Nucleosome Positioning

真核基因组DNA以高度紧凑的形式存在并发挥作用，作为重复的 核小体称为染色质。核小体阻断了包裹它们的DNA的大部分相互作用 与其他基因调节蛋白和酶一起，但核小体积极地帮助招募其他蛋白质到 通过这些其他蛋白质与核小体的组蛋白尾巴相互作用，接近它们包裹的DNA 域名。因此，核小体沿DNA的详细位置可能既有重要的抑制作用 以及对染色体功能的促进作用。本项目的重点是理解以下原则 控制核小体沿基因组放置的位置。在本项目期内，我们获得了数据 证明基因组关心他们的核小体位于哪里，基因组通过一种 核小体定位的DNA序列密码，我们能够部分破译这个密码。这个 我们仅根据我们阅读该代码的能力来预测核小体位置，可以解释至少50%的 体内核小体的实际位置。在下一批赠款期间，我们将在三个关键方面继续研究这些发现 方向。AIM 1的研究将提供新的数据，将改善我们的组蛋白-DNA亲和力“轮廓”， 使其能够更好地预测全基因组的核小体位置。目标2中的研究将阐明和 实验评估位点特异性DNA结合蛋白星座之间的完全竞争 以及核小体，当这些分子在其耦合的动态平衡中共同作用时。AIM中的研究 3将提供关于核小体在不同启动子上的分布和性质的高分辨率数据 并将把这些数据与一种利用个体生活的新的实验方法一起应用 细胞，以阐明差异转录基因中启动子独立的机制。 相关性：本项目将阐明控制核小体沿 基因组。核小体的详细分布影响着染色体功能的方方面面，包括 DNA复制、转录、修复、重组和染色体分裂。对…的理解 这项工作所产生的真核基因组结构将有助于我们理解、诊断和合理 设计治疗癌症、发育和传染病的新疗法。

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.