Novel Bioinformatics Tools for Quantitative Prediction of Primary MicroRNA Processing

用于定量预测初级 MicroRNA 加工的新型生物信息学工具

• 批准号: 10031383
• 负责人: YE DING
• 金额: $ 47.64万
• 依托单位: YALE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-09-01 至 2024-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10031383
• 关键词: Affect; Base Sequence; Biological Assay; Biological Process; Biology; Cells; Cleaved cell; Clustered Regularly Interspaced Short Palindromic Repeats; Communities; Computer Models; Data; Data Set; Databases; Development; Distal; Enzymes; Evaluation; Gene Expression; Gene Expression Regulation; Genes; Genetic Variation; Goals; Human; Human Genetics; Human Genome; Knowledge; Laboratories; Lead; Licensing; Literature; Mediating; Messenger RNA; Methods; MicroRNAs; Modeling; Mus; Nucleotides; Performance; Play; Process; Production; Proteins; RNA; RNA Computations; RNA Folding; RNA Sequences; RNA Splicing; RNASE3L gene; Regulation; Reporter; Ribonuclease III; Role; Single Nucleotide Polymorphism; Structural Models; Structure; Transcript; Untranslated RNA; Validation; base; bioinformatics tool; genetic variant; genome editing; genome-wide; genomic profiles; human disease; interest; method development; mouse genome; novel; pri-miRNA; protein complex; tool; user-friendly

PROJECT SUMMARY MiRNAs play important roles in diverse biological processes and their dysregulation can lead to human diseases. A critical step in the control of miRNA expression is the processing of the hairpin-containing primary miRNA transcripts (pri-miRNAs), catalyzed by protein complexes consisting of RNase III enzyme DROSHA, its partner DGCR8 and other proteins. Pri-miRNAs possess cis- structural and sequence determinants to license them for processing, the disruption of which, such as by human single-nucleotide polymorphisms (SNPs), can affect processing. However, the existing cis-regulatory rules are insufficient to adequately explain the processing of all canonical miRNAs, and currently there is a lack of a method that can perform sequence-based prediction of pri-miRNA processing efficiency. Likewise, the impact of human genetic variations on pri-miRNA processing is poorly understood. In addition to miRNAs, the pri-miRNA processing machinery is also known to cleave some hairpin-containing messenger RNAs and long noncoding RNAs, regulating their abundance and splicing. However, there is no method that can predict which RNAs can be processed by DROSHA. This interdisciplinary proposal will develop first-of-its-kind sequence-based methods to quantitatively predict the processing efficiency of mammalian pri-miRNAs. We will also utilize these tools toward predicting the influence of human SNPs on pri- miRNA processing and non-miRNA DROSHA substrates. Leveraging on the computational and experimental expertise of the two PIs, four aims will be carried out to achieve the overall goal. In the first aim, we will use a combined computational and experimental approach to develop four quantitative models that generate sequence-based predictions of pri-miRNA processing efficiency, which incorporate the influence of hairpin- flanking sequences largely ignored to date. In the second aim, we will predict and validate the effects of human single-nucleotide polymorphisms on pri-miRNA processing. In the third aim, we will predict and evaluate non- miRNA DROSHA substrates. In the fourth aim, we will develop a user-friendly online database for easy community access of our predictions. The methods and database generated from this proposal will fill an existing knowledge gap by providing quantitative predictions of pri-miRNA processing, the impact of SNPs in the regulation of processing, and non-miRNA transcripts processed similar to pri-miRNAs. These tools and results can fuel further studies by the community, e.g., to study cis- and trans- regulation of pri-miRNA processing, to evaluate the functions of genetic variants around miRNA loci, and to study mechanisms of gene expression control.

项目摘要 miRNAs在多种生物学过程中发挥重要作用，其失调可导致人类 疾病控制miRNA表达的一个关键步骤是加工含有发夹的初级RNA， miRNA转录物（pri-miRNAs），由RNase III酶DROSHA组成的蛋白质复合物催化，其 DGCR 8和其他蛋白质。Pri-miRNAs具有顺式结构和序列决定簇， 它们用于加工，其破坏，例如通过人类单核苷酸多态性（SNP），可以 影响加工。然而，现有的顺式监管规则不足以充分解释处理 所有典型的miRNAs，目前缺乏一种方法，可以进行基于序列的预测 pri-miRNA的加工效率。同样，人类遗传变异对pri-miRNA加工的影响 是很难理解的。除了miRNAs，pri-miRNAs加工机制也已知切割一些miRNAs。 含有发夹的信使RNA和长的非编码RNA，调节它们的丰度和剪接。 然而，没有方法可以预测哪些RNA可以被DROSHA加工。这个跨学科 一项提案将开发第一种基于序列的方法来定量预测处理效率 哺乳动物pri-miRNAs。我们还将利用这些工具预测人类SNP对原发性肝癌的影响。 miRNA加工和非miRNA DROSHA底物。利用计算和实验 我们将利用两名专业人员的专业知识，实现四个目标，以实现总体目标。在第一个目标中，我们将使用 结合计算和实验方法，开发四个定量模型， 基于序列的pri-miRNA加工效率预测，其中包括发夹的影响， 侧翼序列至今被忽略。在第二个目标中，我们将预测和验证人类的影响， pri-miRNA加工的单核苷酸多态性。在第三个目标中，我们将预测和评估非- miRNA DROSHA底物。在第四个目标中，我们将开发一个用户友好的在线数据库， 社区访问我们的预测。本提案产生的方法和数据库将填补现有的 通过提供pri-miRNA加工的定量预测， 调节加工，以及非miRNA转录物加工类似于pri-miRNA。这些工具和成果 可以推动社区的进一步研究，例如，研究pri-miRNA加工的顺式和反式调节， 评估miRNA位点周围的遗传变异的功能，并研究基因表达的机制 控制