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

Michiel J.L. De Hoon; Ryan J. Taft; Takehiro Hashimoto; Mutsumi Kanamori-Katayama; Hideya Kawaji; Mitsuoki Kawano; Mami Kishima; Timo Lassmann; Geoffrey J. Faulkner; John S. Mattick; Carsten O. Daub; Piero Carninci; Jun Kawai; Harukazu Suzuki; Yoshihide Hayashizaki

doi:10.1101/gr.095273.109

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

Michiel J.L. De Hoon, Ryan J. Taft, Takehiro Hashimoto, Mutsumi Kanamori-Katayama, Hideya Kawaji, Mitsuoki Kawano, Mami Kishima, Timo Lassmann, Geoffrey J. Faulkner, John S. Mattick, Carsten O. Daub, Piero Carninci, Jun Kawai, Harukazu Suzuki, Yoshihide Hayashizaki

Research output: Contribution to journal › Article › peer-review

112 Citations (Scopus)

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.

Original language	English
Pages (from-to)	257-264
Number of pages	8
Journal	Genome Research
Volume	20
Issue number	2
DOIs	https://doi.org/10.1101/gr.095273.109
Publication status	Published - Feb 2010
Externally published	Yes

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De Hoon, M. J. L., Taft, R. J., Hashimoto, T., Kanamori-Katayama, M., Kawaji, H., Kawano, M., Kishima, M., Lassmann, T., Faulkner, G. J., Mattick, J. S., Daub, C. O., Carninci, P., Kawai, J., Suzuki, H., & Hayashizaki, Y. (2010). Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries. Genome Research, 20(2), 257-264. https://doi.org/10.1101/gr.095273.109

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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.",

author = "{De Hoon}, {Michiel J.L.} and Taft, {Ryan J.} and Takehiro Hashimoto and Mutsumi Kanamori-Katayama and Hideya Kawaji and Mitsuoki Kawano and Mami Kishima and Timo Lassmann and Faulkner, {Geoffrey J.} and Mattick, {John S.} and Daub, {Carsten O.} and Piero Carninci and Jun Kawai and Harukazu Suzuki and Yoshihide Hayashizaki",

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De Hoon, MJL, Taft, RJ, Hashimoto, T, Kanamori-Katayama, M, Kawaji, H, Kawano, M, Kishima, M, Lassmann, T, Faulkner, GJ, Mattick, JS, Daub, CO, Carninci, P, Kawai, J, Suzuki, H & Hayashizaki, Y 2010, 'Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries', Genome Research, vol. 20, no. 2, pp. 257-264. https://doi.org/10.1101/gr.095273.109

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AU - De Hoon, Michiel J.L.

AU - Taft, Ryan J.

AU - Hashimoto, Takehiro

AU - Kanamori-Katayama, Mutsumi

AU - Kawaji, Hideya

AU - Kawano, Mitsuoki

AU - Kishima, Mami

AU - Lassmann, Timo

AU - Faulkner, Geoffrey J.

AU - Mattick, John S.

AU - Daub, Carsten O.

AU - Carninci, Piero

AU - Kawai, Jun

AU - Suzuki, Harukazu

AU - Hayashizaki, Yoshihide

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

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