ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2008
Characteristics and prediction of RNA editing sites in transcripts of the Moss Takakia lepidozioides chloroplast.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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11 citing papers in PubMed, 16 citations in OpenAlex.
- Complete sequencing of the mitochondrial genome of tea plantFrontiers in plant science · 2025Article
- A Comprehensive Evolutionary Study of Chloroplast RNA Editing in Gymnosperms: A Novel Type of G-to-A RNA Editing Is Common in Gymnosperms.International journal of molecular sciences · 2022Article
- The complete plastid genome sequence of the enigmatic moss, Takakia lepidozioides (Takakiopsida, Bryophyta): evolutionary perspectives on the largest collection of genes in mosses and the intensive RNA editing.Plant molecular biology · 2021Article
- Resolution of the ordinal phylogeny of mosses using targeted exons from organellar and nuclear genomes.Nature communications · 2019Article
- Variable frequency of plastid RNA editing among ferns and repeated loss of uridine-to-cytidine editing from vascular plants.PloS one · 2015Article
- Organellar genomes of the four-toothed moss, Tetraphis pellucida.BMC genomics · 2014Article
- Nuclear DYW-type PPR gene families diversify with increasing RNA editing frequencies in liverwort and moss mitochondria.Journal of molecular evolution · 2012Article
- Editing site analysis in a gymnosperm mitochondrial genome reveals similarities with angiosperm mitochondrial genomes.Current genetics · 2010Article
- RESOPS: a database for analyzing the correspondence of RNA editing sites to protein three-dimensional structures.Plant & cell physiology · 2009Article
- CURE-Chloroplast: a chloroplast C-to-U RNA editing predictor for seed plants.BMC bioinformatics · 2009Article
- Post-transcriptional control of chloroplast gene expression.Gene regulation and systems biology · 2009Article
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Authors and funding
5 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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; approximately 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.
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