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Volumn 94, Issue 2, 2009, Pages 117-124

Contrast features of CpG islands in the promoter and other regions in the dog genome

Author keywords

CpG islands; Dog; Domestication; Essential genes; Gene Ontology; Genome evolution; Homologous genes; Housekeeping genes; Promoter

Indexed keywords

ARTICLE; CONTROLLED STUDY; CPG ISLAND; DOG; GENE SEQUENCE; GENETIC MARKER; GENETIC RECOMBINATION; HUMAN; KARYOTYPE; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE;

EID: 67649967535     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2009.04.007     Document Type: Article
Times cited : (20)

References (51)
  • 1
    • 0037159691 scopus 로고    scopus 로고
    • The domestication of social cognition in dogs
    • Hare B., Brown M., Williamson C., and Tomasello M. The domestication of social cognition in dogs. Science 298 (2002) 1634-1636
    • (2002) Science , vol.298 , pp. 1634-1636
    • Hare, B.1    Brown, M.2    Williamson, C.3    Tomasello, M.4
  • 2
    • 35748957135 scopus 로고    scopus 로고
    • Lessons learned from the dog genome
    • Wayne R.K., and Ostrander E.A. Lessons learned from the dog genome. Trends Genet. 23 (2007) 557-567
    • (2007) Trends Genet. , vol.23 , pp. 557-567
    • Wayne, R.K.1    Ostrander, E.A.2
  • 3
    • 0033373189 scopus 로고    scopus 로고
    • A complete comparative chromosome map for the dog, red fox, and human and its integration with canine genetic maps
    • Yang F., et al. A complete comparative chromosome map for the dog, red fox, and human and its integration with canine genetic maps. Genomics 62 (1999) 189-202
    • (1999) Genomics , vol.62 , pp. 189-202
    • Yang, F.1
  • 4
    • 0034667333 scopus 로고    scopus 로고
    • Use of flow-sorted canine chromosomes in the assignment of canine linkage, radiation hybrid, and syntenic groups to chromosomes: refinement and verification of the comparative chromosome map for dog and human
    • Sargan D.R., et al. Use of flow-sorted canine chromosomes in the assignment of canine linkage, radiation hybrid, and syntenic groups to chromosomes: refinement and verification of the comparative chromosome map for dog and human. Genomics 69 (2000) 182-195
    • (2000) Genomics , vol.69 , pp. 182-195
    • Sargan, D.R.1
  • 5
    • 2442653898 scopus 로고    scopus 로고
    • Genetic structure of the purebred domestic dog
    • Parker H.G., et al. Genetic structure of the purebred domestic dog. Science 304 (2004) 1160-1164
    • (2004) Science , vol.304 , pp. 1160-1164
    • Parker, H.G.1
  • 6
    • 0141596080 scopus 로고    scopus 로고
    • The dog genome: survey sequencing and comparative analysis
    • Kirkness E.F., et al. The dog genome: survey sequencing and comparative analysis. Science 301 (2003) 1898-1903
    • (2003) Science , vol.301 , pp. 1898-1903
    • Kirkness, E.F.1
  • 7
    • 28644447707 scopus 로고    scopus 로고
    • Genome sequence, comparative analysis and haplotype structure of the domestic dog
    • Lindblad-Toh K., et al. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 438 (2005) 803-819
    • (2005) Nature , vol.438 , pp. 803-819
    • Lindblad-Toh, K.1
  • 9
    • 2542502350 scopus 로고    scopus 로고
    • IDID: inherited diseases in dogs: web-based information for canine inherited disease genetics
    • Sargan D.R. IDID: inherited diseases in dogs: web-based information for canine inherited disease genetics. Mamm. Genome 15 (2004) 503-506
