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Volumn 358, Issue 1, 2007, Pages 336-341

Prediction of C-to-U RNA editing sites in higher plant mitochondria using only nucleotide sequence features

Author keywords

C to U; Prediction; RNA editing; SVM; Triplets

Indexed keywords

CYTIDINE; RNA;

EID: 34248221207     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2007.04.130     Document Type: Article
Times cited : (17)

References (41)
  • 1
    • 33748607688 scopus 로고    scopus 로고
    • Breaking the central dogma by RNA editing
    • Maydanovych O., and Beal P.A. Breaking the central dogma by RNA editing. Chem. Rev. 106 (2006) 3397-3411
    • (2006) Chem. Rev. , vol.106 , pp. 3397-3411
    • Maydanovych, O.1    Beal, P.A.2
  • 3
    • 0037449753 scopus 로고    scopus 로고
    • C-to-U RNA editing: mechanisms leading to genetic diversity
    • Blanc V., and Davidson N.O. C-to-U RNA editing: mechanisms leading to genetic diversity. J. Biol. Chem. 278 (2002) 1395-1398
    • (2002) J. Biol. Chem. , vol.278 , pp. 1395-1398
    • Blanc, V.1    Davidson, N.O.2
  • 4
    • 33645074681 scopus 로고    scopus 로고
    • RNA editing in plant organelles: machinery, physiological function and evolution
    • Shikanai T. RNA editing in plant organelles: machinery, physiological function and evolution. Cell. Mol. Life Sci. 63 (2006) 698-708
    • (2006) Cell. Mol. Life Sci. , vol.63 , pp. 698-708
    • Shikanai, T.1
  • 5
    • 0022552305 scopus 로고
    • Major transcript of the frameshifted coxII gene from trypanosome mitochondria contains four nucleotides that are not encoded in the DNA
    • Benne R., Burg J.V.D., Brakenhoff J.P.J., Sloof P., Boom J.H.V., and Tromp M.C. Major transcript of the frameshifted coxII gene from trypanosome mitochondria contains four nucleotides that are not encoded in the DNA. Cell 46 (1986) 819-826
    • (1986) Cell , vol.46 , pp. 819-826
    • Benne, R.1    Burg, J.V.D.2    Brakenhoff, J.P.J.3    Sloof, P.4    Boom, J.H.V.5    Tromp, M.C.6
  • 6
    • 0023763122 scopus 로고
    • Biased hypermutation and other genetic changes in defective measles viruses in human brain infections
    • Cattaneo R., Schmid A., Eschle D., Baczko K., Meulen V.t., and Billeter M.A. Biased hypermutation and other genetic changes in defective measles viruses in human brain infections. Cell 55 (1988) 255-265
    • (1988) Cell , vol.55 , pp. 255-265
    • Cattaneo, R.1    Schmid, A.2    Eschle, D.3    Baczko, K.4    Meulen, V.t.5    Billeter, M.A.6
  • 7
    • 0023651359 scopus 로고
    • A novel form of tissue-specific RNA processing produces apolipoprotein-B48 in intestine
    • Powell L.M., Wallis S.C., Pease R.J., Edwards Y.H., Knott T.J., and Scott J. A novel form of tissue-specific RNA processing produces apolipoprotein-B48 in intestine. Cell 50 (1987) 831-840
    • (1987) Cell , vol.50 , pp. 831-840
    • Powell, L.M.1    Wallis, S.C.2    Pease, R.J.3    Edwards, Y.H.4    Knott, T.J.5    Scott, J.6
  • 8
    • 0025995296 scopus 로고
    • RNA editing in brain controls a determinant of ion flow in glutamate-gated channels
    • Sommer B., Köhler M., Sprengel R., and Seeburg P.H. RNA editing in brain controls a determinant of ion flow in glutamate-gated channels. Cell 67 (1991) 11-19
    • (1991) Cell , vol.67 , pp. 11-19
    • Sommer, B.1    Köhler, M.2    Sprengel, R.3    Seeburg, P.H.4
  • 9
    • 0030998440 scopus 로고    scopus 로고
    • Occurrence of plastid RNA editing in all major lineages of land plants
