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，3 'UTR位于mRNA末端的终止密码子和polyA尾之间。它们在基因表达的转录后调控中的重要性正在显现，因为它们含有许多基本上未表征的调控元件，这些调控元件使它们成为miRNA和RNA结合蛋白的核心靶标。 最近，我们的研究小组和其他人已经表明，选择性多聚腺苷酸化（阿帕），一个过程中，相同的mRNA产生不同的3 'UTR亚型，是广泛存在于后生动物。 我们不知道为什么这么多基因转录有多个3 '端，以及加工机制如何区分相同mRNA内的不同切割信号，从而导致替代的3' UTR亚型。阿帕在所有后生动物的转录本中的广泛丰度使我们假设存在更复杂的图片，其中不仅存在通过miRNA的负调控网络，而且存在通过阿帕操作的新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同种型的基因是这些阳性网络的主要驱动因素，要么允许要么逃避miRNA靶向。从这个角度来看，miRNAs和阿帕原则上都可以极大地重塑基因表达输出，这表明它们都在细胞和组织身份的建立和维持中发挥关键作用。这一想法还有待于在活的生物体中进行测试和验证。C的强大遗传学。elegans和无与伦比的可用资源使该模型系统成为理解mRNA 3 '末端形成和转录后调节的基本原理的理想模型。我们希望生产湿工作台和生物信息学工具，以允许产生高质量的组织特异性3 'UTR定位动力学的所有基因在9个主要的体细胞组织，以了解阿帕的基本原理，其动态发展，以及其生产和调节在体内使用系统生物学方法。我们还将研究阿帕的功能，重点是负的miRNA调控，并在三个主要的蠕虫组织中开发miRNA表达和靶向数据，然后将结果与我们的组织特异性阿帕数据相结合，以产生第一个活生物体中的miRNA-APA相互作用组。我们还将对阿帕的产生及其在我们初步结果强调的12个基因中的功能进行机制研究。总之，这些目标结合联合收割机高通量基因组学，生物信息学，遗传学，生物化学和系统生物学的创新方法来研究阿帕及其在转录后基因调控中的作用。