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Volumn 39, Issue 4, 2007, Pages 457-466

Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome

Author keywords

[No Author keywords available]

Indexed keywords

DNA; HISTONE H3; LYSINE; RNA POLYMERASE;

EID: 34047116826     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng1990     Document Type: Article
Times cited : (1783)

References (50)
  • 1
    • 0026708177 scopus 로고
    • Targeted mutation of the DNA methyltransferase gene results in embryonic lethality
    • Li, E., Bestor, T.H. & Jaenisch, R. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 69, 915-926 (1992).
    • (1992) Cell , vol.69 , pp. 915-926
    • Li, E.1    Bestor, T.H.2    Jaenisch, R.3
  • 2
    • 0027378582 scopus 로고
    • Role for DNA methylation in genomic imprinting
    • Li, E., Beard, C. & Jaenisch, R. Role for DNA methylation in genomic imprinting. Nature 366, 362-365 (1993).
    • (1993) Nature , vol.366 , pp. 362-365
    • Li, E.1    Beard, C.2    Jaenisch, R.3
  • 3
    • 0031467130 scopus 로고    scopus 로고
    • X-chromosome inactivation in mammals
    • Heard, E., Clerc, P. & Avner, P. X-chromosome inactivation in mammals. Annu. Rev. Genet. 31, 571-610 (1997).
    • (1997) Annu. Rev. Genet , vol.31 , pp. 571-610
    • Heard, E.1    Clerc, P.2    Avner, P.3
  • 4
    • 2642531973 scopus 로고    scopus 로고
    • Epigenetics in human disease and prospects for epigenetic therapy
    • Egger, G., Liang, G., Aparicio, A. & Jones, P.A. Epigenetics in human disease and prospects for epigenetic therapy. Nature 429, 457-463 (2004).
    • (2004) Nature , vol.429 , pp. 457-463
    • Egger, G.1    Liang, G.2    Aparicio, A.3    Jones, P.A.4
  • 5
    • 0033822364 scopus 로고    scopus 로고
    • Large-scale human promoter mapping using CpG islands
    • Ioshikhes, I.P. & Zhang, M.Q. Large-scale human promoter mapping using CpG islands. Nat. Genet. 26, 61-63 (2000).
    • (2000) Nat. Genet , vol.26 , pp. 61-63
    • Ioshikhes, I.P.1    Zhang, M.Q.2
  • 6
    • 32344450824 scopus 로고    scopus 로고
    • Genomic DNA methylation: The mark and its mediators
    • Klose, R.J. & Bird, A.P. Genomic DNA methylation: the mark and its mediators. Trends Biochem. Sci. 31, 89-97 (2006).
    • (2006) Trends Biochem. Sci , vol.31 , pp. 89-97
    • Klose, R.J.1    Bird, A.P.2
  • 7
    • 0026583975 scopus 로고
    • Repression of genes by DNA methylation depends on CpG density and promoter strength: Evidence for involvement of a methyl-CpG binding protein
    • Boyes, J. & Bird, A. Repression of genes by DNA methylation depends on CpG density and promoter strength: evidence for involvement of a methyl-CpG binding protein. EMBO J. 11, 327-333 (1992).
    • (1992) EMBO J , vol.11 , pp. 327-333
    • Boyes, J.1    Bird, A.2
  • 8
    • 0028106737 scopus 로고
    • Dependence of transcriptional repression on CpG methylation density
    • Hsieh, C.L. Dependence of transcriptional repression on CpG methylation density. Mol. Cell. Biol. 14, 5487-5494 (1994).
    • (1994) Mol. Cell. Biol , vol.14 , pp. 5487-5494
    • Hsieh, C.L.1
  • 9
    • 0027689976 scopus 로고
    • Dynamics of DNA methylation during development
    • Brandeis, M., Ariel, M. & Cedar, H. Dynamics of DNA methylation during development. Bioessays 15, 709-713 (1993).
