High Resolution Mapping of Function Elements in the Yeast Genome

描述（由申请人提供）：核小体是真核生物染色体的基本组成部分。获取编码在染色体中的遗传信息取决于核小体沿DNA的位置。仅仅相隔几个核苷酸的位置就能对基因表达产生深远的影响。然而，大多数染色体和基因调控元件所处的染色质环境在很大程度上仍然未知。这里提出的工作有望生成整个基因组中核小体位置的最高分辨率地图。选择酿酒酵母基因组是因为其简单的基因组复杂性和高度的注释，这将使DNA调控元件和核小体位置之间的关系变得特别明显。标准和翻译后修饰的核小体核心颗粒将被分离出来，它们在整个基因组中的位置将使用三个独立的平台进行定位：基于测序的标记，基于杂交的平铺阵列和基于计算的比较基因组学，旨在绘制核小体定位序列。这些方法有望揭示染色质结构的基本方面，包括定位的DNA序列决定因素，核小体DNA的旋转和翻译设置，特定类别染色体元件的染色质结构，以及核小体拓扑结构和启动子调控元件之间的关系。这项研究与公共卫生有关，因为它为理解动物的基因调控提供了重要的基础。基因表达的错误调控是许多人类疾病的主要原因，因此，更好地了解基因调控机制将为开发治疗方法提供更明智的方法。基因表达的核小体控制在动物中是高度保守的，因此在苍蝇和蠕虫身上学到的经验教训直接适用于人类系统。

DESCRIPTION (provided by applicant): The nucleosome is the fundamental building block of eukaryotic chromosomes. Access to genetic information encoded in chromosomes is dependent upon where nucleosomes reside along the DNA. Alternative locations just a few nucleotides apart can have profound effects on gene expression. Yet the chromatin context in which most chromosomal and gene regulatory elements reside remains largely unknown. The work proposed here is expected to generate the highest resolution map of nucleosome locations throughout a genome. The Saccharomyces cerevisiae genome is chosen because of its simple genomic complexity and high degree of annotation, which will allow relationships between DNA regulatory elements and nucleosome positions to become particularly evident. Standard and post-translationally modified nucleosome core particles will be isolated and their locations throughout the genome mapped using three independent platforms: sequencing-based tagging, hybridization-based tiling arrays, and computationally-based comparative genomics that seeks to map nucleosome positioning sequences. These approaches are expected to reveal the fundamental aspects of chromatin architecture including DNA sequence determinants of positioning, rotational and translational settings of nucleosomal DNA, chromatin structure at specific classes of chromosomal elements, and the relationship between nucleosomal topology and promoter regulatory elements. This research is relevant to public health in that it provides an important foundation upon which gene regulation can be understood in animals. Mis-regulation of gene expression is a central cause of many human diseases, and thus a better understanding of gene regulatory mechanisms will provide more informed approaches in developing therapeutics. Nucleosomal control of gene expression is highly conserved among animals, thus lessons learned in flies and worms are directly applicable to human systems.