title: Accurate identification of human Alu and non-Alu RNA editing sites.
abstract: 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.
authors.affiliation: Department of Genetics, Stanford University, California, USA.
authors.forename: Gokul
authors.initials: G
authors.lastname: Ramaswami
authors.forename: Wei
authors.initials: W
authors.lastname: Lin
authors.forename: Robert
authors.initials: R
authors.lastname: Piskol
authors.forename: Meng How
authors.initials: MH
authors.lastname: Tan
authors.forename: Carrie
authors.initials: C
authors.lastname: Davis
authors.forename: Jin Billy
authors.initials: JB
authors.lastname: Li
mesh_terms: D000071479:APOBEC-1 Deaminase; D020087:Alu Elements; D002460:Cell Line; D003564:Cytidine Deaminase / Q000378:metabolism; D006801:Humans; D009710:Nucleotide Mapping / Q000379:methods; D017393:RNA Editing; D012330:RNA, Double-Stranded; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D012330:RNA, Double-Stranded; D000071479:APOBEC-1 Deaminase; C000605089:APOBEC1 protein, human; D003564:Cytidine Deaminase