Identifying RNA editing sites in miRNAs by deep sequencing.

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.

[1]  A. Hatzigeorgiou,et al.  Redirection of Silencing Targets by Adenosine-to-Inosine Editing of miRNAs , 2007, Science.

[2]  P. Seeburg,et al.  Modulation of microRNA processing and expression through RNA editing by ADAR deaminases , 2006, Nature Structural &Molecular Biology.

[3]  Gang Xu,et al.  mirTools: microRNA profiling and discovery based on high-throughput sequencing , 2010, Nucleic Acids Res..

[4]  Vincent Moulton,et al.  The UEA sRNA workbench: a suite of tools for analysing and visualizing next generation sequencing microRNA and small RNA datasets , 2012, Bioinform..

[5]  K. Nishikura.  Functions and regulation of RNA editing by ADAR deaminases. , 2010, Annual review of biochemistry.

[6]  Jin Billy Li,et al.  Comment on “Widespread RNA and DNA Sequence Differences in the Human Transcriptome” , 2012, Science.

[7]  Michael Zuker,et al.  Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information , 1981, Nucleic Acids Res..

[8]  J. Kawai,et al.  Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries. , 2010, Genome research.

[9]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[10]  Shahar Alon,et al.  Systematic identification of edited microRNAs in the human brain , 2012, Genome research.

[11]  Y. Hayashizaki,et al.  A comprehensive survey of 3' animal miRNA modification events and a possible role for 3' adenylation in modulating miRNA targeting effectiveness. , 2010, Genome research.

[12]  Mingyao Li,et al.  Widespread RNA and DNA Sequence Differences in the Human Transcriptome , 2011, Science.

[13]  D. Bartel.  MicroRNAs Genomics, Biogenesis, Mechanism, and Function , 2004, Cell.