Journal of Genetic Medicine

Korean Society of Medical Genetics and Genomics (대한의학유전학회)
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Bioinformatics Approaches for the Identification and Annotation of RNA Editing Sites

  • Lee, Soo Youn (Seoul National University Biomedical Informatics (SNUBI) and Systems Biomedical Informatics Research Center) ;
  • Kim, Ju Han (Seoul National University Biomedical Informatics (SNUBI) and Systems Biomedical Informatics Research Center)
  • Received : 2013.06.04
  • Accepted : 2013.06.15
  • Published : 2013.06.30
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Abstract

Post-transcriptional nucleotide sequence modification of transcripts by RNA editing is an important molecular mechanism in the regulation of protein function and is associated with a variety of human disease phenotypes. Identification of RNA editing sites is the basic step for studying RNA editing. Databases and bioinformatics resources are used to annotate and evaluate as well as identify RNA editing sites. No method is free of limitations. Correctly establishing an analytic pipeline and strategic application of both experimental and bioinformatics methods constitute the first step in investigating RNA editing. This review summarizes modern bioinformatics approaches and related resources for RNA editing research.

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References

  1. Park E, Williams B, Wold BJ, Mortazavi A. RNA editing in the human ENCODE RNA-seq data. Genome Res 2012;22:1626-33. https://doi.org/10.1101/gr.134957.111
  2. Kleinman CL, Majewski J. Comment on "Widespread RNA and DNA sequence differences in the human transcriptome". Science 2012;335: 1302; author reply 1302.
  3. Lin W, Piskol R, Tan MH, Li JB. Comment on "Widespread RNA and DNA sequence differences in the human transcriptome". Science 2012;335: 1302; author reply 1302.
  4. Pickrell JK, Gilad Y, Pritchard JK. Comment on "Widespread RNA and DNA sequence differences in the human transcriptome". Science 2012; 335:1302; author reply 1302.
  5. Benne R, Van den Burg J, Brakenhoff JP, Sloof P, Van Boom JH, Tromp MC. Major transcript of the frameshifted coxII gene from trypanosome mitochondria contains four nucleotides that are not encoded in the DNA. Cell 1986;46:819-26. https://doi.org/10.1016/0092-8674(86)90063-2
  6. Nishikura K. Functions and regulation of RNA editing by ADAR deaminases. Annu Rev Biochem 2010;79:321-49. https://doi.org/10.1146/annurev-biochem-060208-105251
  7. Kim U, Wang Y, Sanford T, Zeng Y, Nishikura K. Molecular cloning of cDNA for double-stranded RNA adenosine deaminase, a candidate enzyme for nuclear RNA editing. Proc Natl Acad Sci U S A 1994;91: 11457-61. https://doi.org/10.1073/pnas.91.24.11457
  8. Kumar M, Carmichael GG. Nuclear antisense RNA induces extensive adenosine modifications and nuclear retention of target transcripts. Proc Natl Acad Sci U S A 1997;94:3542-7. https://doi.org/10.1073/pnas.94.8.3542
  9. Wagner RW, Smith JE, Cooperman BS, Nishikura K. A double-stranded RNA unwinding activity introduces structural alterations by means of adenosine to inosine conversions in mammalian cells and Xenopus eggs. Proc Natl Acad Sci U S A 1989;86:2647-51. https://doi.org/10.1073/pnas.86.8.2647
  10. Basilio C, Wahba AJ, Lengyel P, Speyer JF, Ochoa S. Synthetic polynucleotides and the amino acid code. V. Proc Natl Acad Sci U S A 1962;48: 613-6. https://doi.org/10.1073/pnas.48.4.613
  11. Gerber AP, Keller W. RNA editing by base deamination: more enzymes, more targets, new mysteries. Trends Biochem Sci 2001;26:376-84. https://doi.org/10.1016/S0968-0004(01)01827-8
  12. Maas S, Kawahara Y, Tamburro KM, Nishikura K. A-to-I RNA editing and human disease. RNA Biol 2006;3:1-9. https://doi.org/10.4161/rna.3.1.2495
  13. Athanasiadis A, Rich A, Maas S. Widespread A-to-I RNA editing of Alucontaining mRNAs in the human transcriptome. PLoS Biol 2004;2:e391. https://doi.org/10.1371/journal.pbio.0020391
  14. Kim DD, Kim TT, Walsh T, Kobayashi Y, Matise TC, Buyske S, et al. Widespread RNA editing of embedded alu elements in the human transcriptome. Genome Res 2004;14:1719-25. https://doi.org/10.1101/gr.2855504
  15. Nishikura K. Editor meets silencer: crosstalk between RNA editing and RNA interference. Nat Rev Mol Cell Biol 2006;7:919-31. https://doi.org/10.1038/nrm2061
  16. Cenci C, Barzotti R, Galeano F, Corbelli S, Rota R, Massimi L, et al. Down-regulation of RNA editing in pediatric astrocytomas: ADAR2 editing activity inhibits cell migration and proliferation. J Biol Chem 2008;283:7251-60. https://doi.org/10.1074/jbc.M708316200
