Dissecting modular interaction of RNA with protein in chromatin

项目摘要/摘要 当前RNA研究的前沿是了解这种分子令人惊叹的复杂性。那里 人们越来越认识到，RNA的作用是多方面的，远远超出了其编码潜力。 RNA具有多样的结构、大量的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。理解这些是至关重要的 网络从单个分子RNA相互作用的水平上到它们对疾病和 发展。具体地说，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相互作用调节基因表达的功能。以前的研究，仅限于识别 被单个帽子结合的RNA不考虑组合RNA结合。在这里，我透露CAP- RNA网络包含多个结合多个蛋白质的RNA簇。值得注意的是，复梳组和三胸组 CAP(分别为EZH2和WDR5)似乎与类似的RNA相互作用，尽管它们在 染色质修饰。这表明EZH2-和WDR5-RNA的相互作用可能会影响或对抗一种 另一种是，这可能表现为染色质状态的改变。我的目的是阐明不同的CAP-RNA 相互作用相互影响，并表征多个帽子的RNA结合之间的关系。我 假设RNA包含与特定蛋白质相互作用的多个元素或模块，并且 网络中组合相互作用的功能读数可以通过模块化设计原理来理解 核糖核酸。我提出以下目的来研究这个想法，特别是EZH2-和WDR5-RNA 相互作用：(1)建立一种大规模平行RNA分析(MPRNA)来鉴定与 一种特定的蛋白质，(2)利用多个RNA的组合合成来研究模块化原理 揭示了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的框架来研究以RNA为中心的网络，使用两者 实验和计算方法。它将揭示蛋白质-RNA的相互作用原理和机制 交互作用，并检查这些交互作用的功能后果。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 甚至可以洞察在二价位上多梳基和三胸基复合体的控制 染色质。

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.