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（由适用提供）：我们的研究重点是3'未翻译区域（3'UTRS）的生产，活动和功能，这些区域位于终止密码子和Polya尾巴之间的mRNA末端。它们在基因表达的转录后调节中的重要性正在出现，因为它们包含许多很大程度上未表征的调节元素，使它们成为miRNA和RNA结合蛋白的核心靶标。最近，我们的小组和其他人表明，替代的聚腺苷酸化（APA）是在后生动物中广泛扩展的，在这种过程中，具有不同3'UTR同工型产生相同的mRNA。我们不知道为什么如此多的基因被多个3端转录，以及处理机械如何区分同一mRNA中的不同裂解信号，导致替代3'UTR同工型。所有后生动物的转录本中APA的宽度抽象使我们假设存在更复杂的图像，在这种情况下，不仅有MiRNA的负调节网络，而且还具有新型的意外阳性调节网络，但APA则操作。在此观点中，在发育过程中在不同细胞或组织环境中切换3'UTR同工型的基因是这些正网络的主要驱动因素，即允许或逃脱miRNA靶向。从这种角度来看，miRNA和APA原则上都可以显着重塑基因表达输出，这表明它们都在细胞和组织身份的建立和维持中起关键作用。这个想法尚未在生活组织中进行测试和验证。秀丽隐杆线虫的强大遗传学和可用的无与伦比的资源使该模型系统非常适合理解mRNA 3'End形成和转录后调节的基本原理。我们希望生产湿的基础和生物信息学工具，以使九个主要的体细胞组织中所有基因的高质量组织特异性3'UTR定位动力学生成，以便使用系统生物学方法来了解APA的基本原理，其发育动力以及其体内生产和调节。我们还将通过专注于阴性miRNA调节并开发miRNA表达并靶向三个主要的蠕虫组织中的数据，然后将结果叠加到我们组织特定的APA数据中，以在生活组织中产生第一个miRNA-APA Interactome。我们还将对APA产生及其在12个基因中的功能进行机械研究，并由我们的初步结果强调。综上所述，这些目标结合了高通量基因组学，生物信息学，遗传学，生物化学和系统生物学的创新方式，以研究APA及其在转录后基因调节中的作用。