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Volumn 421, Issue 1-2, 2008, Pages 14-19

Lower GC-content in editing exons: Implications for regulation by molecular characteristics maintained by selection

Author keywords

G and Ka Ks; GC content; Purifying selection; RNA editing

Indexed keywords

DNA; NUCLEOTIDE; RNA;

EID: 48549095628     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2008.05.012     Document Type: Article
Times cited : (3)

References (55)
  • 1
    • 0027141519 scopus 로고
    • Number of CpG islands and genes in human and mouse
    • Antequera F., and Bird A. Number of CpG islands and genes in human and mouse. Proc. Natl. Acad. Sci. U. S. A. 90 (1993) 11995-11999
    • (1993) Proc. Natl. Acad. Sci. U. S. A. , vol.90 , pp. 11995-11999
    • Antequera, F.1    Bird, A.2
  • 2
    • 0033962272 scopus 로고    scopus 로고
    • A phylogenetic analysis reveals an unusual sequence conservation within introns involved in RNA editing
    • Aruscavage P.J., and Bass B.L. A phylogenetic analysis reveals an unusual sequence conservation within introns involved in RNA editing. RNA 6 (2000) 257-269
    • (2000) RNA , vol.6 , pp. 257-269
    • Aruscavage, P.J.1    Bass, B.L.2
  • 3
    • 0035997389 scopus 로고    scopus 로고
    • RNA editing by adenosine deaminases that act on RNA
    • Bass B.L. RNA editing by adenosine deaminases that act on RNA. Annu. Rev. Biochem. 71 (2002) 817-846
    • (2002) Annu. Rev. Biochem. , vol.71 , pp. 817-846
    • Bass, B.L.1
  • 4
    • 0037046560 scopus 로고    scopus 로고
    • Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2)
    • Bentley S.D., et al. Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 417 (2002) 141-147
    • (2002) Nature , vol.417 , pp. 141-147
    • Bentley, S.D.1
  • 5
    • 0037108764 scopus 로고    scopus 로고
    • Linkage limits the power of natural selection in Drosophila
    • Betancourt A.J., and Presgraves D.C. Linkage limits the power of natural selection in Drosophila. Proc. Natl. Acad. Sci. U. S. A. 99 (2002) 13616-13620
    • (2002) Proc. Natl. Acad. Sci. U. S. A. , vol.99 , pp. 13616-13620
    • Betancourt, A.J.1    Presgraves, D.C.2
  • 6
    • 0346991738 scopus 로고    scopus 로고
    • The problem of counting sites in the estimation of the synonymous and nonsynonymous substitution rates: implications for the correlation between the synonymous substitution rate and codon usage bias
    • Bierne N., and Eyre-Walker A. The problem of counting sites in the estimation of the synonymous and nonsynonymous substitution rates: implications for the correlation between the synonymous substitution rate and codon usage bias. Genetics 165 (2003) 1587-1597
    • (2003) Genetics , vol.165 , pp. 1587-1597
    • Bierne, N.1    Eyre-Walker, A.2
  • 9
    • 0033527048 scopus 로고    scopus 로고
    • The complete nucleotide sequence of chromosome 3 of Plasmodium falciparum
    • Bowman S., et al. The complete nucleotide sequence of chromosome 3 of Plasmodium falciparum. Nature 400 (1999) 532-538
    • (1999) Nature , vol.400 , pp. 532-538
    • Bowman, S.1
  • 10
    • 0025779286 scopus 로고
    • Synonymous nucleotide substitution rates in mammalian genes: implications for the molecular clock and the relationship of mammalian orders
    • Bulmer M., Wolfe K.H., and Sharp P.M. Synonymous nucleotide substitution rates in mammalian genes: implications for the molecular clock and the relationship of mammalian orders. Proc. Natl. Acad. Sci. U. S. A. 88 (1991) 5974-5978
