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

Nat Methods. 2012 Jun;9(6):579-81. doi: 10.1038/nmeth.1982. Epub 2012 Apr 4.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • APOBEC-1 Deaminase
  • Alu Elements*
  • Cell Line
  • Cytidine Deaminase / metabolism
  • Humans
  • Nucleotide Mapping / methods
  • RNA Editing*
  • RNA, Double-Stranded
  • Sequence Analysis, RNA / methods*


  • RNA, Double-Stranded
  • APOBEC-1 Deaminase
  • APOBEC1 protein, human
  • Cytidine Deaminase