    • (2004) Mamm. Genome , vol.15 , pp. 503-506
    • Sargan, D.R.1
  • 10
    • 32444436681 scopus 로고    scopus 로고
    • Sequence context analysis of 8.2 million single nucleotide polymorphisms in the human genome
    • Zhao Z., and Zhang F. Sequence context analysis of 8.2 million single nucleotide polymorphisms in the human genome. Gene 366 (2006) 316-324
    • (2006) Gene , vol.366 , pp. 316-324
    • Zhao, Z.1    Zhang, F.2
  • 11
    • 29344432096 scopus 로고    scopus 로고
    • Sequence context analysis in the mouse genome: single nucleotide polymorphisms and CpG island sequences
    • Zhao Z., and Zhang F. Sequence context analysis in the mouse genome: single nucleotide polymorphisms and CpG island sequences. Genomics 87 (2006) 68-74
    • (2006) Genomics , vol.87 , pp. 68-74
    • Zhao, Z.1    Zhang, F.2
  • 12
    • 47149116702 scopus 로고    scopus 로고
    • CpG island density and its correlations with genomic features in mammalian genomes
    • Han L., Su B., Li W.H., and Zhao Z. CpG island density and its correlations with genomic features in mammalian genomes. Genome Biol. 9 (2008) R79
    • (2008) Genome Biol. , vol.9
    • Han, L.1    Su, B.2    Li, W.H.3    Zhao, Z.4
  • 13
    • 0019322245 scopus 로고
    • DNA methylation and the frequency of CpG in animal DNA
    • Bird A.P. DNA methylation and the frequency of CpG in animal DNA. Nucleic Acids Res. 8 (1980) 1499-1504
    • (1980) Nucleic Acids Res. , vol.8 , pp. 1499-1504
    • Bird, A.P.1
  • 14
    • 0042329754 scopus 로고    scopus 로고
    • Structure, function and evolution of CpG island promoters
    • Antequera F. Structure, function and evolution of CpG island promoters. Cell. Mol. Life Sci. 60 (2003) 1647-1658
    • (2003) Cell. Mol. Life Sci. , vol.60 , pp. 1647-1658
    • Antequera, F.1
  • 15
    • 0023472826 scopus 로고
    • CpG islands as gene markers in the vertebrate nucleus
    • Bird A.P. CpG islands as gene markers in the vertebrate nucleus. Trends Genet. 3 (1987) 342-347
    • (1987) Trends Genet. , vol.3 , pp. 342-347
    • Bird, A.P.1
  • 16
    • 0023216891 scopus 로고
    • CpG islands in vertebrate genomes
    • Gardiner-Garden M., and Frommer M. CpG islands in vertebrate genomes. J. Mol. Biol. 196 (1987) 261-282
    • (1987) J. Mol. Biol. , vol.196 , pp. 261-282
    • Gardiner-Garden, M.1    Frommer, M.2
  • 17
    • 34047116826 scopus 로고    scopus 로고
    • Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome
    • Weber M., et al. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat. Genet. 39 (2007) 457-466
    • (2007) Nat. Genet. , vol.39 , pp. 457-466
    • Weber, M.1
  • 18
    • 33751505540 scopus 로고    scopus 로고
    • DNA methylation profiling of human chromosomes 6, 20 and 22
    • Eckhardt F., et al. DNA methylation profiling of human chromosomes 6, 20 and 22. Nat. Genet. 38 (2006) 1378-1385
    • (2006) Nat. Genet. , vol.38 , pp. 1378-1385
    • Eckhardt, F.1
  • 19
    • 38949212693 scopus 로고    scopus 로고
    • A novel CpG island set identifies tissue-specific methylation at developmental gene loci
    • Illingworth R., et al. A novel CpG island set identifies tissue-specific methylation at developmental gene loci. PLoS Biol. 6 (2008) e22
    • (2008) PLoS Biol. , vol.6
    • Illingworth, R.1
  • 20
    • 1242296842 scopus 로고    scopus 로고
    • A comprehensive analysis of allelic methylation status of CpG islands on human chromosome 21q
