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

基本信息

批准号：
10297094
负责人：
Marco Mangone
金额：
$ 31.78万
依托单位：
ARIZONA STATE UNIVERSITY-TEMPE CAMPUS
依托单位国家：
美国
项目类别：
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/10297094
关键词：
3&apos Untranslated Regions Alzheimer&apos 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 transcriptome virtual

项目摘要

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

抽象的 3’非翻译区 (3’UTR) 是位于终止密码子和 PolyA 尾之间的 mRNA 末端。包含许多特征不明的监管要素，使其成为后 miRNA 和 RNA 结合蛋白对基因表达的转录调控很小。我们的团队和其他人已经证明，结合 3’UTR 并抑制 mRNA 翻译的调节 RNA。选择性多聚腺苷酸化 (APA)，这是在后生动物中观察到的一种难以捉摸的过程，可产生具有各种 3'UTR 同工型广泛存在，而 APA 经常存在于正常状态和几乎所有状态。疾病，其在细胞和组织中的生物学作用是一个谜，具有较长 3'UTR 的基因具有更大的潜力。调节位点，因此 APA 可能允许基因改变其 3'UTR 长度并逃避 miRNA 的抑制由于 APA 含量丰富，这可以解释为什么没有直接相关性。了解细胞转录组和蛋白质组之间的 3' 端形成的整体机制，APA。功能和 miRNA 靶向将推进转录后修饰的研究。拥有数百个 miRNA 和数千个 3'UTR 同工型，其中大部分在我们对这些网络的运作方式和发育背景知之甚少。尽管它们在控制基因表达方面发挥着关键作用，但我们仍然需要彼此沟通。数据和见解，并通过获取和融合组织来开发高分辨率 miRNA/3’UTR Interactome 我们的 Interactome 将提供特定的 miRNA 定位数据、miRNA 目标数据和 3'UTR 亚型数据。体内转录后基因调控功能的整体基础，阐明其在正常和在我们的第一个 R01 资助中，我们研究了组织特异性 APA 事件和 miRNA 网络。在线虫 C. elegans 中，为了定义和探测线虫 miRNA/3'UTR 互作组，我们鉴定了 3'UTR。八种线虫体细胞组织中的亚型，获得了三个最大和最重要的体细胞组织的 miRNA 表达数据。与疾病相关的秀丽隐杆线虫组织，开发并实施了公正的方法来定位 miRNA 高通量目标，并启动了我们研究中确定的基因中 APA 选择的机制研究。对于这个新提交的内容，我们将：(1) 通过包含新的组织特异性 3'UTR 来完成蠕虫 3'UTRome 同工型，(2) 鉴定八种线虫体细胞组织中的组织特异性 miRNA 群体，(3) 执行我们策划的 3'UTRome 将进行机制研究，以确定 APA 背景下的组织特异性 PAS 选择。成为第一个提供以单碱基分辨率映射的完整后生动物 3’UTRome 的数据库。研究 PAS 选择的三个全局假设可以揭示全局转录后基因调控与组织发育和疾病有关的机制，因此具有很高的影响。这些新研究的影响很大，因为将为全球了解这一问题提供重要结果后生动物转录后基因调控的生物学。 1