메뉴 건너뛰기




Volumn 6, Issue 3-4, 2008, Pages 144-154

Comparative Genomic Study Reveals a Transition from TA Richness in Invertebrates to GC Richness in Vertebrates at CpG Flanking Sites: An Indication for Context-Dependent Mutagenicity of Methylated CpG Sites

Author keywords

CpG deficiency; DNA methylation; GC content; invertebrate genomes

Indexed keywords

5' UNTRANSLATED REGION; ARTICLE; BEE; CAENORHABDITIS ELEGANS; CHICKEN; COMPARATIVE STUDY; CPG ISLAND; DEAMINATION; DNA METHYLATION; DROSOPHILA; GC RICH SEQUENCE; GENE MUTATION; GENE SEQUENCE; GENOME; GENOMICS; HUMAN; INVERTEBRATE; MUTAGENICITY; NONHUMAN; PUFFER FISH; SEA URCHIN; VERTEBRATE; ZEBRA FISH;

EID: 62949240195     PISSN: 16720229     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1672-0229(09)60002-4     Document Type: Article
Times cited : (3)

References (38)
  • 1
    • 0028568008 scopus 로고
    • Heterogeneity of genomes: measures and values
    • Karlin S., et al. Heterogeneity of genomes: measures and values. Proc. Natl. Acad. Sci. USA 91 (1994) 12837-12841
    • (1994) Proc. Natl. Acad. Sci. USA , vol.91 , pp. 12837-12841
    • Karlin, S.1
  • 2
    • 0029060923 scopus 로고
    • Dinucleotide relative abundance extremes: a genomic signature
    • Karlin S., and Burge C. Dinucleotide relative abundance extremes: a genomic signature. Trends Genet. 11 (1995) 283-290
    • (1995) Trends Genet. , vol.11 , pp. 283-290
    • Karlin, S.1    Burge, C.2
  • 3
    • 73049131457 scopus 로고
    • Enzymatic synthesis of deoxyribonucleic acid. VIII. Frequencies of nearest neighbor base sequences in deoxyribonucleic acid
    • Josse J., et al. Enzymatic synthesis of deoxyribonucleic acid. VIII. Frequencies of nearest neighbor base sequences in deoxyribonucleic acid. J. Biol. Chem. 236 (1961) 864-875
    • (1961) J. Biol. Chem. , vol.236 , pp. 864-875
    • Josse, J.1
  • 4
    • 0019322245 scopus 로고
    • DNA methylation and the frequency of CpGinanimalDNA
    • Bird A.P. DNA methylation and the frequency of CpGinanimalDNA. Nucleic Acids Res. 8 (1980) 1499-1504
    • (1980) Nucleic Acids Res. , vol.8 , pp. 1499-1504
    • Bird, A.P.1
  • 5
    • 0023853921 scopus 로고
    • The CpG dinucleotide and human genetic disease
    • Cooper D.N., and Youssoufian H. The CpG dinucleotide and human genetic disease. Hum. Genet. 78 (1988) 151-155
    • (1988) Hum. Genet. , vol.78 , pp. 151-155
    • Cooper, D.N.1    Youssoufian, H.2
  • 6
    • 0025944851 scopus 로고
    • CpG islands, genes and isochores in the genomes of vertebrates
    • Aissani B., and Bernardi G. CpG islands, genes and isochores in the genomes of vertebrates. Gene 106 (1991) 185-195
    • (1991) Gene , vol.106 , pp. 185-195
    • Aissani, B.1    Bernardi, G.2
  • 7
    • 0031593155 scopus 로고    scopus 로고
    • Structural and compositional features of untranslated regions of eukaryotic mRNAs
    • Pesole G., et al. Structural and compositional features of untranslated regions of eukaryotic mRNAs. Gene 205 (1997) 95-102
    • (1997) Gene , vol.205 , pp. 95-102
    • Pesole, G.1
  • 8
    • 0032509187 scopus 로고    scopus 로고
    • CpG doubles, CpG islands and Alu repeats in long human DNA sequences from different isochore families
    • Jabbari K., and Bernardi G. CpG doubles, CpG islands and Alu repeats in long human DNA sequences from different isochore families. Gene 224 (1998) 123-127
    • (1998) Gene , vol.224 , pp. 123-127
    • Jabbari, K.1    Bernardi, G.2
  • 9
    • 14544298936 scopus 로고    scopus 로고
    • CpG mutation rates in the human genome are highly dependent on local GC content
    • Fryxell K.J., and Moon W.J. CpG mutation rates in the human genome are highly dependent on local GC content. Mol. Biol. Evol. 22 (2005) 650-658
    • (2005) Mol. Biol. Evol. , vol.22 , pp. 650-658
    • Fryxell, K.J.1    Moon, W.J.2
  • 10
    • 0034735780 scopus 로고    scopus 로고
    • DNA methylation in Drosophila melanogaster
    • Lyko F., et al. DNA methylation in Drosophila melanogaster. Nature 408 (2000) 538-540
    • (2000) Nature , vol.408 , pp. 538-540
    • Lyko, F.1
  • 11
    • 0034672095 scopus 로고    scopus 로고
    • DNA of Drosophila melanogaster contains 5-methylcytosine
    • Gowher H., et al. DNA of Drosophila melanogaster contains 5-methylcytosine. EMBO J. 19 (2000) 6918-6923