    • (1991) Proc. Natl. Acad. Sci. U. S. A. , vol.88 , pp. 5974-5978
    • Bulmer, M.1    Wolfe, K.H.2    Sharp, P.M.3
  • 11
    • 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
  • 12
    • 0029563023 scopus 로고
    • A method for estimating the numbers of synonymous and nosynonymous subsitutions per site
    • Comeron J.M. A method for estimating the numbers of synonymous and nosynonymous subsitutions per site. J. Mol. Evol. 41 (1995) 1152-1159
    • (1995) J. Mol. Evol. , vol.41 , pp. 1152-1159
    • Comeron, J.M.1
  • 13
    • 0032825011 scopus 로고    scopus 로고
    • K-Estimator: calculation of the number of nucleotide subsitutions per site and the confidence intervals
    • Comeron J.M. K-Estimator: calculation of the number of nucleotide subsitutions per site and the confidence intervals. Bioinformatics. 15 (1999) 763-764
    • (1999) Bioinformatics. , vol.15 , pp. 763-764
    • Comeron, J.M.1
  • 14
    • 1042289731 scopus 로고    scopus 로고
    • Structure and sequence determinants required for the RNA editing of ADAR2 substrates
    • Dawson T., Sansam C., and Emeson R. Structure and sequence determinants required for the RNA editing of ADAR2 substrates. J. Biol. Chem. 279 (2004) 4941-4951
    • (2004) J. Biol. Chem. , vol.279 , pp. 4941-4951
    • Dawson, T.1    Sansam, C.2    Emeson, R.3
  • 15
    • 0036889468 scopus 로고    scopus 로고
    • Evolution of synonymous codon usage in metazoans
    • Duret L. Evolution of synonymous codon usage in metazoans. Curr. Opin. Genet. Dev. 12 (2002) 640-649
    • (2002) Curr. Opin. Genet. Dev. , vol.12 , pp. 640-649
    • Duret, L.1
  • 17
    • 0019776838 scopus 로고
    • Chromosome structure and the C-value paradox
    • Gall J.G. Chromosome structure and the C-value paradox. J. Cell Biol. 91 (1981) 3s-14s
    • (1981) J. Cell Biol. , vol.91
    • Gall, J.G.1
  • 18
    • 12744257602 scopus 로고    scopus 로고
    • Chromosome 2 sequence of the human malaria parasite Plasmodium falciparum
    • Gardner M.J., et al. Chromosome 2 sequence of the human malaria parasite Plasmodium falciparum. Science 282 (1998) 1126-1132
    • (1998) Science , vol.282 , pp. 1126-1132
    • Gardner, M.J.1
  • 19
    • 0014468084 scopus 로고
    • Deoxyribonucleic acid base composition in the taxonomy of Staphylococcus
    • Garrity F.L., Detrick B., and Dennedy E.R. Deoxyribonucleic acid base composition in the taxonomy of Staphylococcus. J. Bacteriol. 97 (1969) 557-560
    • (1969) J. Bacteriol. , vol.97 , pp. 557-560
    • Garrity, F.L.1    Detrick, B.2    Dennedy, E.R.3
  • 20
    • 0035090476 scopus 로고    scopus 로고
    • Coincidence, coevolution, or causation? DNA content, cell size, and the C-value enigma
    • Gregory T.R. Coincidence, coevolution, or causation? DNA content, cell size, and the C-value enigma. Biol. Rev. Camb. Philos. Soc. 76 (2001) 65-101
    • (2001) Biol. Rev. Camb. Philos. Soc. , vol.76 , pp. 65-101
    • Gregory, T.R.1
  • 22
    • 0029877296 scopus 로고    scopus 로고
    • Q/R site editing in kainate receptor GluR5 and GluR6 pre-mRNAs requires distant intronic sequences
    • Herb A., Higuchi M., Sprengel R., and Seeburg P.H. Q/R site editing in kainate receptor GluR5 and GluR6 pre-mRNAs requires distant intronic sequences. Proc. Natl. Acad. Sci. U. S. A. 93 (1996) 1875-1880
    • (1996) Proc. Natl. Acad. Sci. U. S. A. , vol.93 , pp. 1875-1880
    • Herb, A.1    Higuchi, M.2    Sprengel, R.3    Seeburg, P.H.4
  • 23
    • 0027772363 scopus 로고
