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Volumn 22, Issue 1, 2012, Pages 142-150

Accurate identification of A-to-I RNA editing in human by transcriptome sequencing

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Indexed keywords

TRANSCRIPTOME;

EID: 84855320189     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.124107.111     Document Type: Article
Times cited : (278)

References (58)
  • 2
    • 12344300804 scopus 로고    scopus 로고
    • Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome
    • doi: 10.1371/journal.pbio.0020391
    • Athanasiadis A, Rich A,Maas S. 2004.Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome. PLoS Biol 2: e391. doi: 10.1371/journal.pbio.0020391.
    • (2004) PLoS Biol , vol.2
    • Athanasiadis, A.1    Rich, A.2    Maas, S.3
  • 3
    • 0028685490 scopus 로고
    • Fitting a mixture model by expectation maximization to discover motifs in biopolymers
    • Bailey TL, Elkan C. 1994. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 2: 28-36.
    • (1994) Proc Int Conf Intell Syst Mol Biol , vol.2 , pp. 28-36
    • Bailey, T.L.1    Elkan, C.2
  • 4
    • 0035997389 scopus 로고    scopus 로고
    • RNA editing by adenosine deaminases that act on RNA
    • DOI 10.1146/annurev.biochem.71.110601.135501
    • Bass BL. 2002. RNA editing by adenosine deaminases that act on RNA. Annu Rev Biochem 71: 817-846. (Pubitemid 34800236)
    • (2002) Annual Review of Biochemistry , vol.71 , pp. 817-846
    • Bass, B.L.1
  • 6
    • 33746882054 scopus 로고    scopus 로고
    • Gene expression profiling of acute myeloid leukemia with translocation t(8;16)(p11;p13) and MYST3-CREBBP rearrangement reveals a distinctive signature with a specific pattern of HOX gene expression
    • DOI 10.1158/0008-5472.CAN-05-4601
    • Camos M, Esteve J, Jares P, Colomer D, Rozman M, Villamor N, Costa D, Carrio A, Nomdedeu J, Montserrat E, et al. 2006. Gene expression profiling of acute myeloid leukemia with translocation t(8;16)(p11;p13) and MYST3-CREBBP rearrangement reveals a distinctive signature with a specific pattern of HOX gene expression. Cancer Res 66: 6947-6954. (Pubitemid 44197669)
    • (2006) Cancer Research , vol.66 , Issue.14 , pp. 6947-6954
    • Camos, M.1    Esteve, J.2    Jares, P.3    Colomer, D.4    Rozman, M.5    Villamor, N.6    Costa, D.7    Carrio, A.8    Nomdedeu, J.9    Montserrat, E.10    Campo, E.11
  • 8
    • 76749101197 scopus 로고    scopus 로고
    • U87MG decoded: The genomic sequence of a cytogenetically aberrant human cancer cell line
    • doi: 10.1371/journal.pgen.1000832
    • Clark MJ, Homer N, O'Connor BD, Chen Z, Eskin A, Lee H, Merriman B, Nelson SF. 2010. U87MG decoded: the genomic sequence of a cytogenetically aberrant human cancer cell line. PLoS Genet 6: e1000832. doi: 10.1371/journal.pgen.1000832.
    • (2010) PLoS Genet , vol.6
    • Clark, M.J.1    Homer, N.2    O'Connor, B.D.3    Chen, Z.4    Eskin, A.5    Lee, H.6    Merriman, B.7    Nelson, S.F.8
  • 11
    • 77951922861 scopus 로고    scopus 로고
    • Molecular diversity through RNA editing: A balancing act
    • Farajollahi S, Maas S. 2010. Molecular diversity through RNA editing: a balancing act. Trends Genet 26: 221-230.
    • (2010) Trends Genet , vol.26 , pp. 221-230
    • Farajollahi, S.1    Maas, S.2
  • 12
    • 54349084037 scopus 로고    scopus 로고
    • A-to-I RNA editing and cancer: From pathology to basic science
    • Gallo A, Galardi S. 2008. A-to-I RNA editing and cancer: from pathology to basic science. RNA Biol 5: 135-139.
