Genetics and Genomics of Alternative Polyadenylation and miRNA Regulation in C. elegans

线虫中选择性多聚腺苷酸化和 miRNA 调控的遗传学和基因组学

• 批准号: 9081441
• 负责人: Marco Mangone
• 金额: $ 30.83万
• 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 2021-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9081441
• 关键词: 3' Untranslated Regions; Anecdotes; Biochemistry; Bioinformatics; Biological; Biological Models; Biology; Caenorhabditis elegans; Cell Line; Cell Maintenance; Cells; Code; Codon Nucleotides; Complex; Data; Data Set; Development; Disease; Dissection; Elements; Event; Gene Expression; Gene Expression Regulation; Generations; Genes; Genetic; Genomics; Gold; Heterogeneity; Human; Knowledge; Lead; Life; Link; Maps; Messenger RNA; MicroRNAs; Muscle; Nematoda; Organism; Output; Play; Polyadenylation; Post-Transcriptional Regulation; Process; Production; Protein Isoforms; Proteins; RNA-Binding Proteins; Regulation; Regulator Genes; Regulatory Element; Research; Resources; Role; Signal Transduction; Switch Genes; System; Systems Biology; Tail; Testing; Thinking; Tissues; Trans-Activators; Transcript; Transgenic Organisms; Translating; Validation; Variant; base; cDNA Library; cancer cell; combinatorial; high throughput technology; human disease; in vivo; innovation; insight; miRNA expression profiling; novel; prospective; public health relevance; tool; vector

 DESCRIPTION (provided by applicant): Our research focuses on the production, activity and function of 3' Untranslated Regions (3'UTRs), which are located at the end of mRNAs between the STOP codon and the polyA tail. Their importance in post- transcriptional regulation of gene expression is emerging as they contain numerous, largely uncharacterized regulatory elements that make them a core target for miRNAs and RNA binding proteins. Recently our group and others have shown that alternative polyadenylation (APA), a process where the same mRNA is produced with different 3'UTR isoforms, is widespread in metazoans. We do not know why so many genes are transcribed with multiple 3'ends, and how the processing machinery discriminates between different cleavage signals within the same mRNA leading to alternative 3'UTR isoforms. The widespread abundance of APA in transcripts of all metazoans led us to hypothesize the presence of a more complex picture, where there are not only negative regulatory networks though miRNAs, but also novel unexplored positive regulatory networks operated though APA. In this view genes that switch 3'UTR isoforms in different cellular or tissue contexts during development are the main drivers of these positive networks, either allowing or escaping miRNA targeting. In this view, both miRNAs and APA can in principle dramatically reshape gene expression output, suggesting they both play key roles in the establishment and maintenance of cell and tissue identity. This idea has yet to be tested and validated in a living organism. The powerful genetics of C. elegans and the unparalleled resources available make this model system ideal for understanding the basic principles of mRNA 3'end formation and post-transcriptional regulation. We want to produce wet-bench and bioinformatic tools to allow the generation of high-quality tissue-specific 3'UTR localization dynamics for all genes in nine major somatic tissues, in order to understand the basic principles of APA, its dynamics in development, as well as its production and regulation in vivo using a systems biology approach. We will also study the function of APA by focusing on negative miRNA regulation and developing miRNA expression and targeting data in three major worm tissues, and then superimpose the results to our tissue specific APA data to produce the first miRNA-APA Interactome in a living organism. We will also perform mechanistic studies of APA production and their function in 12 genes highlighted by our preliminary results. Taken together, these aims combine high-throughput genomics, bioinformatics, genetics, biochemistry and systems biology in innovative ways to study APA and its role in post-transcriptional gene regulation.

 描述（由申请人提供）：我们的研究重点是 3' 非翻译区 (3'UTR) 的产生、活性和功能，这些区域位于 mRNA 末端的终止密码子和 PolyA 尾部之间，它们在后转录中的重要性。基因表达的转录调控正在兴起，因为它们含有大量未表征的调控元件，这使它们成为 miRNA 和 RNA 结合蛋白的核心靶标。用不同的 3'UTR 亚型产生相同 mRNA 的过程在后生动物中很普遍，我们不知道为什么这么多基因用多个 3' 末端转录，以及处理机制如何区分同一 mRNA 内的不同切割信号。导致替代的 3'UTR 同工型 APA 在所有后生动物的转录物中广泛存在，使我们能够解决更复杂的问题，其中不仅存在通过 miRNA 的负调控网络，而且还存在负调控网络。在此观点中，在发育过程中在不同的细胞或组织环境中切换3'UTR同种型的基因是这些正向网络的主要驱动力，允许或逃避miRNA的靶向。原则上，APA 可以显着重塑基因表达输出，这表明它们在细胞和身份的建立和维持中都发挥着关键作用，这一想法尚未在活生物体中得到测试和验证。线虫和无与伦比的可用资源使该模型系统成为了解 mRNA 3' 末端形成和转录后调控基本原理的理想选择。我们希望生产湿台和生物信息学工具，以生成高质量的组织。我们还将研究九个主要体细胞组织中所有基因的特定 3'UTR 定位动力学，以便了解 APA 的基本原理、其发育动力学以及使用系统生物学方法在体内的产生和调节。我们还将通过关注负 miRNA 调节并开发 miRNA 表达和三个主要蠕虫组织中的靶向数据来研究 APA 的功能，然后将结果与我们的组织特异性 APA 数据叠加到活体生物体中的第一个 miRNA-APA 相互作用组中。我们的初步结果强调了 APA 产生及其在 12 个基因中的功能的机制研究，这些目标以创新的方式将高通量基因组学、生物信息学、遗传学、生物化学和系统生物学结合起来。研究 APA 及其在转录后基因调控中的作用。