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Volumn 39, Issue 14, 2011, Pages 6044-6055

Complete characterization of the edited transcriptome of the mitochondrion of Physarum polycephalum using deep sequencing of RNA

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY RNA; DINUCLEOTIDE; TRANSCRIPTOME; TRANSFER RNA;

EID: 80051751272     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr180     Document Type: Article
Times cited : (35)

References (42)
  • 1
    • 79951578730 scopus 로고    scopus 로고
    • When you can't trust the DNA: RNA editing changes transcript sequences
    • Knoop, V. (2011) When you can't trust the DNA: RNA editing changes transcript sequences. Cell Mol. Life Sci., 68, 567-586.
    • (2011) Cell Mol. Life Sci. , vol.68 , pp. 567-586
    • Knoop, V.1
  • 2
    • 0037449753 scopus 로고    scopus 로고
    • C-to-U RNA editing: Mechanisms leading to genetic diversity
    • DOI 10.1074/jbc.R200024200
    • Blanc, V. and Davidson, N.O. (2003) C-to-U RNA editing: mechanisms leading to genetic diversity. J. Biol. Chem., 278, 1395-1398. (Pubitemid 36801361)
    • (2003) Journal of Biological Chemistry , vol.278 , Issue.3 , pp. 1395-1398
    • Blanc, V.1    Davidson, N.O.2
  • 3
    • 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
  • 5
    • 0036303481 scopus 로고    scopus 로고
    • Widespread and extensive editing of mitochondrial mRNAS in dinoflagellates
    • DOI 10.1016/S0022-2836(02)00468-0
    • Lin, S., Zhang, H., Spencer, D.F., Norman, J.E. and Gray, M.W. (2002) Widespread and extensive editing of mitochondrial mRNAS in dinoflagellates. J. Mol. Biol., 320, 727-739. (Pubitemid 34729401)
    • (2002) Journal of Molecular Biology , vol.320 , Issue.4 , pp. 727-739
    • Lin, S.1    Zhang, H.2    Spencer, D.F.3    Norman, J.E.4    Gray, M.W.5
  • 6
    • 0032992906 scopus 로고    scopus 로고
    • A novel nucleotide incorporation activity implicated in the editing of mitochondrial transfer RNAs in Acanthamoeba castellanii
    • DOI 10.1017/S1355838299981840
    • Price, D.H. and Gray, M.W. (1999) A novel nucleotide incorporation activity implicated in the editing of mitochondrial transfer RNAs in Acanthamoeba castellanii. RNA, 5, 302-317. (Pubitemid 29079289)
    • (1999) RNA , vol.5 , Issue.2 , pp. 302-317
    • Price, D.H.1    Gray, M.W.2
  • 7
    • 13244296941 scopus 로고    scopus 로고
    • In vitro characterization of a tRNA editing activity in the mitochondria of Spizellomyces punctatus, a chytridiomycete fungus
    • DOI 10.1074/jbc.M411273200
    • Bullerwell, C.E. and Gray, M.W. (2005) In vitro characterization of a tRNA editing activity in the mitochondria of Spizellomyces punctatus, a Chytridiomycete fungus. J. Biol. Chem., 280, 2463-2470. (Pubitemid 40189346)
    • (2005) Journal of Biological Chemistry , vol.280 , Issue.4 , pp. 2463-2470
    • Bullerwell, C.E.1    Gray, M.W.2
  • 8
    • 0034507456 scopus 로고    scopus 로고
    • Functions and mechanisms of RNA editing
    • DOI 10.1146/annurev.genet.34.1.499
    • Gott, J.M. and Emeson, R.B. (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
  • 9
    • 0026090511 scopus 로고
    • RNA editing by cytidine insertion in mitochondria of Physarum polycephalum
    • Mahendran, R., Spottswood, M.R. and Miller, D.L. (1991) RNA editing by cytidine insertion in mitochondria of Physarum polycephalum. Nature, 349, 434-438. (Pubitemid 21926108)
    • (1991) Nature , vol.349 , Issue.6308 , pp. 434-438
    • Mahendran, R.1    Spottswood, M.R.2    Miller, D.L.3
  • 10
    • 77950223517 scopus 로고    scopus 로고
    • Insertion/deletion editing in Physarum polycephalum
    • Goringer, H.U. (ed.) Springer, Berlin
    • Gott, J.M. and Rhee, A.C. (2007) Insertion/deletion editing in Physarum polycephalum. In Goringer, H.U. (ed.), RNA editing, Vol. 20. Springer, Berlin, pp. 85-104.