    • (2008) RNA Biol , vol.5 , pp. 135-139
    • Gallo, A.1    Galardi, S.2
  • 14
    • 70349524975 scopus 로고    scopus 로고
    • RNA editing: A driving force for adaptive evolution?
    • Gommans WM, Mullen SP, Maas S. 2009. RNA editing: a driving force for adaptive evolution? Bioessays 31: 1137-1145.
    • (2009) Bioessays , vol.31 , pp. 1137-1145
    • Gommans, W.M.1    Mullen, S.P.2    Maas, S.3
  • 15
    • 0034507456 scopus 로고    scopus 로고
    • Functions and mechanisms of RNA editing
    • DOI 10.1146/annurev.genet.34.1.499
    • Gott JM, Emeson RB. 2000. Functions and mechanisms of RNA editing. Annu Rev Genet 34: 499-531. (Pubitemid 32065931)
    • (2000) Annual Review of Genetics , vol.34 , pp. 499-531
    • Gott, J.M.1    Emeson, R.B.2
  • 17
    • 0042528670 scopus 로고    scopus 로고
    • Nervous system targets of RNA editing identified by comparative genomics
    • DOI 10.1126/science.1086763
    • Hoopengardner B, Bhalla T, Staber C, Reenan R. 2003. Nervous system targets of RNA editing identified by comparative genomics. Science 301: 832-836. (Pubitemid 36962624)
    • (2003) Science , vol.301 , Issue.5634 , pp. 832-836
    • Hoopengardner, B.1    Bhalla, T.2    Staber, C.3    Reenan, R.4
  • 18
    • 79960914208 scopus 로고    scopus 로고
    • Extensive genomic and transcriptional diversity identified through massively parallel DNA and RNA sequencing of 18 Korean individuals
    • Ju YS, Kim JI, Kim S, Hong D, Park H, Shin JY, Lee S, Lee WC, Yu SB, Park SS, et al. 2011. Extensive genomic and transcriptional diversity identified through massively parallel DNA and RNA sequencing of 18 Korean individuals. Nat Genet 43: 745-752.
    • (2011) Nat Genet , vol.43 , pp. 745-752
    • Ju, Y.S.1    Kim, J.I.2    Kim, S.3    Hong, D.4    Park, H.5    Shin, J.Y.6    Lee, S.7    Lee, W.C.8    Yu, S.B.9    Park, S.S.10
  • 19
    • 33847317017 scopus 로고    scopus 로고
    • Redirection of silencing targets by adenosine-to-inosine editing of miRNAs
    • DOI 10.1126/science.1138050
    • Kawahara Y, Zinshteyn B, Sethupathy P, Iizasa H, Hatzigeorgiou AG, Nishikura K. 2007. Redirection of silencing targets by adenosine-toinosine editing of miRNAs. Science 315: 1137-1140. (Pubitemid 46328026)
    • (2007) Science , vol.315 , Issue.5815 , pp. 1137-1140
    • Kawahara, Y.1    Zinshteyn, B.2    Sethupathy, P.3    Iizasa, H.4    Hatzigeorgiou, A.G.5    Nishikura, K.6
  • 21
    • 0036226603 scopus 로고    scopus 로고
    • BLAT: The BLAST-like alignment tool
    • Kent WJ. 2002. BLAT: the BLAST-like alignment tool. Genome Res 12: 656-664.
    • (2002) Genome Res , vol.12 , pp. 656-664
    • Kent, W.J.1
  • 23
    • 77954505224 scopus 로고    scopus 로고
    • DARNED: A DAtabase of RNa EDiting in humans
    • Kiran A, Baranov PV. 2010. DARNED: a DAtabase of RNa EDiting in humans. Bioinformatics 26: 1772-1776.
    • (2010) Bioinformatics , vol.26 , pp. 1772-1776
    • Kiran, A.1    Baranov, P.V.2
  • 25
    • 33947649553 scopus 로고    scopus 로고
    • Evolutionary history of 7SL RNA-derived SINEs in Supraprimates
    • DOI 10.1016/j.tig.2007.02.002, PII S0168952507000376
    • Kriegs JO, Churakov G, Jurka J, Brosius J, Schmitz J. 2007. Evolutionary history of 7SL RNA-derived SINEs in supraprimates. Trends Genet 23: 158-161. (Pubitemid 46497508)
    • (2007) Trends in Genetics , vol.23 , Issue.4 , pp. 158-161
    • Kriegs, J.O.1    Churakov, G.2    Jurka, J.3    Brosius, J.4    Schmitz, J.5
  • 26
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • doi: 10.1186/gb-2009-10-3-r25
    • Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25. doi: 10.1186/gb-2009-10-3-r25.
