Accurate identification of human Alu and non-Alu RNA editing sites

A computational framework is reported for the accurate and sensitive identification of RNA editing sites from whole-genome DNA and RNA sequences from the same individual. We developed a computational framework to robustly identify RNA editing sites using transcriptome and genome deep-sequencing data from the same individual. As compared with previous methods, our approach identified a large number of Alu and non- Alu RNA editing sites with high specificity. We also found that editing of non- Alu sites appears to be dependent on nearby edited Alu sites, possibly through the locally formed double-stranded RNA structure.