Dynamics in Eukaryotic Dormancy: Gene Expression and Aging

项目摘要 休眠是一种状态，在这种状态下，几乎所有的细胞内活动，如基因表达，都被认为是 （几乎）停止了。许多生物体和细胞在面临诸如缺乏营养等可怕的条件时会进入休眠状态。 营养素尽管它无处不在，休眠状态仍然知之甚少，探索不足。一个主要 开放的问题是哪些细胞内过程可能仍然发生在休眠，到什么程度，以及是否和 它们对休眠期的生存有多么重要这个问题与微生物孢子的休眠、癌症 细胞、植物种子、蠕虫、人体细胞等。微生物孢子特别重要，因为 自然界中的许多微生物通常以休眠孢子而不是营养细胞的形式存在。许多真菌孢子 因为它们是传染性的，并且由于未知的原因难以用现有的药物杀死。 我的实验室的目标是回答上面提出的理解休眠的关键问题。我们使用 休眠酵母（酿酒酵母）孢子作为研究真核休眠的模型系统。 对于休眠的酵母孢子，我们专注于生命的两个基本方面： (1)休眠过程中基因表达的动态与调控 (2)休眠老化的动力学和决定因素 我的实验室在单细胞和全基因组水平上进行定量测量， 基因调控的数学模型我们最近发现，酵母孢子表达一些基因， 休眠（即，在没有任何营养物的水中），并且令人惊讶的是，一些表达水平可以高达 如植物性酵母。为了扩展这一发现，我们采用了一种基于RNA-Seq的技术来检测所有新鲜的 在休眠的酵母孢子中制造RNA我们发现休眠的酵母孢子转录了65%的基因， 其中核糖体蛋白是转录最高的蛋白之一。用显微镜技术检测 mRNA和蛋白质的生产在同一个单孢子和数学模型，筛选各种形式的 基因调控，我们现在正在发现全球（全基因组）协调转录的迹象， 我们的目标是在未来五年内阐明其机制。我们正在进行的工作也揭示了 休眠的酵母孢子分泌分子，帮助彼此生存，延长寿命，调节基因 表情我们将阐明这种“集体休眠”的机制和休眠酵母老化的迹象 孢子一个全面的基因缺失酵母菌株库将帮助我们确定每个基因如何加速 或减缓休眠孢子的老化及其在集体休眠中的作用。我们的工作将推进- 通过建立基因基础知识，对真核生物、微生物休眠有了初步认识 调节和老化的休眠与定量的方法，很少被应用到这些主题。 更广泛地说，我们希望我们的工作将提供一般静止细胞的概念见解。

PROJECT SUMMARY Dormancy is a state in which virtually all intracellular activities, such as gene expression, are thought to have (nearly) stopped. Many organisms and cells become dormant when they face dire conditions such as lack of nutrients. Despite its ubiquity, the state of dormancy remains poorly understood and underexplored. A major open question is which intracellular processes might still occur in dormancy, to what extent, and whether and how they are important for surviving dormancy. This question is relevant to dormancy of microbial spores, cancer cells, plant seeds, worms, cells in human body, and others. Microbial spores are particularly important because many microbes in nature often exist as dormant spores rather than as vegetative cells. Many fungal spores are of interest because they are infectious and are difficult to kill with existing drugs for unknown reasons. My laboratory's goal is to answer the critical question posed above for understanding dormancy. We use the dormant yeast (Saccharomyces cerevisiae) spores as a model system for studying eukaryotic dormancy. With dormant yeast spores, we focus on two fundamental aspects of life: (1) Dynamics and regulation of gene expression in dormancy (2) Dynamics and determinants of aging in dormancy My lab makes quantitative measurements at single-cell and genome-wide levels and combines them with mathematical models of gene regulations. We recently discovered that yeast spores express some genes while dormant (i.e., in water without any nutrients) and that, surprisingly, some of the expression levels can be as high as in vegetative yeasts. To extend this discovery, we adapted an RNA-Seq-based technique to detect all freshly made RNAs in dormant yeast spores. We discovered that dormant yeast spores transcribe ~65% of their genes, with ribosomal proteins being one of the most highly transcribed. With microscope-based techniques that detect mRNA and protein productions in the same single spore and mathematical models that screen various forms of gene regulation, we are now uncovering signs of globally (genome-wide) coordinated transcription and translation whose mechanisms we aim to elucidate in the next five years. Our ongoing work is also uncovering dormant yeast spores secreting molecules that help each other survive, extend lifespans, and regulate gene expression. We will elucidate the mechanisms of this "collective dormancy" and signs of aging in dormant yeast spores. A comprehensive library of gene-deleted yeast strains will help us determine how each gene accelerates or decelerates aging in dormant spores and its role in collective dormancy. Our work will advance the still- primitive understanding of eukaryotic, microbial dormancy by establishing foundational knowledge on gene regulation and aging in dormancy with quantitative approaches that have rarely been applied to these topics. More broadly, we expect that our work will provide conceptual insights into quiescent cells in general.