    • (1993) Bioessays , vol.15 , pp. 709-713
    • Brandeis, M.1    Ariel, M.2    Cedar, H.3
  • 10
    • 0036144048 scopus 로고    scopus 로고
    • DNA methylation patterns and epigenetic memory
    • Bird, A. DNA methylation patterns and epigenetic memory. Genes Dev. 16, 6-21 (2002).
    • (2002) Genes Dev , vol.16 , pp. 6-21
    • Bird, A.1
  • 11
    • 0036613432 scopus 로고    scopus 로고
    • Role for DNA methylation in the control of cell type specific maspin expression
    • Futscher, B.W. et al. Role for DNA methylation in the control of cell type specific maspin expression. Nat. Genet. 31, 175-179 (2002).
    • (2002) Nat. Genet , vol.31 , pp. 175-179
    • Futscher, B.W.1
  • 12
    • 14744267496 scopus 로고    scopus 로고
    • Association of tissue-specific differentially methylated regions (TDMs) with differential gene expression
    • Song, F. et al. Association of tissue-specific differentially methylated regions (TDMs) with differential gene expression. Proc. Natl. Acad. Sci. USA 102, 3336-3341 (2005).
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 3336-3341
    • Song, F.1
  • 13
    • 0032901199 scopus 로고    scopus 로고
    • Cytosine methylation and mammalian development
    • Walsh, C.P. & Bestor, T.H. Cytosine methylation and mammalian development. Genes Dev. 13, 26-34 (1999).
    • (1999) Genes Dev , vol.13 , pp. 26-34
    • Walsh, C.P.1    Bestor, T.H.2
  • 14
    • 0032906457 scopus 로고    scopus 로고
    • DNA methylation profile of the mouse skeletal alpha-actin promoter during development and differentiation
    • Warnecke, P.M. & Clark, S.J. DNA methylation profile of the mouse skeletal alpha-actin promoter during development and differentiation. Mol. Cell. Biol. 19, 164-172 (1999).
    • (1999) Mol. Cell. Biol , vol.19 , pp. 164-172
    • Warnecke, P.M.1    Clark, S.J.2
  • 15
    • 0035875049 scopus 로고    scopus 로고
    • Excessive CpG island hypermethylation in cancer cell lines versus primary human malignancies
    • Smiraglia, D.J. et al. Excessive CpG island hypermethylation in cancer cell lines versus primary human malignancies. Hum. Mol. Genet. 10, 1413-1419 (2001).
    • (2001) Hum. Mol. Genet , vol.10 , pp. 1413-1419
    • Smiraglia, D.J.1
  • 16
    • 0018185292 scopus 로고
    • Molecular basis of base substitution hotspots in Escherichia coli
    • Coulondre, C., Miller, J.H., Farabaugh, P.J. & Gilbert, W. Molecular basis of base substitution hotspots in Escherichia coli. Nature 274, 775-780 (1978).
    • (1978) Nature , vol.274 , pp. 775-780
    • Coulondre, C.1    Miller, J.H.2    Farabaugh, P.J.3    Gilbert, W.4
  • 17
    • 0028358421 scopus 로고
    • The rate of hydrolytic deamination of 5-methylcytosine in double-stranded DNA
    • Shen, J.C., Rideout, W.M., III. & Jones, P.A. The rate of hydrolytic deamination of 5-methylcytosine in double-stranded DNA. Nucleic Acids Res. 22, 972-976 (1994).
    • (1994) Nucleic Acids Res , vol.22 , pp. 972-976
    • Shen, J.C.1    Rideout III, W.M.2    Jones, P.A.3
  • 18
    • 0033575886 scopus 로고    scopus 로고
    • The thymine glycosylase MBD4 can bind to the product of deamination at methylated CpG sites
    • Hendrich, B., Hardeland, U., Ng, H.H., Jiricny, J. & Bird, A. The thymine glycosylase MBD4 can bind to the product of deamination at methylated CpG sites. Nature 401, 301-304 (1999).
