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: 10246941
• 负责人: YE DING
• 金额: $ 45.28万
• 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/10246941
• 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; Genomics; 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; 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.

项目概要 miRNA 在多种生物过程中发挥着重要作用，它们的失调可能导致人类 疾病。控制 miRNA 表达的关键步骤是含有发夹的初级片段的加工 miRNA 转录本（pri-miRNA），由 RNase III 酶 DROSHA 组成的蛋白质复合物催化，其 伙伴 DGCR8 和其他蛋白质。 Pri-miRNA 拥有顺式结构和序列决定簇，可获得许可 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过程 所有典型的miRNA，目前缺乏一种可以进行基于序列的预测的方法 pri-miRNA 加工效率。同样，人类遗传变异对 pri-miRNA 加工的影响 人们对此知之甚少。除了 miRNA 之外，pri-miRNA 加工机制也可以切割一些 含有发夹的信使 RNA 和长非编码 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 处理。这个跨学科 该提案将开发首个基于序列的方法来定量预测处理效率 哺乳动物 pri-miRNA。我们还将利用这些工具来预测人类 SNP 对优先性的影响。 miRNA 处理和非 miRNA DROSHA 底物。利用计算和实验 根据两位PI的专业知识，将实施四个目标来实现总体目标。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，生成 基于序列的 pri-miRNA 处理效率预测，其中纳入了发夹结构的影响 迄今为止，侧翼序列基本上被忽略。在第二个目标中，我们将预测并验证人类的影响 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。第四个目标，我们将开发一个用户友好的在线数据库，以方便 社区访问我们的预测。该提案生成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、SNP 在 处理的调节，非 miRNA 转录物的处理与 pri-miRNA 类似。这些工具和结果 可以促进社区的进一步研究，例如研究 pri-miRNA 加工的顺式和反式调节， 评估 miRNA 位点周围遗传变异的功能，并研究基因表达机制 控制。