메뉴 건너뛰기




Volumn 12, Issue , 2011, Pages

Genome-wide survey reveals dynamic widespread tissue-specific changes in DNA methylation during development

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; CADHERIN; HOMEODOMAIN PROTEIN;

EID: 79955777417     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-12-231     Document Type: Article
Times cited : (115)

References (57)
  • 1
    • 0019322245 scopus 로고
    • DNA methylation and the frequency of CpG in animal DNA
    • 10.1093/nar/8.7.1499, 324012, 6253938
    • Bird AP. DNA methylation and the frequency of CpG in animal DNA. Nucleic Acids Res 1980, 8:1499-1504. 10.1093/nar/8.7.1499, 324012, 6253938.
    • (1980) Nucleic Acids Res , vol.8 , pp. 1499-1504
    • Bird, A.P.1
  • 2
    • 0027141519 scopus 로고
    • Number of CpG islands and genes in human and mouse
    • 10.1073/pnas.90.24.11995, 48112, 7505451
    • Antequera F, Bird A. Number of CpG islands and genes in human and mouse. Proc Natl Acad Sci USA 1993, 90:11995-11999. 10.1073/pnas.90.24.11995, 48112, 7505451.
    • (1993) Proc Natl Acad Sci USA , vol.90 , pp. 11995-11999
    • Antequera, F.1    Bird, A.2
  • 3
    • 0030840954 scopus 로고    scopus 로고
    • Cytosine methylation and the ecology of intragenomic parasites
    • 10.1016/S0168-9525(97)01181-5, 9260521
    • Yoder JA, Walsh CP, Bestor TH. Cytosine methylation and the ecology of intragenomic parasites. Trends Genet 1997, 13:335-340. 10.1016/S0168-9525(97)01181-5, 9260521.
    • (1997) Trends Genet , vol.13 , pp. 335-340
    • Yoder, J.A.1    Walsh, C.P.2    Bestor, T.H.3
  • 5
    • 0026740497 scopus 로고
    • Developmental pattern of gene-specific DNA methylation in the mouse embryo and germ line
    • 10.1101/gad.6.5.705, 1577268
    • Kafri T, Ariel M, Brandeis M, Shemer R, Urven L, McCarrey J, Cedar H, Razin A. Developmental pattern of gene-specific DNA methylation in the mouse embryo and germ line. Genes Dev 1992, 6:705-714. 10.1101/gad.6.5.705, 1577268.
    • (1992) Genes Dev , vol.6 , pp. 705-714
    • Kafri, T.1    Ariel, M.2    Brandeis, M.3    Shemer, R.4    Urven, L.5    McCarrey, J.6    Cedar, H.7    Razin, A.8
  • 6
    • 0023119242 scopus 로고
    • Temporal and regional changes in DNA methylation in the embryonic, extraembryonic and germ cell lineages during mouse embryo development
    • Monk M, Boubelik M, Lehnert S. Temporal and regional changes in DNA methylation in the embryonic, extraembryonic and germ cell lineages during mouse embryo development. Development 1987, 99:371-382.
    • (1987) Development , vol.99 , pp. 371-382
    • Monk, M.1    Boubelik, M.2    Lehnert, S.3
  • 7
    • 0035839126 scopus 로고    scopus 로고
    • Epigenetic reprogramming in mammalian development
    • 10.1126/science.1063443, 11498579
    • Reik W, Dean W, Walter J. Epigenetic reprogramming in mammalian development. Science 2001, 293:1089-1093. 10.1126/science.1063443, 11498579.
    • (2001) Science , vol.293 , pp. 1089-1093
    • Reik, W.1    Dean, W.2    Walter, J.3
  • 8
    • 0037376702 scopus 로고    scopus 로고
    • Expression of various genes is controlled by DNA methylation during mammalian development
    • 10.1002/jcb.10464, 12616529
    • Ehrlich M. Expression of various genes is controlled by DNA methylation during mammalian development. J Cell Biochem 2003, 88:899-910. 10.1002/jcb.10464, 12616529.
