Exploring functional complexes and disease networks within human RNA-binding protein interactomes

探索人类 RNA 结合蛋白相互作用组中的功能复合物和疾病网络

• 批准号: 10200550
• 负责人: Kristopher Brannan
• 金额: $ 12.49万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-08-01 至 2021-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10200550
• 关键词: ALS patients; Affinity; Alternative Splicing; Amyotrophic Lateral Sclerosis; Binding; Binding Proteins; Biological Process; Biology; Biomedical Research; Biotechnology; C9ORF72; Catalogs; Categories; Cell Nucleus; Cells; Cellular Stress; Code; Complex; Computing Methodologies; Cytoplasm; DNA Binding; Disease; Environment; Gene Expression; Genetic Transcription; Goals; Guanosine Triphosphate Phosphohydrolases; Heart; Human; Institutes; Life Cycle Stages; Maps; Mass Spectrum Analysis; Mediating; Mentors; Methods; Modeling; Molecular; Motor Neurons; Mutate; Neurodegenerative Disorders; Nuclear; Nuclear Pore Complex; Nucleocytoplasmic Transport Proteins; Pathology; Patients; Phase; Phenotype; Post-Transcriptional Regulation; Protein Isoforms; Proteins; Proteomics; Publishing; RAN GTPase Activating Protein 1; RANGAP1 gene; RNA; RNA Binding; RNA Computations; RNA Probes; RNA Recognition Motif; RNA Transport; RNA metabolism; RNA-Binding Proteins; RNA-Protein Interaction; Reporting; Research; Research Institute; Research Proposals; Resources; Role; Sensitivity and Specificity; Training; Training Programs; Transcript; Translations; Untranslated RNA; Validation; base; experience; experimental study; genome-wide; induced pluripotent stem cell; mRNA Precursor; motor control; mutant; nervous system disorder; nucleocytoplasmic transport; programs; protein protein interaction; stem cell biology; stress granule; transcription factor; transcriptome sequencing

PROJECT SUMMARY RNA binding proteins (RBPs) bind to both coding and non-coding RNA to influence every step of the RNA life- cycle, including pre-mRNA processing, RNA localization, and control of translation and degradation. More and more evidence reveals that disruption of RNA metabolism is a hallmark of many human neurodegenerative diseases including Amyotrophic Lateral Sclerosis. Understanding how RBPs act in coordinated networks to regulate RNA fate is key to uncovering the molecular mechanisms underlying these disease pathologies. A complete catalogue of human RBPs is elusive due to the emergence of new classes of RBPs that interact with unpolyadenylated pre-mRNAs or non-canonical RBPs that lack characterized RNA-binding domains, and thus evade traditional RNA-interactome capture studies. We developed a computational RBP classifier based on the observation that protein-protein interaction networks that depend on co-binding of RNA molecules can be used to discover new classes of RBPs. This proposal seeks to utilize predictions from this classifier to accomplish 3 main goals. 1. Phase 1: Determine the biological function of RNA-binding by the disease-associated non-canonical nucleocytoplasmic transport related candidate RBP RANGAP1. 2. Phase 2: Determine the biological function of RNA-binding for an expanded group of disease- associated non-canonical nucleocytoplasmic transport related candidate RBPs. 3. Phase 2: Build an RBP centered protein-protein interaction network to expand the repertoire of human RBPs to characterize ALS relevant higher order RNP complexes. My extensive experience in the study of DNA and RNA binding proteins makes me an ideal candidate to perform the research proposed here. These aims will build towards the completion of a comprehensive list of human RBPs that will help provide detailed maps of RNA regulatory networks. The Yeo lab at UCSD is a leader in the field of RNA biology, and therefore is an excellent environment to perform the proposed training and build an independent research program. The Yeo lab is situated at the heart of a major biomedical research hub at UCSD, adjacent to the Salk Institute, and other research institutes and biotechnology companies in La Jolla. Conducting the proposed training program here will give me access to leaders in stem cell biology and proteomic methods that I hope to master as I transition to independence.

项目摘要 RNA结合蛋白（RBP）与编码和非编码RNA结合，以影响RNA寿命的每个步骤 循环，包括前MRNA处理，RNA定位以及翻译和降解的控制。更多和 更多证据表明，RNA代谢的破坏是许多人类神经退行性的标志 包括肌萎缩性侧硬化症在内的疾病。了解RBP在协调网络中的作用 调节RNA命运是揭示这些疾病病理学基础的分子机制的关键。一个 由于出现了与之相互作用的新类RBP，因此人RBP的完整目录难以捉摸 缺乏表征RNA结合域的非溶解二苯基的前MRNA或非典型的RBP，因此 逃避传统的RNA相互作用捕获研究。我们开发了一个基于 观察到依赖RNA分子共同结合的蛋白质 - 蛋白质相互作用网络可以是 用于发现新的RBP。该建议旨在利用该分类器的预测 实现3个主要目标。 1。阶段1：确定与疾病相关的非典型的RNA结合的生物学功能 核细胞转运相关的候选RBP RAGAP1。 2。阶段2：确定RNA结合的生物学功能，用于扩展的一组疾病 - 相关的非经典核细胞转运相关的候选RBP。 3。阶段2：建立一个以RBP为中心的蛋白质 - 蛋白质相互作用网络，以扩大人类的曲目 RBP表征ALS相关的高阶RNP复合物。 我在研究DNA和RNA结合蛋白方面的丰富经验使我成为了我的理想候选者 在此处进行研究。这些目标将建立在完成的综合列表中 将有助于提供RNA调节网络的详细地图的人RBP。 UCSD的YEO实验室是 RNA生物学领域的领导者，因此是进行拟议培训的绝佳环境 并建立一个独立的研究计划。 YEO实验室位于主要生物医学的心脏 UCSD的研究中心，毗邻SALK研究所以及其他研究机构和生物技术 La Jolla的公司。在这里进行拟议的培训计划将使我与STEM的领导者访问 我希望在过渡到独立时掌握的细胞生物学和蛋白质组学方法。