Published in

Cold Spring Harbor Laboratory Press, Genome Research, 2(20), p. 257-264, 2010

DOI: 10.1101/gr.095273.109

Links

Tools

Export citation

Search in Google Scholar

Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries

Journal article published in 2010 by Michiel J. L. de Hoon, Ryan J. Taft, Takehiro Hashimoto, Mutsumi Kanamori-Katayama, Hideya Kawaji, Mitsuoki Kawano, Mami Kishima, Timo Lassmann ORCID, Geoffrey J. Faulkner, John S. Mattick ORCID, Carsten O. Daub, Piero Carninci, Jun Kawai, Harukazu Suzuki, Yoshihide Hayashizaki
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

Full text: Download

Green circle
Preprint: archiving allowed
Upload
Red circle
Postprint: archiving forbidden
Orange circle
Published version: archiving restricted
Upload
Policy details
Data provided by SHERPA/RoMEO

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.