    • RNA editing of AMPA receptor subunit GluR-B: a base-paired intron-exon structure determines position and efficiency
    • Higuchi M., Single F.N., Kohler M., Sommer B., Sprengel R., and Seeburg P.H. RNA editing of AMPA receptor subunit GluR-B: a base-paired intron-exon structure determines position and efficiency. Cell 75 (1993) 1361-1370
    • (1993) Cell , vol.75 , pp. 1361-1370
    • Higuchi, M.1    Single, F.N.2    Kohler, M.3    Sommer, B.4    Sprengel, R.5    Seeburg, P.H.6
  • 24
    • 0042528670 scopus 로고    scopus 로고
    • Nerous system targets of RNA editing identified by comparative genomics
    • Hoopengardner B., Bhalla T., Staber C., and Reenan R. Nerous system targets of RNA editing identified by comparative genomics. Science 301 (2003) 832-836
    • (2003) Science , vol.301 , pp. 832-836
    • Hoopengardner, B.1    Bhalla, T.2    Staber, C.3    Reenan, R.4
  • 25
    • 7244245762 scopus 로고    scopus 로고
    • Finishing the euchromatic sequence of the human genome
    • International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature 431 (2004) 931-945
    • (2004) Nature , vol.431 , pp. 931-945
    • International Human Genome Sequencing Consortium1
  • 26
    • 33748118463 scopus 로고    scopus 로고
    • The nicotinic acetylcholine receptor gene family of the honey bee, Apis mellifera
    • Jones A.K., Raymond-Delpech V., Thany S.H., Gauthier M., and Sattelle D.B. The nicotinic acetylcholine receptor gene family of the honey bee, Apis mellifera. Genome Res. 16 (2006) 1422-1430
    • (2006) Genome Res. , vol.16 , pp. 1422-1430
    • Jones, A.K.1    Raymond-Delpech, V.2    Thany, S.H.3    Gauthier, M.4    Sattelle, D.B.5
  • 27
    • 36049014434 scopus 로고    scopus 로고
    • The cys-loop ligand-gated ion channel gene superfamily of the red flour beetle, Tribolium castaneum
    • Jones A.K., and Sattelle D.B. The cys-loop ligand-gated ion channel gene superfamily of the red flour beetle, Tribolium castaneum. BMC Genomics. 8 (2007) 327
    • (2007) BMC Genomics. , vol.8 , pp. 327
    • Jones, A.K.1    Sattelle, D.B.2
  • 30
    • 0036640951 scopus 로고    scopus 로고
    • Human SNP variability and mutation rate are higher in regions of high recombination
    • Lercher M.J., and Hurst L.D. Human SNP variability and mutation rate are higher in regions of high recombination. Trends Genet. 18 (2002) 337-340
    • (2002) Trends Genet. , vol.18 , pp. 337-340
    • Lercher, M.J.1    Hurst, L.D.2
  • 33
    • 33746541594 scopus 로고    scopus 로고
    • The role of a metastable RNA secondary structure in hepatitis delta virus genotype III RNA editing
    • Linnstaedt S.D., Kasprzak W.K., Shapiro B.A., and Casey J.L. The role of a metastable RNA secondary structure in hepatitis delta virus genotype III RNA editing. RNA 12 (2006) 1-13
    • (2006) RNA , vol.12 , pp. 1-13
    • Linnstaedt, S.D.1    Kasprzak, W.K.2    Shapiro, B.A.3    Casey, J.L.4
  • 34
    • 15844368815 scopus 로고    scopus 로고
    • Structural requirements for RNA editing in glutamate receptor pre-mRNAs by recombinant double-stranded RNA adenosine deaminase
    • Maas S., Melcher T., Herb A., Seeburg P.H., Keller W., Krause S., Higuchi M., and O'Connell M.A. Structural requirements for RNA editing in glutamate receptor pre-mRNAs by recombinant double-stranded RNA adenosine deaminase. J. Biol. Chem. 271 (1996) 12221-12226
    • (1996) J. Biol. Chem. , vol.271 , pp. 12221-12226
    • Maas, S.1    Melcher, T.2    Herb, A.3    Seeburg, P.H.4    Keller, W.5    Krause, S.6    Higuchi, M.7    O'Connell, M.A.8
