Dynamics of DNA-histone interactions

DNA-组蛋白相互作用的动力学

• 批准号: 10551382
• 负责人: Tae-Hee Lee
• 金额: $ 58.81万
• 依托单位: PENNSYLVANIA STATE UNIVERSITY, THE
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-08-01 至 2028-07-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10551382
• 关键词: Address; Affect; Area; Biochemical; Complex; Core Protein; DNA; DNA Methylation; Development; Diagnosis; Disease; Enzyme Interaction; Enzymes; Eukaryota; Failure; Fluorescence; Fluorescence Resonance Energy Transfer; Gene Expression Regulation; Genes; Genetic; Goals; Histone Acetylation; Histones; Investigation; Methods; Methylation; Molecular; Molecular Conformation; Molecular Machines; Motion; Multienzyme Complexes; Neurodegenerative Disorders; Nucleosomes; Optics; Pathogenesis; Play; Process; Public Health; RNA Polymerase II; Reporting; Research; Role; Structure; Sumoylation Pathway; System; Variant; cancer type; centromere protein A; chromatin modification; ds-DNA; improved; leukemia; programs; single molecule; structural biology; tool; ultra high resolution

Project Summary The overarching goal of my research program is to elucidate the roles of dynamic DNA-histone interactions in the nucleosome in regulating gene accessibility from single-molecule approaches. The nucleosome is the fundamental packing unit of genes in eukaryotes and plays important roles in gene regulation. Errors in gene regulation often lead to developmental failure and lethal diseases such as various types of cancer. The nucleosome is made of ~147 bp ds-DNA with an octameric histone protein core. DNA and histones are targets for various chromatin modifications that are often critically implicated in gene regulation mechanisms. We reported several important changes in the structure and structural dynamics of the nucleosome induced by various chromatin modifications and histone variants such as DNA methylation, histone acetylations, SUMOylation, CENP-A, and H2A.Z in the context of their roles in gene regulation. As these changes are heterogeneous, unsynchronized, and/or complex, they are often impossible to resolve with ensemble-averaging biochemical, genetic, and static structural biology tools. We develop and improve single- molecule fluorescence methods and systems, mainly based on FRET, FCS, and colocalization at an optical super-resolution to address these problems. We will continue pushing the boundaries of these experimental systems and methods to support our future research that will center around three synergistic themes: how (1) chromatin modifications and histone variants, (2) spontaneous molecular motions and interactions, and (3) active and passive molecular machines and enzymes affect DNA-histone dynamics in nucleosomes and nucleosome arrays and how the effects are implicated in gene regulation mechanisms. We recently started evolving our mostly nucleosome-focused experimental systems by combining various enzymes that act on the nucleosome and expanding them to include nucleosome arrays. Based on these systems, our research will continue largely in three topical areas in the next five years: (1) nucleosome dynamics during its interaction with complex enzymes such as RNA polymerase II and Dot1L, a key player in H3K79 methylation-dependent leukemia pathogenesis, (2) the effects of chromatin modifications on the structure and dynamics of the nucleosome and their implications in nucleosome-enzyme interactions, (3) conformations and dynamics of nucleosome arrays and the effects of chromatin modifications on nucleosome dynamics in nucleosome arrays. Investigations in these areas will help understand the fundamental molecular processes that regulate nucleosome dynamics and gene accessibility during nucleosome-enzyme interactions in a nucleosome and a nucleosome-array context and at depth and clarity afforded by our highly-refined tractable single-molecule systems.

项目摘要 我的研究计划的首要目标是阐明动态DNA组蛋白的作用 核小体中的相互作用通过单分子方法调节基因可及性。的 核小体是真核生物基因的基本包装单位，在基因表达中起着重要的作用。 调控基因调控中的错误通常会导致发育失败和致命疾病，例如各种 癌症的类型。核小体由约147 bp的双链DNA组成，具有八聚体组蛋白核心。DNA和 组蛋白是各种染色质修饰的靶标，这些染色质修饰通常与基因调控密切相关 机制等我们报道了几个重要的变化，在结构和结构动力学的， 核小体由各种染色质修饰和组蛋白变体如DNA甲基化诱导， 组蛋白乙酰化、SUMO化、CENP-A和H2A.Z在基因调控中的作用。作为 这些变化是异构的、不同步的和/或复杂的， 整体平均生化，遗传和静态结构生物学工具。我们致力于开发和改进单- 分子荧光方法和系统，主要基于FRET，FCS和光学共定位 超分辨率来解决这些问题。我们将继续推动这些实验性的边界 系统和方法，以支持我们未来的研究，将围绕三个协同主题：如何（1） 染色质修饰和组蛋白变体，（2）自发分子运动和相互作用，以及（3） 主动和被动分子机器和酶影响核小体中的DNA-组蛋白动力学， 核小体阵列和如何影响基因调控机制。 我们最近开始发展我们主要以核小体为中心的实验系统， 作用于核小体并将其扩展为包括核小体阵列的各种酶。基于 这些系统，我们的研究将继续主要在三个主题领域在未来五年：（1）核小体 在与RNA聚合酶II和Dot 1 L等复杂酶相互作用期间， H3 K79甲基化依赖性白血病发病机制，（2）染色质修饰对H3 K79甲基化依赖性白血病发病机制的影响。 核小体的结构和动力学及其在核小体-酶相互作用中的意义，（3） 核小体阵列的构象和动力学以及染色质修饰对核小体的影响 核小体阵列的动力学在这些领域的研究将有助于了解基本的分子 在核小体-酶相互作用期间调节核小体动力学和基因可及性的过程 在核小体和核小体阵列背景下，以及我们高度精炼的 易处理的单分子系统。