Functional RNA elements in the human genome

人类基因组中的功能性RNA元件

基本信息

批准号：
8773860
负责人：
XIANG-DONG FU
金额：
$ 69.75万
依托单位：
UNIVERSITY OF CALIFORNIA, SAN DIEGO
依托单位国家：
美国
项目类别：
财政年份：
2008
资助国家：
美国
起止时间：
2008-06-01 至 2017-06-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8773860
关键词：
Alternative Splicing Binding Cells Code Collection Complement Complex Computing Methodologies Coupling Custom Data Data Set Development Disease Dissection Double-Stranded RNA Ectopic Expression Epigenetic Process Event Functional RNA Funding Gene Expression Gene Expression Regulation Gene Mutation Generations Genes Genetic Transcription Genomics Grant Health Human Human Genome Indium Individual Laboratories Length Libraries Link Malignant Neoplasms Mammalian Cell Mediating Messenger RNA Molecular Mutation National Human Genome Research Institute Nerve Degeneration Neurodegenerative Disorders Open Reading Frames Pathway Analysis Pathway interactions Positioning Attribute Process Productivity Protein Binding Protein Isoforms Proteins Proteomics Publications Publishing RNA RNA Interference RNA Processing RNA Splicing RNA analysis RNA-Binding Proteins Reagent Regulation Regulator Genes Research Resources Ribonucleases Series Signal Pathway Signaling Molecule Structure System Technology Translations base cell type cis acting element computerized tools effective therapy gain of function genome-wide human disease innovation insight leukemia mammalian genome novel overexpression predictive modeling protein TDP-43 protein complex protein protein interaction response screening small hairpin RNA tool transcriptome sequencing transcriptomics treatment strategy two-dimensional

项目摘要

DESCRIPTION (provided by applicant): This proposal seeks renewal of a multi-PI project (Fu and Yeo) to use global approaches to elucidate regulatory principles in the regulation of alternative splicing in mammalian genomes. Built upon our accomplishments in the past funding cycle, including extensive preliminary results, we propose to conduct several systematic loss- and gain-of-function studies to identify genes, gene networks, and pathways involved in the regulation of alternative splicing in three specific aims. The first aim is to perform large-scale network analysis of regulated alternative splicing. Using the two-dimensional mRNA isoform profiling platform developed in our labs, we propose to conduct both genome-wide RNAi and overexpression screening in HEK293 cells and score a set of commonly regulated splicing events (~400) in each treatment condition. We will also complement these genome-wide perturbation studies with transcriptomic analyses by comprehensive RNA-seq against shRNA-mediated depletion (already completed) and ectopic expression of ~300 carefully selected RNA binding proteins (RBPs). These data will help identify new splicing factors, integrate RBPs into transcription, epigenetic and signaling pathways, and decipher both unique and dominant functions of individual RBPs. In the second aim, we propose to analyze RBP-centric protein-protein interaction networks. In particular, we propose to take full advantage of our validated library of open reading frames encoding RBPs for quantitative proteomic analysis of 300 RBPs with and without RNase treatment to identify both RNA-dependent and independent interactions within the framework of RBP complexes. Using the large datasets of functional RNA targets (Aim 1) and RBP-centric protein-protein interactions (Aim 2), we will in Aim 3 perform integrated analysis of RNA genomics data to build predictive models of the regulation of alternative splicing by RBPs. We will use or develop a set of computational tools to predict novel RBP targets, refine individual RBP-central gene networks, and most importantly, integrate comprehensive RBP cis and trans interactomes with system-wide perturbation to build predictive models for cell-specific regulation of alternative splicing. We believe that such integrated analysis will have major impacts on our understanding of regulated splicing and associated disease mechanisms.

描述（由申请人提供）：该提案寻求更新一个多PI项目（FU和YEO），以使用全球方法来阐明哺乳动物基因组中替代剪接的调节原理。我们基于在过去的融资周期中的成就，包括广泛的初步结果，我们建议进行几项系统的损失和功能收益研究，以识别在三个特定目标中调节替代剪接的基因，基因网络以及涉及的途径。第一个目的是对受调节的替代剪接进行大规模网络分析。我们使用实验室中开发的二维mRNA同工型分析平台，我们建议在HEK293细胞中同时进行全基因组RNAi和过表达筛选，并在每种治疗条件下对一组普通调节的剪接事件（〜400）进行评分。我们还将通过针对SHRNA介导的耗竭（已经完成）的全面RNA-Seq进行转录组分析来补充这些全基因组扰动研究（已经完成）和〜300个精心选择的RNA结合蛋白（RBP）的异位表达。这些数据将有助于确定新的剪接因子，将RBP整合到转录，表观遗传和信号通路中，并破译单个RBP的独特和主导功能。在第二个目标中，我们建议分析以RBP为中心的蛋白质 - 蛋白质相互作用网络。特别是，我们建议在编码RBP的开放阅读框架的经过验证的库中充分利用，以进行定量的300 RBP的蛋白质组学分析，进行有没有RNase处理的情况下，以识别RNE依赖性和独立的相互作用在RBP复合物的框架内。使用功能性RNA靶标的大数据集（AIM 1）和以RBP为中心的蛋白质 - 蛋白质相互作用（AIM 2），我们将在AIM 3中对RNA基因组学数据进行综合分析，以构建RBPS调节替代剪接的预测模型。我们将使用或开发一组计算工具来预测新颖的RBP目标，完善单个RBP中心基因网络，最重要的是，将综合的RBP顺式和反式相互作用与系统范围的扰动整合在一起，以构建用于替代拼接细胞特异性调节的细胞特异性调节的预测模型。我们认为，这种综合分析将对我们对受调节的剪接和相关疾病机制的理解产生重大影响。