Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas, United States of America.
PLoS One. 2012;7(3):e34394. doi: 10.1371/journal.pone.0034394. Epub 2012 Mar 28.
MicroRNAs (miRNAs) are small non-coding RNAs that regulate a variety of biological processes. The latest version of the miRBase database (Release 18) includes 1,157 mouse and 680 rat mature miRNAs. Only one new rat mature miRNA was added to the rat miRNA database from version 16 to version 18 of miRBase, suggesting that many rat miRNAs remain to be discovered. Given the importance of rat as a model organism, discovery of the completed set of rat miRNAs is necessary for understanding rat miRNA regulation. In this study, next generation sequencing (NGS), microarray analysis and bioinformatics technologies were applied to discover novel miRNAs in rat kidneys. MiRanalyzer was utilized to analyze the sequences of the small RNAs generated from NGS analysis of rat kidney samples. Hundreds of novel miRNA candidates were examined according to the mappings of their reads to the rat genome, presence of sequences that can form a miRNA hairpin structure around the mapped locations, Dicer cleavage patterns, and the levels of their expression determined by both NGS and microarray analyses. Nine novel rat hairpin precursor miRNAs (pre-miRNA) were discovered with high confidence. Five of the novel pre-miRNAs are also reported in other species while four of them are rat specific. In summary, 9 novel pre-miRNAs (14 novel mature miRNAs) were identified via combination of NGS, microarray and bioinformatics high-throughput technologies.
微小 RNA（miRNAs）是一类小的非编码 RNA，可以调控多种生物过程。miRBase 数据库的最新版本（版本 18）包括 1157 个小鼠成熟 miRNA 和 680 个大鼠成熟 miRNA。从 miRBase 的版本 16 到版本 18，大鼠 miRNA 数据库只增加了一个新的大鼠成熟 miRNA，这表明还有许多大鼠 miRNA 有待发现。鉴于大鼠作为模式生物的重要性，发现完整的大鼠 miRNA 集对于理解大鼠 miRNA 的调控是必要的。在这项研究中，我们应用下一代测序（NGS）、微阵列分析和生物信息学技术来发现大鼠肾脏中的新 miRNA。利用 miRanalyzer 分析了大鼠肾脏样本 NGS 分析产生的小 RNA 序列。根据它们的reads 与大鼠基因组的映射、在映射位置周围形成 miRNA 发夹结构的序列的存在、Dicer 切割模式以及通过 NGS 和微阵列分析确定的表达水平，对数百个新的 miRNA 候选物进行了检查。发现了 9 个具有高可信度的新大鼠发夹前体 miRNA（pre-miRNA）。其中 5 个新的 pre-miRNA 也在其他物种中报道过，而另外 4 个是大鼠特有的。总之，通过 NGS、微阵列和生物信息学高通量技术的组合，鉴定了 9 个新的 pre-miRNA（14 个新的成熟 miRNA）。