    • (2009) Genome Biol , vol.10
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 27
    • 33645765165 scopus 로고    scopus 로고
    • RNA editing and alternative splicing: The importance of co-transcriptional coordination
    • Laurencikiene J, Kallman AM, Fong N, Bentley DL, Ohman M. 2006. RNA editing and alternative splicing: the importance of co-transcriptional coordination. EMBO Rep 7: 303-307.
    • (2006) EMBO Rep , vol.7 , pp. 303-307
    • Laurencikiene, J.1    Kallman, A.M.2    Fong, N.3    Bentley, D.L.4    Ohman, M.5
  • 28
    • 0034711082 scopus 로고    scopus 로고
    • Double-stranded RNA adenosine deaminases ADAR1 and ADAR2 have overlapping specificities
    • Lehmann KA, Bass BL. 2000. Double-stranded RNA adenosine deaminases ADAR1 and ADAR2 have overlapping specificities. Biochemistry 39: 12875-12884.
    • (2000) Biochemistry , vol.39 , pp. 12875-12884
    • Lehmann, K.A.1    Bass, B.L.2
  • 30
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows- Wheeler transform
    • Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows- Wheeler transform. Bioinformatics 25: 1754-1760.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 32
    • 66449114324 scopus 로고    scopus 로고
    • SNP detection for massively parallel whole-genome resequencing
    • Li R, Li Y, Fang X, Yang H, Wang J, Kristiansen K. 2009b. SNP detection for massively parallel whole-genome resequencing. Genome Res 19: 1124-1132.
    • (2009) Genome Res , vol.19 , pp. 1124-1132
    • Li, R.1    Li, Y.2    Fang, X.3    Yang, H.4    Wang, J.5    Kristiansen, K.6
  • 34
    • 33947719472 scopus 로고    scopus 로고
    • Hypothesis: RNA editing of microRNA target sites in humans?
    • DOI 10.1261/rna.296407
    • Liang H, Landweber LF. 2007. Hypothesis: RNA editing of microRNA target sites in humans? RNA 13: 463-467. (Pubitemid 46506929)
    • (2007) RNA , vol.13 , Issue.4 , pp. 463-467
    • Liang, H.1    Landweber, L.F.2
  • 35
    • 79952460585 scopus 로고    scopus 로고
    • Gene regulation through RNA editing
    • Maas S. 2010. Gene regulation through RNA editing. Discov Med 10: 379-386.
    • (2010) Discov Med , vol.10 , pp. 379-386
    • Maas, S.1
  • 36
    • 33748607688 scopus 로고    scopus 로고
    • Breaking the central dogma by RNA editing
    • DOI 10.1021/cr050314a
    • Maydanovych O, Beal PA. 2006. Breaking the central dogma by RNA editing. Chem Rev 106: 3397-3411. (Pubitemid 44376942)
    • (2006) Chemical Reviews , vol.106 , Issue.8 , pp. 3397-3411
    • Maydanovych, O.1    Beal, P.A.2
  • 37
    • 46249106990 scopus 로고    scopus 로고
    • Mapping and quantifying mammalian transcriptomes by RNA-Seq
    • DOI 10.1038/nmeth.1226, PII NMETH.1226
    • Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. 2008. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5: 621-628. (Pubitemid 351911867)
    • (2008) Nature Methods , vol.5 , Issue.7 , pp. 621-628
    • Mortazavi, A.1    Williams, B.A.2    McCue, K.3    Schaeffer, L.4    Wold, B.5
  • 38
    • 77952293063 scopus 로고    scopus 로고
    • Functions and regulation of RNA editing by ADAR deaminases
    • Nishikura K. 2010. Functions and regulation of RNA editing by ADAR deaminases. Annu Rev Biochem 79: 321-349.