  • 35
    • 1142302213 scopus 로고    scopus 로고
    • Selection on codon usage in Drosophila Americana
    • Maside X., Lee A.W., and Charlesworth B. Selection on codon usage in Drosophila Americana. Curr Biol. 14 (2005) 150-154
    • (2005) Curr Biol. , vol.14 , pp. 150-154
    • Maside, X.1    Lee, A.W.2    Charlesworth, B.3
  • 36
    • 0027153966 scopus 로고
    • Codon usage bias and base composition of nuclear genes in Drosophila
    • Moriyama E.N., and Hartl D.L. Codon usage bias and base composition of nuclear genes in Drosophila. Genetics 134 (1993) 847-858
    • (1993) Genetics , vol.134 , pp. 847-858
    • Moriyama, E.N.1    Hartl, D.L.2
  • 37
    • 28544447032 scopus 로고    scopus 로고
    • A method to find tissue-specific novel sites of selective adenosine deamination
    • Ohlson J., Ensterö M., Sjöberg B.M., and Öhman M. A method to find tissue-specific novel sites of selective adenosine deamination. Nucleic Acids Res. 33 (2005) e167
    • (2005) Nucleic Acids Res. , vol.33
    • Ohlson, J.1    Ensterö, M.2    Sjöberg, B.M.3    Öhman, M.4
  • 39
    • 0035252113 scopus 로고    scopus 로고
    • The RNA world meets behavior: A→I pre-mRNA editing in animals
    • Reenan R.A. The RNA world meets behavior: A→I pre-mRNA editing in animals. Trends Genet. 17 (2001) 53-56
    • (2001) Trends Genet. , vol.17 , pp. 53-56
    • Reenan, R.A.1
  • 40
    • 15244351357 scopus 로고    scopus 로고
    • Molecular determinants and guided evolution of species-specific RNA editing
    • Reenan R.A. Molecular determinants and guided evolution of species-specific RNA editing. Nature 434 (2005) 409-413
    • (2005) Nature , vol.434 , pp. 409-413
    • Reenan, R.A.1
  • 41
    • 0033529064 scopus 로고    scopus 로고
    • Regulation of alternative splicing by RNA editing
    • Rueter S.M., Dawson T.R., and Emeson R.B. Regulation of alternative splicing by RNA editing. Nature 399 (1999) 75-80
    • (1999) Nature , vol.399 , pp. 75-80
    • Rueter, S.M.1    Dawson, T.R.2    Emeson, R.B.3
  • 42
    • 0037449779 scopus 로고    scopus 로고
    • RNA editing minireview series
    • Samuel C.E. RNA editing minireview series. J. Biol. Chem. 278 (2003) 1389-1390
    • (2003) J. Biol. Chem. , vol.278 , pp. 1389-1390
    • Samuel, C.E.1
  • 43
    • 35649025709 scopus 로고    scopus 로고
    • The nicotinic acetylcholine receptor gene family of the silkworm, Bombyx mori
    • Shao Y.M., Dong K., and Zhang C.X. The nicotinic acetylcholine receptor gene family of the silkworm, Bombyx mori. BMC Genomics. 8 (2007) 324
    • (2007) BMC Genomics. , vol.8 , pp. 324
    • Shao, Y.M.1    Dong, K.2    Zhang, C.X.3
  • 44
    • 33748102415 scopus 로고    scopus 로고
    • Nucleotide substitution pattern in rice paralogues: implication for negative correlation between the synonymous substitution rate and codon usage bias
    • Shi X., Wang X., Li Z., Zhu Q., Tang W., Ge S., and Luo J. Nucleotide substitution pattern in rice paralogues: implication for negative correlation between the synonymous substitution rate and codon usage bias. Gene. 367 (2006) 199-206
    • (2006) Gene. , vol.367 , pp. 199-206
    • Shi, X.1    Wang, X.2    Li, Z.3    Zhu, Q.4    Tang, W.5    Ge, S.6    Luo, J.7
  • 45
    • 0007245956 scopus 로고
    • Agreement between deoxyribonucleic acid base composition and taxometric classification of gram-positive cocci
    • Silvestri L.G., and Hill L.G. Agreement between deoxyribonucleic acid base composition and taxometric classification of gram-positive cocci. J. Bacteriol. 90 (1965) 136-140
