NUCLEOSOME POSITIONING

细胞功能的底物包括转录， 复制、重组和染色体分裂都是染色质， 裸DNA这些功能对儿童的发育和健康至关重要。 所有的有机体。在染色体组织的初始阶段，DNA是 压缩成重复排列的核小体。详细定位 核小体的沿着DNA可能是必不可少的其他消极或积极的 基因调控核小体独特的局部排列是 在端粒和着丝粒上，在已知基因的附近， 调节区域，以及其他染色体位置;这些特定的 排列被认为是染色体功能所必需的。的 DNA本身的序列强烈地偏向于核小体的位置 DNA被包裹在其中，某些DNA序列规则或基序 参与核小体位置的蛋白质。这些研究结果意味着 基因组DNA序列的进化是为了促进它们的功能 通过影响它们的染色质结构。长期目标是 工作是阐明分子结构之间的关系， 染色体和它们的功能。本项目的目标是 探讨基因组DNA序列、核小体 定位和染色体功能。关键事实可能缺失。有 需要进行系统的定量分析，需要新的 实验工具我们将从三个方面着手实现这些目标。这些 研究建立在我们最近完成的SLEX实验的基础上， 大量非天然DNA序列具有特别高的亲和力 组蛋白八聚体，因此，异常强大的核小体 定位力(i)我们将采取类似的方法从 在整个酵母基因组中，这些区域对DNA具有最大的影响力， 序列指导的核小体定位。这些序列将是 其特征在于，它们用于核小体定位的自由能被量化， 并分析了它们对染色体功能的贡献。(ii)我们将使用 我们现有的选择定位序列来操纵和研究 核小体定位在体内，我们将使用生物物理方法， 体外分析DNA的结构和机械性能， 负责他们强大的定位能力。(iii)我们两个都要 进化和设计方法，以创造下一代甚至 更强的定位序列，用于未来的体外研究和 vivo.

The substrates for cellular functions including transcription, replication, recombination, and chromosome division are chromatin, not naked DNA. These functions are essential for the development and health of all organisms. In the initial level of chromosome organization, DNA is compacted into a repeating array of nucleosomes. The detailed positioning of nucleosomes along DNA can be essential for other negative or positive gene regulation. Distinctive local arrangements of nucleosomes are reported at telomeres and centromeres, in the vicinity of known gene regulatory regions, and at other chromosomal locations; these particular arrangements are believed to be essential for chromosome function. The sequence of the DNA itself strongly biases the position of the nucleosomes into which the DNA is wrapped, and certain DNA sequence rules or motifs involved in nucleosome position have been elucidated. These findings imply that genomic DNA sequences are evolved to facilitate their function through effects on their chromatin structure. The long term aim of this work is to elucidate the relationship between the molecular architecture of chromosomes and their function. The goal of the present project is to explore the relationships between genomic DNA sequence, nucleosome positioning, and chromosome function. May key facts are missing. There is a need for systematic and quantitative analyses, and a need for new experimental tools. We will attack these goals in three ways. These studies build on our recent completion of SLEX experiment which yielded a large number of non-natural DNA sequences have exceptionally high affinity for histone octamer and, consequently, exceptionally strong nucleosome positioning power. (i) We will take similar approaches to select from the entire yeast genome those regions have the greatest power for DNA sequence-directed nucleosome positioning. These sequences will be characterized, their free energy for nucleosome positioning quantified, and their contributions to chromosome function analyzed. (ii) We will use our existing selected positioning sequences to manipulate and study nucleosome positioning in vivo and we will use biophysical approaches in vitro to analyze the DNA structural and mechanical properties that are responsible for their strong positioning power. (iii) We will take both evolutionary and design approaches to create a next generation of even stronger positioning sequences for use in future studies in vitro and in vivo.