    • (2010) Annu Rev Biochem , vol.79 , pp. 321-349
    • Nishikura, K.1
  • 41
    • 70449711243 scopus 로고    scopus 로고
    • Computation for ChIP-seq and RNAseq studies
    • Pepke S, Wold B, Mortazavi A. 2009. Computation for ChIP-seq and RNAseq studies. Nat Methods 6 (11 Suppl): S22-S32.
    • (2009) Nat Methods , vol.6 , Issue.11 SUPPL.
    • Pepke, S.1    Wold, B.2    Mortazavi, A.3
  • 42
    • 77955812141 scopus 로고    scopus 로고
    • Large-scale detection and analysis of RNA editing in grape mtDNA by RNA deep-sequencing
    • Picardi E, Horner DS, Chiara M, Schiavon R, Valle G, Pesole G. 2010. Large-scale detection and analysis of RNA editing in grape mtDNA by RNA deep-sequencing. Nucleic Acids Res 38: 4755-4767.
    • (2010) Nucleic Acids Res , vol.38 , pp. 4755-4767
    • Picardi, E.1    Horner, D.S.2    Chiara, M.3    Schiavon, R.4    Valle, G.5    Pesole, G.6
  • 43
    • 52949093215 scopus 로고    scopus 로고
    • Mouse let-7 miRNA populations exhibit RNA editing that is constrained in the 5′-seed/cleavage/anchor regions and stabilize predicted mmu-let-7a:mRNA duplexes
    • Reid JG, Nagaraja AK, Lynn FC, Drabek RB, Muzny DM, Shaw CA, Weiss MK, Naghavi AO, Khan M, Zhu H, et al. 2008. Mouse let-7 miRNA populations exhibit RNA editing that is constrained in the 5′-seed/cleavage/anchor regions and stabilize predicted mmu-let-7a:mRNA duplexes. Genome Res 18: 1571-1581.
    • (2008) Genome Res , vol.18 , pp. 1571-1581
    • Reid, J.G.1    Nagaraja, A.K.2    Lynn, F.C.3    Drabek, R.B.4    Muzny, D.M.5    Shaw, C.A.6    Weiss, M.K.7    Naghavi, A.O.8    Khan, M.9    Zhu, H.10
  • 44
    • 63849136153 scopus 로고    scopus 로고
    • Protein kinase C isoforms: Multi-functional regulators of cell life and death
    • Reyland ME. 2009. Protein kinase C isoforms: multi-functional regulators of cell life and death. Front Biosci 14: 2386-2399.
    • (2009) Front Biosci , vol.14 , pp. 2386-2399
    • Reyland, M.E.1
  • 45
    • 0024273119 scopus 로고
    • The accuracy of reverse transcriptase from HIV-1
    • Roberts JD, Bebenek K, Kunkel TA. 1988. The accuracy of reverse transcriptase from HIV-1. Science 242: 1171-1173. (Pubitemid 19007043)
    • (1988) Science , vol.242 , Issue.4882 , pp. 1171-1173
    • Roberts, J.D.1    Bebenek, K.2    Kunkel, T.A.3
  • 46
  • 47
    • 0033529064 scopus 로고    scopus 로고
    • Regulation of alternative splicing by RNA editing
    • Rueter SM, Dawson TR, Emeson RB. 1999. Regulation of alternative splicing by RNA editing. Nature 399: 75-80.
    • (1999) Nature , vol.399 , pp. 75-80
    • Rueter, S.M.1    Dawson, T.R.2    Emeson, R.B.3
  • 48
    • 34547121502 scopus 로고    scopus 로고
    • Regulation of glutamate receptor B pre-mRNA splicing by RNA editing
    • DOI 10.1093/nar/gkm314
    • Schoft VK, Schopoff S, Jantsch MF. 2007. Regulation of glutamate receptor B pre-mRNA splicing by RNA editing. Nucleic Acids Res 35: 3723-3732. (Pubitemid 47244665)
    • (2007) Nucleic Acids Research , vol.35 , Issue.11 , pp. 3723-3732
    • Schoft, V.K.1    Schopoff, S.2    Jantsch, M.F.3
  • 51
    • 38649084399 scopus 로고    scopus 로고
    • A-to-I editing sites are a genomically encoded G: Implications for the evolutionary significance and identification of novel editing sites
    • DOI 10.1261/rna.797108
    • Tian N, Wu X, Zhang Y, Jin Y. 2008. A-to-I editing sites are a genomically encoded G: implications for the evolutionary significance and identification of novel editing sites. RNA 14: 211-216. (Pubitemid 351171581)
    • (2008) RNA , vol.14 , Issue.2 , pp. 211-216
    • Tian, N.1    Wu, X.2    Zhang, Y.3    Jin, Y.4
  • 52
    • 65449136284 scopus 로고    scopus 로고
    • TopHat: Discovering splice junctions with RNA-Seq
    • Trapnell C, Pachter L, Salzberg SL. 2009. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25: 1105-1111.
