Modeling Chromatin Organization and Function

描述(由申请人提供)：了解染色体组织及其对基因表达的控制是最基本和最重要的开放生物学挑战之一。在不同的空间和时间尺度上对染色质的折叠状态进行建模是解开最基本的细胞功能的关键，包括转录激活、基因沉默和表观遗传控制。在这份提案中，我们继续我们始于2000年的染色质建模创新建模项目，该项目提供了关于染色质组织和动力学的新颖和高影响力的出版物，以纳入扩大模型范围和影响重大生物学问题的新因素。我们还增加了一位实验合作者，谢尔盖·格里戈里耶夫博士，他已经成功地与我们合作，[以及斯坦福大学Simbios国家生物医学计算中心的一个团队，帮助传播我们的软件工具，增强我们项目的影响力。]我们的长期目标是整合染色质组织的结构和动力学方面，以描述通过蛋白质因子、表观遗传标记和环境条件介导的转录调控的热力学机制。为了推进这一目标，我们将研究：(1)染色质结构及其与多价离子的折叠和离子的动态分布；(2)染色质二级结构在不同内外因素下的折叠；(3)二价离子、染色质纤维浓度和结构蛋白的三级染色质组织。在目标1中，我们将结合Poisson-Boltzmann理论，一种改进的屏蔽势函数表示法，以及一种计算染色质构象变化时屏蔽势的方法，建立染色质与多价离子折叠的严格模型。在目标2中，我们将探索DNA连接物长度变异性、组蛋白变体、表观遗传修饰和外力[使用中尺度、多分辨率和全原子模型的创新组合]对30 nm染色质纤维结构的影响。在目标3中，我们将对多价离子、集中的纤维环境和结合蛋白诱导的三级染色质结构进行建模，以揭示纤维-纤维相互作用和纤维环形成的结构机制，并通过染色质折叠的大规模变化来促进我们对转录调控的理解。这些在描绘染色质组织、能量和动力学方面具有挑战性的研究，通过创新的建模和实验技术进行检验，将有助于阐明从根本上调节基因组组织和表达的关键结构/功能连接。与格里戈耶夫博士的实验合作将有助于将实验与理论结合起来；[与斯坦福大学Simbios的R.Altman博士合作将有助于传播我们开发的工具，并增强项目的影响力。]所建立的模型和方法也适用于其他复杂的大分子体系。最终，这项工作的结果通过影响控制核小体组成和染色质折叠的试剂的设计而具有实际应用价值。 与公共健康相关：染色质组织影响最基本和最重要的细胞功能，包括转录调控和表观遗传控制。我们的项目将通过使用创新的建模和模拟工具在不同的空间和时间尺度上模拟染色质的折叠状态来阐明染色质组织的结构机制。了解这些机制对于解释细胞功能的正常和异常状态以及设计生物医学应用中影响这些过程的药物非常重要。

DESCRIPTION (provided by applicant): Understanding chromosome organization and its control of gene expression represents one of the most fundamental and significant open biological challenges. Modeling the folding states of chromatin on various spatial and temporal scales is key for unraveling the most basic cellular functions, including transcription activation, gene silencing, and epigenetic control. In this proposal, we continue our innovative modeling project on chromatin modeling started in 2000 that has provided novel and high-impact publications concerning chromatin organization and dynamics to incorporate new factors that expand the model scope and impact significant biological problems. We also add an experimental collaborator, Dr. Sergei Grigoryev, with whom we have already worked successfully, [and a team at Stanford's Simbios National Center for Biomedical Computation, to help disseminate our software tools and enhance our project's impact.] Our long term goal is to integrate structural and dynamical aspects of chromatin organization to delineate the thermodynamic mechanisms of transcriptional regulation mediated through protein factors, epigenetic marks, and environmental conditions. To advance in this goal, we will study: (Aim 1) chromatin structure and folding with multivalent ions and dynamic ionic distribution; (Aim 2) chromatin secondary structure folding under different internal and external factors; (Aim 3) tertiary chromatin organization with divalent ions, chromatin fiber concentration, and architectural proteins. In Aim 1, we will develop a rigorous model of chromatin folding with multivalent ions by using a combination of Poisson-Boltzmann theory, an improved representation of screening potential functions, and a method for computing screening potentials as the chromatin conformation changes. In Aim 2, we will explore the effects in the structure of the 30-nm chromatin fiber of DNA linker length variability, histone variants, epigenetic modifications and external forces [using an innovative combination of mesoscale, multiresolution and all-atom models.] In Aim 3, we will model tertiary chromatin structures induced by multivalent ions, concentrated fiber environments, and bound proteins to unravel the structural mechanisms for fiber-fiber interactions and fiber-loop formation and advance our understanding of transcriptional control via large-scale alterations of chromatin folds. These challenging studies in delineating chromatin organization, energetic, and dynamics examined with innovative modeling and experimental techniques, will help elucidate key structure/function connections that fundamentally regulate genomic organization and expression. The experimental collaboration with Dr. Grigoryev will help integrate experiment and theory; [the collaboration with Dr. R. Altman at Stanford's Simbios will help disseminate our developed tools and enhance project impact.] The developed models and methods are applicable to other complex macromolecules systems. Ultimately, this work's results have practical applications by impacting design of agents that control nucleosome composition and chromatin folds. PUBLIC HEALTH RELEVANCE: Chromatin organization affects the most basic and significant cellular functions including transcription regulation and epigenetic control. Our project will elucidate the structural mechanisms of chromatin organization by modeling the folding states of chromatin on various spatial and temporal scales using innovative modeling and simulation tools. Understanding these mechanisms is important for interpreting normal and aberrant states of cellular function and designing agents that affect these processes for biomedical applications.