    • (2007) RNA Editing , vol.20 , pp. 85-104
    • Gott, J.M.1    Rhee, A.C.2
  • 11
    • 0035869059 scopus 로고    scopus 로고
    • Non-templated addition of nucleotides to the 3′ end of nascent RNA during RNA editing in Physarum
    • DOI 10.1093/emboj/20.6.1405
    • Cheng, Y.W., Visomirski-Robic, L.M. and Gott, J.M. (2001) Non-templated addition of nucleotides to the 30 end of nascent RNA during RNA editing in Physarum. EMBO J., 20, 1405-1414. (Pubitemid 32233980)
    • (2001) EMBO Journal , vol.20 , Issue.6 , pp. 1405-1414
    • Cheng, Y.-W.1    Visomirski-Robic, L.M.2    Gott, J.M.3
  • 12
    • 24944546687 scopus 로고    scopus 로고
    • Discovery of new genes and deletion editing in Physarum mitochondria enabled by a novel algorithm for finding edited mRNAs
    • DOI 10.1093/nar/gki820
    • Gott, J.M., Parimi, N. and Bundschuh, R. (2005) Discovery of new genes and deletion editing in Physarum mitochondria enabled by a novel algorithm for finding edited mRNAs. Nucleic Acids Res., 33, 5063-5072. (Pubitemid 41487814)
    • (2005) Nucleic Acids Research , vol.33 , Issue.16 , pp. 5063-5072
    • Gott, J.M.1    Parimi, N.2    Bundschuh, R.3
  • 13
    • 0027373196 scopus 로고
    • Substitutional and insertional RNA editing of the cytochrome c oxidase subunit 1 mRNA of Physarum polycephalum
    • Gott, J.M., Visomirski, L.M. and Hunter, J.L. (1993) Substitutional and insertional RNA editing of the cytochrome c oxidase subunit 1 mRNA of Physarum polycephalum. J. Biol. Chem., 268, 25483-25486. (Pubitemid 23358154)
    • (1993) Journal of Biological Chemistry , vol.268 , Issue.34 , pp. 25483-25486
    • Gott, J.M.1    Visomirski, L.M.2    Hunter, J.L.3
  • 14
    • 77149166632 scopus 로고    scopus 로고
    • Two forms of RNA editing are required for tRNA maturation in Physarum mitochondria
    • Gott, J.M., Somerlot, B.H. and Gray, M.W. (2010) Two forms of RNA editing are required for tRNA maturation in Physarum mitochondria. RNA, 16, 482-488.
    • (2010) RNA , vol.16 , pp. 482-488
    • Gott, J.M.1    Somerlot, B.H.2    Gray, M.W.3
  • 15
    • 0344113707 scopus 로고    scopus 로고
    • RNA editing in Physarum mitochondria
    • Grosjean, H. and Benne, R. (eds) ASM Press, Washington DC
    • Gott, J.M. and Visomirski-Robic, L.M. (1998) RNA editing in Physarum mitochondria. In Grosjean, H. and Benne, R. (eds), Modification and Editing of RNA. ASM Press, Washington DC, pp. 395-411.
    • (1998) Modification and Editing of RNA , pp. 395-411
    • Gott, J.M.1    Visomirski-Robic, L.M.2
  • 18
    • 37249023728 scopus 로고    scopus 로고
    • The process of RNA editing in plant mitochondria
    • DOI 10.1016/j.mito.2007.09.004, PII S1567724907002437, Unique Aspects of Plant Motichondria
    • Takenaka, M., Verbitskiy, D., van der Merwe, J.A., Zehrmann, A. and Brennicke, A. (2008) The process of RNA editing in plant mitochondria. Mitochondrion, 8, 35-46. (Pubitemid 350263734)
    • (2008) Mitochondrion , vol.8 , Issue.1 , pp. 35-46
    • Takenaka, M.1    Verbitskiy, D.2    Van Der Merwe, J.A.3    Zehrmann, A.4    Brennicke, A.5
  • 19
    • 79954584259 scopus 로고    scopus 로고
    • A unique transcriptome: 1782 positions of RNA editing alter 1406 codon identities in mitochondrial mRNAs of the lycophyte Isoetes engelmannii
    • doi:10.1093/nar/gkq1227 [Epub ahead of print, 7 December 2010]
    • Grewe, F., Herres, S., Viehover, P., Polsakiewicz, M., Weisshaar, B. and Knoop, V. (2010) A unique transcriptome: 1782 positions of RNA editing alter 1406 codon identities in mitochondrial mRNAs of the lycophyte Isoetes engelmannii. Nucleic Acids Res., doi:10.1093/nar/gkq1227 [Epub ahead of print, 7 December 2010].
    • (2010) Nucleic Acids Res.
