Browse > Article
http://dx.doi.org/10.5734/JGM.2013.10.1.27

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)
Publication Information
Journal of Genetic Medicine / v.10, no.1, 2013 , pp. 27-32 More about this Journal
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.
Keywords
RNA editing; RNA-Seq; Bioinformatics;
Citations & Related Records
연도 인용수 순위
  • Reference
1 Park E, Williams B, Wold BJ, Mortazavi A. RNA editing in the human ENCODE RNA-seq data. Genome Res 2012;22:1626-33.   DOI
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.   DOI
6 Nishikura K. Functions and regulation of RNA editing by ADAR deaminases. Annu Rev Biochem 2010;79:321-49.   DOI
7 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.   DOI
8 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.   DOI
9 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.   DOI
10 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.   DOI
11 Gerber AP, Keller W. RNA editing by base deamination: more enzymes, more targets, new mysteries. Trends Biochem Sci 2001;26:376-84.   DOI
12 Maas S, Kawahara Y, Tamburro KM, Nishikura K. A-to-I RNA editing and human disease. RNA Biol 2006;3:1-9.   DOI
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.   DOI
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.   DOI
15 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.   DOI
16 Nishikura K. Editor meets silencer: crosstalk between RNA editing and RNA interference. Nat Rev Mol Cell Biol 2006;7:919-31.   DOI
17 Huang WH, Tseng CN, Tang JY, Yang CH, Liang SS, Chang HW. RNA editing and drug discovery for cancer therapy. ScientificWorldJournal 2013;2013:804505.
18 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.   DOI
19 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.   DOI
20 Decher N, Netter MF, Streit AK. Putative impact of RNA editing on drug discovery. Chem Biol Drug Des 2013;81:13-21.   DOI
21 Chakravarti A. Widespread promiscuous genetic information transfer from DNA to RNA. Circ Res 2011;109:1202-3.   DOI
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.   DOI
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.   DOI
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.   DOI
25 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.   DOI
26 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.   DOI
27 Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009;25:1105-11.   DOI
28 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.   DOI
29 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.   DOI
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.   DOI
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.   DOI
32 Kiran A, Baranov PV. DARNED: a DAtabase of RNa EDiting in humans. Bioinformatics 2010;26:1772-6.   DOI
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.   DOI
34 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.   DOI
35 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.   DOI
36 Picardi E, Regina TM, Brennicke A, Quagliariello C. REDIdb: the RNA editing database. Nucleic Acids Res 2007;35(Database issue):D173-7.   DOI
37 Smigielski EM, Sirotkin K, Ward M, Sherry ST. dbSNP: a database of single nucleotide polymorphisms. Nucleic Acids Res 2000;28:352-5.   DOI
38 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.   DOI
39 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.   DOI
40 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.   DOI