Structured RNAs Binding to Proteins Containing the dsRBD

描述（由申请人提供）：双链RNA结合域（dsRBD）存在于所有生命领域，特别是高等真核生物中。越来越多的证据表明，含有 dsRBD（又名 dsRBP）的蛋白质在基本分子和细胞功能、感染和免疫以及发育中发挥着关键作用。 dsRBP 功能的一个关键共同主题是通过 dsRBD 与结构化 RNA 配体结合。虽然完美双链 dsRNA 通常用作体外结合伴侣，但最近的研究表明内源性 RNA 配体更加多样化。然而，迄今为止，这些生物学相关的体内RNA配体仅在小规模实验中进行了零星的检查，导致数据不完整。在本提案中，我们计划开发在一些常用细胞系中对 dsRBDs/dsRBPs RNA 配体进行深度测序的实验方法，并通过计算探索它们的序列和结构特征以及生物网络。 公共健康相关性：含有双链 RNA 结合域 (dsRBD) 的蛋白质（称为 dsRBP）在正常和病理条件下都具有关键作用。它们功能的一个关键方面是与结构化 RNA 的结合。人们对这些 RNA 伴侣知之甚少。通过使用深度测序技术和生物信息学，该项目将检查并编录与人类 dsRBP 家族成员相互作用的不同 RNA 物种群体。这些数据将有助于了解 RNA-蛋白质相互作用及其作用，预测目前未知的 dsRBP 功能，并可能产生迄今尚未发现的 RNA 种类。

DESCRIPTION (provided by applicant): The double-stranded RNA binding domain (dsRBD) is present in all kingdoms of life, particularly in higher eukaryotes. Growing lines of evidence indicate that proteins containing dsRBDs, a.k.a. dsRBPs, play pivotal roles in essential molecular and cellular functions, infection and immunity, and development. A key common theme of dsRBP functions is binding to structured RNA ligands via dsRBDs. While perfectly duplexed dsRNAs are typically employed as binding partners in vitro, recent studies have indicated that endogenous RNA ligands are much more diverse. However, to date, these biologically relevant in vivo RNA ligands have been examined only sporadically and in small-scale experiments, resulting in fragmentary data. In this proposal, we plan to develop experimental methods for deep sequencing RNA ligands of dsRBDs/dsRBPs in a number of commonly used cell lines and to computationally explore their sequence and structure features and biological networks. PUBLIC HEALTH RELEVANCE: Proteins that contain the double-stranded RNA binding domain (dsRBD), known as dsRBPs, have pivotal roles in both normal and pathological conditions. A critical aspect of their functions is binding to structured RNAs. These RNA partners are poorly understood. By using deep sequencing technology and bioinformatics, this project will examine and catalog the distinct populations of RNA species interacting with members of the human dsRBP family. The data will help understand the RNA-protein interactions and their roles, will predict dsRBP functions that are presently unknown, and will probably yield hitherto undiscovered RNA species.