Functional RNA elements in the human genome

人类基因组中的功能性RNA元件

• 批准号: 9381421
• 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
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-06-01 至 2020-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9381421
• 关键词: Address; Alternative Splicing; Area; Binding; Binding Proteins; Binding Sites; Bioinformatics; Biology; Chromatin; Clustered Regularly Interspaced Short Palindromic Repeats; Coupling; DNA; DNA Polymerase II; DNA-Directed RNA Polymerase; Data Set; Development; Disease; Dissection; Elements; Epigenetic Process; Event; Funding; Gene Expression; Genes; Genetic Transcription; Genomic approach; Genomics; Goals; Grant; Human Genome; Individual; Lead; Mammalian Cell; Mass Spectrum Analysis; Messenger RNA; Metabolism; Methodology; Methods; Molecular; National Human Genome Research Institute; Nuclear Export; Nuclear Pore; Pathology; Pathway Analysis; Pathway interactions; Pattern; Phase; Polyadenylation; Positioning Attribute; Productivity; Protein Analysis; Proteins; Publications; RANGAP1 gene; RNA; RNA Binding; RNA Processing; RNA Recognition Motif; RNA Splicing; RNA analysis; RNA-Binding Proteins; RNA-Protein Interaction; Reaction; Recruitment Activity; Regulation; Regulatory Pathway; Reproducibility; Research; Role; Sequence Homology; Series; Testing; Transcriptional Regulation; Untranslated RNA; Zinc Fingers; computerized tools; effective therapy; genome-wide; genomic RNA; genomic tools; human disease; infancy; innovation; insight; mRNA Precursor; mammalian genome; novel; novel strategies; nucleocytoplasmic transport; protein profiling; protein protein interaction; screening; technological innovation; transcription factor; transcriptome; treatment strategy

Project Summary This proposal seeks competitive renewal of a multi-PI project (Fu and Yeo), which aims to use global approaches to elucidate the regulatory principles of RNA binding proteins (RBPs) in mammalian genomes. Built upon our accomplishments in the past funding cycle, we propose to leverage the powerful experimental and computational tools we have developed to pursue four specific aims. In Aim 1, we will couple gain- and lost-of-function multi-target screens to deduce regulatory pathways at both splicing and polyadenylation levels. We will focus on determining the specific function of different RNA polymerase II (Pol II) subunits, rather than by the Pol II CTD alone, in the recruitment of RNA processing machineries for co-transcriptional RNA processing. In Aim 2, we will develop a general strategy for systematic identification of chromatin-associated RBPs to determine direct contribution of some RBPs to transcription and co-transcriptional RNA processing reactions. We will concentrate our efforts in dissecting a potential new pathway in epigenetic control of alternative splicing as well as broader roles of specific RBPs in direct transcriptional control. In Aim 3, we will use a novel strategy for identification and characterization of non-canonical RBPs. Focusing on a large number of newly identified finger zinc (Znf) proteins, we propose to determine their roles in binding to both DNA and RNA and deduce their transcriptome-wide interactions with RNA. We also propose to pursue a specific paradigm in this aim on a newly identified RBP known to associate with the nuclear pore to determine its role in selective mRNA nuclear export, which is pertinent to an ALS-regulated disease pathology. Combined, we believe that this comprehensive, interconnected, and hypothesis-driven research plan will greatly advance our understanding of regulated RNA processing and associated disease mechanisms.

项目摘要 该提案寻求多PI项目（Fu和Yeo）的竞争性更新，该项目旨在使用全球 阐明哺乳动物基因组中RNA结合蛋白（RBP）调控原理的方法。 基于我们在过去的资助周期中取得的成就，我们建议利用强大的实验性 和计算工具，我们已经开发了追求四个具体目标。在目标1中，我们将增益和 功能丧失的多靶筛选以推断剪接和多聚腺苷酸化水平的调节途径。 我们将集中在确定不同的RNA聚合酶II（Pol II）亚基的具体功能，而不是 通过单独的Pol II CTD，在共转录RNA的RNA加工机器的募集中， 处理.在目标2中，我们将开发一种系统鉴定染色质相关的 RBP以确定一些RBP对转录和共转录RNA加工的直接贡献 反应.我们将集中我们的努力解剖一个潜在的新途径，在表观遗传控制， 选择性剪接以及特定RBP在直接转录控制中的更广泛作用。在目标3中，我们 使用一种新的策略来识别和表征非规范RBP。专注于大型 一些新发现的指状锌（Znf）蛋白，我们建议确定它们的作用，结合两者 DNA和RNA，并推导出它们与RNA的转录组范围内的相互作用。我们亦建议推行一项 在这个目标的特定范例上，新鉴定的已知与核孔相关的RBP确定 它在选择性mRNA核输出中的作用，这与ALS调节的疾病病理学有关。 结合起来，我们相信，这一全面的，相互关联的，假设驱动的研究计划将 极大地推进了我们对RNA加工调控和相关疾病机制的理解。