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

de Hoon, Michiel J. L., Taft, Ryan J., Hashimoto, Takehiro, Kanamori-Katayama, Mutsumi, Kawaji, Hideya, Kawano, Mitsuoki, Kishima, Mami, Lassmann, Timo, Faulkner, Geoffrey J., Mattick, John S., Daub, Carsten O., Carninci, Piero, Kawai, Jun, Suzuki, Harukazu and Hayashizaki, Yoshihide (2010) Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries. Genome Research, 20 2: 257-264. doi:10.1101/gr.095273.109


Author de Hoon, Michiel J. L.
Taft, Ryan J.
Hashimoto, Takehiro
Kanamori-Katayama, Mutsumi
Kawaji, Hideya
Kawano, Mitsuoki
Kishima, Mami
Lassmann, Timo
Faulkner, Geoffrey J.
Mattick, John S.
Daub, Carsten O.
Carninci, Piero
Kawai, Jun
Suzuki, Harukazu
Hayashizaki, Yoshihide
Title Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries
Journal name Genome Research   Check publisher's open access policy
ISSN 1088-9051
1549-5469
Publication date 2010-02
Sub-type Article (original research)
DOI 10.1101/gr.095273.109
Open Access Status DOI
Volume 20
Issue 2
Start page 257
End page 264
Total pages 14
Place of publication Cold Spring Harbor, NY, United States
Publisher Cold Spring Harbor Laboratory Press
Collection year 2011
Language eng
Formatted 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.
Keyword Post transcriptional regulation
Small RNAs
Expression
Biogenesis
Modulation
Precursor
Alignment
Genomics
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2011 Collection
Institute for Molecular Bioscience - Publications
 
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Citation counts: TR Web of Science Citation Count  Cited 70 times in Thomson Reuters Web of Science Article | Citations
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Created: Sun, 21 Feb 2010, 00:07:36 EST