    • (2003) J Cell Biochem , vol.88 , pp. 899-910
    • Ehrlich, M.1
  • 9
  • 10
    • 0016692220 scopus 로고
    • X inactivation, differentiation, and DNA methylation
    • 10.1159/000130315, 1093816
    • Riggs AD. X inactivation, differentiation, and DNA methylation. Cytogenet Cell Genet 1975, 14:9-25. 10.1159/000130315, 1093816.
    • (1975) Cytogenet Cell Genet , vol.14 , pp. 9-25
    • Riggs, A.D.1
  • 11
    • 0031662164 scopus 로고    scopus 로고
    • Transcription of IAP endogenous retroviruses is constrained by cytosine methylation
    • 10.1038/2413, 9771701
    • Walsh CP, Chaillet JR, Bestor TH. Transcription of IAP endogenous retroviruses is constrained by cytosine methylation. Nat Genet 1998, 20:116-117. 10.1038/2413, 9771701.
    • (1998) Nat Genet , vol.20 , pp. 116-117
    • Walsh, C.P.1    Chaillet, J.R.2    Bestor, T.H.3
  • 12
    • 34047116826 scopus 로고    scopus 로고
    • Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome
    • 10.1038/ng1990, 17334365
    • Weber M, Hellmann I, Stadler MB, Ramos L, Paabo S, Rebhan M, Schubeler D. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet 2007, 39:457-466. 10.1038/ng1990, 17334365.
    • (2007) Nat Genet , vol.39 , pp. 457-466
    • Weber, M.1    Hellmann, I.2    Stadler, M.B.3    Ramos, L.4    Paabo, S.5    Rebhan, M.6    Schubeler, D.7
  • 13
    • 0016439429 scopus 로고
    • DNA modification mechanisms and gene activity during development
    • 10.1126/science.1111098, 1111098
    • Holliday R, Pugh JE. DNA modification mechanisms and gene activity during development. Science 1975, 187:226-232. 10.1126/science.1111098, 1111098.
    • (1975) Science , vol.187 , pp. 226-232
    • Holliday, R.1    Pugh, J.E.2
  • 14
    • 0026708177 scopus 로고
    • Targeted mutation of the DNA methyltransferase gene results in embryonic lethality
    • 10.1016/0092-8674(92)90611-F, 1606615
    • Li E, Bestor TH, Jaenisch R. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 1992, 69:915-926. 10.1016/0092-8674(92)90611-F, 1606615.
    • (1992) Cell , vol.69 , pp. 915-926
    • Li, E.1    Bestor, T.H.2    Jaenisch, R.3
  • 15
    • 0033615717 scopus 로고    scopus 로고
    • DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development
    • 10.1016/S0092-8674(00)81656-6, 10555141
    • Okano M, Bell DW, Haber DA, Li E. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 1999, 99:247-257. 10.1016/S0092-8674(00)81656-6, 10555141.
    • (1999) Cell , vol.99 , pp. 247-257
    • Okano, M.1    Bell, D.W.2    Haber, D.A.3    Li, E.4
  • 16
    • 0026052179 scopus 로고
    • A genomic scanning method for higher organisms using restriction sites as landmarks
    • 10.1073/pnas.88.21.9523, 52750, 1946366
    • Hatada I, Hayashizaki Y, Hirotsune S, Komatsubara H, Mukai T. A genomic scanning method for higher organisms using restriction sites as landmarks. Proc Natl Acad Sci USA 1991, 88:9523-9527. 10.1073/pnas.88.21.9523, 52750, 1946366.