    • (1999) Nature , vol.401 , pp. 301-304
    • Hendrich, B.1    Hardeland, U.2    Ng, H.H.3    Jiricny, J.4    Bird, A.5
  • 19
    • 0027383758 scopus 로고
    • The purification of a mismatch-specific thymine-DNA glycosylase from HeLa cells
    • Neddermann, P. & Jiricny, J. The purification of a mismatch-specific thymine-DNA glycosylase from HeLa cells. J. Biol. Chem. 268, 21218-21224 (1993).
    • (1993) J. Biol. Chem , vol.268 , pp. 21218-21224
    • Neddermann, P.1    Jiricny, J.2
  • 20
    • 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, 157-163 (2006).
    • (2006) Genome Res , vol.16 , pp. 157-163
    • Rollins, R.A.1
  • 21
    • 31944432339 scopus 로고    scopus 로고
    • A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters
    • Saxonov, S., Berg, P. & Brutlag, D.L. A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc. Natl. Acad. Sci. USA 103, 1412-1417 (2006).
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , pp. 1412-1417
    • Saxonov, S.1    Berg, P.2    Brutlag, D.L.3
  • 22
    • 23044514626 scopus 로고    scopus 로고
    • Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells
    • Weber, M. et al. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat. Genet. 37, 853-862 (2005).
    • (2005) Nat. Genet , vol.37 , pp. 853-862
    • Weber, M.1
  • 23
    • 0037133565 scopus 로고    scopus 로고
    • Comprehensive analysis of CpG islands in human chromosomes 21 and 22
    • Takai, D. & Jones, P.A. Comprehensive analysis of CpG islands in human chromosomes 21 and 22. Proc. Natl. Acad. Sci. USA 99, 3740-3745 (2002).
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 3740-3745
    • Takai, D.1    Jones, P.A.2
  • 24
    • 0023216891 scopus 로고
    • CpG islands in vertebrate genomes
    • Gardiner-Garden, M. & Frommer, M. CpG islands in vertebrate genomes. J. Mol. Biol. 196, 261-282 (1987).
    • (1987) J. Mol. Biol , vol.196 , pp. 261-282
    • Gardiner-Garden, M.1    Frommer, M.2
  • 25
    • 23844519339 scopus 로고    scopus 로고
    • A high-resolution map of active promoters in the human genome
    • Kim, T.H. et al. A high-resolution map of active promoters in the human genome. Nature 436, 876-880 (2005).
    • (2005) Nature , vol.436 , pp. 876-880
    • Kim, T.H.1
  • 26
    • 15044366201 scopus 로고    scopus 로고
    • Methylation of histones: Playing memory with DNA
    • Peters, A.H. & Schubeler, D. Methylation of histones: playing memory with DNA. Curr. Opin. Cell Biol. 17, 230-238 (2005).
    • (2005) Curr. Opin. Cell Biol , vol.17 , pp. 230-238
    • Peters, A.H.1    Schubeler, D.2
  • 27
    • 2642570305 scopus 로고    scopus 로고
    • The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote
    • Schubeler, D. et al. The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote. Genes Dev. 18, 1263-1271 (2004).
    • (2004) Genes Dev , vol.18 , pp. 1263-1271
    • Schubeler, D.1
  • 28
    • 4644300141 scopus 로고    scopus 로고
    • Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution
    • Hwang, D.G. & Green, P. Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution. Proc. Natl. Acad. Sci. USA 101, 13994-14001 (2004).
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 13994-14001
    • Hwang, D.G.1    Green, P.2
  • 29
    • 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. USA 101, 6062-6067 (2004).
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 6062-6067
    • Su, A.I.1
  • 30
    • 33745845526 scopus 로고    scopus 로고
    • The human cumulus-oocyte complex gene-expression profile
    • Assou, S. et al. The human cumulus-oocyte complex gene-expression profile. Hum. Reprod. 21, 1705-1719 (2006).
    • (2006) Hum. Reprod , vol.21 , pp. 1705-1719
    • Assou, S.1
  • 31
    • 4344711733 scopus 로고    scopus 로고
    • Frequent nonrandom activation of germ-line genes in human cancer
    • Koslowski, M. et al. Frequent nonrandom activation of germ-line genes in human cancer. Cancer Res. 64, 5988-5993 (2004).