    • (1965) J. Bacteriol. , vol.90 , pp. 136-140
    • Silvestri, L.G.1    Hill, L.G.2
  • 46
    • 0034750390 scopus 로고    scopus 로고
    • Nucleotide substitution rate estimation in enterobacteria: approximate and maximum-likelihood methods lead to similar conclusions
    • Smith N.G., and Eyre-Walker A. Nucleotide substitution rate estimation in enterobacteria: approximate and maximum-likelihood methods lead to similar conclusions. Mol. Biol. Evol. 18 (2001) 2124-2126
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 2124-2126
    • Smith, N.G.1    Eyre-Walker, A.2
  • 47
    • 33751081282 scopus 로고    scopus 로고
    • RNA editing in Drosophila melanogaster: new targets and functional consequences
    • Stapleton M., Carlson J.W., and Celniker S.E. RNA editing in Drosophila melanogaster: new targets and functional consequences. RNA 12 (2006) 1-11
    • (2006) RNA , vol.12 , pp. 1-11
    • Stapleton, M.1    Carlson, J.W.2    Celniker, S.E.3
  • 48
    • 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) 145
    • (2006) BMC Bioinformatics , vol.7 , pp. 145
    • Thompson, J.1    Gopal, S.2
  • 49
    • 0344305774 scopus 로고    scopus 로고
    • Mutations in RNAi rescue aberrant chemotaxis of ADAR mutants
    • Tonkin L.A., and Bass B.L. Mutations in RNAi rescue aberrant chemotaxis of ADAR mutants. Science 302 (2003) 1725
    • (2003) Science , vol.302 , pp. 1725
    • Tonkin, L.A.1    Bass, B.L.2
  • 50
    • 0037388031 scopus 로고    scopus 로고
    • DNA helix: the importance of being GC-rich
    • Vinogradov A.E. DNA helix: the importance of being GC-rich. Nucleic Acids Res. 31 (2003) 1838-1844
    • (2003) Nucleic Acids Res. , vol.31 , pp. 1838-1844
    • Vinogradov, A.E.1
  • 51
    • 1242293743 scopus 로고    scopus 로고
    • Fixation biases affecting human SNPs
    • Webster M.T., and Smith N.G. Fixation biases affecting human SNPs. Trends Genet. 20 (2004) 122-126
    • (2004) Trends Genet. , vol.20 , pp. 122-126
    • Webster, M.T.1    Smith, N.G.2
  • 52
    • 19544384915 scopus 로고    scopus 로고
    • Male-driven biased gene conversion governs the evolution of base composition in human alu repeats
    • Webster M.T., Smith N.G., Hultin-Rosenberg L., Arndt P.F., and Ellegren H. Male-driven biased gene conversion governs the evolution of base composition in human alu repeats. Mol. Biol. Evol. 22 (2005) 1468-1474
    • (2005) Mol. Biol. Evol. , vol.22 , pp. 1468-1474
    • Webster, M.T.1    Smith, N.G.2    Hultin-Rosenberg, L.3    Arndt, P.F.4    Ellegren, H.5
  • 53
    • 15244344826 scopus 로고    scopus 로고
    • Identification of new targets of Drosophila pre-mRNA adenosine deaminase
    • Xia S., Yang J., Su Y., Qian J., Ma E., and Haddad G.G. Identification of new targets of Drosophila pre-mRNA adenosine deaminase. Physiol Genomics. 20 (2005) 195-202
    • (2005) Physiol Genomics. , vol.20 , pp. 195-202
    • Xia, S.1    Yang, J.2    Su, Y.3    Qian, J.4    Ma, E.5    Haddad, G.G.6
  • 55
    • 0036726239 scopus 로고    scopus 로고
    • Patterns of nucleotide substitution among simultaneously duplicated gene pairs in Arabidopsis thaliana
    • Zhang L., Vision T.J., and Gaut B.S. Patterns of nucleotide substitution among simultaneously duplicated gene pairs in Arabidopsis thaliana. Mol. Biol. Evol. 19 (2002) 1464-1473
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 1464-1473
    • Zhang, L.1    Vision, T.J.2    Gaut, B.S.3


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