Using REDItools to Detect RNA Editing Events in NGS Datasets

RNA editing is a post‐transcriptional/co‐transcriptional molecular phenomenon whereby a genetic message is modified from the corresponding DNA template by means of substitutions, insertions, and/or deletions. It occurs in a variety of organisms and different cellular locations through evolutionally and biochemically unrelated proteins. RNA editing has a plethora of biological effects including the modulation of alternative splicing and fine‐tuning of gene expression. RNA editing events by base substitutions can be detected on a genomic scale by NGS technologies through the REDItools package, an ad hoc suite of Python scripts to study RNA editing using RNA‐Seq and DNA‐Seq data or RNA‐Seq data alone. REDItools implement effective filters to minimize biases due to sequencing errors, mapping errors, and SNPs. The package is freely available at Google Code repository (http://code.google.com/p/reditools/) and released under the MIT license. In the present unit we show three basic protocols corresponding to three main REDItools scripts. © 2015 by John Wiley & Sons, Inc.

[1]  M. Jantsch,et al.  Proteome diversification by adenosine to inosine RNA-editing , 2010, RNA biology.

[2]  Ernesto Picardi,et al.  REDIdb: the RNA editing database , 2006, Nucleic Acids Res..

[3]  Giorgio Valle,et al.  Large-scale detection and analysis of RNA editing in grape mtDNA by RNA deep-sequencing , 2010, Nucleic acids research.

[4]  Angela Gallo,et al.  ADARs: allies or enemies? The importance of A‐to‐I RNA editing in human disease: from cancer to HIV‐1 , 2012, Biological reviews of the Cambridge Philosophical Society.

[5]  R. Emeson,et al.  Functions and mechanisms of RNA editing. , 2000, Annual review of genetics.

[6]  Pavel V. Baranov,et al.  Darned in 2013: inclusion of model organisms and linking with Wikipedia , 2012, Nucleic Acids Res..

[7]  F. Kempken,et al.  Cell type-specific loss of atp6 RNA editing in cytoplasmic male sterile Sorghum bicolor. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[8]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[9]  Jin Billy Li,et al.  Accurate identification of human Alu and non-Alu RNA editing sites , 2012, Nature Methods.

[10]  J. Harrow,et al.  Systematic evaluation of spliced alignment programs for RNA-seq data , 2013, Nature Methods.

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

[12]  Ernesto Picardi,et al.  REDItools: high-throughput RNA editing detection made easy , 2013, Bioinform..

[13]  Serban Nacu,et al.  Fast and SNP-tolerant detection of complex variants and splicing in short reads , 2010, Bioinform..

[14]  A. Brennicke,et al.  REDIdb: an upgraded bioinformatics resource for organellar RNA editing sites. , 2011, Mitochondrion.

[15]  Jin Billy Li,et al.  RADAR: a rigorously annotated database of A-to-I RNA editing , 2013, Nucleic Acids Res..