High Resolution Mapping of Function Elements in the Yeast Genome

描述(申请人提供)：核小体是真核细胞染色体的基本构件。对染色体中编码的遗传信息的获取取决于核小体沿DNA的位置。仅相隔几个核苷酸的可选位置就可以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背景在很大程度上仍不清楚。这里提出的工作有望生成整个基因组中最高分辨率的核小体位置图。选择酿酒酵母基因组是因为它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。将分离标准和翻译后修饰的核小体核心颗粒，并使用三个独立的平台绘制它们在基因组中的位置：基于测序的标记、基于杂交的拼接阵列和基于计算的比较基因组学，该比较基因组学寻求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，包括核小体DNA的定位、旋转和平移设置的DNA序列决定因素，特定类型染色体元件的染色质结构，以及核小体拓扑和启动子调控元件之间的关系。这项研究与公共卫生有关，因为它提供了一个重要的基础，可以在此基础上理解动物的基因调控。基因表达的错误调控是许多人类疾病的中心原因，因此，对基因调控机制的更好理解将为开发治疗方法提供更多的信息。核小体对基因表达的控制在动物中是高度保守的，因此在苍蝇和蠕虫中学到的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.