    • Yamada Y., et al. A comprehensive analysis of allelic methylation status of CpG islands on human chromosome 21q. Genome Res. 14 (2004) 247-266
    • (2004) Genome Res. , vol.14 , pp. 247-266
    • Yamada, Y.1
  • 21
    • 34548444095 scopus 로고    scopus 로고
    • Features and trend of loss of promoter-associated CpG islands in the human and mouse genomes
    • Jiang C., et al. Features and trend of loss of promoter-associated CpG islands in the human and mouse genomes. Mol. Biol. Evol. 24 (2007) 1991-2000
    • (2007) Mol. Biol. Evol. , vol.24 , pp. 1991-2000
    • Jiang, C.1
  • 22
    • 31444437920 scopus 로고    scopus 로고
    • Epigenetics provides a new generation of oncogenes and tumour-suppressor genes
    • Esteller M. Epigenetics provides a new generation of oncogenes and tumour-suppressor genes. Br. J. Cancer 94 (2006) 179-183
    • (2006) Br. J. Cancer , vol.94 , pp. 179-183
    • Esteller, M.1
  • 23
    • 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
  • 24
    • 0343621494 scopus 로고    scopus 로고
    • Aberrant CpG-island methylation has non-random and tumour-type-specific patterns
    • Costello J.F., et al. Aberrant CpG-island methylation has non-random and tumour-type-specific patterns. Nat. Genet. 24 (2000) 132-138
    • (2000) Nat. Genet. , vol.24 , pp. 132-138
    • Costello, J.F.1
  • 25
    • 0027893006 scopus 로고
    • Evidence for erosion of mouse CpG islands during mammalian evolution
    • Matsuo K., et al. Evidence for erosion of mouse CpG islands during mammalian evolution. Somat. Cell Mol. Genet. 19 (1993) 543-555
    • (1993) Somat. Cell Mol. Genet. , vol.19 , pp. 543-555
    • Matsuo, K.1
  • 26
    • 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. U. S. A. 99 (2002) 3740-3745
    • (2002) Proc. Natl. Acad. Sci. U. S. A. , vol.99 , pp. 3740-3745
    • Takai, D.1    Jones, P.A.2
  • 27
    • 0026742792 scopus 로고
    • CpG islands as gene markers in the human genome
    • Larsen F., Gundersen G., Lopez R., and Prydz H. CpG islands as gene markers in the human genome. Genomics 13 (1992) 1095-1107
    • (1992) Genomics , vol.13 , pp. 1095-1107
    • Larsen, F.1    Gundersen, G.2    Lopez, R.3    Prydz, H.4
  • 28
    • 1542563409 scopus 로고    scopus 로고
    • Initial sequencing and comparative analysis of the mouse genome
    • Waterston R.H., et al. Initial sequencing and comparative analysis of the mouse genome. Nature 420 (2002) 520-562
    • (2002) Nature , vol.420 , pp. 520-562
    • Waterston, R.H.1
  • 29
    • 33749342164 scopus 로고    scopus 로고
    • Phylogenetic reconstruction of orthology, paralogy, and conserved synteny for dog and human
    • Goodstadt L., and Ponting C.P. Phylogenetic reconstruction of orthology, paralogy, and conserved synteny for dog and human. PLoS Comput. Biol. 2 (2006) e133
    • (2006) PLoS Comput. Biol. , vol.2
    • Goodstadt, L.1    Ponting, C.P.2
  • 30
    • 37648999313 scopus 로고    scopus 로고
    • Distinguishing protein-coding and noncoding genes in the human genome
    • Clamp M., et al. Distinguishing protein-coding and noncoding genes in the human genome. Proc. Natl. Acad. Sci. U. S. A. 104 (2007) 19428-19433
    • (2007) Proc. Natl. Acad. Sci. U. S. A. , vol.104 , pp. 19428-19433
    • Clamp, M.1
  • 31
    • 58049197826 scopus 로고    scopus 로고
    • The dystrobrevin-binding protein 1 gene: features and networks
    • Guo A.Y., et al. The dystrobrevin-binding protein 1 gene: features and networks. Mol. Psychiatry 14 (2009) 18-29
