PMCCPMCCPMCC

Search tips
Search criteria 

Advanced

 
Logo of bmcgenoBioMed Centralsearchsubmit a manuscriptregisterthis articleBMC Genomics
 
BMC Genomics. 2009; 10: 155.
Published online Apr 9, 2009. doi:  10.1186/1471-2164-10-155
PMCID: PMC2674459
Bioinformatics analysis suggests base modifications of tRNAs and miRNAs in Arabidopsis thaliana
Kei Iida,1,2 Hailing Jin,3 and Jian-Kang Zhucorresponding author1
1Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
2Bioinformatics and Systems Engineering Division, RIKEN Yokohama Institute, 1-7-22, Suehiro, Tsurumi, Yokohama 230-0045, Japan
3Department of Plant Pathology, University of California, Riverside, California 92521, USA
corresponding authorCorresponding author.
Kei Iida: kiida/at/base.riken.jp; Hailing Jin: hailing.jin/at/ucr.edu; Jian-Kang Zhu: jian-kang.zhu/at/ucr.edu
Received October 27, 2008; Accepted April 9, 2009.
Abstract
Background
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.
Results
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).
Conclusion
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.
Articles from BMC Genomics are provided here courtesy of
BioMed Central