Abstract
Deep sequencing has many possible applications; one of them is the identification and quantification of RNA editing sites. The most common type of RNA editing is adenosine to inosine (A-to-I) editing. A prerequisite for this editing process is a double-stranded RNA (dsRNA) structure. Such dsRNAs are formed as part of the microRNA (miRNA) maturation process, and it is therefore expected that miRNAs are affected by A-to-I editing. Indeed, tens of editing sites were found in miRNAs, some of which change the miRNA binding specificity. Here, we describe a protocol for the identification of RNA editing sites in mature miRNAs using deep sequencing data.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsSpringer Nature is developing a new tool to find and evaluate Protocols. Learn more
References
Nishikura K (2010) Functions and regulation of RNA editing by ADAR deaminases. Annu Rev Biochem 79:321–349
Yang W, Chendrimada TP, Wang Q et al (2006) Modulation of microRNA processing and expression through RNA editing by ADAR deaminases. Nat Struct Mol Biol 13:13–21
Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281–297
Kawahara Y, Zinshteyn B, Sethupathy P et al (2007) Redirection of silencing targets by adenosine-to-inosine editing of miRNAs. Science 315:1137–1140
Burroughs AM, Ando Y, de Hoon MJL et al (2010) A comprehensive survey of 3′ animal miRNA modification events and a possible role for 3′ adenylation in modulating miRNA targeting effectiveness. Genome Res 20:1398–1410
de Hoon MJL, Taft RJ, Hashimoto T et al (2010) Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries. Genome Res 20:257–264
Alon S, Mor E, Vigneault F et al (2012) Systematic identification of edited microRNAs in the human brain. Genome Res 22:1533–1540
Li M, Wang IX, Li Y et al (2011) Widespread RNA and DNA sequence differences in the human transcriptome. Science 333:53–58
Lin W, Piskol R, Tan MH et al (2012) Comment on “widespread RNA and DNA sequence differences in the human transcriptome”. Science 335:1302
Langmead B, Trapnell C, Pop M et al (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25
Stocks MB, Moxon S, Mapleson D et al (2012) The UEA sRNA workbench: a suite of tools for analysing and visualising next generation sequencing microRNA and small RNA datasets. Bioinformatics 28:2059–2061
Zhu E, Zhao F, Xu G et al (2010) mirTools: microRNA profiling and discovery based on high-throughput sequencing. Nucleic Acids Res 38:W392–W397
Zuker M, Stiegler P (1981) Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res 9:133–148
Acknowledgments
This work was partially supported by a grant from the United States–Israel Binational Science Foundation (grant number 2009/290), Jerusalem, Israel, to EE. SA was supported by a Clore Fellowship.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2013 Springer Science+Business Media New York
About this protocol
Cite this protocol
Alon, S., Eisenberg, E. (2013). Identifying RNA Editing Sites in miRNAs by Deep Sequencing. In: Shomron, N. (eds) Deep Sequencing Data Analysis. Methods in Molecular Biology, vol 1038. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-514-9_9
Download citation
DOI: https://doi.org/10.1007/978-1-62703-514-9_9
Published:
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-62703-513-2
Online ISBN: 978-1-62703-514-9
eBook Packages: Springer Protocols