메뉴 건너뛰기




Volumn 24, Issue 19, 2008, Pages 2157-2164

Is there an acceleration of the CpG transition rate during the mammalian radiation?

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; BIOINFORMATICS; CONTROLLED STUDY; CPG ISLAND; GENE SEQUENCE; HUMAN; MAMMAL; MOUSE; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROBABILITY; PROCESS OPTIMIZATION; RADIATION; REPRODUCIBILITY; SEQUENCE ANALYSIS; SIMULATION;

EID: 52949149017     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btn391     Document Type: Article
Times cited : (6)

References (45)
  • 1
    • 3543110745 scopus 로고    scopus 로고
    • Regional and time-resolved mutation patterns of the human genome
    • Arndt,P. and Hwa,T. (2004) Regional and time-resolved mutation patterns of the human genome. Bioinformatics, 20, 1482-1485.
    • (2004) Bioinformatics , vol.20 , pp. 1482-1485
    • Arndt, P.1    Hwa, T.2
  • 2
    • 19544383635 scopus 로고    scopus 로고
    • Identification and measurement of neighbor-dependent nucleotide substitution processes
    • Arndt,P. and Hwa,T. (2005) Identification and measurement of neighbor-dependent nucleotide substitution processes. Bioinformatics 21, 2322-2328.
    • (2005) Bioinformatics , vol.21 , pp. 2322-2328
    • Arndt, P.1    Hwa, T.2
  • 3
    • 0242666279 scopus 로고    scopus 로고
    • Distinct changes of genomic biases in nucleotide substitution at the time of mammalian radiation
    • Arndt,P. et al. (2003a) Distinct changes of genomic biases in nucleotide substitution at the time of mammalian radiation. Mol. Biol. Evol., 20, 1887-1896.
    • (2003) Mol. Biol. Evol , vol.20 , pp. 1887-1896
    • Arndt, P.1
  • 4
    • 0242659321 scopus 로고    scopus 로고
    • DNA sequence evolution with neighbor-dependent mutation
    • Arndt,P. et al. (2003b) DNA sequence evolution with neighbor-dependent mutation. J. Comp. Biol., 10, 313-322.
    • (2003) J. Comp. Biol , vol.10 , pp. 313-322
    • Arndt, P.1
  • 5
    • 21244454414 scopus 로고    scopus 로고
    • Substantial regional variation in substitution rates in the human genome: Importance of GC content, gene density, and telomere-specific effects
    • Arndt,P. et al. (2005) Substantial regional variation in substitution rates in the human genome: Importance of GC content, gene density, and telomere-specific effects. J. Mol. Evol., 60, 748-763.
    • (2005) J. Mol. Evol , vol.60 , pp. 748-763
    • Arndt, P.1
  • 6
    • 0026631005 scopus 로고
    • The influence of nearest neighbors on the rate and pattern of spontaneous point mutations
    • Blake,R. et al. (1992) The influence of nearest neighbors on the rate and pattern of spontaneous point mutations. J. Mol. Evol., 34, 189-200.
    • (1992) J. Mol. Evol , vol.34 , pp. 189-200
    • Blake, R.1
  • 7
    • 0028354234 scopus 로고
    • Pervasive CpG suppression in animal mitrochondrial genomes
    • Cardon,L. et al. (1994) Pervasive CpG suppression in animal mitrochondrial genomes. Proc. Natl Acad. Sci USA, 91, 3799-3803.
    • (1994) Proc. Natl Acad. Sci USA , vol.91 , pp. 3799-3803
    • Cardon, L.1
  • 8
    • 0024342297 scopus 로고
    • Cytosine methylation and the fate of CpG dinucleotides in vertebrate genomes
    • Cooper,D. and Krawczak,M. (1989) Cytosine methylation and the fate of CpG dinucleotides in vertebrate genomes. Hu.m Genet., 83, 181-188.
    • (1989) Hu.m Genet , vol.83 , pp. 181-188
    • Cooper, D.1    Krawczak, M.2
  • 9
    • 0018185292 scopus 로고
    • Molecular basis of base substitution hotspots in Escherichia coli
    • Coulondre,C. et al. (1978) Molecular basis of base substitution hotspots in Escherichia coli. Nature, 274, 775-780.
