Characteristics and prediction of rna editing sites in transcripts of the moss takakia lepidozioides chloroplast

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

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)309-321
Number of pages13
JournalDNA Research
Volume15
Issue number5
DOIs
Publication statusPublished - 2008

Fingerprint

RNA Editing
Bryophyta
Chloroplasts
Chloroplast Genes
Organelles
Chloroplast RNA
Embryophyta
Cytidine
Uridine
RNA Precursors
Sequence Analysis
Proteins
Nucleotides
Complementary DNA
Gene Expression
Amino Acids

Keywords

  • Bioinformatics
  • Chloroplast
  • Computational biology
  • Plant organelle
  • Singlet and doublet propensities
  • Takakia lepidozioides

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology
  • Medicine(all)

Cite this

Characteristics and prediction of rna editing sites in transcripts of the moss takakia lepidozioides chloroplast. / Yura, Kei; Miyata, Yuki; Arikawa, Tomotsugu; Higuchi, Masanobu; Sugita, Mamoru.

In: DNA Research, Vol. 15, No. 5, 2008, p. 309-321.

Research output: Contribution to journalArticle

Yura, Kei ; Miyata, Yuki ; Arikawa, Tomotsugu ; Higuchi, Masanobu ; Sugita, Mamoru. / Characteristics and prediction of rna editing sites in transcripts of the moss takakia lepidozioides chloroplast. In: DNA Research. 2008 ; Vol. 15, No. 5. pp. 309-321.
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