Transcriptional Architecture and Chromatin Landscape of Circadian Clocks in Aging

描述（由申请人提供）：热量限制（CR）是少数几种提高哺乳动物寿命的方案之一，但这种有益作用的机制尚不清楚。在大多数CR研究中的混淆是，食物摄入的时间限制几乎总是伴随着热量限制。已知时间限制或限制进食（RF）是哺乳动物中昼夜节律的强有力的夹带刺激，并且可以改变外周器官系统（例如肝脏）的整个昼夜代谢谱。有趣的是，CR 与RF组合的电生理信号已经被证明是甚至更有效的夹带信号，并且可以重置视交叉上核（SCN）中的中枢起搏器以及外周组织中的昼夜节律振荡器。考虑到昼夜节律的恶化是衰老的标志之一，并且考虑到人类和动物模型中的昼夜节律破坏导致心血管和代谢紊乱，这种“昼夜节律顺序”（内部节律的一致性和同步性）的时间破坏可能显著有助于衰老和长寿。在初步数据中，我们发现RF对全基因组昼夜节律转录结构、基因表达和RNA聚合酶II募集和启动以及涉及组蛋白甲基化和乙酰化的染色质修饰具有广泛和复杂的影响。这些变化导致节律性基因表达模式和影响途径的阶段发生大的变化，这些途径对衰老过程至关重要，包括能量利用和代谢途径、胰岛素信号传导、mTOR信号传导、异生物质解毒和泛素介导的蛋白水解。降低的昼夜节律幅度和不适当的阶段性节律是衰老的标志，改善昼夜节律功能的治疗与健康和更长的寿命有关。因此，热量限制范例的有益效果可能部分或全部源于食物摄入的时间限制，而不是热量的减少。因此，我们假设，在热量限制期间，中枢和外周振荡器的同步化改善了激素、生化和生理功能，从而导致衰老的减弱和寿命的延长。在这些实验中，我们将产生全面的昼夜节律谱的生物钟转录因子结合，基因表达和染色质修饰，以评估在衰老过程中发生的全基因组变化。我们将使用一个实验设计，区分热量限制和时间限制的贡献。使用隐马尔可夫模型和相关矩阵分析作为衰老的函数的昼夜节律转录景观将为发现对昼夜节律、衰老和长寿至关重要的基因组和表观基因组签名和机制提供基础。

DESCRIPTION (provided by applicant): Caloric restriction (CR) is one of the few regimens that enhances longevity in mammals, yet the mechanisms underlying this beneficial effect have been elusive. A confound in the majority of CR studies is that temporal restriction of food intake almost always accompanies caloric restriction. Temporal restriction or restricted feeding (RF) is known to be a potent entraining stimulus for circadian rhythms in mammals and can shift the entire circadian metabolic profile of peripheral organ systems such as the liver. Interestingly, CR combined with RF has been shown to be an even more potent entraining signal and can reset both the central pacemaker in the suprachiasmatic nucleus (SCN) as well as circadian oscillators in peripheral tissues. Given that deterioration of circadian rhythms is one of the hallmarks of aging and given that circadian disruptions in both human and animal models lead to cardiovascular and metabolic disorders, such temporal disruptions of "circadian order" (coherence and synchrony of internal rhythms) could contribute significantly to aging and longevity. In preliminary data we have found that RF has wide-ranging and complex effects on genome-wide circadian transcriptional architecture, gene expression and RNA polymerase II recruitment and initiation as well as chromatin modifications involving histone methylation and acetylation. These changes result in large shifts in the phases of rhythmic gene expression patterns and impact pathways that are central to the aging process including energy utilization and metabolic pathways, insulin signaling, mTOR signaling, xenobiotic detoxification, and ubiquitin mediated proteolysis. Lowered circadian amplitude and inappropriately phased rhythms are hallmarks of aging, and treatments that improve circadian function have been linked to well-being and longer lifespan. Therefore, it is possible that the beneficial effects of caloric restriction paradigms originates partially or fully from the temporal restriction of food intake, rather than the reduction in calories. Thus, we hypothesize that synchronization of central and peripheral oscillators during caloric restriction improves hormonal, biochemical and physiological functions, which can then lead to attenuation of aging and increased life span. In these experiments we will generate comprehensive circadian profiles of circadian clock transcription factor binding, gene expression and chromatin modifications to assess genome-wide changes that occur during the aging process. We will use an experimental design that distinguishes the contributions of caloric restriction from those of temporal restrictions. Analyse of the circadian transcriptional landscape as a function of aging using Hidden Markov Models and correlation matrices will provide a foundation for discovery of genomic and epigenomic signatures and mechanisms critical to circadian rhythms, aging and longevity.