Nucleosome Positioning

真核生物基因组DNA以高度紧凑的形式存在和发挥作用，作为一个重复的DNA序列。 称为染色质的核小体。核小体将包裹它们的大部分DNA从相互作用中封闭起来 与其他基因调控蛋白和酶，但核小体积极帮助招募其他蛋白质， 通过这些其他蛋白质与核小体的组蛋白尾部的相互作用， 域.因此，核小体沿着DNA的详细位置可能具有重要的抑制作用， 和染色体功能的促进作用。这个项目的重点是了解的原则， 控制着核小体沿着基因组沿着的位置。在本项目期间，我们获得了数据 证明了基因组关心它们的核小体的位置，基因组通过一种 DNA序列编码核小体定位，我们能够部分破译这一代码。的 我们仅仅根据我们阅读这些代码的能力来预测核小体的位置， 体内核小体的位置。在下一个资助期，我们将在三个关键领域继续研究这些发现。 方向目标1中的研究将提供新的数据，这将改善我们的组蛋白-DNA亲和力“概况”， 使其能够更好地预测基因组范围内的核小体位置。目标2中的研究将阐明 通过实验评估位点特异性DNA结合蛋白的星座之间的充分竞争， 和核小体，当这些分子在它们的耦合动态平衡中一起作用时。研究目的 3将提供关于核小体在趋异启动子上的分布和性质的高分辨率数据 全基因组，并将这些数据与一种新的实验方法一起应用，利用个人生活 细胞，阐明机制的启动子的独立性，在不同的转录基因。 相关性：本项目将阐明核小体在细胞中沿着排列的基本规则。 基因组核小体的详细分布影响染色体功能的各个方面，包括 DNA复制、转录、修复、重组和染色体分裂。的理解 这项工作产生的真核基因组结构将有助于我们理解，诊断， 为癌症、发育和传染病设计新的治疗方法。

Eukaryotic genomic DNA exists and functions in a highly compacted form, as a repeating array of nucleosomes called chromatin. Nucleosomes occlude much of the DNA that wraps them from interaction with other gene regulatory proteins and enzymes, yet nucleosomes actively help recruit other proteins to the vicinity of their wrapped DNA, through interaction of these other proteins with the nucleosomes' histone tail domains. Thus, the detailed locations of nucleosomes along the DNA may have both important inhibitory and facilitatory roles for chromosome function. This project is focused on understanding the principles that govern where nucleosomes are placed along the genome. In the current project period, we obtained data proving that genomes care where their nucleosomes are located, that genomes manifest this care through a DNA sequence code for nucleosome positioning, and that we are able partially to decipher this code. The nucleosome positions that we predict based only on our ability to read this code explain at least 50% of actual in vivo nucleosome positions. In the next grant period, we will pursue these findings in three key directions. Studies in Aim 1 will provide new data that will improve our histone-DNA affinity "profile", enabling it to better-predict nucleosome locations genome wide. Studies in Aim 2 will elucidate and experimentally evaluate the full competition between the constellation of site-specific DNA binding proteins and nucleosomes, when these molecules act together in their coupled dynamic equilibrium. Studies in Aim 3 will provide high resolution data on the distribution and nature of nucleosomes over divergent promoters genome-wide, and will apply these data together with a new experimental approach utilizing individual living cells, to elucidate the mechanism of promoter independence in divergently transcribed genes. Relevance: This project will elucidate the basic rules that govern where nucleosomes are placed along the genome. The detailed distribution of nucleosomes influences all aspects of chromosome function, including DNA replication, transcription, repair, recombination, and chromosome division. The understanding of eukaryotic genome structure that results from this work will help us understand, diagnose, and rationally design new kinds of therapies for, cancers and developmental and infectious diseases.