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

• 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
• 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
• 来源: https://reporter.nih.gov/project-details/10501107
• 关键词: 3-Dimensional; Architecture; Behavior; Biological Assay; Biology; Cell Nucleus; Cells; Chromatin; Chromatin Fiber; Chromatin Structure; Crowding; DNA; DNA Sequence; Development; Dimensions; Disease; Environment; Epigenetic Process; Free Energy; Genes; Genome; Genomic Instability; Genomics; Imaging Device; In Vitro; Individual; Investigation; Lead; Measurement; Measures; Modeling; Organism; Partition Coefficient; Play; Process; Proteins; Reaction; Regulation; Research; Resolution; Role; Structure; Testing; Tube; Work; biophysical properties; cohesion; experimental study; genetic information; in vivo; laser tweezer; novel; organizational structure; programs; single molecule

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.

摘要 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 我的建议的核心是努力开发一个框架，将体外实验与其对应的实验联系起来 in vivo.我们将通过采用新颖的体外实验平台来实现这一目标，这些平台具有独特的优势， 中尺度物质(1)DNA和染色质幕，这是一个高分辨率，高通量的单一， 用于成像长延伸DNA和染色质纤维上的相互作用的分子工具。(2)光镊， 以极高的分辨率测量DNA或染色质上的力。和（3）液滴实验，它允许 我们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。使用 通过这些分析，我实验室的研究旨在了解染色质是如何浓缩成紧凑结构的 以及压实在生物学中的作用。此外，我们正在研究表观遗传信息是如何 沿着染色质纤维传播以及染色质如何动态分配到具有相似功能的区域 原子核拟议的研究计划旨在将体内测量与机械学联系起来。 通过追踪跨尺度的反应来构建单个蛋白质作用的框架。具体来说，我们的方法提供了 利用这个机会，从试管中分离的分子中增加特定反应的复杂性， 一维反应的扩展分子，到无序的三维环境， 凝聚，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攻击 染色质生物学中关于调控和结构域形成的重要问题，至今仍是难以捉摸的。 最终，将推动我们走向一个有凝聚力的模型，我们的遗传信息是如何获得，管理， 打包好的