Novel Bioinformatics Tools for Quantitative Prediction of Primary MicroRNA Processing

项目总结 MiRNAs在多种生物学过程中发挥着重要作用，其失调可导致人类 疾病。控制miRNA表达的关键步骤是处理含有发夹的初级 MiRNA转录本(pri-miRNAs)，由RNaseIII酶DROSHA组成的蛋白质复合体催化，ITS 伴侣Dgcr8和其他蛋白质。PrI-miRNAs拥有要许可的顺式结构和序列决定簇 它们用于加工，其中断，例如由人类单核苷酸多态(SNPs)，可以 影响处理。然而，现有的顺式监管规则不足以充分解释这一过程 在所有规范的miRNAs中，目前还缺乏一种可以进行基于序列的预测的方法 Pri-miRNA的处理效率。同样，人类基因变异对pri-miRNA加工的影响 人们对此知之甚少。除了miRNAs，Pri-miRNA处理机制也被认为能切割一些 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处理。这一交叉学科 提案将开发首个基于序列的方法来定量预测处理效率 哺乳动物的pri-miRNAs。我们还将利用这些工具来预测人类SNPs对原生基因的影响。 MiRNA加工和非miRNA DROSHA底物。利用计算和实验 在两个绩效指标的专业知识基础上，将实现四个目标，以实现总体目标。在第一个目标中，我们将使用 计算和实验相结合的方法来开发四个定量模型，以生成 基于序列的Pri-miRNA处理效率的预测，其中包括发夹的影响- 到目前为止，侧翼序列基本上被忽视。在第二个目标中，我们将预测和验证人类活动的影响 Pri-miRNA加工中的单核苷酸多态性。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，以方便 对我们的预测进行社区访问。由该提案生成的方法和数据库将填补现有的 通过提供对pri-miRNA加工的定量预测，SNPs在 加工的调控，以及非miRNA转录本的加工类似于pri-miRNAs。这些工具和结果 可以推动社区进行进一步的研究，例如研究pri-miRNA加工的顺式和反式调节，以 评估miRNA基因座周围的遗传变异的功能，并研究基因表达的机制 控制力。

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.