    • Freyer R., Kiefer-Meyer M.-C., and Kössel H. Occurrence of plastid RNA editing in all major lineages of land plants. Proc. Natl. Acad. Sci. USA 94 (1997) 6285-6290
    • (1997) Proc. Natl. Acad. Sci. USA , vol.94 , pp. 6285-6290
    • Freyer, R.1    Kiefer-Meyer, M.-C.2    Kössel, H.3
  • 10
    • 0027972519 scopus 로고
    • Evidence for RNA editing in mitochondria of all major groups of land plants except the Bryophyta
    • Hiesel R., Combettes B., and Brennicke A. Evidence for RNA editing in mitochondria of all major groups of land plants except the Bryophyta. Proc. Natl. Acad. Sci. USA 91 (1994) 629-633
    • (1994) Proc. Natl. Acad. Sci. USA , vol.91 , pp. 629-633
    • Hiesel, R.1    Combettes, B.2    Brennicke, A.3
  • 11
    • 0029863292 scopus 로고    scopus 로고
    • RNA editing in bryophytes and a molecular phylogeny of land plants
    • Malek O., Lättig K., Hiesel R., Brennicke A., and Knoop V. RNA editing in bryophytes and a molecular phylogeny of land plants. EMBO J. 15 (1996) 1403-1411
    • (1996) EMBO J. , vol.15 , pp. 1403-1411
    • Malek, O.1    Lättig, K.2    Hiesel, R.3    Brennicke, A.4    Knoop, V.5
  • 13
    • 12344300804 scopus 로고    scopus 로고
    • Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome
    • Athanasiadis A., Rich A., and Maas S. Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome. PLoS Biol. 2 (2004) e391
    • (2004) PLoS Biol. , vol.2
    • Athanasiadis, A.1    Rich, A.2    Maas, S.3
  • 14
    • 20744459167 scopus 로고    scopus 로고
    • A bioinformatic screen for novel A-I RNA editing sites reveals recoding editing in BC10
    • Clutterbuck D.R., Leroy A., O'Connell M.A., and Semple C.A.M. A bioinformatic screen for novel A-I RNA editing sites reveals recoding editing in BC10. Bioinformatics 21 (2005) 2590-2595
    • (2005) Bioinformatics , vol.21 , pp. 2590-2595
    • Clutterbuck, D.R.1    Leroy, A.2    O'Connell, M.A.3    Semple, C.A.M.4
  • 17
    • 0037062438 scopus 로고    scopus 로고
    • RNA hairpins in noncoding regions of human brain and Caenorhabditis elegans mRNA are edited by adenosine deaminases that act on RNA
    • Morse D.P., Aruscavage P.J., and Bass B.L. RNA hairpins in noncoding regions of human brain and Caenorhabditis elegans mRNA are edited by adenosine deaminases that act on RNA. Proc. Natl. Acad. Sci. USA 99 (2002) 7906-7911
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 7906-7911
    • Morse, D.P.1    Aruscavage, P.J.2    Bass, B.L.3
  • 18
    • 0032980354 scopus 로고    scopus 로고
    • RNA editing site recognition in higher plant mitochondria
    • Mulligan R.M., Williams M.A., and Shanahan M.T. RNA editing site recognition in higher plant mitochondria. J. Hered. 90 (1999) 338-344
    • (1999) J. Hered. , vol.90 , pp. 338-344
    • Mulligan, R.M.1    Williams, M.A.2    Shanahan, M.T.3
  • 19
    • 0027131046 scopus 로고
    • RNA editing in plant mitochondria: [alpha]-phosphate is retained during C-to-U conversion in mRNAs
    • Rajasekhar V.K., and Mulligan R.M. RNA editing in plant mitochondria: [alpha]-phosphate is retained during C-to-U conversion in mRNAs. Plant Cell 5 (1993) 1843-1852
    • (1993) Plant Cell , vol.5 , pp. 1843-1852
    • Rajasekhar, V.K.1    Mulligan, R.M.2
  • 20
    • 0029095915 scopus 로고
    • Evidence for a site-specific cytidine deamination reaction involved in C-to-U RNA editing of plant mitochondria
    • Yu W., and Schuster W. Evidence for a site-specific cytidine deamination reaction involved in C-to-U RNA editing of plant mitochondria. J. Biol. Chem. 270 (1995) 18227-18233
