Mechanism of Distant Communication in Chromatin

染色质远距离通讯机制

• 批准号: 1050470
• 负责人: Vasily Studitsky
• 金额: $ 57万
• 依托单位: Rutgers, The State University of New Jersey-RBHS-Robert Wood
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-04-01 至 2014-05-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1050470&HistoricalAwards=false
• 关键词: Mechanism; Distant; Communication; Chromatin

Intellectual merit: The first step in gene expression (RNA synthesis, or transcription) of the vast majority of eukaryotic genes is regulated by enhancers, which are DNA sequences that bind specific proteins and activate transcription over large distances. Enhancer-target communication (ETC) leads to direct interaction of enhancers with the target promoters, the sites of transcription initiation, via formation of a DNA loop. ETC can be prevented by insulators, which are DNA elements that form alternative DNA loops and can isolate enhancers from the targets. Thus, gene regulation in human cells involves formation of DNA loops of variable sizes. The mechanisms of efficient communication between enhancers and promoters and the mechanisms by which such communication is prevented by insulators remain unknown. In particular, neither structural nor dynamic aspects of DNA looping have been rationalized. Recently, it has been shown that DNA loops bound to histone proteins are a highly efficient communication device. These observations indicate that ETC could constitute a critical step in gene regulation and raise the following important questions: What elements of the DNA-histone complexes mediate efficient ETC, and how can ETC be inhibited or facilitated by various factors? In this project, a highly purified and functionally active experimental system has been established that allows quantitative analysis of the rate of ETC in the DNA-histone complexes. This system will be used as a tool to analyze structural and dynamic properties of the DNA-histone complexes that dictate the rate of ETC. The objectives of this research are to evaluate the mechanisms of efficient distant communication and inhibition of communication by insulators and to identify factors affecting distant communication and evaluate their effect on the dynamics of the DNA-histone complexes.Broader impacts: This project will provide an enhanced learning experience for several undergraduate and two graduate students involved in the project. They will participate weekly in four different meetings; namely (1) laboratory meetings in which they will have the opportunity to present their own research every 2-3 months, (2) laboratory discussion of recent publications on chromatin structure/dynamics/function, (3) problem solving sessions with a small group of students and senior researchers that focuses on technical challenges, and (4) Departmental Progress Reports where all Departmental students present their research annually. This project is well suited for student participation, as it provides a solid conceptual foundation and utilizes methodologies applicable to many areas of research, and at the same time is paradigm-driven, providing an intuitive transition from the classroom to the bench. The laboratory regularly trains underrepresented minority undergraduates (within the UMDNJ Summer Research Program). New technologies/strategies for analysis of structure/dynamics of the DNA-histone complexes will be developed. Some of them will be of general use in the field of biology. The project is a multi- disciplinary study to examine a complex biological question, and incorporates recent advances in computational science and structural biology at the interface between chemistry, physics and biology.

智力优点：绝大多数真核基因的基因表达（RNA合成或转录）的第一步是由增强子调节的，增强子是结合特定蛋白质并远距离激活转录的DNA序列。增强子-靶通讯（ETC）通过形成DNA环导致增强子与靶启动子（转录起始位点）的直接相互作用。ETC可以通过绝缘体来防止，绝缘体是形成替代DNA环的DNA元件，可以将增强子与靶标隔离。因此，人类细胞中的基因调控涉及可变大小的DNA环的形成。增强子和启动子之间有效通讯的机制以及绝缘子阻止这种通讯的机制仍然未知。特别是，DNA循环的结构和动力学方面都没有得到合理化。最近，研究表明，与组蛋白结合的DNA环是一种高效的通讯装置。这些观察结果表明，ETC可能构成基因调控的关键步骤，并提出了以下重要问题：什么元素的DNA-组蛋白复合物介导有效的ETC，ETC如何被抑制或促进各种因素？本研究建立了一个高纯度、高活性的DNA-组蛋白复合物中ETC的定量分析系统。该系统将被用作分析DNA-组蛋白复合物的结构和动力学性质的工具，这些性质决定了ETC的速率。本研究的目的是评估有效的远距离通信和绝缘体抑制通信的机制，并确定影响远距离通信的因素，评估它们对DNA-组蛋白复合物动力学的影响。这个项目将为参与该项目的几名本科生和两名研究生提供增强的学习经验。他们将每周参加四次不同的会议;即（1）实验室会议，其中他们将有机会每2-3个月展示他们自己的研究，（2）关于染色质结构/动力学/功能的最新出版物的实验室讨论，（3）与一小群学生和高级研究人员的问题解决会议，其关注技术挑战，和（4）部门进展报告，所有部门的学生每年提出他们的研究。该项目非常适合学生参与，因为它提供了坚实的概念基础，并利用适用于许多研究领域的方法，同时是范式驱动的，提供了从课堂到板凳的直观过渡。该实验室定期培训代表性不足的少数民族本科生（在UMDNJ夏季研究计划内）。将开发用于分析DNA-组蛋白复合物的结构/动力学的新技术/策略。其中一些将在生物学领域具有普遍用途。该项目是一项多学科研究，旨在研究一个复杂的生物学问题，并在化学，物理和生物学之间的界面上结合了计算科学和结构生物学的最新进展。