Genetics and Genomics of Alternative Polyadenylation and miRNA Regulation in C. e - Renewal - 1

C. e 中替代多聚腺苷酸化和 miRNA 调控的遗传学和基因组学 - Renewal - 1

• 批准号: 10454976
• 负责人: Marco Mangone
• 金额: $ 31.61万
• 依托单位: ARIZONA STATE UNIVERSITY-TEMPE CAMPUS
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-06-01 至 2025-05-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10454976
• 关键词: 3' Untranslated Regions; Alzheimer' s Disease; Biochemistry; Bioinformatics; Biological; Biological Models; Biology; Caenorhabditis elegans; Cell Lineage; Cells; Cloning; Communities; Complex; Coupled; Data; Data Set; Databases; Development; Disease; Elements; Event; Gene Expression; Gene Expression Regulation; Gene Rearrangement; Genes; Genetic; Genetic Transcription; Genetic Translation; Genome; Genomics; Goals; Grant; Human; Immunoprecipitation; Intestines; Knowledge; Length; Light; Malignant Neoplasms; Manuals; Maps; Mechanics; Messenger RNA; Methods; MicroRNAs; Modification; Molecular; Muscle; Muscular Dystrophies; N-Methylaspartate; Nematoda; Neurons; Nuclear; Organism; Pattern; Pharyngeal structure; Physiological; Polyadenylation; Population; Post-Transcriptional Regulation; Process; Production; Protein Isoforms; Proteome; RNA Binding; RNA-Binding Proteins; Reaction; Regulation; Regulator Genes; Regulatory Element; Repression; Research; Research Project Grants; Resolution; Resources; Role; Signal Transduction; Site; Sorting - Cell Movement; Subcutaneous Tissue; Tail; Terminator Codon; Testing; Tissues; Update; Validation; base; cis acting element; dosage; experimental study; genetic manipulation; genetic signature; human disease; improved; in vivo; insight; member; novel; tool; transcription regulatory network; transcriptome; virtual

Abstract 3’ Untranslated Regions (3’UTR) are mRNA ends located between the STOP codon and the polyA tail. They contain numerous regulatory elements that are poorly characterized, making them a core target for post- transcriptional regulation of gene expression by miRNAs and RNA binding proteins. MiRNAs are small regulatory RNAs that bind 3’UTRs and repress mRNA translation. Our group and others have shown that alternative polyadenylation (APA), an elusive process observed in metazoans that gives rise to genes with various 3’UTR isoforms, is widespread. While APA is frequently present in normal states and in virtually all diseases, its biological role in cells and tissues is a mystery. Genes with longer 3’UTRs have more potential regulatory sites, thus APA may allow genes to alter their 3’UTR length and escape the repression by miRNAs and RNA binding proteins. Since APA is abundant this could explain why there is not a direct correlation between cellular transcriptomes and proteomes. Understanding the global mechanics of 3’end formation, APA function, and miRNA targeting would advance research on post-transcriptional modifications. Metazoans possess hundreds of miRNAs and thousands of 3’UTR isoforms, most of which are expressed and function in different tissues and developmental contexts. We know little about how these networks operate and communicate with each other, despite their critical role in controlling gene expression. We need to gain new data and insights, and develop a high-resolution miRNAs/3’UTRs Interactome by acquiring and fusing tissue- specific miRNA localization data, miRNA target data, and 3’UTRs isoform data. Our Interactome will provide the global basis of post-transcriptional gene regulation function in vivo, elucidating its role in both normal and disease states in metazoans. In our first R01 grant we studied tissue-specific APA events and miRNA networks in the nematode C. elegans, to define and probe the worm miRNAs/3’UTRs Interactome. We identified 3’UTR isoforms in eight C. elegans somatic tissues, acquired miRNA expression data for the three largest and disease-relevant C. elegans worm tissues, developed and implemented unbiased methods to map miRNA targets in high throughput, and initiated mechanistic studies of APA selection in genes identified in our studies. For this new submission we will, (1) complete the worm 3’UTRome by including new tissue-specific 3’UTR isoforms, (2) identify tissue-specific miRNA populations in eight worm somatic tissues and, (3) perform mechanistic studies to determine tissue-specific PAS choice in the context of APA. Our curated 3’UTRome will be the first database to provide a complete metazoan 3’UTRome mapped at a single base resolution. Investigating three global hypotheses of PAS choice can uncover global post-transcriptional gene regulatory mechanisms implicated in tissue development and disease, and therefore of high impact. We believe that the impact of these new studies is high since will provide important results toward a global understanding the biology of post-transcriptional gene regulation in metazoans. 1

摘要 3‘非翻译区(3’UTR)是位于终止密码子和Polya尾部之间的mRNA末端。他们 包含许多特征不佳的监管要素，使其成为后 MiRNAs和RNA结合蛋白对基因表达的转录调控。MiRNAs很小 结合3‘端非编码区并抑制信使核糖核酸翻译的调控RNA。我们的团队和其他人已经证明 交替多聚腺苷化(APA)，在后生动物中观察到的一种难以捉摸的过程，导致基因与 各种3‘非编码区亚型广泛存在。虽然APA经常存在于正常状态和几乎所有 对于疾病，它在细胞和组织中的生物学作用是一个谜。3‘端UTR值较长的基因更具潜力 因此，APA可能允许基因改变其3‘UTR长度，从而逃避miRNAs的抑制 和RNA结合蛋白。由于APA丰富，这可以解释为什么没有直接的相关性 在细胞转录组和蛋白质组之间。了解3‘端形成的全球机制 功能，而miRNA靶向将促进转录后修饰的研究。后生动物 拥有数以百计的miRNA和数以千计的3‘非编码区异构体，其中大多数在 不同的组织和发育环境。我们对这些网络是如何运作的知之甚少 相互交流，尽管它们在控制基因表达方面发挥了关键作用。我们需要获得新的 数据和见解，并开发高分辨率miRNAs/3‘UTRS交互作用组，通过获取和融合组织- 特定的miRNA定位数据、miRNA靶标数据和3‘UTRS异构体数据。我们的互动组将提供 体内转录后基因调控功能的整体基础，阐明其在正常和 后生动物的疾病状态。在我们的第一个R01拨款中，我们研究了特定于组织的APA事件和miRNA网络 在线虫线虫中，定义和探测蠕虫miRNAs/3‘UTRs相互作用组。我们确定了3‘非编码区 在8个线虫体细胞组织中的异构体，获得了三个最大的和 与疾病相关的线虫组织，开发并实施了无偏方法来定位miRNA 高通量的目标，并启动了我们研究中确定的基因中APA选择的机制研究。 对于这个新的提交，我们将：(1)通过包括新的组织特异性3‘UTR来完成蠕虫3’UT罗马 异构体，(2)鉴定八种蠕虫体细胞组织中的组织特异性miRNA群体，以及(3)执行 在APA的背景下确定组织特异性PAS选择的机制研究。我们策划的3‘UT罗马将会 是第一个以单一基本分辨率提供完整的后生动物3‘UT罗马地图的数据库。 研究PAS选择的三个全球假说可以揭示全球转录后基因调控 与组织发育和疾病有关的机制，因此影响很大。我们相信， 这些新研究的影响很大，因为这将为全球理解 后生动物转录后基因调控的生物学。 1