; Genes; Genetic Transcription; Genome; Goals; Human; Intervention; Light; Link; Mammalian Cell; Messenger RNA; Metabolic; Metabolic Pathway; Metabolic syndrome; Metabolism; Modeling; Molecular; Mutation; Neurospora; Neurospora crassa; Organism; Outcome; Output; Pathway interactions; Pattern; Periodicity; Phase; Photoreceptors; Physiology; Proteins; Regulation; Regulon; Reproduction spores; Role; Route; Shapes; System; Systems Biology; Testing; Time; Transcript; Work; circadian pacemaker; genetic manipulation; human disease; metabolomics; network models; nucleotide metabolism; promoter; public health relevance; shift work; stem; transcription factor; transcription factor USF; transcriptome sequencing

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.

描述（由申请人提供）： 生物钟是一种进化上保守的时间保持机制，通过调节有节奏的基因表达，协调生物体的生理与日常环境周期。由于人体生理和行为的几乎所有方面都与生物钟有关，昼夜节律系统的异常与多种疾病有关，包括影响高达40%的50岁以上成年人的代谢综合征。因此，了解哪些基因受生物钟的调控，以及这种调控的机制，对于了解生物钟相关疾病是必要的。此外，时钟控制的转录在昼夜节律周期的所有可能阶段达到峰值;然而，我们缺乏对控制阶段的基本了解。为了开始理解昼夜节律输出基因网络，我们确定了粗糙脉孢菌中核心时钟组件和转录因子（TF）WCC的直接靶标，并在大约200个直接靶标中发现了TF的过度表达。在这些第一层TF中，ADV-1被证明是稳健的节律性的，在时钟控制的发育中有缺陷，并且与下游代谢网络密切相关。我们还发现，除了WCC之外，几个第一层TF结合到ADV-1启动子，并且ADV-1反馈结合到这些相同TF的启动子。这些相同的TF也结合并潜在地相互共调节，以及ADV-1的直接靶标。此外，我们对ADV-1的直接靶点的分析揭示了参与发育、代谢和转录控制的基因的富集。总之，这些数据表明，一个复杂的调控网络连接WCC ADV-1和下游发育和代谢基因。我们的数据还表明，这个网络的功能之一是产生不同的时间动态的基因表达的生物功能的强大的节奏至关重要。通过结合计算和实验生物学，我们将在我们的具体目标中直接测试这个想法。我们将确定上游网络如何塑造ADV-1（Aim 1）的节奏，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）。我们将结合联合收割机的上游和下游网络模型来预测和验证哪些遗传变化将选择性地改变由ADV-1节律性控制的特定代谢途径的表达阶段（目的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，以减少生物钟中断对人类疾病的严重影响，例如与轮班工作相关的代谢综合征。