Posttranscriptional regulation by mRNA-binding shuttling and transport proteins

mRNA 结合穿梭和转运蛋白的转录后调节

• 批准号: 8412350
• 负责人: Uwe Ohler
• 金额: $ 91.06万
• 依托单位: ROCKEFELLER UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-09-30 至 2017-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8412350
• 关键词: Address; Amyotrophic Lateral Sclerosis; Attention; Automobile Driving; Binding; Binding Proteins; Binding Sites; Biochemical; Biochemistry; Biology; Carrier Proteins; Cell Nucleus; Cells; Chromatin; Complement; Computational Biology; Computer Analysis; Cytoplasm; Data; Dendrites; Development; Disease; Elements; Experimental Models; Exportins; FMRP; Fragile X Syndrome; Functional RNA; Future; Gene Expression; Gene Expression Regulation; Genes; Genetic Translation; Genetic Variation; Genome; Goals; Human; Human Genetics; Human Genome; Immunoprecipitation; Joints; Karyopherins; Knowledge; Libraries; Ligands; Maps; Mental Retardation; Messenger RNA; Methods; Mining; Modeling; Mutation; Nuclear Export; Nuclear RNA; Nucleic Acid Regulatory Sequences; Outcome; Play; Polyadenylation; Preparation; Proteins; RNA; RNA Processing; RNA Sequences; RNA Splicing; RNA Transport; RNA-Binding Proteins; RNA-Protein Interaction; Recombinant Proteins; Regulation; Regulatory Element; Ribonucleic Acid Regulatory Sequences; Ribonucleoproteins; Ribonucleosides; Role; Running; Site; Staging; Structure; System; Technology; Theoretical model; Transcript; Translational Regulation; Translations; Transport Process; Variant; Work; autism spectrum disorder; combinatorial; crosslink; design; genome-wide; high reward; high risk; insight; mRNA Expression; member; messenger ribonucleoprotein; multidisciplinary; nucleocytoplasmic transport; particle; structural biology

DESCRIPTION (provided by applicant): All mRNA molecules are subject to posttranscriptional gene regulation (PTGR) involving sequence-dependent modulation of splicing, cleavage and polyadenylation, editing, transport, stability, and translation. In recent years, a paradigm shift has occurred in our understanding of PTGR, triggered by discoveries of regulatory RNAs and extensive RNA processing including alternative polyadenylation and splicing. These developments have led to the realization that virtually every human gene is subject to some degree of PTGR. Understanding the mechanisms of target RNA recognition, and the function of the hundreds of mRNA-binding proteins encod- ed in the human genome, is therefore an open challenge that requires the joint effort of multidisciplinary teams. The recent introduction of deep sequencing technologies has enabled the development of new methods for precisely mapping interaction sites between RNA-binding proteins (RBPs) and their RNA target sites in human cells. It is only now possible to resolve interdependencies and redundancies of binding of RBPs and ribonucleoprotein particles (RNPs) to mRNA molecules and evaluate their contribution to gene regulation in the context of organismal development or normal and disease states. The broad aim of this application is to identify and characterize the interaction networ of mRNA-binding proteins at the sequence, structural and functional level, with a particular focus on transport and shuttling - crucial PTGR mechanisms that have received little attention. A driving concept is whether larger "chromatin"- like packaging of RNPs facilitates transport and translational regulation. The specific aims include: (1) Global identification of target RNA site for a comprehensive panel of nucleocytoplasmic transport and shuttling proteins by Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR- CLIP) involving deep sequencing of libraries for all proteins and computational analysis. (2) Integrated annotation of binding sites on transcripts across libraries, using a probabilistic graphical modeling approach to identify prevalent site configurations from heterogenenous data. PAR-CLIP data, complemented by expression as well as sequence and RNA structural features, will allow for the identification of targets for combinatorial and redundant regulation. (3) Development of experimental systems for assessment of the phenotypic outcomes of the perturbation of the transporter interaction network and elucidation of its role in normal and disease states. (4) Perform biophysical and structural studies substantiating the biochemical and computational findings. Natural, as well as designed RNA-recognition element (RRE)-representing RNA ligands, will by co-crystallized with their respective recombinant proteins placing emphasis on obtaining larger RNP structures. The proposed work will thus establish the first theoretical and experimental models that relate global maps of protein-RNA interactions to RNA transport, setting the stage for future systems-wide studies of PTGR. PUBLIC HEALTH RELEVANCE: The control of gene expression at the mRNA level plays a larger role than previously anticipated. This proposal aims to resolve the joint contribution of dozens of mRNA-binding proteins shuttling between nucleus and cytoplasm, as well of proteins participating in nucleocytoplasmic transport. This approach will identify numerous important regulatory regions in mRNAs, as well as uncover mRNAs and RNA-binding proteins particularly vulnerable to mutation and deregulation in disease states.

描述（由申请人提供）：所有mRNA分子都受转录后基因调控（PTGR）的影响，包括剪接、切割和聚腺苷化、编辑、运输、稳定性和翻译的序列依赖性调节。近年来，一种范式发生了转变