| 基于BLAST与比较基因组学方法计算鉴定青鳉鱼的microRNA前体 |
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| 引用本文： | 刘沅,郑新娟,姜毅,孙远东,罗野婯,谭树华,金元昌,严明理,袁志栋.基于BLAST与比较基因组学方法计算鉴定青鳉鱼的microRNA前体[J].广西农业生物科学,2014(1):179-187. |
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| 作者姓名： | 刘沅 郑新娟 姜毅 孙远东 罗野婯 谭树华 金元昌 严明理 袁志栋 |
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| 作者单位： | 湖南科技大学生命科学学院,湘潭411201 |
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| 基金项目： | 国家自然科学基金青年项目（31100914）; 湖南省普通高等学校教学改革研究项目“水产养殖实践教学基地的建设与研究”（教育厅批准号220）; 湖南科技大学博士启动基金（E51178）共同资助
致谢 本研究由国家自然科学基金青年项目（31100914）、湖南省普通高等学校教学改革研究项目“水产养殖实践教学基地的建设与研究”（教育厅批准号220）和湖南科技大学博士启动基金（E51178）共同资助,特此致谢! |
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| 摘 要： | microRNA（miRNA）是一类长度为18～25 nt的单链小分子RNA。它可以调控基因的表达调控。通过与目标mRNA的特定位点的结合,从而抑制蛋白质的翻译或诱导该mRNA的降解。目前鱼类miRNA方面以斑马鱼miRNA的研究较多。为发掘另一种鱼类模式生物——青鳉鱼（Oryzias latipes,medeka）的miRNA,利用BLAST同源搜索方法与比较基因组学方法,并根据成熟miRNA的序列保守性以及miRNA前体（premiRNA）的二级结构的特征,对该模式生物的pre-miRNA进行了计算鉴定与分析。通过与miRBase19中已经发布的miRNA进行比较,在青鳉鱼基因组中共找到了56条新序列。设定miRNA基因间距的阈值为5000nt,新发现的与已知的pre-miRNA共形成31个基因簇。同时,这56条新发现的pre-miRNA可以划分到33个已知的基因家族中,并分析了新发现的、保守miRNA的靶标与功能。
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| 关 键 词： | miRNA BLAST 比较基因组学 青鳉鱼 |
Computational Identification of Medaka Pre-miRNAs Using BLAST and the Comparative Genomic Approach |
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| Liu Yuan,Zheng Xinjuan,Jiang Yi,Sun Yuandong,Luo Yeli,Tan Shuhua,Jin Yuanchang,Yan Mingli,Yuan Zhidong.Computational Identification of Medaka Pre-miRNAs Using BLAST and the Comparative Genomic Approach[J].Journal of Guangxi Agricultural and Biological Science,2014(1):179-187. |
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| Authors: | Liu Yuan Zheng Xinjuan Jiang Yi Sun Yuandong Luo Yeli Tan Shuhua Jin Yuanchang Yan Mingli Yuan Zhidong |
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| Institution: | ( School of Life Sciences, Hunan University of Science and Technology, Xiangtan, 411201) |
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| Abstract: | MicroRNAs （miRNAs） are a kind of small single-strand RNA molecules whose length are 18-25 nt. miRNAs could regulate the gene expression by combining with the specific sites in mRNAs, which is subject to suppress the translation of proteins or induce degradation of the target mRNAs. Among fish species, zebra fish is the most studied organism on miRNA studies. To identify the miRNA precursors （pre-miRNAs）of model organism, medaka （Oryzias latipes）, two methods including the BLAST method and comparative genomic approach, and two characters, such as the conservation of mature miRNA sequences and the characters of precursor＇s hairpin structure have been used in this research. By comparing with the data from miRBase19, 56 novel pre-miRNAs have been determined from the predicted pre-miRNAs. The 56 new pre-miRNAs and the 165 known pre-miRNAs in the miRBase19 could form into 31 gene clusters along the chromosomes with the threshold of gene interval was set at 5 000 nt. And these new pre-miRNAs could be classified into 33 miRNA gene families. Moreover, the targets and their functions of the new pre-miRNAs have also been analyzed. |
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| Keywords: | miRNA BLAST Comparative genomics Medaka |
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