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 C-to-U RNA editing sites is still unknown. In recent years, many efforts have been made to computationally predict C-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.
Du
Pufeng
P
Bioinformatics Division, Tsinghua National Laboratory for Information Science and Technology (TNLIST), Department of Automation, Tsinghua University, Beijing 100084, China.
He
Tao
T
Li
Yanda
Y
D000465:Algorithms; D001483:Base Sequence; D008928:Mitochondria / Q000235:genetics*; D009711:Nucleotides / Q000235:genetics*; D010944:Plants / Q000235:genetics* / Q000648:ultrastructure; D017393:RNA Editing; D018749:RNA, Plant / Q000235:genetics*; D017423:Sequence Analysis, RNA
D009711:Nucleotides; D018749:RNA, Plant