    • (2000) EMBO J. , vol.19 , pp. 6918-6923
    • Gowher, H.1
  • 12
    • 33750486851 scopus 로고    scopus 로고
    • Functional CpG methylation system in a social insect
    • Wang Y., et al. Functional CpG methylation system in a social insect. Science 314 (2006) 645-647
    • (2006) Science , vol.314 , pp. 645-647
    • Wang, Y.1
  • 13
    • 0031027468 scopus 로고    scopus 로고
    • Methylation of genomes and genes at the invertebrate-vertebrate boundary
    • Tweedie S., et al. Methylation of genomes and genes at the invertebrate-vertebrate boundary. Mol. Cell. Biol. 17 (1997) 1469-1475
    • (1997) Mol. Cell. Biol. , vol.17 , pp. 1469-1475
    • Tweedie, S.1
  • 14
    • 0033582623 scopus 로고    scopus 로고
    • Nonmethylated transposable elements and methylated genes in a chordate genome
    • Simmen M.W., et al. Nonmethylated transposable elements and methylated genes in a chordate genome. Science 283 (1999) 1164-1167
    • (1999) Science , vol.283 , pp. 1164-1167
    • Simmen, M.W.1
  • 15
    • 0033858879 scopus 로고    scopus 로고
    • Cytosine deamination plays a primary role in the evolution of mammalian isochores
    • Fryxell K.J., and Zuckerkandl E. Cytosine deamination plays a primary role in the evolution of mammalian isochores. Mol. Biol. Evol. 17 (2000) 1371-1383
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 1371-1383
    • Fryxell, K.J.1    Zuckerkandl, E.2
  • 16
    • 34248195006 scopus 로고    scopus 로고
    • CpG methylation is targeted to transcription units in an invertebrate genome
    • Suzuki M.M., et al. CpG methylation is targeted to transcription units in an invertebrate genome. Genome Res. 17 (2007) 625-631
    • (2007) Genome Res. , vol.17 , pp. 625-631
    • Suzuki, M.M.1
  • 17
    • 32044455298 scopus 로고    scopus 로고
    • Large-scale structure of genomic methylation patterns
    • Rollins R.A., et al. Large-scale structure of genomic methylation patterns. Genome Res. 16 (2006) 157-163
    • (2006) Genome Res. , vol.16 , pp. 157-163
    • Rollins, R.A.1
  • 18
    • 0030840954 scopus 로고    scopus 로고
    • Cytosine methylation and the ecology of intragenomic parasites
    • Yoder J.A., et al. Cytosine methylation and the ecology of intragenomic parasites. Trends Genet. 13 (1997) 335-340
    • (1997) Trends Genet. , vol.13 , pp. 335-340
    • Yoder, J.A.1
  • 19
    • 0037133565 scopus 로고    scopus 로고
    • Comprehensive analysis of CpG islands in human chromosomes 21 and 22
    • Takai D., and Jones P.A. Comprehensive analysis of CpG islands in human chromosomes 21 and 22. Proc. Natl. Acad. Sci. USA 99 (2002) 3740-3745
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 3740-3745
    • Takai, D.1    Jones, P.A.2
  • 20
    • 10644283823 scopus 로고    scopus 로고
    • Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
    • International Chicken Genome Sequencing Consortium. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432 (2004) 695-716
    • (2004) Nature , vol.432 , pp. 695-716
    • International Chicken Genome Sequencing Consortium1
  • 21
    • 2042437650 scopus 로고    scopus 로고
    • Initial sequencing and analysis of the human genome
    • International Human Genome Sequecing Consortium. Initial sequencing and analysis of the human genome. Nature 409 (2001) 860-921
    • (2001) Nature , vol.409 , pp. 860-921
    • International Human Genome Sequecing Consortium1
  • 22
    • 0025756961 scopus 로고
    • Non-methylated islands in fish genomes are GC-poor
    • Cross S., et al. Non-methylated islands in fish genomes are GC-poor. Nucleic Acids Res. 19 (1991) 1469-1474
    • (1991) Nucleic Acids Res. , vol.19 , pp. 1469-1474
    • Cross, S.1
  • 23
    • 0032406223 scopus 로고    scopus 로고
    • Methylation of CpG dinucleotides in the lacI gene of the Big Blue transgenic mouse
    • You Y.H., et al. Methylation of CpG dinucleotides in the lacI gene of the Big Blue transgenic mouse. Mutat. Res. 420 (1998) 55-65
    • (1998) Mutat. Res. , vol.420 , pp. 55-65
    • You, Y.H.1
  • 24
    • 0031593201 scopus 로고    scopus 로고
    • Methylation patterns in the isochores of vertebrate genomes
    • Caccio S., et al. Methylation patterns in the isochores of vertebrate genomes. Gene 205 (1997) 119-124
    • (1997) Gene , vol.205 , pp. 119-124
    • Caccio, S.1
