High Resolution Mapping of Function Elements in the Yeast Genome

描述（由申请人提供）：真核DNA被包装成染色质，该染色质具有明确的组织。染色质由核小体组成，其沿DNA的位置决定了基因调控元件的可及性，并最终决定了基因的表达水平。核小体受到多种机制的高度调控，包括：翻译后修饰、由伴侣促进的沉积和排出，以及由染色质重塑复合体促进的重新定位。这种核小体状态通过与特定的基因调控蛋白相互作用进一步调节基因表达。核小体状态如何与基因调控因子相互作用在很大程度上是未知的，这是我们理解疾病中基因表达如何被控制和错误调控的核心。在这里，我们建议通过首先以高分辨率绘制单个核小体状态的基因组位置来进一步了解这种界面，因为模型基因表达程序（热休克和孢子形成）正在展开。核小体状态的例子包括组蛋白修饰、核小体相位、定位和宽度。其次，我们将确定这些状态对染色质组织和基因表达的贡献，通过检查当这些状态通过诱变消除时发生了什么。第三，我们将创建与特定染色质和基因调控因子相互作用的核小体的高分辨率全基因组图谱。这些目标旨在首先以高分辨率描述核小体状态的景观，然后确定它们的功能，然后确定它们与基因调控因子的相互作用，主要使用酵母菌作为模型系统。关键的核小体模式将在后生动物模型系统中进一步探索，以确定这些模式是否代表真核生物的基本原理。

DESCRIPTION (provided by applicant): Eukaryotic DNA is packaged into chromatin, and this chromatin has a well-defined organization. Chromatin is composed of nucleosome building blocks, whose positioning along the DNA dictates the accessibility of gene regulatory elements, and ultimately the expression levels of genes. Nucleosomes are highly regulated through many mechanisms including: post-translational modifications, deposition and eviction that is facilitated by chaperones, and re-positioning facilitated by chromatin remodeling complexes. Such nucleosome states further regulate gene expression by interacting with specific gene regulatory proteins. How nucleosome states interface with gene regulatory factors is largely unknown and is central to our understanding of how gene expression is controlled and mis-regulated in diseases. Here, we propose to further our understanding of this interface by first mapping the genomic position of individual nucleosome states at high resolution as model gene expression programs (heat shock and sporulation) unfold. Examples of nucleosome states include histone modifications, and nucleosome phasing, positioning, and width. Second, we will ascertain the contribution of such states to chromatin organization and gene expression, by examining what fails to happen when such states are eliminated through mutagenesis. Third, we will create high-resolution genome-wide maps of nucleosomes that interact with specific chromatin and gene regulatory factors. These aims are intended to first describe the landscape of nucleosomal states at high resolution, then identify their function, and then ascertain their interplay with gene regulatory factors using primarily Saccharomyces as a model system.Key nucleosomal patterns will be further explored in metazoan model systems, to ascertain whether such patterns represent fundamental principles in eukaryotes. PUBLIC HEALTH RELEVANCE: Since nucleosome positioning and regulation play central roles in controlling gene expression from yeast to man, and gene expression is the origin of both normal and diseased cellular behavior, knowledge of the genomic organizational state of nucleosomes is key toward maintaining proper cell physiology and rectifying aberrant states. This project is intended to provide a greater understanding of nucleosomal states in relation to gene expression.