Harnessing the chromatin conformational code for epigenetic regulation

利用染色质构象密码进行表观遗传调控

• 批准号: 10473051
• 负责人: Serena Sanulli
• 金额: $ 141.66万
• 依托单位: STANFORD UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-09-01 至 2025-08-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10473051
• 关键词: 3-Dimensional; Architecture; Biological; Biological Markers; Biophysics; Cells; Chromatin; Chromatin Structure; Code; Cryoelectron Microscopy; DNA; Defect; Disease; Epigenetic Process; Genetic; Genetic Transcription; Genome; Histones; In Vitro; Interdisciplinary Study; Investigation; Knowledge; Libraries; Link; Malignant Neoplasms; Molecular; Molecular Conformation; Nuclear; Nucleosome Core Particle; Nucleosomes; Pathologic; Pharmaceutical Preparations; Physiology; Post-Translational Protein Processing; Regulation; Research; Science; Shapes; Tail; Testing; Textbooks; Therapeutic; Translational Research; United States National Institutes of Health; Work; base; epigenetic regulation; flexibility; gene repression; high reward; high risk; in vivo; innovation; insight; macromolecular assembly; nanobodies; new therapeutic target; novel; novel strategies; novel therapeutics; programs; sensor; therapeutic biomarker; tool

Project summary Eukaryotic DNA is wrapped around nucleosomes, which form chains of chromatin that are further folded into three-dimensional assemblies. The architecture of these assemblies regulates many nuclear functions, including genome 3D folding and transcription, and ultimately dictates cellular identity. Nucleosomes are a well-known hub of chromatin regulation, most of which is thought to occur via a variety of post-translational modifications on the protruding flexible tails of histones. Based on the assumption that most regulation of chromatin's structure and interactions with other factors occurs at these histone tails, the globular core of nucleosomes has been considered rigid and minimally regulatory. Excitingly, my recent work has revealed a new insight: that the nucleosome core is malleable and that this plasticity regulates chromatin folding and gene repression. I therefore propose that the globular, malleable core of nucleosomes is a hub for genetic and epigenetic regulation as well as a potential novel therapeutic target. To test this provocative hypothesis that challenges the textbook paradigm of chromatin regulation, novel tools capable of probing both in vitro and in vivo atomic-scale dynamics of large macromolecular assemblies such as chromatin must be developed. My lab will close this gap by developing conformation-specific nanobodies (NanoNucs) that act as sensors of distinct nucleosome conformations. NanoNucs will be discovered from a synthetic library containing >2 x 109 distinct nanobodies. We will employ NanoNucs to gain structural and biophysical insights into nucleosome conformational dynamics and to probe and perturb the nucleosome conformational code in cells. Specifically, we will: (i) obtain atomic understanding of nucleosome alternative states by combining NMR, HDX-MS, and cryo-EM; (ii) identify chromatin factors that sense and leverage nucleosome plasticity; (iii) search for nucleosome conformations that are biological or pathological biomarkers; and (iv) develop a novel strategy to manipulate nucleosome shapes and chromatin states in cells. By carrying out this highly ambitious, integrated, and multidisciplinary research program, my lab will unveil the molecular mechanisms and therapeutical potential of the nucleosome conformational code. I anticipate that these high-risk, high-reward investigations will reveal new fundamental principles of genome regulation that shift the long-standing paradigm of rigid histone units and that will broadly impact biomedical science over the short and long terms. Exploring the structural flexibility of nucleosomes represents an opportunity to identify novel therapeutic biomarkers and drugs for diseases linked to epigenetics defects, such as cancer. Ultimately, with critical support from the NIH Director's New Innovator Program, our studies will enrich our knowledge of the function and physiology of chromatin with atomic-scale biophysical insights into the chromatin architecture itself.

项目概要 真核 DNA 包裹在核小体周围，核小体形成染色质链，进一步折叠成 三维组件。这些组件的架构调节许多核功能，包括 基因组 3D 折叠和转录，并最终决定细胞身份。核小体是众所周知的枢纽 染色质调控，其中大部分被认为是通过各种翻译后修饰发生的 突出的组蛋白柔性尾部。基于染色质结构的大部分调节和 与其他因素的相互作用发生在这些组蛋白尾部，核小体的球状核心已被 被认为是严格且最低限度的监管。令人兴奋的是，我最近的工作揭示了一个新的见解： 核小体核心具有可塑性，这种可塑性调节染色质折叠和基因抑制。我因此 提出核小体的球状、可延展的核心也是遗传和表观遗传调控的中心 作为潜在的新型治疗靶点。检验这一挑战教科书范式的挑衅性假设 染色质调控的新工具，能够探测大分子的体外和体内原子级动力学 必须开发诸如染色质之类的大分子组装体。我的实验室将通过开发来缩小这一差距 构象特异性纳米抗体（NanoNucs）充当不同核小体构象的传感器。 NanoNucs 将从包含 >2 x 109 个不同纳米抗体的合成文库中发现。我们将聘用 NanoNucs 获得核小体构象动力学的结构和生物物理见解并进行探索 并扰乱细胞中的核小体构象密码。具体来说，我们将：（i）获得原子理解 通过结合 NMR、HDX-MS 和冷冻电镜来确定核小体的替代状态； (ii) 确定染色质因子 感知并利用核小体可塑性； (iii) 寻找生物或生物的核小体构象 病理生物标志物； (iv) 开发一种新的策略来操纵核小体形状和染色质 细胞中的状态。通过开展这项雄心勃勃、综合性、多学科的研究计划，我的实验室 将揭示核小体构象密码的分子机制和治疗潜力。我 预计这些高风险、高回报的研究将揭示基因组的新基本原理 改变刚性组蛋白单元长期存在范式并将广泛影响生物医学的监管 短期和长期的科学。探索核小体的结构灵活性代表了 有机会识别与表观遗传学缺陷相关的疾病的新型治疗生物标志物和药物，例如 作为癌症。最终，在 NIH 主任新创新者计划的大力支持下，我们的研究将丰富 我们对染色质功能和生理学的了解以及对染色质的原子尺度生物物理学见解 染色质结构本身。