    • (1995) J. Biol. Chem. , vol.270 , pp. 18227-18233
    • Yu, W.1    Schuster, W.2
  • 21
    • 0033592907 scopus 로고    scopus 로고
    • RNA editing in arabidopsis mitochondria effects 441 C-to-U changes in ORFs
    • Giegé P., and Brennicke A. RNA editing in arabidopsis mitochondria effects 441 C-to-U changes in ORFs. Proc. Natl. Acad. Sci. USA 96 (1999) 15324-15329
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 15324-15329
    • Giegé, P.1    Brennicke, A.2
  • 22
    • 0344442430 scopus 로고    scopus 로고
    • The complete nucleotide sequence and RNA editing content of the mitochondrial genome of rapeseed (Brassica napus L.): comparative analysis of the mitochondrial genomes of rapeseed and Arabidopsis thaliana
    • Handa H. The complete nucleotide sequence and RNA editing content of the mitochondrial genome of rapeseed (Brassica napus L.): comparative analysis of the mitochondrial genomes of rapeseed and Arabidopsis thaliana. Nucleic Acids Res. 31 (2003) 5907-5916
    • (2003) Nucleic Acids Res. , vol.31 , pp. 5907-5916
    • Handa, H.1
  • 23
    • 0036456491 scopus 로고    scopus 로고
    • The complete sequence of the rice (Oryza sativa L.) mitochondrial genome: frequent DNA sequence acquisition and loss during the evolution of flowering plants
    • Notsu Y., Masood S., Nishikawa T., Kubo N., Akiduki G., Nakazono M., Hirai A., and Kadowaki K. The complete sequence of the rice (Oryza sativa L.) mitochondrial genome: frequent DNA sequence acquisition and loss during the evolution of flowering plants. Mol. Genet. Genomics 268 (2002) 434-445
    • (2002) Mol. Genet. Genomics , vol.268 , pp. 434-445
    • Notsu, Y.1    Masood, S.2    Nishikawa, T.3    Kubo, N.4    Akiduki, G.5    Nakazono, M.6    Hirai, A.7    Kadowaki, K.8
  • 24
    • 0024419064 scopus 로고
    • RNA editing in plant mitochondria
    • Covello P.S., and Gray M.W. RNA editing in plant mitochondria. Nature 341 (1989) 662-666
    • (1989) Nature , vol.341 , pp. 662-666
    • Covello, P.S.1    Gray, M.W.2
  • 25
    • 0024414676 scopus 로고
    • RNA editing in wheat mitochondria results in the conservation of protein sequences
    • Gualberto J.M., Lamattina L., Bonnard G., Weil J.-H., and Grienenberger J.-M. RNA editing in wheat mitochondria results in the conservation of protein sequences. Nature 341 (1989) 660-662
    • (1989) Nature , vol.341 , pp. 660-662
    • Gualberto, J.M.1    Lamattina, L.2    Bonnard, G.3    Weil, J.-H.4    Grienenberger, J.-M.5
  • 27
    • 13244255317 scopus 로고    scopus 로고
    • Simple statistical models predict C-to-U edited sites in plant mitochondrial RNA
    • Cummings M.P., and Myers D.S. Simple statistical models predict C-to-U edited sites in plant mitochondrial RNA. BMC Bioinformatics 5 (2004)
    • (2004) BMC Bioinformatics , vol.5
    • Cummings, M.P.1    Myers, D.S.2
  • 28
    • 25444502084 scopus 로고    scopus 로고
    • PREP-Mt: predictive RNA editor for plant mitochondrial genes
    • Mower J.P. PREP-Mt: predictive RNA editor for plant mitochondrial genes. BMC Bioinformatics 6 (2005)
    • (2005) BMC Bioinformatics , vol.6
    • Mower, J.P.1
  • 29
    • 33646545074 scopus 로고    scopus 로고
    • Genetic algorithm learning as a robust approach to RNA editing site prediction
    • Thompson J., and Gopal S. Genetic algorithm learning as a robust approach to RNA editing site prediction. BMC Bioinformatics 7 (2006)
