Dissecting modular interaction of RNA with protein in chromatin

解析染色质中 RNA 与蛋白质的模块化相互作用

• 批准号: 10471444
• 负责人: Taeyoung Hwang
• 金额: $ 24.89万
• 依托单位: LIEBER INSTITUTE, INC.
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-09-01 至 2024-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10471444
• 关键词: Affect; Amaze; Base Sequence; Binding; Binding Proteins; Biochemical; Biological; Biological Assay; Biology; CREBBP gene; Cell physiology; Cells; Cellular biology; Chromatin; Code; Combinatorial Synthesis; Complex; Computational algorithm; Computing Methodologies; DNA; Data Set; Development; Disease; EZH2 gene; Elements; Foundations; Gene Expression; Gene Expression Regulation; Genomics; High-Throughput Nucleotide Sequencing; Histones; Human; Individual; Mediating; Medicine; Modeling; Modification; Molecular; Mutation; Nature; Oligonucleotides; Output; Polycomb; Proteins; RNA; RNA Binding; RNA-Binding Proteins; RNA-Protein Interaction; Reporter; Research; Rest; Role; Site; Structure; Telomerase RNA Component; Tertiary Protein Structure; Testing; Untranslated RNA; base; chromatin modification; combinatorial; design; experimental study; high throughput screening; insight; protein protein interaction; protein structure; scaffold; scale up; tool

Project summary / Abstract The forefront of current RNA research centers on understanding the amazing complexity of this molecule. There is an expanding appreciation that the roles of RNA are multifaceted and extend far beyond its coding potential. RNA has the capacity for diverse structures, numerous modifications, and combinatorial interactions, and thus RNA is a foundational component for many complex regulatory networks. It is crucial to understand these networks from the level of individual molecular RNA interactions up through their effects on disease and development. In particular, many chromatin-associated proteins (CAPs) additionally interact with RNA, and may function in regulating gene expression by way of these RNA interactions. Previous studies, limited to identifying the RNAs bound by individual CAPs, did not consider combinatorial RNA binding. Here, I reveal that the CAP- RNA network contains clusters of RNAs that bind multiple proteins. Notably, Polycomb group and Trithorax group CAPs (EZH2 and WDR5, respectively) seem to interact with similar RNAs despite their opposing roles in chromatin modification. This suggests that EZH2- and WDR5- RNA interactions may affect or counter one another, and that this could manifest in altered chromatin states. I aim to elucidate how different CAP-RNA interactions affect one another and to characterize the relationship among RNA-binding of multiple CAPs. I hypothesize that RNA contains multiple elements, or modules, that interact with specific proteins, and that the functional readout of combinatorial interactions in a network can be understood by modular design principles of RNA. I propose the following aims to investigate this idea, particularly focusing on EZH2- and WDR5- RNA interactions: (1) development of a massively-parallel RNA assay (MPRNA) to identify RNA elements that bind to a particular protein, (2) investigating the modular principle using combinatorial synthesis of multiple RNA elements, (3) uncovering the underlying mechanism of RNA element organization and protein interaction. This approach will establish an interdisciplinary framework for studying RNA-centric networks, using both experimental and computational methods. It will reveal interaction principles and mechanisms of protein-RNA interactions, and examine functional consequences of these interactions. It will increase our understanding of RNA-based regulatory networks, particularly in the context of chromatin and CAP-mediated gene regulation. It may even provide insight into the control of Polycomb- and Trithorax- group complexes at sites of bivalent chromatin.

项目概要/摘要 当前 RNA 研究的前沿集中于了解这种分子惊人的复杂性。那里 人们越来越认识到 RNA 的作用是多方面的，并且远远超出了其编码潜力。 RNA 具有多种结构、大量修饰和组合相互作用的能力，因此 RNA 是许多复杂调控网络的基本组成部分。了解这些很重要 从单个分子 RNA 相互作用的水平到它们对疾病和疾病的影响 发展。特别是，许多染色质相关蛋白 (CAP) 还与 RNA 相互作用，并且可能 通过这些 RNA 相互作用来调节基因表达。先前的研究仅限于识别 单个 CAP 结合的 RNA 没有考虑组合 RNA 结合。在此，我向大家透露，CAP- RNA 网络包含结合多种蛋白质的 RNA 簇。值得注意的是，Polycomb 群和 Trithorax 群 CAP（分别为 EZH2 和 WDR5）似乎与相似的 RNA 相互作用，尽管它们在 染色质修饰。这表明 EZH2- 和 WDR5- RNA 相互作用可能会影响或抵消一种 另一个，这可能会体现在染色质状态的改变中。我的目的是阐明 CAP-RNA 有何不同 相互作用相互影响并表征多个 CAP 的 RNA 结合之间的关系。我 假设 RNA 包含多个与特定蛋白质相互作用的元件或模块，并且 网络中组合相互作用的功能读出可以通过模块化设计原理来理解 核糖核酸。我提出以下目标来研究这个想法，特别关注 EZH2- 和 WDR5- RNA 相互作用：（1）开发大规模并行RNA测定（MPRNA）来识别结合的RNA元件 特定蛋白质，(2) 使用多种 RNA 的组合合成研究模块化原理 (3)揭示RNA元件组织和蛋白质相互作用的潜在机制。这 方法将建立一个跨学科框架来研究以 RNA 为中心的网络，同时使用 实验和计算方法。揭示蛋白质-RNA相互作用原理和机制 相互作用，并检查这些相互作用的功能后果。它将增加我们对 基于 RNA 的调控网络，特别是在染色质和 CAP 介导的基因调控的背景下。它 甚至可以深入了解 Polycomb 和 Trithorax 基团复合物在二价位点的控制 染色质。