    • (1991) Proc Natl Acad Sci USA , vol.88 , pp. 9523-9527
    • Hatada, I.1    Hayashizaki, Y.2    Hirotsune, S.3    Komatsubara, H.4    Mukai, T.5
  • 17
    • 0027723111 scopus 로고
    • Methylation profiles of genomic DNA of mouse developmental brain detected by restriction landmark genomic scanning (RLGS) method
    • 10.1093/nar/21.24.5604, 310523, 8284204
    • Kawai J, Hirotsune S, Hirose K, Fushiki S, Watanabe S, Hayashizaki Y. Methylation profiles of genomic DNA of mouse developmental brain detected by restriction landmark genomic scanning (RLGS) method. Nucleic Acids Res 1993, 21:5604-5608. 10.1093/nar/21.24.5604, 310523, 8284204.
    • (1993) Nucleic Acids Res , vol.21 , pp. 5604-5608
    • Kawai, J.1    Hirotsune, S.2    Hirose, K.3    Fushiki, S.4    Watanabe, S.5    Hayashizaki, Y.6
  • 18
    • 0036734599 scopus 로고    scopus 로고
    • Epigenetic marks by DNA methylation specific to stem, germ and somatic cells in mice
    • 10.1046/j.1365-2443.2002.00574.x, 12296826
    • Shiota K, Kogo Y, Ohgane J, Imamura T, Urano A, Nishino K, Tanaka S, Hattori N. Epigenetic marks by DNA methylation specific to stem, germ and somatic cells in mice. Genes Cells 2002, 7:961-969. 10.1046/j.1365-2443.2002.00574.x, 12296826.
    • (2002) Genes Cells , vol.7 , pp. 961-969
    • Shiota, K.1    Kogo, Y.2    Ohgane, J.3    Imamura, T.4    Urano, A.5    Nishino, K.6    Tanaka, S.7    Hattori, N.8
  • 19
    • 14744267496 scopus 로고    scopus 로고
    • Association of tissue-specific differentially methylated regions (TDMs) with differential gene expression
    • 10.1073/pnas.0408436102, 552919, 15728362
    • Song F, Smith JF, Kimura MT, Morrow AD, Matsuyama T, Nagase H, Held WA. Association of tissue-specific differentially methylated regions (TDMs) with differential gene expression. Proc Natl Acad Sci USA 2005, 102:3336-3341. 10.1073/pnas.0408436102, 552919, 15728362.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 3336-3341
    • Song, F.1    Smith, J.F.2    Kimura, M.T.3    Morrow, A.D.4    Matsuyama, T.5    Nagase, H.6    Held, W.A.7
  • 27
    • 33846066292 scopus 로고    scopus 로고
    • A unique configuration of genome-wide DNA methylation patterns in the testis
    • 10.1073/pnas.0607521104, 1765440, 17190809
    • Oakes CC, La SS, Smiraglia DJ, Robaire B, Trasler JM. A unique configuration of genome-wide DNA methylation patterns in the testis. Proc Natl Acad Sci USA 2007, 104:228-233. 10.1073/pnas.0607521104, 1765440, 17190809.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 228-233
    • Oakes, C.C.1    La, S.S.2    Smiraglia, D.J.3    Robaire, B.4    Trasler, J.M.5
  • 29
    • 33748055105 scopus 로고    scopus 로고
    • MIRA-assisted microarray analysis, a new technology for the determination of DNA methylation patterns, identifies frequent methylation of homeodomain-containing genes in lung cancer cells
    • 10.1158/0008-5472.CAN-06-1888, 16912168
    • Rauch T, Li H, Wu X, Pfeifer GP. MIRA-assisted microarray analysis, a new technology for the determination of DNA methylation patterns, identifies frequent methylation of homeodomain-containing genes in lung cancer cells. Cancer Res 2006, 66:7939-7947. 10.1158/0008-5472.CAN-06-1888, 16912168.
    • (2006) Cancer Res , vol.66 , pp. 7939-7947
    • Rauch, T.1    Li, H.2    Wu, X.3    Pfeifer, G.P.4
  • 30
    • 34547476585 scopus 로고    scopus 로고
    • Global, comparative analysis of tissue-specific promoter CpG methylation
    • 10.1016/j.ygeno.2007.04.011, 17582736
    • Schilling E, Rehli M. Global, comparative analysis of tissue-specific promoter CpG methylation. Genomics 2007, 90:314-323. 10.1016/j.ygeno.2007.04.011, 17582736.
