Systems Biology and Biomedical Informatics (SBBI) Laboratory, Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
Brief Bioinform. 2018 May 1;19(3):415-424. doi: 10.1093/bib/bbw140.
Small RNA sequencing is the most widely used tool for microRNA (miRNA) discovery, and shows great potential for the efficient study of miRNA cross-species transport, i.e., by detecting the presence of exogenous miRNA sequences in the host species. Because of the increased appreciation of dietary miRNAs and their far-reaching implication in human health, research interests are currently growing with regard to exogenous miRNAs bioavailability, mechanisms of cross-species transport and miRNA function in cellular biological processes. In this article, we present microRNA Discovery (miRDis), a new small RNA sequencing data analysis pipeline for both endogenous and exogenous miRNA detection. Specifically, we developed and deployed a Web service that supports the annotation and expression profiling data of known host miRNAs and the detection of novel miRNAs, other noncoding RNAs, and the exogenous miRNAs from dietary species. As a proof-of-concept, we analyzed a set of human plasma sequencing data from a milk-feeding study where 225 human miRNAs were detected in the plasma samples and 44 show elevated expression after milk intake. By examining the bovine-specific sequences, data indicate that three bovine miRNAs (bta-miR-378, -181* and -150) are present in human plasma possibly because of the dietary uptake. Further evaluation based on different sets of public data demonstrates that miRDis outperforms other state-of-the-art tools in both detection and quantification of miRNA from either animal or plant sources. The miRDis Web server is available at: http://sbbi.unl.edu/miRDis/index.php.
小 RNA 测序是最广泛使用的 microRNA（miRNA）发现工具，对于有效研究 miRNA 跨物种运输具有很大的潜力，即通过检测宿主物种中外源 miRNA 序列的存在。由于人们对膳食 miRNA 的认识不断提高，以及它们对人类健康的深远影响，目前对外源 miRNA 的生物利用度、跨物种运输机制以及 miRNA 在细胞生物学过程中的功能的研究兴趣正在增长。在本文中，我们提出了 microRNA Discovery（miRDis），这是一种用于检测内源性和外源性 miRNA 的新小 RNA 测序数据分析管道。具体来说，我们开发并部署了一个 Web 服务，该服务支持已知宿主 miRNA 的注释和表达谱数据，以及新型 miRNA、其他非编码 RNA 和膳食物种的外源性 miRNA 的检测。作为概念验证，我们分析了一组来自母乳喂养研究的人类血浆测序数据，在这些血浆样本中检测到 225 个人类 miRNA，其中 44 个在摄入牛奶后表达水平升高。通过检查牛特异性序列，数据表明三种牛 miRNA（bta-miR-378、-181*和-150）可能存在于人类血浆中，因为这些 miRNA 是通过膳食摄入的。基于不同公共数据集的进一步评估表明，miRDis 在检测和定量来自动物或植物来源的 miRNA 方面均优于其他最先进的工具。miRDis Web 服务器可在以下网址获得：http://sbbi.unl.edu/miRDis/index.php。