    • (1978) Nature , vol.274 , pp. 775-780
    • Coulondre, C.1
  • 11
    • 17744381573 scopus 로고    scopus 로고
    • A genomic region evolving toward different GC contents in humans and chimpanzees indicates a recent and regionally limited shift in the mutation pattern
    • Ebersberger,I. and Meyer,M. (2005) A genomic region evolving toward different GC contents in humans and chimpanzees indicates a recent and regionally limited shift in the mutation pattern. Mol. Biol. Evol. 22, 1240-1245.
    • (2005) Mol. Biol. Evol , vol.22 , pp. 1240-1245
    • Ebersberger, I.1    Meyer, M.2
  • 12
    • 0022648672 scopus 로고
    • DNA cytosine methylation and heat-induced deamination
    • Ehrlich,M. et al. (1986) DNA cytosine methylation and heat-induced deamination. Biosci. Rep., 6, 387-393.
    • (1986) Biosci. Rep , vol.6 , pp. 387-393
    • Ehrlich, M.1
  • 13
    • 52949130649 scopus 로고    scopus 로고
    • Ewens,J. and Grant,G. (2005) Statistical Methods in Bioinfomtatics: An Introduction. Springer Science, New York, NY.
    • Ewens,J. and Grant,G. (2005) Statistical Methods in Bioinfomtatics: An Introduction. Springer Science, New York, NY.
  • 14
    • 0033858879 scopus 로고    scopus 로고
    • Cytosine deamination plays a primary role in the evoluduon of mammalian isochores
    • Fryxell,K. and Zuckerkandl,E. (2000) Cytosine deamination plays a primary role in the evoluduon of mammalian isochores. Mol. Biol. Evol., 17, 1371-1383.
    • (2000) Mol. Biol. Evol , vol.17 , pp. 1371-1383
    • Fryxell, K.1    Zuckerkandl, E.2
  • 15
    • 23744486255 scopus 로고    scopus 로고
    • The scale of mutational variation in the murid genome
    • Gaffney,D. and Keightley,P. (2005) The scale of mutational variation in the murid genome. Genome Res., 15, 1086-1094.
    • (2005) Genome Res , vol.15 , pp. 1086-1094
    • Gaffney, D.1    Keightley, P.2
  • 16
    • 0025815687 scopus 로고
    • Two guidelines for bootstrap hypothesis testing
    • Hall,P. and Wilson,S. (1991) Two guidelines for bootstrap hypothesis testing. Biometrics, 47, 757-762.
    • (1991) Biometrics , vol.47 , pp. 757-762
    • Hall, P.1    Wilson, S.2
  • 17
    • 18544404720 scopus 로고    scopus 로고
    • Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution
    • Hardison,R. et al. (2003) Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. Genome Res., 13, 13-26.
    • (2003) Genome Res , vol.13 , pp. 13-26
    • Hardison, R.1
  • 18
    • 0022376704 scopus 로고
    • Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
    • Hasegawa,M. et al. (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol., 22, 160-174.
    • (1985) J. Mol. Evol , vol.22 , pp. 160-174
    • Hasegawa, M.1
  • 19
    • 0037406067 scopus 로고    scopus 로고
    • The methyl-CpG binding domain and evolving role of DNA methylation in animals
    • Hendricb,B. and Tweedie,S. (2003) The methyl-CpG binding domain and evolving role of DNA methylation in animals. Trend Genet., 19 269-277.
    • (2003) Trend Genet , vol.19 , pp. 269-277
    • Hendricb, B.1    Tweedie, S.2
  • 20
    • 0028294455 scopus 로고
    • Wide variations in neighbor-dependent substitution rates
    • Hess,S. et al. (1994) Wide variations in neighbor-dependent substitution rates. J. Mol. Biol., 236, 1022-1033.
    • (1994) J. Mol. Biol , vol.236 , pp. 1022-1033
    • Hess, S.1
  • 21
    • 4644300141 scopus 로고    scopus 로고
    • Baysian Markov chain monte carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution
    • Hwang,D. and Green,P. (2004) Baysian Markov chain monte carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution. Proc. Natl Acad, Sci. USA, 101, 13994-14001.
    • (2004) Proc. Natl Acad, Sci. USA , vol.101 , pp. 13994-14001
    • Hwang, D.1    Green, P.2
  • 22
    • 0031593251 scopus 로고    scopus 로고
    • Eolutionary changes in CpG and methylation levels in the genome of vertebrates
    • Jabbari,K. et al. (1997) Eolutionary changes in CpG and methylation levels in the genome of vertebrates. Gene, 205, 109-118.