    • (2007) Genomics , vol.90 , pp. 314-323
    • Schilling, E.1    Rehli, M.2
  • 31
    • 35948981875 scopus 로고    scopus 로고
    • Genome-wide profiling of DNA methylation reveals a class of normally methylated CpG island promoters
    • 2041996, 17967063
    • Shen L, Kondo Y, Guo Y, Zhang J, Zhang L, Ahmed S, Shu J, Chen X, Waterland RA, Issa JP. Genome-wide profiling of DNA methylation reveals a class of normally methylated CpG island promoters. PLoS Genet 2007, 3:2023-2036. 2041996, 17967063.
    • (2007) PLoS Genet , vol.3 , pp. 2023-2036
    • Shen, L.1    Kondo, Y.2    Guo, Y.3    Zhang, J.4    Zhang, L.5    Ahmed, S.6    Shu, J.7    Chen, X.8    Waterland, R.A.9    Issa, J.P.10
  • 32
    • 58149490976 scopus 로고    scopus 로고
    • Tissue specific differentially methylated regions (TDMR): Changes in DNA methylation during development
    • 10.1016/j.ygeno.2008.09.003, 2658018, 18952162
    • Song F, Mahmood S, Ghosh S, Liang P, Smiraglia DJ, Nagase H, Held WA. Tissue specific differentially methylated regions (TDMR): Changes in DNA methylation during development. Genomics 2009, 93:130-139. 10.1016/j.ygeno.2008.09.003, 2658018, 18952162.
    • (2009) Genomics , vol.93 , pp. 130-139
    • Song, F.1    Mahmood, S.2    Ghosh, S.3    Liang, P.4    Smiraglia, D.J.5    Nagase, H.6    Held, W.A.7
  • 33
    • 23044514626 scopus 로고    scopus 로고
    • Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells
    • 10.1038/ng1598, 16007088
    • Weber M, Davies JJ, Wittig D, Oakeley EJ, Haase M, Lam WL, Schubeler D. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet 2005, 37:853-862. 10.1038/ng1598, 16007088.
    • (2005) Nat Genet , vol.37 , pp. 853-862
    • Weber, M.1    Davies, J.J.2    Wittig, D.3    Oakeley, E.J.4    Haase, M.5    Lam, W.L.6    Schubeler, D.7
  • 34
    • 57149092605 scopus 로고    scopus 로고
    • DNA methylation profile of tissue-dependent and differentially methylated regions (T-DMRs) in mouse promoter regions demonstrating tissue-specific gene expression
    • 10.1101/gr.074070.107, 2593572, 18971312
    • Yagi S, Hirabayashi K, Sato S, Li W, Takahashi Y, Hirakawa T, Wu G, Hattori N, Hattori N, Ohgane J, Tanaka S, Liu XS, Shiota K. DNA methylation profile of tissue-dependent and differentially methylated regions (T-DMRs) in mouse promoter regions demonstrating tissue-specific gene expression. Genome Res 2008, 18:1969-1978. 10.1101/gr.074070.107, 2593572, 18971312.
    • (2008) Genome Res , vol.18 , pp. 1969-1978
    • Yagi, S.1    Hirabayashi, K.2    Sato, S.3    Li, W.4    Takahashi, Y.5    Hirakawa, T.6    Wu, G.7    Hattori, N.8    Hattori, N.9    Ohgane, J.10    Tanaka, S.11    Liu, X.S.12    Shiota, K.13
  • 37
  • 38
    • 33847304609 scopus 로고    scopus 로고
    • Gene body-specific methylation on the active × chromosome
    • 10.1126/science.1136352, 17322062
    • Hellman A, Chess A. Gene body-specific methylation on the active × chromosome. Science 2007, 315:1141-1143. 10.1126/science.1136352, 17322062.
