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Mechanism and Function of Chromatin Positional Dynamics in Interphase

间期染色质位置动力学的机制和功能

基本信息

批准号：
9118319
负责人：
Alexandra Zidovska
金额：
$ 24.9万
依托单位：
NEW YORK UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2013
资助国家：
美国
起止时间：
2013-09-01 至 2018-07-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/9118319
关键词：
ATP phosphohydrolase Acute leukemia Address Aftercare Antineoplastic Agents Award BRD2 gene Behavior Binding Binding Proteins Biochemical Biochemistry Biological Biological Process Biology Bromodomain Cancer cell line Carcinoma Cell Cycle Regulation Cell Line Cell Nucleus Cell physiology Cells Cellular biology Centromere Chromatin Chromosome Territory Chromosomes Complement Complex Cultured Cells Cytoskeleton DNA DNA Packaging DNA Polymerase II DNA Repair DNA Topoisomerases Data Diagnostic Doctor of Philosophy Embryo Evolution Family Fellowship Foundations Future Gene Expression Genes Genetic Transcription Goals Hela Cells Histone H2B Histones Image In Situ Interphase Knowledge Label Lamins Laws Learning Life Malignant Neoplasms Mammalian Cell Maps Measurement Measures Mentors Methodology Methods Modeling Molecular Molecular Biology Motor Multiple Myeloma Nature Nuclear Nuclear Fusion Nuclear Proteins Paper Pattern Phase Physics Poison Polymers Positioning Attribute Postdoctoral Fellow Property Proteins Proteomics Publications RNA Interference RNA interference screen Research Resolution Role Site Spectrum Analysis System Testing Time Training Velocimetries Work abstracting analytical tool cancer cell cell motility cell type chromatin remodeling condensed matter physics fly in vivo inhibitor/antagonist knock-down live cell microscopy particle particle spectroscopy physical model physical science post-doctoral training screening segregation single molecule skills small molecule small molecule inhibitor telomere tool

项目摘要

Project Summary/Abstract The goal of the proposed research is (1) to measure spatially and temporally resolved chromatin dynamics in mammalian cells in interphase in vivo and (2) determine the origin and function of these dynamical behaviors by combining quantitative approaches derived from physical sciences with tools from molecular biology and biochemistry. The dynamic behavior of chromatin (DNA and associated proteins) has traditionally been studied by live cell microscopy of nuclear proteins, single genes, subchromosomal foci and chromosomal territories [Marshall et al. 1997; Belmont et al. 1998; Levi et al. 2005; Kumaran et al. 2008; Stixova et al. 2011]. Such studies are highly informative, but in practice one can only investigate a few sites simultaneously. Approaches that provide a picture of an overall chromatin dynamics have been slow to develop [Abney et al. 1997]. In the proposed research we will use our newly developed method of velocity correlation spectroscopy (VCS) [Zidovska et al. 2012a], combined with established methods like particle image velocimetry (PIV) and spatio-temporal image correlation spectroscopy (STICS), to measure high-resolution chromatin velocity maps and spatio-temporal evolution of chromatin dynamics over an entire nucleus for the first time (aim 1). In previous work using VCS we found local coherence in spatio-temporal chromatin dynamics, showing that chromatin dynamics is correlated over micron and second scale [Zidovska et al. 2012b]. Our preliminary studies also showed that chromatin dynamics uses ATP, but is independent of the cytoskeleton, hinting at nuclear ATPases being responsible for the observed dynamics. We will probe the origin of the observed chromatin dynamics by specifically inhibiting major nuclear ATPases (polymerase II, DNA polymerase and topoisomerase) using molecular poisons or RNA interference and analyzing the spatio-temporal changes in the pattern of measured chromatin dynamics (aim 2). An exciting preliminary finding showed that chromatin dynamics are largely blocked by a recently-described small molecule JQ1, which binds specifically to four BET family bromodomain proteins, antagonizing their binding to histones [Filippakopoulos et al. 2010]. By investigating how JQ1 blocks chromatin motility we will gain new information on the role of BET proteins in chromatin dynamics. Since JQ1 has demonstrated efficacy in translational models of poorly differentiated carcinoma, multiple myeloma and acute leukemia [Delmore et al. 2011; Zuber et al. 2011], this work may also help elucidate the cellular effects of a promising anti-cancer agent. Finally, we extend this approach to a small panel of cancer and non-cancer cell lines (aim 3) to ask whether chromatin dynamics are perturbed in cancer. If so, VCS analysis might prove useful as a diagnostic tool. Our discoveries in this project will provide a framework for a mechanistic picture of the origins and functional importance of chromatin dynamics in mammalian cells.

项目总结/摘要本研究的目标是：（1）测量空间和时间分辨的染色质动力学，哺乳动物细胞在间期在体内和（2）确定这些动力学行为的起源和功能通过将物理科学的定量方法与分子生物学的工具相结合，生物化学染色质（DNA和相关蛋白质）的动力学行为传统上是通过核蛋白、单基因、亚染色体病灶和染色体区域的活细胞显微镜检查 [马歇尔等人，1997;贝尔蒙特等人，1998; Levi等人，2005; Kumaran等人，2008; Stixova等人，2011]。等研究提供的信息量很大，但实际上只能同时调查几个地点。方法提供整个染色质动力学图像的方法发展缓慢[Abney et al.1997]。在这项研究中，我们将使用我们新开发的速度相关光谱方法 (VCS)[Zidovska等人，2012 a]，结合粒子图像测速法（PIV）和时空图像相关光谱（STICS），用于测量高分辨率染色质速度图以及首次在整个细胞核上染色质动力学的时空演化（aim 1）。在先前的工作，我们发现局部相干时空染色质动力学，显示，染色质动力学在微米和秒级上相关[Zidovska et al. 2012 b]。我们的初步研究还表明，染色质动力学使用ATP，但不依赖于细胞骨架，暗示核ATP酶负责观察到的动力学。我们将探索观察到的通过特异性抑制主要的核ATP酶（聚合酶II、DNA聚合酶和拓扑异构酶）使用分子毒药或RNA干扰，并分析拓扑异构酶的时空变化。染色质动力学模式（AIM 2）。一项令人兴奋的初步发现表明，动力学在很大程度上被最近描述的小分子JQ 1阻断，该小分子JQ 1特异性结合四种BET，家族布罗莫结构域蛋白，拮抗其与组蛋白的结合[Filippakopoulos et al. 2010]。通过通过研究JQ 1如何阻断染色质运动，我们将获得关于BET蛋白在细胞内作用的新信息。染色质动力学由于JQ 1已在低分化癌的转化模型中证明了疗效，癌症、多发性骨髓瘤和急性白血病[Delmore et al. 2011; Zuber et al. 2011]，这项工作也可能有助于阐明一种有前途的抗癌剂的细胞效应。最后，我们将这种方法扩展到一小组癌症和非癌症细胞系（aim 3），染色质动力学是否在癌症中受到干扰。如果是这样的话，工具.我们在这个项目中的发现将为起源的机械图提供一个框架，哺乳动物细胞中染色质动力学的功能重要性。