    • (2009) Mol. Psychiatry , vol.14 , pp. 18-29
    • Guo, A.Y.1
  • 32
    • 0024537065 scopus 로고
    • Similarity and divergence among rodent repetitive DNA-sequences
    • Bains W., and Templesmith K. Similarity and divergence among rodent repetitive DNA-sequences. J. Mol. Evol. 28 (1989) 191-199
    • (1989) J. Mol. Evol. , vol.28 , pp. 191-199
    • Bains, W.1    Templesmith, K.2
  • 33
    • 28844501661 scopus 로고    scopus 로고
    • Short interspersed elements (SINEs) are a major source of canine genomic diversity
    • Wang W., and Kirkness E.F. Short interspersed elements (SINEs) are a major source of canine genomic diversity. Genome Res. 15 (2005) 1798-1808
    • (2005) Genome Res. , vol.15 , pp. 1798-1808
    • Wang, W.1    Kirkness, E.F.2
  • 34
    • 33750329496 scopus 로고    scopus 로고
    • CpGcluster: a distance-based algorithm for CpG-island detection
    • Hackenberg M., et al. CpGcluster: a distance-based algorithm for CpG-island detection. BMC Bioinformatics 7 (2006) 446
    • (2006) BMC Bioinformatics , vol.7 , pp. 446
    • Hackenberg, M.1
  • 35
    • 62249118461 scopus 로고    scopus 로고
    • CpG islands or CpG clusters: how to identify functional GC-rich regions in a genome?
    • Han L., and Zhao Z. CpG islands or CpG clusters: how to identify functional GC-rich regions in a genome?. BMC Bioinformatics 10 (2009) 65
    • (2009) BMC Bioinformatics , vol.10 , pp. 65
    • Han, L.1    Zhao, Z.2
  • 36
    • 2442651458 scopus 로고    scopus 로고
    • Recombination drives the evolution of GC-content in the human genome
    • Meunier J., and Duret L. Recombination drives the evolution of GC-content in the human genome. Mol. Biol. Evol. 21 (2004) 984-990
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 984-990
    • Meunier, J.1    Duret, L.2
  • 37
    • 39749162243 scopus 로고    scopus 로고
    • Evolution of the genomic rate of recombination in mammals
    • Dumont B.L., and Payseur B.A. Evolution of the genomic rate of recombination in mammals. Evolution 62 (2008) 276-294
    • (2008) Evolution , vol.62 , pp. 276-294
    • Dumont, B.L.1    Payseur, B.A.2
  • 38
    • 33845874371 scopus 로고    scopus 로고
    • Methylation-dependent transition rates are dependent on local sequence lengths and genomic regions
    • Zhao Z., and Jiang C. Methylation-dependent transition rates are dependent on local sequence lengths and genomic regions. Mol. Biol. Evol. 24 (2007) 23-25
    • (2007) Mol. Biol. Evol. , vol.24 , pp. 23-25
    • Zhao, Z.1    Jiang, C.2
  • 39
    • 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
  • 40
    • 33746731132 scopus 로고    scopus 로고
    • Relaxation of selective constraint on dog mitochondrial DNA following domestication
    • Bjornerfeldt S., Webster M.T., and Vila C. Relaxation of selective constraint on dog mitochondrial DNA following domestication. Genome Res. 16 (2006) 990-994
    • (2006) Genome Res. , vol.16 , pp. 990-994
    • Bjornerfeldt, S.1    Webster, M.T.2    Vila, C.3
  • 41
    • 33344458581 scopus 로고    scopus 로고
    • The accumulation of deleterious mutations in rice genomes: a hypothesis on the cost of domestication
    • Lu J., et al. The accumulation of deleterious mutations in rice genomes: a hypothesis on the cost of domestication. Trends Genet. 22 (2006) 126-131
    • (2006) Trends Genet. , vol.22 , pp. 126-131
    • Lu, J.1
  • 42
