title: Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries.
abstract: MicroRNAs (miRNAs) are short (20-23 nt) RNAs that are sequence-specific mediators of transcriptional and post-transcriptional regulation of gene expression. Modern high-throughput technologies enable deep sequencing of such RNA species on an unprecedented scale. We find that the analysis of small RNA deep-sequencing libraries can be affected by cross-mapping, in which RNA sequences originating from one locus are inadvertently mapped to another. Similar to cross-hybridization on microarrays, cross-mapping is prevalent among miRNAs, as they tend to occur in families, are similar or derived from repeat or structural RNAs, or are post-transcriptionally modified. Here, we develop a strategy to correct for cross-mapping, and apply it to the analysis of RNA editing in mature miRNAs. In contrast to previous reports, our analysis suggests that RNA editing in mature miRNAs is rare in animals.
authors.affiliation: Omics Science Center, RIKEN Yokohama Institute, Tsurumi, Yokohama 230-0045, Japan.
authors.forename: Michiel J L
authors.initials: MJ
authors.lastname: de Hoon
authors.forename: Ryan J
authors.initials: RJ
authors.lastname: Taft
authors.forename: Takehiro
authors.initials: T
authors.lastname: Hashimoto
authors.forename: Mutsumi
authors.initials: M
authors.lastname: Kanamori-Katayama
authors.forename: Hideya
authors.initials: H
authors.lastname: Kawaji
authors.forename: Mitsuoki
authors.initials: M
authors.lastname: Kawano
authors.forename: Mami
authors.initials: M
authors.lastname: Kishima
authors.forename: Timo
authors.initials: T
authors.lastname: Lassmann
authors.forename: Geoffrey J
authors.initials: GJ
authors.lastname: Faulkner
authors.forename: John S
authors.initials: JS
authors.lastname: Mattick
authors.forename: Carsten O
authors.initials: CO
authors.lastname: Daub
authors.forename: Piero
authors.initials: P
authors.lastname: Carninci
authors.forename: Jun
authors.initials: J
authors.lastname: Kawai
authors.forename: Harukazu
authors.initials: H
authors.lastname: Suzuki
authors.forename: Yoshihide
authors.initials: Y
authors.lastname: Hayashizaki
mesh_terms: D000818:Animals; D001483:Base Sequence; D015723:Gene Library; D057166:High-Throughput Screening Assays; D006801:Humans; D051379:Mice; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D017393:RNA Editing / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D035683:MicroRNAs; C542687:mirnlet7 microRNA, mouse