Functional RNA elements in the human genome

人类基因组中的功能性RNA元件

• 批准号: 8471148
• 负责人: XIANG-DONG FU
• 金额: $ 64.94万
• 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 2014-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8471148
• 关键词: Address; Affect; Alternative Splicing; Award; Beryllium; Binding; Biochemical; Biological Process; Biology; Cell Line; Cell physiology; Cells; Cistrons; Code; Complex; Computational Biology; DNA-Binding Proteins; Development; Dissection; Epigenetic Process; Eukaryota; Event; Excision; Exons; Functional RNA; Gene Expression; Gene Expression Regulation; Genes; Genetic; Genome; Genomics; Goals; Grant; Hereditary Disease; Heterogeneous-Nuclear Ribonucleoproteins; Human; Human Cell Line; Human Genetics; Human Genome; Immunoprecipitation; Indium; Individual; Introns; Knowledge; Leadership; Machine Learning; Malignant Neoplasms; Maps; Measurement; Mediating; MicroRNAs; Modeling; Molecular; National Human Genome Research Institute; Output; Pathway interactions; Play; Process; Protein Isoforms; Proteins; Proteome; Publications; Publishing; RNA; RNA Interference; RNA Splicing; RNA-Binding Proteins; RNA-Protein Interaction; Regulation; Regulatory Pathway; Relative (related person); Reporter; Research; Role; Sampling; Series; Signal Transduction; Site; System; Technology; Tissues; Vertebrates; base; cell type; cost effective; crosslink; empowered; functional group; functional outcomes; genome wide association study; genome-wide; homologous recombination; human disease; innovation; interest; mRNA Precursor; mammalian genome; new technology; novel; predictive modeling; programs; response

DESCRIPTION (provided by applicant): Pre-mRNA splicing is essential for proper gene expression in higher eukaryotic genomes, as the vast majority of genes contain introns that have to be accurately recognized and removed. Recent studies have revealed that >90% of the genes undergo alternative splicing, which is believed to contribute to the complexity of the proteome in different cell types and tissues in vertebrates and abundant evidence suggests that altered splicing causes a variety of human diseases. Despite extensive knowledge on the splicing mechanism based on biochemical dissection of model minigenes, we know little about how many genes are involved in the regulation of alternative splicing and where the functional RNA elements are embedded in the human genome. Built on our productive research in the current award period, we now propose a bold plan to systematically attack the critical gap of our knowledge about the regulation of alternative splicing. We will pursue three major lines of research by utilizing the latest and innovative genomics technologies. (1) We will use a new, automated platform recently developed in our lab to profile hundreds of conserved alternative splicing events against every annotated genes in the human genome. This unbiased approach will generate unprecedented information to uncover novel splicing regulators and deduce pathways in regulated splicing. (2) We will focus on RNA binding proteins involved in individual regulatory pathways to elucidate the molecular basis for regulated splicing by mapping their physical interactions with expressed RNA. For this purpose, we will construct a large panel of cell lines based on FLP-In 293 cells to express individual RNA binding proteins as a V5-tagged protein at the C- terminus, which will permit large-scale mapping of RNA-protein interactions by CLIP-seq (CrossLinking ImmunoPrecipitation followed by high throughput sequencing) under a similar and optimized set of conditions. (3) Our third goal is to use the information generated from the proposed mapping and functional studies to develop an integrated framework for de novo prediction of splicing regulation by using machine-learning and graphical models. This research has the potential to fundamentally change our view on splicing control and its contribution to human disease.

描述（由申请人提供）：前MRNA剪接对于在较高的真核基因组中适当的基因表达至关重要，因为绝大多数基因包含必须准确识别和去除的内含子。最近的研究表明，> 90％的基因经历了替代剪接，这被认为有助于脊椎动物中不同细胞类型和组织中蛋白质组的复杂性，并且大量证据表明，改变剪接会导致各种人类疾病。尽管基于模型微型元素的生化解剖学的剪接机理的广泛了解，但我们对调节替代剪接的调节以及功能性RNA元素的调节以及人类基因组中的功能性RNA元件的位置知之甚少。基于当前奖励期间的生产研究，我们现在提出了一个大胆的计划，以系统地攻击我们有关调节替代剪接的知识的关键差距。我们将利用最新和创新的基因组技术来进行三项主要研究。 （1）我们将使用最近在实验室开发的新的自动化平台，以针对人类基因组中每个带注释的基因的数百个保守的替代剪接事件。这种公正的方法将产生前所未有的信息，以发现新颖的剪接调节器并推断受调节剪接的途径。 （2）我们将专注于参与单个调节途径的RNA结合蛋白，以通过映射其与表达的RNA的物理相互作用来阐明调节剪接的分子基础。为此，我们将基于FLP-IN 293细胞构建大型细胞系，以在C末端表达单个RNA结合蛋白作为V5标记的蛋白，这将允许通过夹克SEQ（clip-seq）进行大规模的RNA蛋白相互作用（在较高的遍及序列上进行交联的免疫接收和优化序列）。 （3）我们的第三个目标是使用从提出的映射和功能研究中生成的信息来开发通过使用机器学习和图形模型从头开始对剪接调控的集成框架。这项研究有可能从根本上改变我们对剪接控制及其对人类疾病的贡献的看法。