Nucleosome Positioning

描述（由申请人提供）：真核生物基因组DNA以高度紧密的形式存在并发挥作用，作为称为染色质的核小体重复阵列。核小体阻断了包裹它们的DNA与其他基因调控蛋白和酶的相互作用，然而核小体通过其他蛋白质与核小体组蛋白尾部结构域的相互作用，积极地帮助招募其他蛋白质到它们包裹的DNA附近。因此，核小体沿DNA的详细位置可能对染色体功能具有重要的抑制和促进作用。这个项目的重点是理解控制核小体沿基因组位置的原则。在当前的项目期间，我们获得的数据证明基因组关心它们的核小体的位置，基因组通过核小体定位的DNA序列代码表明这种关心，并且我们能够部分地破译这个代码。我们仅基于我们读取该代码的能力预测的核小体位置解释了至少50%的实际体内核小体位置。在下一个资助期，我们将在三个关键方向继续研究这些发现。Aim 1的研究将提供新的数据，以改善我们的组蛋白- dna亲和力“谱”，使其能够更好地预测全基因组范围内的核小体位置。Aim 2的研究将阐明和实验评估位点特异性DNA结合蛋白和核小体之间的充分竞争，当这些分子在耦合动态平衡中一起作用时。Aim 3的研究将提供核小体在不同启动子全基因组上的分布和性质的高分辨率数据，并将这些数据与利用单个活细胞的新实验方法一起应用，以阐明不同转录基因中启动子独立性的机制。相关性：该项目将阐明控制核小体沿基因组放置位置的基本规则。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。这项工作对真核生物基因组结构的理解将有助于我们理解、诊断和合理设计癌症、发育和感染性疾病的新疗法。

DESCRIPTION (provided by applicant): 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 this 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.