Transcriptional Architecture and Chromatin Landscape of Circadian Clocks in Aging

描述(由申请人提供)：卡路里限制(CR)是为数不多的延长哺乳动物寿命的方案之一，但这种有益效果背后的机制一直难以捉摸。大多数CR研究中的一个困惑是，食物摄入量的时间限制几乎总是伴随着卡路里限制。时间限制或限制摄食(RF)被认为是哺乳动物昼夜节律的一种强有力的诱导性刺激，并可以改变肝脏等周围器官系统的整个昼夜代谢谱。有趣的是，CR 与射频相结合被证明是一种更有效的诱导信号，可以重置视交叉上核(SCN)的中央起搏器以及周围组织的昼夜振荡。鉴于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紊乱会导致心血管和代谢紊乱，这种昼夜节律的短暂紊乱(内部节律的一致性和同步性)可能会对衰老和长寿做出重大贡献。在初步的数据中，我们发现RF对全基因组的昼夜节律转录结构、基因表达、RNA聚合酶II的招募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而复杂的影响。这些变化导致了在衰老过程中起核心作用的节律性基因表达模式和影响途径的阶段发生了巨大变化，包括能量利用和代谢途径、胰岛素信号、mTOR信号、外源解毒和泛素介导的蛋白质分解。昼夜节律幅度降低和不适当的相位节律是衰老的标志，改善昼夜节律功能的治疗被认为与幸福感和更长的寿命有关。因此，卡路里限制模式的有益影响可能部分或全部源于对食物摄入量的时间限制，而不是卡路里的减少。因此，我们假设，在热量限制期间，中枢和外周振荡器的同步改善了激素、生化和生理功能，从而可能导致延缓衰老和延长寿命。在这些实验中，我们将生成生物钟转录因子结合、基因表达和染色质修饰的全面昼夜节律曲线，以评估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，区分卡路里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函数的昼夜节律转录图谱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特征和机制提供基础。

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.