Understanding the Gene Regulatory Mechanisms That Underlie Age-Induced Changes in the Circadian System and Neurodegeneration

了解年龄引起的昼夜节律系统变化和神经退行性疾病背后的基因调控机制

• 批准号: 10404992
• 负责人: David Anthony Hendrix
• 金额: $ 36.14万
• 依托单位: OREGON STATE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-09-30 至 2024-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10404992
• 关键词: ATAC-seq; Affect; Age; Age of Onset; Aging; Alzheimer' s Disease; Alzheimer' s disease related dementia; Animal Model; Automobile Driving; Autopsy; Behavior; Behavioral; Binding; Biological; Biological Markers; Biology of Aging; Brain; Cell physiology; ChIP-seq; Chromatin; Chronobiology; Circadian Dysregulation; Circadian Rhythms; Clinical Research; Computational Biology; Computer Models; DNA Binding; Data; Dementia; Disease; Drosophila genus; Elderly; Epigenetic Process; Erythroid; Event; Gene Expression; Gene Expression Regulation; Genes; Genetic; Genetic Transcription; Genome; Genomics; Head; Health; Heat shock factor; Homeostasis; Human; Hyperoxia; Hypoxia Inducible Factor; Individual; Knock-out; Lead; Life Cycle Stages; Longevity; Mammals; Measurement; Measures; MicroRNAs; Molecular; Mus; Nerve Degeneration; Neurodegenerative Disorders; Neurons; Neurophysiology - biologic function; Nuclear; Output; Oxidative Stress; Pathology; Pathway interactions; Patients; Pattern; Periodicity; Persons; Phenocopy; Physiological Processes; Play; Post-Transcriptional Regulation; Predisposition; Publications; Publishing; RNA Interference; RNA Polymerase II; Regulator Genes; Rodent; Role; Sleep; Small RNA; Stress; System; Systems Biology; Testing; Time; Work; age related; age related neurodegeneration; base; biological adaptation to stress; circadian; circadian pacemaker; circadian transcriptome; combat; data modeling; flexibility; fly; follow-up; genetic manipulation; genome-wide; genomic data; healthy aging; heat shock transcription factor; in vivo evaluation; innovation; insight; kinetic model; network models; novel; overexpression; oxidative damage; pre-clinical; predictive modeling; prevent; promoter; response; tool; transcription factor; transcriptome; transcriptome sequencing

PROJECT SUMMARY: The circadian system is an important network hub coordinating cellular functions and homeostasis. Age-related alterations in the human circadian system are implicated in Alzheimer’s and other neuronal pathologies. Recent evidence in fruit flies and mice suggests correlation between disrupted rhythms and neurodegeneration; however, very little is known about mechanisms involved. To investigate these mechanisms, we compared circadian transcriptome in heads of young and old Drosophila using RNA-seq. We found that several genes, early-life cyclers (ELCs), that were expressed in young flies in a rhythmic fashion lose cycling pattern to become constitutively low or high in old flies. We also uncovered a group of genes, which we termed late life cyclers (LLCs), that were low and arrhythmic in heads of young flies but became strongly rhythmic in heads of old flies. This group contains known stress- responsive genes that are induced in young flies in response to oxidative stress or hyperoxia. Based on these findings from our recently published data, we hypothesize that the circadian system is rewired during aging through a combination of alterations in inputs from, and outputs to, stress-response pathways, and changes in post-transcriptional regulation by age-altered microRNA expression. Because of the connections between the circadian system and neurodegeneration, we expect some of these changes could be harmful for neuronal heath, and others could be part of a protective mechanism. In Aim 1, we will measure genome-wide binding of the core circadian transcription factors (TFs) CLK and CYC, stress responsive TFs, and RNA Polymerase II through ChIP-Seq and identify age-specific binding events that could be responsible for these regulatory changes. In addition, we will perform ATAC-seq to measure chromatin accessibility. In Aim 2, we will develop network models of gene regulation by combining this new data, along with our existing RNA-seq data and forthcoming small RNA-seq data. We will build computational models and analyze genomic data to create a mechanistic understanding of the epigenetic changes leading to the observed age-onset changes in diurnal expression patterns. By comparing the networks that we will build for young and old flies, we will be able to identify candidate regulators of aging, neurodegeneration (CRANs) that we will follow up on. In Aim 3, we will study the role of these CRANs in neuronal health, lifespan, and behavioral rhythms. We will use genetic manipulation to determine the causative gene regulatory events responsible for changes in health and neurodegeneration. The proposed work should reveal clock-controlled pathways that protect the brain from age-related damage, as well as examples of age-onset dysregulation of the clock network or connected pathways. Given the conserved molecular basis of circadian clock and aging biology, we expect these pathways will also function in humans. !

项目概要： 昼夜节律系统是协调细胞功能的重要网络枢纽， 体内平衡人类昼夜节律系统中与睡眠有关的改变涉及到 老年痴呆症和其他神经病变。最近在果蝇和老鼠身上发现的证据表明 节律紊乱与神经退行性变之间的相关性;然而， 有关的机制。为了研究这些机制，我们比较了昼夜节律 使用RNA-seq的年轻和年老果蝇头部的转录组。我们发现， 基因，早期生命周期蛋白（ELC），在年轻的果蝇中以有节奏的方式表达， 循环模式，成为组成性低或高的老苍蝇。我们还发现了一组 基因，我们称之为晚期生命周期因子（LLCs），在年轻人的头部中是低的和低表达的。 但在老苍蝇的头上变得有强烈的节奏感。这个群体包含已知的压力- 在幼蝇中诱导的对氧化应激或高氧的反应基因。 根据我们最近发表的数据，我们假设昼夜节律 在老化过程中，通过输入和输出的组合变化， 应激反应途径，以及年龄改变的转录后调节的变化。 microRNA表达。由于昼夜节律系统和 神经变性，我们预计其中一些变化可能对神经元健康有害， 其他的可能是保护机制的一部分。在目标1中，我们将测量全基因组结合 核心昼夜节律转录因子（TF）CLK和CYC、应激反应TF和RNA 聚合酶II通过ChIP-Seq和鉴定年龄特异性结合事件， 对这些监管变化负责。此外，我们将执行ATAC-seq来测量 染色质可及性在目标2中，我们将开发基因调控的网络模型， 将这些新数据与我们现有的RNA-seq数据和即将推出的小RNA-seq数据相结合， 数据我们将建立计算模型，分析基因组数据， 了解表观遗传变化导致观察到的昼夜变化的年龄发作 表达模式通过比较我们将为年轻和年老的果蝇建立的网络，我们将 能够确定我们将遵循的衰老，神经退行性变（CRAN）的候选调节因子 在目标3中，我们将研究这些CRAN在神经元健康，寿命和 行为节奏我们将使用基因操作来确定致病基因 负责健康和神经退化变化的调节事件。拟议工作 应该揭示时钟控制的途径，保护大脑免受年龄相关的损害，以及 作为时钟网络或相关通路的年龄发病失调的例子。鉴于 生物钟和衰老生物学的保守分子基础，我们预计这些途径将 也在人类中发挥作用。 !

项目成果

Age-dependent effects of blue light exposure on lifespan, neurodegeneration, and mitochondria physiology in Drosophila melanogaster.

• DOI: 10.1038/s41514-022-00092-z
• 发表时间: 2022-07-27
• 期刊: NPJ AGING
• 作者: Song, Yujuan;Yang, Jun;Law, Alexander D;Hendrix, David A;Kretzschmar, Doris;Robinson, Matthew;Giebultowicz, Jadwiga M
• 通讯作者: Giebultowicz, Jadwiga M