    • (1997) Gene , vol.205 , pp. 109-118
    • Jabbari, K.1
  • 23
    • 0000732090 scopus 로고
    • Evolution of protein molecules
    • Munro,H, ed, Academic Press, New York, pp
    • Jukes,T. and Cantor,C. (1969) Evolution of protein molecules. In Munro,H. (ed.), Mannalian Protein Metabolism. Academic Press, New York, pp. 121-132.
    • (1969) Mannalian Protein Metabolism , pp. 121-132
    • Jukes, T.1    Cantor, C.2
  • 24
    • 0030923586 scopus 로고    scopus 로고
    • Compositional differences within and between eukaryotic genomes
    • Karlin,S. and Mrázek,J. (1997) Compositional differences within and between eukaryotic genomes. Proc. Natl Acad. Sci. USA, 94, 10227-10232.
    • (1997) Proc. Natl Acad. Sci. USA , vol.94 , pp. 10227-10232
    • Karlin, S.1    Mrázek, J.2
  • 25
    • 38949102309 scopus 로고    scopus 로고
    • Exponential decay of GC content detected by strand-symmetric substitution rates influences the evolution of isochore structure
    • Karro,J. et al. (2008) Exponential decay of GC content detected by strand-symmetric substitution rates influences the evolution of isochore structure. Mol. Biol. Evol., 25, 362-374.
    • (2008) Mol. Biol. Evol , vol.25 , pp. 362-374
    • Karro, J.1
  • 26
    • 0036079158 scopus 로고    scopus 로고
    • The human genome browser at UCSC
    • Kent,W. et al. (2002) The human genome browser at UCSC. Genome Res., 12, 996-1006.
    • (2002) Genome Res , vol.12 , pp. 996-1006
    • Kent, W.1
  • 27
    • 33750472316 scopus 로고    scopus 로고
    • Heterogeneous genomic molecular clocks in primates
    • Kim,S. et al. (2006) Heterogeneous genomic molecular clocks in primates. PLoS Genet., 2, 1527-1534.
    • (2006) PLoS Genet , vol.2 , pp. 1527-1534
    • Kim, S.1
  • 28
    • 0032416149 scopus 로고    scopus 로고
    • Model of molecular evolution and phylogeny
    • Lio,P. and Goldman,N. (1998) Model of molecular evolution and phylogeny. Genome Res., 8, 1233-1244.
    • (1998) Genome Res , vol.8 , pp. 1233-1244
    • Lio, P.1    Goldman, N.2
  • 29
    • 0032976213 scopus 로고    scopus 로고
    • Evolution of DNA base composition under no-strand-bias conditions when the substitution rates are not constant
    • Lobry,J. and Lobry,C. (1999) Evolution of DNA base composition under no-strand-bias conditions when the substitution rates are not constant. Mol. Biol. Evol., 16, 719-723.
    • (1999) Mol. Biol. Evol , vol.16 , pp. 719-723
    • Lobry, J.1    Lobry, C.2
  • 30
    • 13244276706 scopus 로고    scopus 로고
    • A nucleotide substitution model with nearest-neighbour interactions
    • Lunter,G. and Hein,J. (2004) A nucleotide substitution model with nearest-neighbour interactions. Bioinformatics, 20, 216-223.
    • (2004) Bioinformatics , vol.20 , pp. 216-223
    • Lunter, G.1    Hein, J.2
  • 31
    • 2442651458 scopus 로고    scopus 로고
    • Recombination drives the evolution of GC-content in the human genome
    • Meunier,J. and Duret,L. (2004) Recombination drives the evolution of GC-content in the human genome. Mol. Biol. Evol., 21, 984-990.
    • (2004) Mol. Biol. Evol , vol.21 , pp. 984-990
    • Meunier, J.1    Duret, L.2
  • 32
    • 17244367011 scopus 로고    scopus 로고
    • Homology-dependent methylation in primate repetitive DNA
    • Meunier,J. et al. (2005) Homology-dependent methylation in primate repetitive DNA. Proc. Natl Acad. Sci. USA, 102, 5471-5476.
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 5471-5476
    • Meunier, J.1
  • 33
    • 22144435948 scopus 로고    scopus 로고
    • On studentising and blocklength selection for the bootstrap on time series
    • Peifer,M. et al. (2005) On studentising and blocklength selection for the bootstrap on time series. Biometr. J., 47, 346-357.
    • (2005) Biometr. J , vol.47 , pp. 346-357
    • Peifer, M.1
  • 34
    • 0019318994 scopus 로고
    • DNA methylation and gene function
    • Razin,C. and Riggs,A. (1980) DNA methylation and gene function. Science, 210, 604-610.