    • (2004) Cancer Res , vol.64 , pp. 5988-5993
    • Koslowski, M.1
  • 32
    • 0025836937 scopus 로고
    • DNA hypomethylation and germ cell-specific expression of testis-specific H2B histone gene
    • Choi, Y.C. & Chae, C.B. DNA hypomethylation and germ cell-specific expression of testis-specific H2B histone gene. J. Biol. Chem. 266, 20504-20511 (1991).
    • (1991) J. Biol. Chem , vol.266 , pp. 20504-20511
    • Choi, Y.C.1    Chae, C.B.2
  • 33
    • 0033761974 scopus 로고    scopus 로고
    • Testis-specific histone H1t gene is hypermethylated in nongerminal cells in the mouse
    • Singal, R. et al. Testis-specific histone H1t gene is hypermethylated in nongerminal cells in the mouse. Biol. Reprod. 63, 1237-1244 (2000).
    • (2000) Biol. Reprod , vol.63 , pp. 1237-1244
    • Singal, R.1
  • 34
    • 0034458963 scopus 로고    scopus 로고
    • Genomic targeting of methylated DNA: Influence of methylation on transcription, replication, chromatin structure, and histone acetylation
    • Schubeler, D. et al. Genomic targeting of methylated DNA: influence of methylation on transcription, replication, chromatin structure, and histone acetylation. Mol. Cell. Biol. 20, 9103-9112 (2000).
    • (2000) Mol. Cell. Biol , vol.20 , pp. 9103-9112
    • Schubeler, D.1
  • 35
    • 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, 1378-1385 (2006).
    • (2006) Nat. Genet , vol.38 , pp. 1378-1385
    • Eckhardt, F.1
  • 36
    • 33645777446 scopus 로고    scopus 로고
    • CpG island methylation in human lymphocytes is highly correlated with DNA sequence, repeats, and predicted DNA structure
    • Bock, C. et al. CpG island methylation in human lymphocytes is highly correlated with DNA sequence, repeats, and predicted DNA structure. PLoS Genet 2, e26 (2006).
    • (2006) PLoS Genet , vol.2
    • Bock, C.1
  • 37
    • 8644278033 scopus 로고    scopus 로고
    • Binding to nonmethylated CpG DNA is essential for target recognition, transactivation, and myeloid transformation by an MLL oncoprotein
    • Ayton, P.M., Chen, E.H. & Cleary, M.L. Binding to nonmethylated CpG DNA is essential for target recognition, transactivation, and myeloid transformation by an MLL oncoprotein. Mol. Cell. Biol. 24, 10470-10478 (2004).
    • (2004) Mol. Cell. Biol , vol.24 , pp. 10470-10478
    • Ayton, P.M.1    Chen, E.H.2    Cleary, M.L.3
  • 38
    • 29244438472 scopus 로고    scopus 로고
    • CpG-binding protein (CXXC finger protein 1) is a component of the mammalian Set1 histone H3-Lys4 methyltransferase complex, the analogue of the yeast Set1/COMPASS complex
    • Lee, J.H. & Skalnik, D.G. CpG-binding protein (CXXC finger protein 1) is a component of the mammalian Set1 histone H3-Lys4 methyltransferase complex, the analogue of the yeast Set1/COMPASS complex. J. Biol. Chem. 280, 41725-41731 (2005).
    • (2005) J. Biol. Chem , vol.280 , pp. 41725-41731
    • Lee, J.H.1    Skalnik, D.G.2
  • 39
    • 14644406272 scopus 로고    scopus 로고
    • Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping
    • Roh, T.Y., Cuddapah, S. & Zhao, K. Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping. Genes Dev. 19, 542-552 (2005).
    • (2005) Genes Dev , vol.19 , pp. 542-552
    • Roh, T.Y.1    Cuddapah, S.2    Zhao, K.3
  • 40
    • 0028940587 scopus 로고
    • Gene number, noise reduction and biological complexity
    • Bird, A.P. Gene number, noise reduction and biological complexity. Trends Genet. 11, 94-100 (1995).
