Nucleosome Positioning

核小体定位

• 批准号: 8213542
• 负责人: OLKE C UHLENBECK
• 金额: $ 43.7万
• 依托单位: NORTHWESTERN UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 1999
• 资助国家: 美国
• 起止时间: 1999-01-01 至 2013-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8213542
• 关键词: Affinity; Architecture; Binding; Binding Sites; Cell Cycle; Cells; Chemicals; Chromatin; Chromatin Fiber; Chromosomes; DNA; DNA Binding; DNA Sequence; DNA biosynthesis; Data; Development; Disease; Engineering; Equilibrium; Eukaryota; Face; Gene Expression; Gene Expression Regulation; Genome; Genomics; Goals; Grant; Health; Higher Order Chromatin Structure; Histones; Kinetics; Laboratories; Lead; Learning; Link; Location; Maps; Measures; Micrococcal Nuclease; Modeling; Nature; Noise; Nucleosomes; Organism; Output; Paper; Positioning Attribute; Problem Solving; Process; Proteins; Recruitment Activity; Reporter; Research; Resolution; Role; Site; Surface; Tail; Testing; Thermodynamics; Time; Transcription Coactivator; Transcription Repressor/Corepressor; Transgenes; Work; base; design; genome-wide; improved; in vivo; novel; novel diagnostics; novel therapeutics; predictive modeling; preference; programs; promoter; public health relevance; research study; structural biology; three dimensional structure; transcription factor

DESCRIPTION (provided by applicant): The long-term aim of this research program is to develop a quantitative understanding of eukaryotic gene regulation. In eukaryotes, the genomic DNA is wrapped in nucleosomes, which occlude much of the surface of the wrapped DNA and strongly distort it; yet, nucleosomes also recruit other proteins through interactions with their histone tail domains. Thus, the detailed locations of nucleosomes have important inhibitory and facilitatory roles in gene regulation, and is essential for the health and development of all eukaryotes. In the current project period we advanced the understanding of where nucleosomes are located along the DNA, the principles that govern these locations, and how these influence competition with other factors and gene expression. In the next grant period, we propose to extend these findings in three directions. Studies in Aim 1 will measure nucleosome-factor competition directly and quantitatively, genome-wide, as synchronized pools of cells progress through the cell cycle; and also at specific engineered transgenes, where we will measure not just nucleosome positioning and occupancy but also the identities, locations, and occupancies of bound factors. These data will test our current understanding of nucleosome-factor competition and the thermodynamic equilibrium hypothesis on which our ideas are based. Studies in Aim 2 seek to measure the exact locations of nucleosomes to the basepair. This information is needed in order to: understand where nucleosomes will or will not compete with factors binding at adjacent target sites; to define the intrinsic 3- dimensional structure of the chromatin fiber; to establish the detailed structural biology of promoters; and to define the true nucleosome-DNA sequence preferences. Studies in Aim 3 will develop and experimentally test a quantitative predictive model for predicting the gene expression output given the genomic DNA sequence, and the concentrations, binding sites, and affinities of a set of transcription factors active in the cell. PUBLIC HEALTH RELEVANCE: The proper regulation of genes is essential for the development and health of all organisms. We discovered a previously unrecognized aspect of gene regulation, in which the genomic DNA sequence influences its own organization into chromosomes, and thereby influences diverse essential chromosome functions. Our hope is that a better understanding of the nature of this novel information, and how it influences gene expression and DNA replication will lead, over the long term, to a better understanding of fundamental mechanisms in disease processes, and from there, to new diagnostics and therapeutics.

描述（由申请人提供）：本研究计划的长期目标是发展对真核基因调控的定量理解。在真核生物中，基因组DNA被包裹在核小体中，核小体封闭包裹的DNA的大部分表面并强烈扭曲它;然而，核小体也通过与它们的组蛋白尾部结构域的相互作用招募其他蛋白质。因此，核小体的详细位置在基因调控中具有重要的抑制和促进作用，并且对所有真核生物的健康和发育至关重要。在当前的项目期间，我们加深了对核小体沿着DNA的位置、控制这些位置的原则以及这些如何影响与其他因素的竞争和基因表达的理解。在下一个资助期内，我们建议在三个方向扩展这些研究结果。目标1中的研究将直接和定量地测量核小体因子竞争，全基因组范围内，随着细胞周期的同步化细胞库的进展;也在特定的工程转基因中，我们将不仅测量核小体定位和占用，而且还测量结合因子的身份，位置和占用。这些数据将检验我们目前对核小体因子竞争的理解以及我们的想法所基于的热力学平衡假设。目标2中的研究试图测量核小体相对于碱基对的精确位置。这些信息是必要的，以便：了解核小体将或将不竞争的因素结合在相邻的目标网站，以确定固有的三维结构的染色质纤维，建立详细的结构生物学的启动子，并确定真正的核小体DNA序列的偏好。目标3的研究将开发和实验测试一种定量预测模型，用于预测给定基因组DNA序列的基因表达输出，以及细胞中一组转录因子的浓度，结合位点和亲和力。 公共卫生相关性：基因的适当调节对所有生物体的发育和健康至关重要。我们发现了基因调控的一个以前未被认识的方面，其中基因组DNA序列影响其自身的染色体组织，从而影响多种重要的染色体功能。我们希望，从长远来看，更好地理解这种新信息的性质以及它如何影响基因表达和DNA复制，将有助于更好地理解疾病过程中的基本机制，并从那里获得新的诊断和治疗方法。

项目成果

A map of nucleosome positions in yeast at base-pair resolution.

• DOI: 10.1038/nature11142
• 发表时间: 2012-06-28
• 期刊: NATURE
• 影响因子: 64.8
• 作者: Brogaard, Kristin;Xi, Liqun;Wang, Ji-Ping;Widom, Jonathan
• 通讯作者: Widom, Jonathan

A locally convoluted cluster model for nucleosome positioning signals in chemical map.

化学图中核小体定位信号的局部卷积聚类模型。

• DOI: 10.1080/01621459.2013.862169
• 发表时间: 2014-01-01
• 期刊: Journal of the American Statistical Association
• 影响因子: 3.7
• 作者: Xi L;Brogaard K;Zhang Q;Lindsay B;Widom J;Wang JP
• 通讯作者: Wang JP

Differential Nucleosome Occupancies across Oct4-Sox2 Binding Sites in Murine Embryonic Stem Cells.

小鼠胚胎干细胞中 Oct4-Sox2 结合位点的不同核小体占据。

• DOI: 10.1371/journal.pone.0127214
• 发表时间: 2015
• 期刊: PloS one
• 影响因子: 3.7
• 作者: Sebeson,Amy;Xi,Liqun;Zhang,Quanwei;Sigmund,Audrey;Wang,Ji-Ping;Widom,Jonathan;Wang,Xiaozhong
• 通讯作者: Wang,Xiaozhong

A chemical approach to mapping nucleosomes at base pair resolution in yeast.

• DOI: 10.1016/b978-0-12-391938-0.00014-8
• 发表时间: 2012
• 期刊: METHODS IN ENZYMOLOGY
• 作者: Brogaard, Kristin R.;Xi, Liqun;Wang, Ji-Ping;Widom, Jonathan
• 通讯作者: Widom, Jonathan