Computational and experimental insights into the structure and dynamics of heterochromatin

对异染色质结构和动力学的计算和实验见解

• 批准号: 9885690
• 负责人: Nathaniel A. Hathaway
• 金额: $ 30.42万
• 依托单位: UNIV OF NORTH CAROLINA CHAPEL HILL
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-12-01 至 2023-11-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9885690
• 关键词: Algorithms; Architecture; Behavior; Biochemical Reaction; Biological Assay; Biology; Calibration; Cell Culture Techniques; Cells; Chemical Structure; Chemicals; Chromatin; Chromatin Fiber; Chromatin Structure; Complement; Complex; Computer Models; DNA; Data; Data Set; Development; Disease; Doxycycline; Enzymes; Epigenetic Process; Equilibrium; Event; Feedback; Fiber; Gene Expression Profiling; Genes; Goals; Grain; Heterochromatin; Individual; Investigation; Knowledge; Language; Lentivirus Vector; Life; Malignant Neoplasms; Measures; Mediating; Methodology; Methods; Modeling; Molecular; Molecular Profiling; Molecular Structure; Mus; Pathogenesis; Pathway interactions; Phase; Physics; Physiological; Process; Production; Proteins; Regenerative Medicine; Regulatory Element; Repression; Research; Resolution; Role; Running; Signal Transduction; Sirolimus; Stochastic Processes; Structure; System; Technology; Testing; Time; Tretinoin; Visualization; Work; base; cancer therapy; chromosome conformation capture; computational platform; computerized tools; embryonic stem cell; experimental study; gene repression; heterochromatin-specific nonhistone chromosomal protein HP-1; improved; in vivo; induced pluripotent stem cell; insight; interest; mechanical properties; methylation pattern; overexpression; particle; physical property; pluripotency; promoter; protein protein interaction; real time monitoring; recruit; response; simulation; small hairpin RNA; temporal measurement

Abstract Chemical, molecular and structural transformations of chromatin are intimately involved in critical cellular phenomena, including differentiation, signaling, and pathogenesis. A detailed knowledge of how molecular complexes involving multiple kilobases of DNA and hundreds of proteins respond to the finest changes in chemical structure is key to elucidating the role of chromatin transformations in life and disease. The overarching goal of this project is to develop and apply computational tools to investigate how the structure and dynamics of chromatin determine its functional states. Our central hypothesis is that physical properties and behavior of the chromatin fiber and associated proteins lend themselves to encoding into efficient and useful ultra-coarse- grained (UCG) representations. Our strategy to reach the goal is by bridging together several computational and experimental methodologies. We initiated the development of Molecular Biosystems (MB), a computational platform for UCG simulations specifically adapted to the chromatin biology. MB methodology represents a blend of physics-based mechanisms, such as dynamics of the chromatin fiber, with stochastic processes encompassing protein-protein interactions and enzymatic reactions. MB studies will be complemented by all-atom MD and CG simulations and experimentally tested using a unique chromatin in vivo assay (CiA) methodology. Specifically, we will investigate the chromatin-mediated repression of Oct4, a key gene regulating embryonic stem (ES) cell pluripotency at defined points in mammalian development. This is important because the ability to reverse the Oct4 repression would streamline production of induced pluripotent cells (iPSC) and advance regenerative medicine. The CiA technology at the Oct4 locus in mouse ES cells will be used for the exploration of changes to chromatin structure, as well as for testing the adequacy of MB simulations. Experimental endpoints that are directly comparable to computational hypotheses will be produced: (1) fraction of Oct4-repressed cells in cell culture; (2) H3K9 methylation patterns on Oct4 promoter; and (3) chromatin conformation capture. Three main components of our research are: (i) Extending and enhancing the UCG MB approach; (ii) Multi- scale simulations of chromatin processes to elucidate the structure and dynamics of heterochromatin of Oct4 regulatory elements; (iii) Experimental real-time monitoring of heterochromatin molecular signatures using Chromatin in vivo Assay (CiA) to study mechanisms and time course of Oct4 de-repression and provide feedback for the computational models. This work is important because of its focus on the physics of the gene repression, whose understanding will bring us one step forward toward the promise of regenerative medicine and new prospects for cancer therapy.

抽象的 染色质的化学、分子和结构转变与关键的细胞密切相关 现象，包括分化、信号传导和发病机制。详细了解分子如何 涉及数千个 DNA 碱基和数百个蛋白质的复合物对最细微的变化做出反应 化学结构是阐明染色质转化在生命和疾病中的作用的关键。首要的 该项目的目标是开发和应用计算工具来研究结构和动力学如何 染色质决定其功能状态。我们的中心假设是物理特性和行为 染色质纤维和相关蛋白质有助于编码成有效且有用的超粗颗粒 粒度（UCG）表示。我们实现这一目标的策略是将多个计算和 实验方法。我们启动了分子生物系统 (MB) 的开发，这是一种计算 特别适合染色质生物学的 UCG 模拟平台。 MB 方法代表了一种混合 基于物理的机制，例如染色质纤维的动力学，其中随机过程包括 蛋白质-蛋白质相互作用和酶促反应。 MB 研究将得到全原子 MD 和 CG 的补充 使用独特的染色质体内测定 (CiA) 方法进行模拟和实验测试。 具体来说，我们将研究染色质介导的 Oct4 抑制，Oct4 是调节胚胎的关键基因。 哺乳动物发育过程中特定点的干细胞 (ES) 多能性。这很重要，因为能力 逆转 Oct4 抑制将简化诱导多能细胞 (iPSC) 的生产并推进 再生医学。小鼠 ES 细胞 Oct4 位点的 CiA 技术将用于探索 染色质结构的变化，以及测试 MB 模拟的充分性。实验终点 将产生可直接与计算假设进行比较的结果：(1) Oct4 抑制细胞的分数 在细胞培养中； (2)Oct4启动子上的H3K9甲基化模式； (3)染色质构象捕获。 我们研究的三个主要组成部分是： (i) 扩展和增强 UCG MB 方法； (ii) 多 染色质过程的规模模拟，以阐明 Oct4 异染色质的结构和动态 监管要素； (iii) 使用异染色质分子特征进行实验实时监测 染色质体内测定 (CiA)，用于研究 Oct4 去抑制的机制和时间过程并提供反馈 对于计算模型。 这项工作很重要，因为它关注基因抑制的物理学，其理解将 使我们朝着再生医学的承诺和癌症治疗的新前景迈进了一步。