  • 25
    • 0028358421 scopus 로고
    • The rate of hydrolytic deamination of 5-methylcytosine in double-stranded DNA
    • Shen J.C., et al. The rate of hydrolytic deamination of 5-methylcytosine in double-stranded DNA. Nucleic Acids Res. 22 (1994) 972-976
    • (1994) Nucleic Acids Res. , vol.22 , pp. 972-976
    • Shen, J.C.1
  • 26
    • 2942594082 scopus 로고    scopus 로고
    • Cytosine methylation and CpG, TpG (CpA) and TpA frequencies
    • Jabbari K., and Bernardi G. Cytosine methylation and CpG, TpG (CpA) and TpA frequencies. Gene 333 (2004) 143-149
    • (2004) Gene , vol.333 , pp. 143-149
    • Jabbari, K.1    Bernardi, G.2
  • 27
    • 33750460281 scopus 로고    scopus 로고
    • Insights into social insects from the genome of the honeybee Apis mellifera
    • Honeybee Genome Sequencing Consortium. Insights into social insects from the genome of the honeybee Apis mellifera. Nature 443 (2006) 931-949
    • (2006) Nature , vol.443 , pp. 931-949
    • Honeybee Genome Sequencing Consortium1
  • 28
    • 0031593251 scopus 로고    scopus 로고
    • Evolutionary changes in CpG and methylation levels in the genome of vertebrates
    • Jabbari K., et al. Evolutionary changes in CpG and methylation levels in the genome of vertebrates. Gene 205 (1997) 109-118
    • (1997) Gene , vol.205 , pp. 109-118
    • Jabbari, K.1
  • 29
    • 34547473804 scopus 로고    scopus 로고
    • DNA methylation and body temperature in fishes
    • Varriale A., and Bernardi G. DNA methylation and body temperature in fishes. Gene 385 (2006) 111-121
    • (2006) Gene , vol.385 , pp. 111-121
    • Varriale, A.1    Bernardi, G.2
  • 30
    • 0021810948 scopus 로고
    • The mosaic genome of warm-blooded vertebrates
    • Bernardi G., et al. The mosaic genome of warm-blooded vertebrates. Science 228 (1985) 953-958
    • (1985) Science , vol.228 , pp. 953-958
    • Bernardi, G.1
  • 31
    • 0034520771 scopus 로고    scopus 로고
    • Assessment of compositional heterogeneity within and between eukaryotic genomes
    • Nekrutenko A., and Li W.H. Assessment of compositional heterogeneity within and between eukaryotic genomes. Genome Res. 10 (2000) 1986-1995
    • (2000) Genome Res. , vol.10 , pp. 1986-1995
    • Nekrutenko, A.1    Li, W.H.2
  • 33
    • 0034989085 scopus 로고    scopus 로고
    • Local rates of recombination are positively correlated with GC content in the human genome
    • Fullerton S.M., et al. Local rates of recombination are positively correlated with GC content in the human genome. Mol. Biol. Evol. 18 (2001) 1139-1142
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 1139-1142
    • Fullerton, S.M.1
  • 34
    • 84985461479 scopus 로고
    • How genetics got a chemical education
    • Chargaff E. How genetics got a chemical education. Ann. N Y Acad. Sci. 325 (1979) 344-360
    • (1979) Ann. N Y Acad. Sci. , vol.325 , pp. 344-360
    • Chargaff, E.1
  • 35
    • 0036166794 scopus 로고    scopus 로고
    • Symmetry observations in long nucleotide sequences: a commentary on the Discovery Note of Qi and Cuticchia
    • Forsdyke D.R. Symmetry observations in long nucleotide sequences: a commentary on the Discovery Note of Qi and Cuticchia. Bioinformatics 18 (2002) 215-217
    • (2002) Bioinformatics , vol.18 , pp. 215-217
    • Forsdyke, D.R.1
  • 36
    • 0034949341 scopus 로고    scopus 로고
    • Compositional symmetries in complete genomes
    • Qi D., and Cuticchia A.J. Compositional symmetries in complete genomes. Bioinformatics 17 (2001) 557-559
    • (2001) Bioinformatics , vol.17 , pp. 557-559
    • Qi, D.1    Cuticchia, A.J.2
  • 37
    • 0034736520 scopus 로고    scopus 로고
    • Chargaff's legacy
    • Forsdyke D.R., and Mortimer J.R. Chargaff's legacy. Gene 261 (2000) 127-137
    • (2000) Gene , vol.261 , pp. 127-137
    • Forsdyke, D.R.1    Mortimer, J.R.2
  • 38
    • 0022555861 scopus 로고
    • Nonviral retroposons: genes, pseudogenes, and transposable elements generated by the reverse flow of genetic information
    • Weiner A.M., et al. Nonviral retroposons: genes, pseudogenes, and transposable elements generated by the reverse flow of genetic information. Annu. Rev. Biochem. 55 (1986) 631-661
    • (1986) Annu. Rev. Biochem. , vol.55 , pp. 631-661
    • Weiner, A.M.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.