    • (1980) Science , vol.210 , pp. 604-610
    • Razin, C.1    Riggs, A.2
  • 35
    • 0000120766 scopus 로고
    • Estimating the dimension of a model
    • Schwarz,G. (1978) Estimating the dimension of a model. Ann. Stat., 6, 461-464.
    • (1978) Ann. Stat , vol.6 , pp. 461-464
    • Schwarz, G.1
  • 36
    • 1542510106 scopus 로고    scopus 로고
    • Phylogenctic estimation of context-dependent substitution rates by maximum likelihood
    • Siepel,A. and Haussler,D. (2004) Phylogenctic estimation of context-dependent substitution rates by maximum likelihood. Mol. Biol. Evol., 21, 468-488.
    • (2004) Mol. Biol. Evol , vol.21 , pp. 468-488
    • Siepel, A.1    Haussler, D.2
  • 37
    • 52949120669 scopus 로고    scopus 로고
    • Smit,A. et al. (1996-2004) Repeatmasker open-3.0.
    • Smit,A. et al. (1996-2004) Repeatmasker open-3.0.
  • 38
    • 10344241529 scopus 로고    scopus 로고
    • Genomic data support the hominoid slowdown and an early obligocene estimate for the hoinoid-cercopithecoid divergence
    • Steiper,M. et al. (2004) Genomic data support the hominoid slowdown and an early obligocene estimate for the hoinoid-cercopithecoid divergence. Proc. Natl Acad. Sci. USA, 101, 17021-17026.
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 17021-17026
    • Steiper, M.1
  • 39
    • 0028922156 scopus 로고
    • Intrastrand parity rules of DNA base composition and usage biases of synonymous codons
    • Sueoka,N. (1995) Intrastrand parity rules of DNA base composition and usage biases of synonymous codons. J. Mol. Evol., 40, 318-325.
    • (1995) J. Mol. Evol , vol.40 , pp. 318-325
    • Sueoka, N.1
  • 40
    • 0031027468 scopus 로고    scopus 로고
    • Methylation of genomes and genes at the boundary of invertebrate-vertebrate boundary
    • Tweedie,S. et al. (1997) Methylation of genomes and genes at the boundary of invertebrate-vertebrate boundary. Mol. Cell. Biol., 17, 1469-1475.
    • (1997) Mol. Cell. Biol , vol.17 , pp. 1469-1475
    • Tweedie, S.1
  • 41
    • 47149088853 scopus 로고    scopus 로고
    • Human-macaque comparisons illuminate variation in neutral substitution rates
    • Tyekucheva,S. et al. (2008) Human-macaque comparisons illuminate variation in neutral substitution rates. Genome Biol., 9, R76.
    • (2008) Genome Biol , vol.9
    • Tyekucheva, S.1
  • 42
    • 1542563409 scopus 로고    scopus 로고
    • Initial sequencing and comparative analysis of the mouse genome
    • Waterston,R. et al. (2002) Initial sequencing and comparative analysis of the mouse genome. Nature, 420, 520-562.
    • (2002) Nature , vol.420 , pp. 520-562
    • Waterston, R.1
  • 43
    • 33646884615 scopus 로고    scopus 로고
    • Strong regional biases in nucleotide substitution in the chicken genome
    • Webster,M. et al. (2006) Strong regional biases in nucleotide substitution in the chicken genome. Mol. Biol. Evol., 23, 1203-1216.
    • (2006) Mol. Biol. Evol , vol.23 , pp. 1203-1216
    • Webster, M.1
  • 44
    • 0027351512 scopus 로고
    • The repair of 5-methylcytosine deamination damage
    • Jost,J. and Saluz,H, eds, Birkhäuser Verlag, Basel, pp
    • Wiebauer,K. et al. (1993) The repair of 5-methylcytosine deamination damage. In Jost,J. and Saluz,H. (eds), DNA Methylation: Molecular Biology and Biological Significance. Birkhäuser Verlag, Basel, pp. 510-522.
    • (1993) DNA Methylation: Molecular Biology and Biological Significance , pp. 510-522
    • Wiebauer, K.1
  • 45
    • 0036897666 scopus 로고    scopus 로고
    • Slow molecular clocks in old world monkeys, apes and humans
    • Yi,S. et al. (2002) Slow molecular clocks in old world monkeys, apes and humans. Mol. Biol. Evol., 19, 2191-2198.
    • (2002) Mol. Biol. Evol , vol.19 , pp. 2191-2198
    • Yi, S.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.