    • (2009) Bioinformatics , vol.25 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3
  • 53
    • 33745622868 scopus 로고    scopus 로고
    • Two Sample Logo: A graphical representation of the differences between two sets of sequence alignments
    • DOI 10.1093/bioinformatics/btl151
    • Vacic V, Iakoucheva LM, Radivojac P. 2006. Two Sample Logo: a graphical representation of the differences between two sets of sequence alignments. Bioinformatics 22: 1536-1537. (Pubitemid 43985328)
    • (2006) Bioinformatics , vol.22 , Issue.12 , pp. 1536-1537
    • Vacic, V.1    Iakoucheva, L.M.2    Radivojac, P.3
  • 54
    • 0036567270 scopus 로고    scopus 로고
    • A putative RNA editing from U to C in a mouse mitochondrial transcript
    • Villegas J, Muller I, Arredondo J, Pinto R, Burzio LO. 2002. A putative RNA editing from U to C in a mouse mitochondrial transcript. Nucleic Acids Res 30: 1895-1901. (Pubitemid 34537583)
    • (2002) Nucleic Acids Research , vol.30 , Issue.9 , pp. 1895-1901
    • Villegas, J.1    Muller, I.2    Arredondo, J.3    Pinto, R.4    Burzio, L.O.5
  • 55
    • 66449129109 scopus 로고    scopus 로고
    • Large-scale mRNA sequencing determines global regulation of RNA editing during brain development
    • Wahlstedt H, Daniel C, Enstero M, Ohman M. 2009. Large-scale mRNA sequencing determines global regulation of RNA editing during brain development. Genome Res 19: 978-986.
    • (2009) Genome Res , vol.19 , pp. 978-986
    • Wahlstedt, H.1    Daniel, C.2    Enstero, M.3    Ohman, M.4
  • 56
    • 78751569755 scopus 로고    scopus 로고
    • Elucidating the inosinome: Global approaches to adenosine-to-inosineRNA editing
    • Wulff BE, Sakurai M, Nishikura K. 2010. Elucidating the inosinome: global approaches to adenosine-to-inosineRNA editing. Nat Rev Genet 12: 81-85.
    • (2010) Nat Rev Genet , vol.12 , pp. 81-85
    • Wulff, B.E.1    Sakurai, M.2    Nishikura, K.3
  • 57
    • 47949099524 scopus 로고    scopus 로고
    • A-to-I RNA editing alters less-conserved residues of highly conserved coding regions: Implications for dual functions in evolution
    • Yang Y, Lv J, Gui B, Yin H, Wu X, Zhang Y, Jin Y. 2008. A-to-I RNA editing alters less-conserved residues of highly conserved coding regions: implications for dual functions in evolution. RNA 14: 1516-1525.
    • (2008) RNA , vol.14 , pp. 1516-1525
    • Yang, Y.1    Lv, J.2    Gui, B.3    Yin, H.4    Wu, X.5    Zhang, Y.6    Jin, Y.7
  • 58
    • 77953180687 scopus 로고    scopus 로고
    • A survey of genomic traces reveals a common sequencing error, RNA editing, and DNA editing
    • doi: 10.1371/journal.pgen.1000954
    • Zaranek AW, Levanon EY, Zecharia T, Clegg T, Church GM. 2010. A survey of genomic traces reveals a common sequencing error, RNA editing, and DNA editing. PLoS Genet 6: e1000954. doi: 10.1371/journal.pgen.1000954.
    • (2010) PLoS Genet , vol.6
    • Zaranek, A.W.1    Levanon, E.Y.2    Zecharia, T.3    Clegg, T.4    Church, G.M.5


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