Mapeamento cruzado e a identificação de sítios de edição em microRNAs

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

Michiel J.L. de Hoon1,4, Ryan J. Taft2, Takehiro Hashimoto1, Mutsumi Kanamori-Katayama1, Hideya Kawaji1, Mitsuoki Kawano1, Mami Kishima1, Timo Lassmann1, Geoffrey J. Faulkner3, John S. Mattick2, Carsten O. Daub1, Piero Carninci1, Jun Kawai1, Harukazu Suzuki1 and Yoshihide Hayashizaki1

- Author Affiliations

1Omics Science Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan;

2Institute for Molecular Bioscience, The University of Queensland, St. Lucia QLD 4072, Australia;

3Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Roslin EH25 9PS, United Kingdom

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.

Footnotes

↵4 Corresponding author.

E-mail mdehoon@gsc.riken.jp; fax 81-45-5039216.

[Supplemental material is available online at http://www.genome.org.]

Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.095273.109.
Received July 1, 2009.

Accepted November 24, 2009.

Copyright © 2010 by Cold Spring Harbor Laboratory Press

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