High Resolution Mapping of Functional Elements in the Yeast Genome

描述（由申请人提供）： 真核DNA被包装成染色质，并且该染色质具有明确的组织。染色质由核小体构建块组成，其沿DNA的沿着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。核小体在基因上以规则的重复间隔出现。这些阵列通过许多机制高度调节，包括：翻译后修饰、由分子伴侣促进的沉积和驱逐，以及由染色质重塑复合物促进的重新定位。我们建议在基因组尺度上进一步理解核小体阵列。在目标1中，我们将使用我们新开发的超高分辨率ChIP-exo检测来确定组蛋白标记沿着核小体阵列在整个基因组中的亚核小体组织。在目标2中，我们将使用ChIP-exo绘制染色质重塑的核小体和亚核小体组织。它们在特定核小体上的位置以及它们在核小体表面上的方向应该提供对它们在基因组尺度上如何发挥功能的洞察。在目标3中，我们将使用我们最近开发的正确定位的核小体阵列的全基因组重构来探测染色质重塑定向阵列形成的生化机制。这些目标的完成，预计将提供核小体阵列的基本原理和它们在调节基因表达的作用的理解。

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 occur in regular repeating intervals on genes. These arrays are highly regulated through many mechanisms including: post- translational modifications, deposition and eviction that are facilitated by chaperones, and re-positioning facilitated by chromatin remodeling complexes. We propose to further our understanding of nucleosomal arrays on a genomic scale. In aim 1, we will use our newly developed ultra-high resolution ChIP-exo assay to determine the subnucleosomal organization of histone marks along nucleosomal arrays across a genome. In aim 2, we will map the nucleosomal and subnucleosomal organization of chromatin remodelers using ChIP-exo. Their placement at specific nucleosomes, and their orientation on the nucleosome surface should provide insight into how they function on a genomic scale. In aim 3, we will use our recently developed genome-wide reconstitution of properly positioned nucleosomal arrays to probe biochemical mechanisms of chromatin remodeler-directed array formation. Completion of these aims is expected to provide an understanding of fundamental principles of nucleosomal array and their role in regulating gene expression.