    • (2006) BMC Bioinformatics , vol.7
    • Thompson, J.1    Gopal, S.2
  • 30
    • 33646545074 scopus 로고    scopus 로고
    • Correction: genetic algorithm learning as a robust approach to RNA editing site prediction
    • Thompson J., and Gopal S. Correction: genetic algorithm learning as a robust approach to RNA editing site prediction. BMC Bioinformatics 7 (2006)
    • (2006) BMC Bioinformatics , vol.7
    • Thompson, J.1    Gopal, S.2
  • 31
    • 0034802513 scopus 로고    scopus 로고
    • cis Recognition elements in plant mitochondrion RNA editing
    • Farre J.-C., Leon G., Jordana X., and Araya A. cis Recognition elements in plant mitochondrion RNA editing. Mol. Cell. Biol. 21 (2001) 6731-6737
    • (2001) Mol. Cell. Biol. , vol.21 , pp. 6731-6737
    • Farre, J.-C.1    Leon, G.2    Jordana, X.3    Araya, A.4
  • 32
    • 33748755541 scopus 로고    scopus 로고
    • Sequence elements critical for efficient RNA editing of a tobacco chloroplast transcript in vivo and in vitro
    • Hayes M.L., Reed M.L., Hegeman C.E., and Hanson M.R. Sequence elements critical for efficient RNA editing of a tobacco chloroplast transcript in vivo and in vitro. Nucleic Acids Res. 34 (2006) 3742-3754
    • (2006) Nucleic Acids Res. , vol.34 , pp. 3742-3754
    • Hayes, M.L.1    Reed, M.L.2    Hegeman, C.E.3    Hanson, M.R.4
  • 33
    • 3442882802 scopus 로고    scopus 로고
    • Complex cis-elements determine an RNA editing site in pea mitochondria
    • Takenaka M., Neuwirt J., and Brennicke A. Complex cis-elements determine an RNA editing site in pea mitochondria. Nucleic Acids Res. 32 (2004) 4137-4144
    • (2004) Nucleic Acids Res. , vol.32 , pp. 4137-4144
    • Takenaka, M.1    Neuwirt, J.2    Brennicke, A.3
  • 34
    • 34248166744 scopus 로고    scopus 로고
    • J.-H. Hung, W.-C. Wang, H.-D. Huang, Systematic identification and repository of RNA editing site in human genome, in: International Computer Symposium, 2006, pp. 1386-1391.
  • 35
    • 33846048733 scopus 로고    scopus 로고
    • dbRES: a web-oriented database for annotated RNA editing sites
    • He T., Du P., and Li Y. dbRES: a web-oriented database for annotated RNA editing sites. Nucleic Acids Res. 35 Database Issue (2007) D141-D144
    • (2007) Nucleic Acids Res. , vol.35 , Issue.Database Issue
    • He, T.1    Du, P.2    Li, Y.3
  • 37
    • 13444252846 scopus 로고    scopus 로고
    • Different patterns in the recognition of editing sites in plant mitochondria
    • Choury D., Farre J.-C., Jordana X., and Arays A. Different patterns in the recognition of editing sites in plant mitochondria. Nucleic Acids Res. 32 (2004) 6397-6406
    • (2004) Nucleic Acids Res. , vol.32 , pp. 6397-6406
    • Choury, D.1    Farre, J.-C.2    Jordana, X.3    Arays, A.4
  • 38
    • 0030770731 scopus 로고    scopus 로고
    • Identification of critical nucleotide positions for plastid RNA editing site recognition
    • Bock R., Hermann M., and Fuchs M. Identification of critical nucleotide positions for plastid RNA editing site recognition. RNA 3 (1997) 1194-1200
    • (1997) RNA , vol.3 , pp. 1194-1200
    • Bock, R.1    Hermann, M.2    Fuchs, M.3
  • 40
    • 34248203345 scopus 로고    scopus 로고
    • V.N. Vapnik, The Nature of Statistical Learning Theory, second ed., Tsinghua University Press, Beijing, 2000 (in Chinese).
  • 41
    • 34248160705 scopus 로고    scopus 로고
    • C.-C. Chang, C.-J. Lin, LIBSVM: a library for support vector machines, 2001.


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