    • (1995) Trends Genet , vol.11 , pp. 94-100
    • Bird, A.P.1
  • 41
    • 33749396836 scopus 로고    scopus 로고
    • DNA methylation is a primary mechanism for silencing post-migratory primordial germ cell genes in both germ cell and somatic cell lineages
    • Maatouk, D.M. et al. DNA methylation is a primary mechanism for silencing post-migratory primordial germ cell genes in both germ cell and somatic cell lineages. Development 133, 3411-3418 (2006).
    • (2006) Development , vol.133 , pp. 3411-3418
    • Maatouk, D.M.1
  • 42
    • 20144379783 scopus 로고    scopus 로고
    • A role for E2F6 in the restriction of male-germ-cell-specific gene expression
    • Pohlers, M. et al. A role for E2F6 in the restriction of male-germ-cell-specific gene expression. Curr. Biol. 15, 1051-1057 (2005).
    • (2005) Curr. Biol , vol.15 , pp. 1051-1057
    • Pohlers, M.1
  • 43
    • 2442654138 scopus 로고    scopus 로고
    • Promoter-dependent mechanism leading to selective hypomethylation within the 5′ region of gene MAGE-A1 in tumor cells
    • De Smet, C., Loriot, A. & Boon, T. Promoter-dependent mechanism leading to selective hypomethylation within the 5′ region of gene MAGE-A1 in tumor cells. Mol. Cell. Biol. 24, 4781-4790 (2004).
    • (2004) Mol. Cell. Biol , vol.24 , pp. 4781-4790
    • De Smet, C.1    Loriot, A.2    Boon, T.3
  • 44
    • 0035735265 scopus 로고    scopus 로고
    • Computational identification of promoters and first exons in the human genome
    • Davuluri, R.V., Grosse, I. & Zhang, M.Q. Computational identification of promoters and first exons in the human genome. Nat. Genet. 29, 412-417 (2001).
    • (2001) Nat. Genet , vol.29 , pp. 412-417
    • Davuluri, R.V.1    Grosse, I.2    Zhang, M.Q.3
  • 45
    • 15244353967 scopus 로고    scopus 로고
    • X-inactivation profile reveals extensive variability in X-linked gene expression in females
    • Carrel, L. & Willard, H.F. X-inactivation profile reveals extensive variability in X-linked gene expression in females. Nature 434, 400-404 (2005).
    • (2005) Nature , vol.434 , pp. 400-404
    • Carrel, L.1    Willard, H.F.2
  • 46
    • 0038692119 scopus 로고    scopus 로고
    • Human housekeeping genes are compact
    • Eisenberg, E. & Levanon, E.Y. Human housekeeping genes are compact. Trends Genet. 19, 362-365 (2003).
    • (2003) Trends Genet , vol.19 , pp. 362-365
    • Eisenberg, E.1    Levanon, E.Y.2
  • 48
    • 0038492517 scopus 로고    scopus 로고
    • A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells
    • Li, Z. et al. A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells. Proc. Natl. Acad. Sci. USA 100, 8164-8169 (2003).
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 8164-8169
    • Li, Z.1
  • 49
    • 0031172451 scopus 로고    scopus 로고
    • Monoallelic expression of human PEG1/MEST is paralleled by parent-specific methylation in fetuses
    • Riesewijk, A.M. et al. Monoallelic expression of human PEG1/MEST is paralleled by parent-specific methylation in fetuses. Genomics 42, 236-244 (1997).
    • (1997) Genomics , vol.42 , pp. 236-244
    • Riesewijk, A.M.1
  • 50
    • 0842263778 scopus 로고    scopus 로고
    • The multicoloured world of promoter recognition complexes
    • Muller, F. & Tora, L. The multicoloured world of promoter recognition complexes. EMBO J. 23, 2-8 (2004).
    • (2004) EMBO J , vol.23 , pp. 2-8
    • Muller, F.1    Tora, L.2


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