Biochemical and Biophysical Research Communications, Vol.358, No.1, 336-341, 2007
Prediction of C-to-U RNA editing sites in higher plant mitochondria using only nucleotide sequence features
RNA editing is a class of post-transcriptional processing which contributes to the organism complexity. C-to-U RNA editing is commonly observed in higher plant mitochondria. The in vivo mechanism of recognizing G-to-U RNA editing sites is still unknown. In recent years, many efforts have been made to computationally predict G-to-U RNA editing sites. But all existing methods require using knowledge other than an RNA sequence. In the present work, we propose the first method for predicting C-to-U RNA editing sites using only nucleotide sequence features. This method was developed based on the SVM algorithm combined with a triplet scoring model. Our method can achieve 84% overall accuracy which is comparable to other methods. We also computationally found that several triplets never appear upstream near an edited cytidine, indicating that these triplets may protect a cytidine from being edited. This discovery suggests the need for further experimental research and may be helpful in understanding the editing site recognition mechanism. (c) 2007 Elsevier Inc. All rights reserved.