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

项目总结： 昼夜节律系统是协调细胞功能和功能的重要网络中枢 动态平衡。人类昼夜节律系统中与年龄相关的变化与 阿尔茨海默氏症和其他神经元病理。最近在果蝇和老鼠身上的证据表明 节律紊乱与神经退行性变之间的相关性；然而，我们知之甚少 关于涉及的机制。为了研究这些机制，我们比较了昼夜节律 用RNA-seq技术研究幼龄和老年果蝇头部的转录组。我们发现有几个 在幼蝇体内以有节奏的方式表达的早期生命周期蛋白(ELCs)基因丢失 在老年果蝇身上变得天生的低或高的骑行模式。我们还发现了一组 我们称之为晚期生命周期蛋白(LLC)的基因，在年轻人的大脑中是低和心律不齐的 苍蝇，但在老苍蝇的头上变得有强烈的节奏。这一组包含已知的压力- 在幼龄果蝇体内诱导的对氧化应激或高氧反应的反应基因。 根据我们最近发表的数据的这些发现，我们假设昼夜节律 系统在老化期间通过输入和输出的组合改变而重新布线 TO、应激反应通路和年龄改变对转录后调节的影响 MicroRNA的表达。因为昼夜节律系统和 神经退化，我们预计其中一些变化可能对神经元健康有害，并且 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、应激反应因子和RNA 聚合酶II通过ChIP-Seq并识别可能是 对这些监管变化负责。此外，我们还将执行ATAC-SEQ来测量 染色质可及性。在目标2中，我们将通过以下方式开发基因调控的网络模型 将这一新数据与我们现有的RNA-SEQ数据和即将到来的小RNA-SEQ结合在一起 数据。我们将建立计算模型并分析基因组数据，以创建一种机制 对导致观察到的昼夜年龄变化的表观遗传学变化的理解 表情模式。通过比较我们将为年轻苍蝇和老年苍蝇建立的网络，我们将 能够确定我们将遵循的老化、神经退行性变(CRAN)的候选调节器 准备好了。在目标3中，我们将研究这些CRAN在神经元健康、寿命和 行为节律。我们将使用基因操作来确定致病基因 导致健康和神经退行性变的调节事件。拟议中的工作 也应该揭示时钟控制的通路，保护大脑免受年龄相关的损害 作为年龄起病的时钟网络或连接通路失调的例子。给定 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 在人类身上也有作用。 好了！

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. !