    • Grewe, F.1    Herres, S.2    Viehover, P.3    Polsakiewicz, M.4    Weisshaar, B.5    Knoop, V.6
  • 20
    • 77955812141 scopus 로고    scopus 로고
    • Large-scale detection and analysis of RNA editing in grape mtDNA by RNA deep-sequencing
    • Picardi, E., Horner, D.S., Chiara, M., Schiavon, R., Valle, G. and 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
  • 21
    • 66349122954 scopus 로고    scopus 로고
    • Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing
    • Li, J.B., Levanon, E.Y., Yoon, J.-K., Aach, J., Xie, B., LeProust, E., Zhang, K., Gao, Y. and Church, G.M. (2009) Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing. Science, 324, 1210-1213.
    • (2009) Science , vol.324 , pp. 1210-1213
    • Li, J.B.1    Levanon, E.Y.2    Yoon, J.-K.3    Aach, J.4    Xie, B.5    Leproust, E.6    Zhang, K.7    Gao, Y.8    Church, G.M.9
  • 23
    • 77956850975 scopus 로고
    • Methods of culture for plasmodial myxomycetes
    • Prescott, D.M. (ed.) Academic Press, New York, NY
    • Daniel, J.W. and Baldwin, H.H. (1964) Methods of culture for plasmodial myxomycetes. In Prescott, D.M. (ed.), Methods in cell physiology. Academic Press, New York, NY, pp. 9-41.
    • (1964) Methods in Cell Physiology , pp. 9-41
    • Daniel, J.W.1    Baldwin, H.H.2
  • 26
    • 13244290067 scopus 로고    scopus 로고
    • Complex management: RNA editing in trypanosomes
    • DOI 10.1016/j.tibs.2004.12.006, PII S0968000404003202
    • Stuart, K.D., Schnaufer, A., Ernst, N.L. and Panigrahi, A.K. (2005) Complex management: RNA editing in trypanosomes. Trends Biochem. Sci., 30, 97-105. (Pubitemid 40187302)
    • (2005) Trends in Biochemical Sciences , vol.30 , Issue.2 , pp. 97-105
    • Stuart, K.D.1    Schnaufer, A.2    Ernst, N.L.3    Panigrahi, A.K.4
  • 27
    • 4444336611 scopus 로고    scopus 로고
    • Unexpectedly complex editing patterns at dinucleotide insertion sites in Physarum mitochondria
    • DOI 10.1128/MCB.24.18.7821-7828.2004
    • Byrne, E.M. and Gott, J.M. (2004) Unexpectedly complex editing patterns at dinucleotide insertion sites in Physarum mitochondria. Mol. Cell Biol., 24, 7821-7828. (Pubitemid 39167434)
    • (2004) Molecular and Cellular Biology , vol.24 , Issue.18 , pp. 7821-7828
    • Byrne, E.M.1    Gott, J.M.2
  • 28
    • 0031753256 scopus 로고    scopus 로고
    • Insertional editing of mitochondrial tRNAs of Physarum polycephalum and Didymium nigripes
    • Antes, T., Costandy, H., Mahendran, R., Spottswood, M. and Miller, D. (1998) Insertional editing of mitochondrial tRNAs of Physarum polycephalum and Didymium nigripes. Mol. Cell Biol., 18, 7521-7527. (Pubitemid 28533070)
    • (1998) Molecular and Cellular Biology , vol.18 , Issue.12 , pp. 7521-7527
    • Antes, T.1    Costandy, H.2    Mahendran, R.3    Spottswood, M.4    Miller, D.5
  • 30
    • 0025355799 scopus 로고
    • Mitochondrial DNA of Physarum polycephalum: Physical mapping, cloning and transcription mapping
    • DOI 10.1007/BF00314881
    • Jones, E.P., Mahendran, R., Spottswood, M.R., Yang, Y.C. and Miller, D.L. (1990) Mitochondrial DNA of Physarum polycephalum: physical mapping, cloning and transcription mapping. Curr. Genet., 17, 331-337. (Pubitemid 20161794)
    • (1990) Current Genetics , vol.17 , Issue.4 , pp. 331-337
    • Jones, E.P.1    Mahendran, R.2    Spottswood, M.R.3    Yang, Y.-C.4    Miller, D.L.5
  • 32
    • 0025189769 scopus 로고
    • A model for RNA editing in kinetoplastid mitochondria: "guide" RNA molecules transcribed from maxicircle DNA provide the edited information
    • Blum, B., Bakalara, N. and Simpson, L. (1990) A model for RNA editing in kinetoplastid mitochondria: "guide" RNA molecules transcribed from maxicircle DNA provide the edited information. Cell, 60, 189-198.
