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：
10501107
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如何组织和访问基因组信息。在我的提议的核心是开发一个框架，可以在体外实验与对应物进行体外实验体内。我们将采用新颖的体外实验平台来做到这一点，这些平台独特地准备与之合作中尺度材料。（1）DNA和染色质窗帘，它们是高分辨率的高通量单个用于长延伸DNA和染色质纤维上的分子工具。（2）光学镊子，测量DNA或染色质上的力至异常高的分辨率。（3）液滴实验，这允许美国测量关键的生物物理参数，例如自由能，分区系数和相对迁移率。使用这些测定法，我的实验室研究旨在了解染色质如何将染色质凝结成紧凑的结构以及压实在生物学中所起的作用。此外，我们正在研究表观遗传信息沿染色质纤维传播，以及染色质如何动态分配到相似功能的区域中核。拟议的研究计划旨在将体内测量与机械性联系起来通过追踪跨尺度的反应来实现单个蛋白质作用的框架。具体而言，我们的方法负担得起我们有机会增加从试管中分离的分子的特定反应的复杂性，扩展分子的一维反应，与无序的三维环境凝结，最后是核。我们认为，在调查中跨过秤，停下来这些中间的观察水平现在已经丢失了，这将使我们能够成功攻击关于调节和领域形成的染色质生物学中的重要问题，这些问题仍然难以捉摸。最终，将使我们朝着如何访问，管理我们的遗传信息以及包装。