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: 9278244
• 负责人: Marco Mangone
• 金额: $ 30.7万
• 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/9278244
• 关键词: 3' Untranslated Regions; Anecdotes; Biochemistry; Bioinformatics; Biological; Biological Models; Biology; Caenorhabditis elegans; Cell Line; Cell Maintenance; Cells; Code; Complex; Data; Data Set; Development; Disease; Dissection; Elements; Event; Gene Expression; Gene Expression Regulation; Generations; Genes; Genetic; Genetic Transcription; Genomics; Gold; Heterogeneity; Human; Knowledge; Lead; 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; Terminator Codon; Testing; Time; Tissues; Trans-Activators; Transcript; Transgenic Organisms; Translating; Untranslated Regions; 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，这些区域位于终止密码子和polyA尾之间的mRNA末端。它们在基因表达转录后调控中的重要性正在显现，因为它们含有大量、很大程度上未表征的调控元件，这使得它们成为 miRNA 和 RNA 结合蛋白的核心靶标。 最近，我们的团队和其他人已经表明，替代多腺苷酸化（APA）是一种用不同的 3'UTR 同工型产生相同 mRNA 的过程，在后生动物中广泛存在。 我们不知道为什么如此多的基因以多个 3' 末端转录，也不知道加工机器如何区分同一 mRNA 内的不同切割信号，从而产生替代的 3'UTR 亚型。所有后生动物转录本中 APA 的广泛存在使我们推测存在更复杂的情况，其中不仅存在通过 miRNA 的负调控网络，而且还存在通过 APA 运行的新颖的未探索的正调控网络。在这种观点中，在发育过程中在不同细胞或组织环境中转换 3'UTR 同工型的基因是这些正网络的主要驱动力，允许或逃避 miRNA 靶向。从这个角度来看，miRNA 和 APA 原则上都可以极大地重塑基因表达输出，这表明它们在细胞和组织身份的建立和维持中都发挥着关键作用。这个想法尚未在生物体中得到测试和验证。线虫强大的遗传学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，以便为九种主要体细胞组织中的所有基因生成高质量的组织特异性 3'UTR 定位动力学，以便使用系统生物学方法了解 APA 的基本原理、其发育动力学以及其在体内的产生和调节。我们还将通过关注负 miRNA 调控并开发 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，然后将结果叠加到我们的组织特异性 APA 数据上，以在活体生物体中产生第一个 miRNA-APA 相互作用组。我们还将对初步结果强调的 APA 产生及其在 12 个基因中的功能进行机制研究。总而言之，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。