  17. Paz N, Levanon EY, Amariglio N, Heimberger AB, Ram Z, Constantini S, et al. Altered adenosine-to-inosine RNA editing in human cancer. Genome Res 2007;17:1586-95. https://doi.org/10.1101/gr.6493107
  18. Peng PL, Zhong X, Tu W, Soundarapandian MM, Molner P, Zhu D, et al. ADAR2-dependent RNA editing of AMPA receptor subunit GluR2 determines vulnerability of neurons in forebrain ischemia. Neuron 2006;49:719-33. https://doi.org/10.1016/j.neuron.2006.01.025
  19. Huang WH, Tseng CN, Tang JY, Yang CH, Liang SS, Chang HW. RNA editing and drug discovery for cancer therapy. ScientificWorldJournal 2013;2013:804505.
  20. Decher N, Netter MF, Streit AK. Putative impact of RNA editing on drug discovery. Chem Biol Drug Des 2013;81:13-21. https://doi.org/10.1111/cbdd.12045
  21. Chakravarti A. Widespread promiscuous genetic information transfer from DNA to RNA. Circ Res 2011;109:1202-3. https://doi.org/10.1161/RES.0b013e31823c4992
  22. Li M, Wang IX, Li Y, Bruzel A, Richards AL, Toung JM, et al. Widespread RNA and DNA sequence differences in the human transcriptome. Science 2011;333:53-8. https://doi.org/10.1126/science.1207018
  23. Ramaswami G, Zhang R, Piskol R, Keegan LP, Deng P, O'Connell MA, et al. Identifying RNA editing sites using RNA sequencing data alone. Nat Methods 2013;10:128-32. https://doi.org/10.1038/nmeth.2330
  24. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memoryefficient alignment of short DNA sequences to the human genome. Genome Biol 2009;10:R25. https://doi.org/10.1186/gb-2009-10-3-r25
  25. Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009;25:1105-11. https://doi.org/10.1093/bioinformatics/btp120
  26. Peng Z, Cheng Y, Tan BC, Kang L, Tian Z, Zhu Y, et al. Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome. Nat Biotechnol 2012;30:253-60. https://doi.org/10.1038/nbt.2122
  27. Picardi E, D'Antonio M, Carrabino D, Castrignanò T, Pesole G. ExpEdit: a webserver to explore human RNA editing in RNA-Seq experiments. Bioinformatics 2011;27:1311-2. https://doi.org/10.1093/bioinformatics/btr117
  28. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009; 25:2078-9. https://doi.org/10.1093/bioinformatics/btp352
  29. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 2010; 20:1297-303. https://doi.org/10.1101/gr.107524.110
  30. Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, et al. The variant call format and VCFtools. Bioinformatics 2011;27:2156-8. https://doi.org/10.1093/bioinformatics/btr330
  31. Kiran AM, O'Mahony JJ, Sanjeev K, Baranov PV. Darned in 2013: inclusion of model organisms and linking with Wikipedia. Nucleic Acids Res 2013;41(Database issue):D258-61. https://doi.org/10.1093/nar/gks961
  32. Kiran A, Baranov PV. DARNED: a DAtabase of RNa EDiting in humans. Bioinformatics 2010;26:1772-6. https://doi.org/10.1093/bioinformatics/btq285
  33. He T, Du P, Li Y. dbRES: a web-oriented database for annotated RNA editing sites. Nucleic Acids Res 2007;35(Database issue):D141-4. https://doi.org/10.1093/nar/gkl815
  34. Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, et al. GenBank. Nucleic Acids Res 2013;41(Database issue):D36-42. https://doi.org/10.1093/nar/gks1195
  35. Picardi E, Regina TM, Brennicke A, Quagliariello C. REDIdb: the RNA editing database. Nucleic Acids Res 2007;35(Database issue):D173-7. https://doi.org/10.1093/nar/gkl793
  36. O'Brien EA, Zhang Y, Wang E, Marie V, Badejoko W, Lang BF, et al. GOBASE: an organelle genome database. Nucleic Acids Res 2009;37 (Database issue):D946-50. https://doi.org/10.1093/nar/gkn819
  37. Laganà A, Paone A, Veneziano D, Cascione L, Gasparini P, Carasi S, et al. miR-EdiTar: a database of predicted A-to-I edited miRNA target sites. Bioinformatics 2012;28:3166-8. https://doi.org/10.1093/bioinformatics/bts589
  38. 1000 Genomes Project Consortium, Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, et al. A map of human genome variation from population-scale sequencing. Nature 2010;467:1061-73. https://doi.org/10.1038/nature09534
  39. International HapMap 3 Consortium, Altshuler DM, Gibbs RA, Peltonen L, Altshuler DM, Gibbs RA, et al. Integrating common and rare genetic variation in diverse human populations. Nature 2010;467:52-8. https://doi.org/10.1038/nature09298
  40. Smigielski EM, Sirotkin K, Ward M, Sherry ST. dbSNP: a database of single nucleotide polymorphisms. Nucleic Acids Res 2000;28:352-5. https://doi.org/10.1093/nar/28.1.352