Journal Article

Characteristics and Prediction of RNA Editing Sites in Transcripts of the Moss <i>Takakia lepidozioides</i> Chloroplast

Kei Yura, Yuki Miyata, Tomotsugu Arikawa, Masanobu Higuchi and Mamoru Sugita

in DNA Research

Published on behalf of Kazusa DNA Research Institute

Volume 15, issue 5, pages 309-321
Published in print October 2008 | ISSN: 1340-2838
Published online July 2008 | e-ISSN: 1756-1663 | DOI: http://dx.doi.org/10.1093/dnares/dsn016

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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.

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

Journal Article.  6755 words.  Illustrated.

Subjects: Genetics and Genomics

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