Bioinformatics analysis suggests base modifications of tRNAs and miRNAs in Arabidopsis thaliana.
Bioinformatics analysis suggests base modifications of tRNAs and miRNAs in Arabidopsis thaliana.
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DOI：
10.1186/1471-2164-10-155
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发表时间：
2009-04-09
期刊：
影响因子：
4.4
通讯作者：
Zhu JK
中科院分区：
文献类型：
--
作者：
Iida K;Jin H;Zhu JK
在一些mrna和非编码RNA（包括RNAs、tRNAs和snrna）中发现了RNA碱基的修饰，其中修饰的碱基对RNA的功能很重要。人们对拟南芥的RNA碱基修饰知之甚少。在目前的工作中，我们利用454技术和大规模平行特征测序（MPSS）方法生成的大量小RNA (sRNAs) cDNA序列，对tRNAs和miRNAs中的RNA碱基修饰进行了生物信息学分析。我们寻找映射到具有单碱基错配（OMM）的基因组序列的sRNAs，这表明候选的修饰核苷酸。我们获得了1187个位点，454和MPSS序列都支持可能的RNA碱基修饰。其中703个位点位于tRNA位点内。核苷酸取代通常位于T臂（从A到U或G的取代）、D臂上游（从G到C、U或A）和D臂下游（从G到U）。主要取代位点的位置与tRNAs中已知的RNA碱基修饰相对应：n1 -甲基腺苷（m1A）、n2 -甲基鸟苷（m2G）和n2 - n2 -甲基鸟苷（m22G）。这些结果表明我们的生物信息学方法成功地检测到了trna中的修饰核苷酸。利用这种方法，我们还发现了147个miRNA位点的替代位点。与trna一样，从A到U或G以及从G到C、U或A的替换是常见的，这表明trna和mirna中的碱基修饰可能相似。我们认为miRNA含有修饰的碱基，这种修饰可能对miRNA的成熟和/或功能很重要。
Modifications of RNA bases have been found in some mRNAs and non-coding RNAs including rRNAs, tRNAs, and snRNAs, where modified bases are important for RNA function. Little is known about RNA base modifications in Arabidopsis thaliana. In the current work, we carried out a bioinformatics analysis of RNA base modifications in tRNAs and miRNAs using large numbers of cDNA sequences of small RNAs (sRNAs) generated with the 454 technology and the massively parallel signature sequencing (MPSS) method. We looked for sRNAs that map to the genome sequence with one-base mismatch (OMM), which indicate candidate modified nucleotides. We obtained 1,187 sites with possible RNA base modifications supported by both 454 and MPSS sequences. Seven hundred and three of these sites were within tRNA loci. Nucleotide substitutions were frequently located in the T arm (substitutions from A to U or G), upstream of the D arm (from G to C, U, or A), and downstream of the D arm (from G to U). The positions of major substitution sites corresponded with the following known RNA base modifications in tRNAs: N1-methyladenosine (m1A), N2-methylguanosine (m2G), and N2-N2-methylguanosine (m22G). These results indicate that our bioinformatics method successfully detected modified nucleotides in tRNAs. Using this method, we also found 147 substitution sites in miRNA loci. As with tRNAs, substitutions from A to U or G and from G to C, U, or A were common, suggesting that base modifications might be similar in tRNAs and miRNAs. We suggest that miRNAs contain modified bases and such modifications might be important for miRNA maturation and/or function.