应用生物信息学寻找大鼠中新的microRNA分子及其实验验证

华东师范大学学报(自然科学版) ›› 2012, Vol. 2012 ›› Issue (3): 154-160,170.

应用生物信息学寻找大鼠中新的microRNA分子及其实验验证

王琳，张双，董素珍

华东师范大学脑功能基因组学教育部重点实验室，上海市脑功能基因组学重点实验室，上海 200062

收稿日期:2011-03-01 修回日期:2011-06-01 出版日期:2012-05-25 发布日期:2012-05-22

Computational and experimental identification of novel microRNAs in rats

WANG Lin, ZHANG Shuang, DONG Su-zhen

Key Laboratory of Brain Functional Genomics, Ministory of Education, Shanghai Key Laboratory of Brain Functional Genomics, East China Normal University, Shanghai 200062, China

Received:2011-03-01 Revised:2011-06-01 Online:2012-05-25 Published:2012-05-22

摘要/Abstract

摘要： 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.

关键词: miRNA, 大鼠, 生物信息学, 同源性搜索

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

中图分类号:

王琳，张双，董素珍. 应用生物信息学寻找大鼠中新的microRNA分子及其实验验证[J]. 华东师范大学学报(自然科学版), 2012, 2012(3): 154-160,170.

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.

参考文献

［1］LAGOS-QUINTANA M, RAUHUT R, LENDECKEL W, et al. Identification of novel genes coding for small expressed RNAs［J］. Science, 2001, 294(5543): 853-858.

［2］LAI E C, TOMANCAK P, WILLIAMS R W, et al. Computational identification of drosophila microRNA genes［J］. Genome Biol, 2003, 4(7): R42.

［3］LIM L P, LAU N C, WEINSTEIN E G, et al. The microRNAs of Caenorhabditis elegans［J］. Genes Dev, 2003, 17(8): 991-1008.

［4］WEBER M J. New human and mouse microRNA genes found by homology search［J］. FEBS J, 2005, 272(1): 59-73.

［5］YUE J, SHENG YORWIG K E. Identification of novel homologous microRNA genes in the rhesus macaque genome［J］. BMC Genomics, 2008(9): 8.

［6］SHAO P, ZHOU H, XIAO Z D, et al. Identification of novel chicken microRNAs and analysis of their genomic organization［J］. Gene,2008, 418(1-2): 34-40.

［7］ZHOU M, WANG Q, SUN J, et al. In silico detection and characteristics of novel microRNA genes in the Equus caballus genome using an integrated ab initio and comparative genomic approach［J］. Genomics, 2009, 94(2): 125-131.

［8］BAEV V, DASKALOVA EMINKOV I. Computational identification of novel microRNA homologs in the chimpanzee genome［J］. Comput Biol Chem,2009, 33(1): 62-70.

［9］KAROLCHIK D, BAERTSCH R, DIEKHANS M, et al. The UCSC genome browser database［J］. Nucleic Acids Res,2003, 31(1): 51-54.

［10］ ALTUVIA Y, LANDGRAF P, LITHWICK G, et al. Clustering and conservation patterns of human microRNAs［J］. Nucleic Acids Res, 2005, 33(8): 2697-2706.

［11］ GRIFFITHS J. miRBase［DB/OL］.(2010-04-01)［2011-02-10］.http://www.mirbase.org.

［12］ GRIFFITHS-JONES S, SAINI H K, VAN DONGEN S, et al. miRBase: tools for microRNA genomics［J］. Nucleic Acids Res,2008, 36(Database issue): D154-D158.

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