    • 54149110152 scopus 로고    scopus 로고
    • The legacy of domestication: accumulation of deleterious mutations in the dog genome
    • Cruz F., Vila C., and Webster M.T. The legacy of domestication: accumulation of deleterious mutations in the dog genome. Mol. Biol. Evol. 25 (2008) 2331-2336
    • (2008) Mol. Biol. Evol. , vol.25 , pp. 2331-2336
    • Cruz, F.1    Vila, C.2    Webster, M.T.3
  • 43
    • 2242463993 scopus 로고    scopus 로고
    • Genetic evidence for an East Asian origin of domestic dogs
    • Savolainen P., et al. Genetic evidence for an East Asian origin of domestic dogs. Science 298 (2002) 1610-1613
    • (2002) Science , vol.298 , pp. 1610-1613
    • Savolainen, P.1
  • 44
    • 36048982458 scopus 로고    scopus 로고
    • Initial sequence and comparative analysis of the cat genome
    • Pontius J.U., et al. Initial sequence and comparative analysis of the cat genome. Genome Res. 17 (2007) 1675-1689
    • (2007) Genome Res. , vol.17 , pp. 1675-1689
    • Pontius, J.U.1
  • 45
    • 33749453792 scopus 로고    scopus 로고
    • Mutational spectrum in the recent human genome inferred by single nucleotide polymorphisms
    • Jiang C., and Zhao Z. Mutational spectrum in the recent human genome inferred by single nucleotide polymorphisms. Genomics 88 (2006) 527-534
    • (2006) Genomics , vol.88 , pp. 527-534
    • Jiang, C.1    Zhao, Z.2
  • 46
    • 33750852510 scopus 로고    scopus 로고
    • Analyses of carnivore microsatellites and their intimate association with tRNA-derived SINEs
    • Lopez-Giraldez F., Andres O., Domingo-Roura X., and Bosch M. Analyses of carnivore microsatellites and their intimate association with tRNA-derived SINEs. BMC Genomics 7 (2006) 269
    • (2006) BMC Genomics , vol.7 , pp. 269
    • Lopez-Giraldez, F.1    Andres, O.2    Domingo-Roura, X.3    Bosch, M.4
  • 47
    • 46349099675 scopus 로고    scopus 로고
    • Comparative analysis of CpG islands in four fish genomes
    • Han L., and Zhao Z. Comparative analysis of CpG islands in four fish genomes. Comp. Funct. Genomics (2008) 565631
    • (2008) Comp. Funct. Genomics , pp. 565631
    • Han, L.1    Zhao, Z.2
  • 48
    • 34447637417 scopus 로고    scopus 로고
    • Mouse duplicate genes are as essential as singletons
    • Liao B.Y., and Zhang J. Mouse duplicate genes are as essential as singletons. Trends Genet. 23 (2007) 378-381
    • (2007) Trends Genet. , vol.23 , pp. 378-381
    • Liao, B.Y.1    Zhang, J.2
  • 49
    • 11144358198 scopus 로고    scopus 로고
    • A gene atlas of the mouse and human protein-encoding transcriptomes
    • Su A.I., et al. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc. Natl. Acad. Sci. U. S. A. 101 (2004) 6062-6067
    • (2004) Proc. Natl. Acad. Sci. U. S. A. , vol.101 , pp. 6062-6067
    • Su, A.I.1
  • 50
    • 24744438019 scopus 로고    scopus 로고
    • Gene expression evolves faster in narrowly than in broadly expressed mammalian genes
    • Yang J., Su A.I., and Li W.H. Gene expression evolves faster in narrowly than in broadly expressed mammalian genes. Mol. Biol. Evol. 22 (2005) 2113-2118
    • (2005) Mol. Biol. Evol. , vol.22 , pp. 2113-2118
    • Yang, J.1    Su, A.I.2    Li, W.H.3
  • 51
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
    • Ashburner M., et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25 (2000) 25-29
    • (2000) Nat. Genet. , vol.25 , pp. 25-29
    • Ashburner, M.1


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