    • (1990) Cell , vol.60 , pp. 189-198
    • Blum, B.1    Bakalara, N.2    Simpson, L.3
  • 33
    • 34548577769 scopus 로고    scopus 로고
    • Strategies of kinetoplastid cryptogene discovery and analysis
    • Maslov, D.A. and Simpson, L. (2007) Strategies of kinetoplastid cryptogene discovery and analysis. Methods Enzymol., 424, 127-139.
    • (2007) Methods Enzymol. , vol.424 , pp. 127-139
    • Maslov, D.A.1    Simpson, L.2
  • 35
    • 0028127728 scopus 로고
    • Editing of the mitochondrial small subunit rRNA in Physarum polycephalum
    • Mahendran, R., Spottswood, M.S., Ghate, A., Ling, M.L., Jeng, K. and Miller, D.L. (1994) Editing of the mitochondrial small subunit rRNA in Physarum polycephalum. EMBO J., 13, 232-240.
    • (1994) EMBO J. , vol.13 , pp. 232-240
    • Mahendran, R.1    Spottswood, M.S.2    Ghate, A.3    Ling, M.L.4    Jeng, K.5    Miller, D.L.6
  • 36
    • 0033614039 scopus 로고    scopus 로고
    • Editing of cytochrome b mRNA in Physarum mitochondria
    • DOI 10.1074/jbc.274.5.2725
    • Wang, S.S., Mahendran, R. and Miller, D.L. (1999) Editing of cytochrome b mRNA in Physarum mitochondria. J. Biol. Chem., 274, 2725-2731. (Pubitemid 29075352)
    • (1999) Journal of Biological Chemistry , vol.274 , Issue.5 , pp. 2725-2731
    • Wang, S.S.1    Mahendran, R.2    Miller, D.L.3
  • 37
    • 78049297930 scopus 로고    scopus 로고
    • RNA editing is absent in a single mitochondrial gene of Didymium iridis
    • Hendrickson, P.G. and Silliker, M.E. (2010) RNA editing is absent in a single mitochondrial gene of Didymium iridis. Mycologia, 102, 1288-1294.
    • (2010) Mycologia , vol.102 , pp. 1288-1294
    • Hendrickson, P.G.1    Silliker, M.E.2
  • 38
    • 77953232837 scopus 로고    scopus 로고
    • RNA editing in six mitochondrial ribosomal protein genes of Didymium iridis
    • Hendrickson, P.G. and Silliker, M.E. (2010) RNA editing in six mitochondrial ribosomal protein genes of Didymium iridis. Curr. Genet., 56, 203-213.
    • (2010) Curr. Genet. , vol.56 , pp. 203-213
    • Hendrickson, P.G.1    Silliker, M.E.2
  • 39
    • 27144500686 scopus 로고    scopus 로고
    • A model for codon position bias in RNA editing
    • Liu, T. and Bundschuh, R. (2005) A model for codon position bias in RNA editing. Phys. Rev. Lett., 95, 088101.
    • (2005) Phys. Rev. Lett. , vol.95 , pp. 088101
    • Liu, T.1    Bundschuh, R.2
  • 40
    • 0027225783 scopus 로고
    • A compilation of large subunit (23S and 23S-like) ribosomal RNA structures: 1993
    • Gutell, R.R., Gray, M.W. and Schnare, M.N. (1993) A compilation of large subunit (23S and 23S-like) ribosomal RNA structures: 1993. Nucleic Acids Res., 21, 3055-3074. (Pubitemid 23223605)
    • (1993) Nucleic Acids Research , vol.21 , Issue.13 , pp. 3055-3074
    • Gutell, R.R.1    Gray, M.W.2    Schnare, M.N.3
  • 41
    • 69049120274 scopus 로고    scopus 로고
    • Distinct roles for sequences upstream of and downstream from Physarum editing sites
    • Rhee, A.C., Somerlot, B.H., Parimi, N. and Gott, J.M. (2009) Distinct roles for sequences upstream of and downstream from Physarum editing sites. RNA, 15, 1753-1765.
    • (2009) RNA , vol.15 , pp. 1753-1765
    • Rhee, A.C.1    Somerlot, B.H.2    Parimi, N.3    Gott, J.M.4
  • 42
    • 0025359331 scopus 로고
    • A stuttering model for paramyxovirus P mRNA editing
    • Vidal, S., Curran, J. and Kolakofsky, D. (1990) A stuttering model for paramyxovirus P mRNA editing. EMBO J., 9, 2017-2022.
    • (1990) EMBO J. , vol.9 , pp. 2017-2022
    • Vidal, S.1    Curran, J.2    Kolakofsky, D.3


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