应用生物信息学寻找大鼠中新的microRNA分子及其实验验证

Computational and experimental identification of novel microRNAs in rats

大鼠已公布的microRNA(miRNA)数量明显少于小鼠及人miRNA的数量.本文采用同源搜索的计算方法预测大鼠新的miRNA.从miRBase数据库中下载已知动物的pre-miRNAs,在UCSC数据库中对大鼠的全基因组序列进行了Blat分析,并根据miRNAs的筛选标准,获得45条新的大鼠miRNAs;随后随机选取其中的9条新miRNAs进行RT-PCR实验验证,发现大部分miRNAs在脑、心、肺、肾、肌肉、脾、睾丸和肝8种组织中均有表达.在此基础上,对预测的新miRNAs进行了miRNA成簇分析和miRNA基因家族分析.

The number of miRNAs in rat genome in miRBase is much less than that of mouse and human. One effective method to identify new miRNAs is to utilize the homolog-based bioin- formatrical method. In this report, this method was applied to predict new miRNAs of rats. The known miRNAs sequences were downloaded from miRBase, and used as query sequences to search the rat genome at UCSC Genome Bioinformatics by BLAT analysis. New miRNAs were selected based on commonly-used miRNA standards. As a result, 45 new miRNAs were ob- tained. Nine of them were chosen to be validated by RT-PCR, and most of them were found ex- pressed in brain, heart, lung, kidney, muscle, spleen, testis and liver. Based on the results, miRNA cluster analysis and miRNA gene family analysis were performed in rat genome.