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DNA Research Advance Access published online on July 23, 2008
DNA Research, doi:10.1093/dnares/dsn016
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© The Author 2008. Kazusa DNA Research Institute
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Characteristics and Prediction of RNA Editing Sites in Transcripts of the Moss Takakia lepidozioides Chloroplast

Kei Yura1,* {dagger}, Yuki Miyata2 {dagger}, Tomotsugu Arikawa3, Masanobu Higuchi4 and Mamoru Sugita2

1 Graduate School of Humanities and Sciences, Ochanomizu University, 2-1-1 Otsuka, Bunkyo, Tokyo 112-8610, Japan
2 Center for Gene Research, Nagoya University, Chikusa, Nagoya 464-8602, Japan
3 Department of Biology, Keio University, 4-1-1 Hiyoshi, Kohoku, Yokohama 223-8521, Japan
4 Department of Botany, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba 305-0005, Japan

Received 26 May 2008 ; accepted 26 June 2008.

RNA editing in land plant organelles is a process primarily involving the conversion of cytidine to uridine in pre-mRNAs. The process is required for gene expression in plant organelles, because this conversion alters the encoded amino acid residues and improves the sequence identity to homologous proteins. A recent study uncovered that proteins encoded in the nuclear genome are essential for editing site recognition in chloroplasts; the mechanisms by which this recognition occurs remain unclear. To understand these mechanisms, we determined the genomic and cDNA sequences of moss Takakia lepidozioides chloroplast genes, then computationally analyzed the sequences within –30 to +10 nucleotides of RNA editing sites (neighbor sequences) likely to be recognized by trans-factors. As the T. lepidozioides chloroplast has many RNA editing sites, the analysis of these sequences provides a unique opportunity to perform statistical analyses of chloroplast RNA editing sites. We divided the 302 obtained neighbor sequences into eight groups based on sequence similarity to identify group-specific patterns. The patterns were then applied to predict novel RNA editing sites in T. lepidozioides transcripts; ~60% of these predicted sites are true editing sites. The success of this prediction algorithm suggests that the obtained patterns are indicative of key sites recognized by trans-factors around editing sites of T. lepidozioides chloroplast genes.

Key words: bioinformatics; chloroplast; computational biology; plant organelle; singlet and doublet propensities; Takakia lepidozioides

* To whom correspondence should be addressed. Tel/Fax. +81 3-5978-5514. E-mail: yura.kei{at}ocha.ac.jp

Edited by Kenta Nakai

{dagger} These authors contributed equally to this work.


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