title: A genome-wide map of hyper-edited RNA reveals numerous new sites.
abstract: Adenosine-to-inosine editing is one of the most frequent post-transcriptional modifications, manifested as A-to-G mismatches when comparing RNA sequences with their source DNA. Recently, a number of RNA-seq data sets have been screened for the presence of A-to-G editing, and hundreds of thousands of editing sites identified. Here we show that existing screens missed the majority of sites by ignoring reads with excessive ('hyper') editing that do not easily align to the genome. We show that careful alignment and examination of the unmapped reads in RNA-seq studies reveal numerous new sites, usually many more than originally discovered, and in precisely those regions that are most heavily edited. Specifically, we discover 327,096 new editing sites in the heavily studied Illumina Human BodyMap data and more than double the number of detected sites in several published screens. We also identify thousands of new sites in mouse, rat, opossum and fly. Our results establish that hyper-editing events account for the majority of editing sites.
authors.affiliation: The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel.
authors.forename: Hagit T
authors.initials: HT
authors.lastname: Porath
authors.affiliation: Department of Computer Science, Columbia University, New York, New York 10027, USA.
authors.forename: Shai
authors.initials: S
authors.lastname: Carmi
authors.affiliation: The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel.
authors.forename: Erez Y
authors.initials: EY
authors.lastname: Levanon
mesh_terms: D000241:Adenosine / Q000235:genetics; D000243:Adenosine Deaminase / Q000235:genetics; D000818:Animals; D001921:Brain / Q000502:physiology; D015894:Genome, Human; D006801:Humans; D007288:Inosine / Q000235:genetics; D051379:Mice; D035683:MicroRNAs / Q000235:genetics; D009893:Opossums / Q000235:genetics; D010987:Platypus / Q000235:genetics; D012313:RNA; D017393:RNA Editing; D012330:RNA, Double-Stranded / Q000737:chemistry / Q000235:genetics; D016601:RNA-Binding Proteins / Q000235:genetics; D051381:Rats; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D035683:MicroRNAs; D012330:RNA, Double-Stranded; D016601:RNA-Binding Proteins; D007288:Inosine; D012313:RNA; C000595356:ADAR protein, human; C567955:ADARB1 protein, human; D000243:Adenosine Deaminase; D000241:Adenosine