Physical determinants of DNA recognition and genome organization in crowded environments

摘要 拟议的研究计划试图了解基因组信息是如何组织和获取的。在… 我的提议的核心是努力开发一种框架，将体外实验与同行联系起来 在活体内。我们将通过使用新的体外实验平台来实现这一点，这些平台是独一无二的 中尺度材料。(1)DNA和染色质窗帘，这是一种高分辨率、高通量的单 用于成像延长的DNA和染色质纤维上的相互作用的分子工具。(2)光学镊子，其 测量DNA或染色质上的力以异常高的分辨率。以及(3)液滴实验，它允许 我们将测量关键的生物物理参数，如自由能、分配系数和相对迁移率。vbl.使用 我实验室的这些分析和研究旨在了解染色质是如何浓缩成致密结构的 以及压实在生物学中所起的作用。此外，我们正在调查表观遗传信息是如何 沿染色质纤维传播，以及染色质如何动态划分为相似功能的区域 原子核。拟议的研究计划试图将活体测量与机械测量联系起来 通过追踪不同尺度上的反应，确定单个蛋白质的作用框架。具体地说，我们的方法能够 美国有机会从试管中分离的分子增加特定反应的复杂性，以 扩展分子上的一维反应，到无序的三维环境 凝聚，最后到达原子核。我们觉得在我们的调查中跨过天平，止步于 这些到目前为止还没有的中间观察水平，将使我们能够成功地攻击 染色质生物学中有关调控和结构域形成的重要问题仍然难以捉摸。 最终，将推动我们走向一个关于如何访问、管理和管理我们的遗传信息的凝聚力模型 包装好了。

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.