Physical determinants of DNA recognition and genome organization in crowded environments

拥挤环境中 DNA 识别和基因组组织的物理决定因素

基本信息

批准号：
10669770
负责人：
Sy Redding
金额：
$ 41.88万
依托单位：
UNIV OF MASSACHUSETTS MED SCH WORCESTER
依托单位国家：
美国
项目类别：
财政年份：
2022
资助国家：
美国
起止时间：
2022-07-22 至 2027-06-30
项目状态：
未结题

项目摘要

Abstract The proposed research program seeks to understand how genomic information is organized and accessed. At the core of my proposal is an effort to develop a framework that bridges in vitro experiments to their counterparts in vivo. We will do this by employing novel in vitro experimental platforms that are uniquely poised to work with mesoscale materials. (1) DNA and chromatin curtains, which are a high-resolution, high-throughput single- molecule tool for imaging interactions on long extended DNA and chromatin fibers. (2) Optical tweezers, which measure forces on DNA or chromatin to exceptionally high resolution. And (3) droplet experiments, which allow us to measure key biophysical parameters, like free energies, partition coefficients, and relative mobilities. Using these assays, research in my lab is aimed at understanding how chromatin condenses into compact structures and the role that compaction plays in biology. In addition, we are investigating how epigenetic information is propagated along chromatin fibers and how chromatin dynamically partitions into regions of similar function in the nucleus. The proposed research program seeks to connect in vivo measurements into mechanistic frameworks of individual protein actions by tracing reactions across scales. Specifically, our approaches afford us the opportunity to increase the complexity of a particular reaction from isolated molecules in a test tube, to one dimensional reactions on extended molecules, to the disordered three dimensional environment of condensates, and finally to the nucleus. We feel that stepping across scales in our investigations, stopping at these intermediate levels of observation, which up to now have been missing, will allow us to successfully attack important questions in chromatin biology about regulation and domain formation, which have remained elusive. And ultimately, will drive us toward a cohesive model of how our genetic information is accessed, managed, and packaged.

抽象的拟议的研究计划旨在了解基因组信息是如何组织和访问的。在我提案的核心是努力开发一个框架，将体外实验与同行实验联系起来体内。我们将通过采用独特的新型体外实验平台来实现这一目标介观材料。 (1) DNA 和染色质幕帘，这是一种高分辨率、高通量的单用于对长延伸 DNA 和染色质纤维上的相互作用进行成像的分子工具。 (2) 光镊，以极高的分辨率测量 DNA 或染色质上的力。 (3) 液滴实验，允许我们可以测量关键的生物物理参数，例如自由能、分配系数和相对迁移率。使用这些测定，我实验室的研究旨在了解染色质如何凝结成紧凑的结构以及压实在生物学中发挥的作用。此外，我们正在研究表观遗传信息如何沿着染色质纤维传播以及染色质如何动态划分成具有相似功能的区域核。拟议的研究计划旨在将体内测量与机械测量联系起来通过跨尺度追踪反应来构建单个蛋白质作用的框架。具体来说，我们的方法提供我们有机会增加试管中分离分子的特定反应的复杂性，扩展分子上的一维反应，到无序的三维环境凝结，最后到达原子核。我们认为，在我们的调查中跨越尺度，停在这些迄今为止一直缺失的中间水平的观察将使我们能够成功地进行攻击染色质生物学中关于调控和结构域形成的重要问题仍然难以捉摸。最终，将推动我们建立一个关于如何获取、管理和识别我们的遗传信息的凝聚力模型。包装好的。