Computational and experimental identification of novel microRNAs in rats

Abstract

Abstract: 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 bioinformatrical 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 obtained. Nine of them were chosen to be validated by RT- PCR, and most of them were found expressed 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.

Key words: miRNA, rat, bioinformatics, homology search

CLC Number:

WANG Lin, ZHANG Shuang, DONG Su-zhen. Computational and experimental identification of novel microRNAs in rats[J]. Journal of East China Normal University(Natural Sc, 2012, 2012(3): 154-160,170.

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