    • (2007) Science , vol.315 , pp. 1141-1143
    • Hellman, A.1    Chess, A.2
  • 41
    • 13444267968 scopus 로고    scopus 로고
    • Hox, ParaHox, ProtoHox: facts and guesses
    • 10.1038/sj.hdy.6800621, 15578045
    • Garcia-Fernandez J. Hox, ParaHox, ProtoHox: facts and guesses. Heredity 2005, 94:145-152. 10.1038/sj.hdy.6800621, 15578045.
    • (2005) Heredity , vol.94 , pp. 145-152
    • Garcia-Fernandez, J.1
  • 42
    • 28944438404 scopus 로고    scopus 로고
    • Modulating Hox gene functions during animal body patterning
    • 10.1038/nrg1726, 16341070
    • Pearson JC, Lemons D, McGinnis W. Modulating Hox gene functions during animal body patterning. Nat Rev Genet 2005, 6:893-904. 10.1038/nrg1726, 16341070.
    • (2005) Nat Rev Genet , vol.6 , pp. 893-904
    • Pearson, J.C.1    Lemons, D.2    McGinnis, W.3
  • 44
    • 59849117080 scopus 로고    scopus 로고
    • Multi-stage analysis of gene expression and transcription regulation in C57/B6 mouse liver development
    • 10.1016/j.ygeno.2008.10.006, 2995988, 19015022
    • Li T, Huang J, Jiang Y, Zeng Y, He F, Zhang MQ, Han Z, Zhang X. Multi-stage analysis of gene expression and transcription regulation in C57/B6 mouse liver development. Genomics 2009, 93:235-242. 10.1016/j.ygeno.2008.10.006, 2995988, 19015022.
    • (2009) Genomics , vol.93 , pp. 235-242
    • Li, T.1    Huang, J.2    Jiang, Y.3    Zeng, Y.4    He, F.5    Zhang, M.Q.6    Han, Z.7    Zhang, X.8
  • 46
    • 0035680734 scopus 로고    scopus 로고
    • An intragenic methylated region in the imprinted Igf2 gene augments transcription
    • 10.1093/embo-reports/kve248, 1084166, 11743023
    • Murrell A, Heeson S, Bowden L, Constancia M, Dean W, Kelsey G, Reik W. An intragenic methylated region in the imprinted Igf2 gene augments transcription. EMBO Rep 2001, 2:1101-1106. 10.1093/embo-reports/kve248, 1084166, 11743023.
    • (2001) EMBO Rep , vol.2 , pp. 1101-1106
    • Murrell, A.1    Heeson, S.2    Bowden, L.3    Constancia, M.4    Dean, W.5    Kelsey, G.6    Reik, W.7
  • 47
    • 58849091905 scopus 로고    scopus 로고
    • A human B cell methylome at 100-base pair resolution
    • 10.1073/pnas.0812399106, 2621253, 19139413
    • Rauch TA, Wu X, Zhong X, Riggs AD, Pfeifer GP. A human B cell methylome at 100-base pair resolution. Proc Natl Acad Sci USA 2009, 106:671-678. 10.1073/pnas.0812399106, 2621253, 19139413.
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 671-678
    • Rauch, T.A.1    Wu, X.2    Zhong, X.3    Riggs, A.D.4    Pfeifer, G.P.5
  • 51
    • 0034625064 scopus 로고    scopus 로고
    • Non-CpG methylation is prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a
    • 10.1073/pnas.97.10.5237, 25812, 10805783
    • Ramsahoye BH, Biniszkiewicz D, Lyko F, Clark V, Bird AP, Jaenisch R. Non-CpG methylation is prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a. Proc Natl Acad Sci USA 2000, 97:5237-5242. 10.1073/pnas.97.10.5237, 25812, 10805783.
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 5237-5242
    • Ramsahoye, B.H.1    Biniszkiewicz, D.2    Lyko, F.3    Clark, V.4    Bird, A.P.5    Jaenisch, R.6
  • 52
    • 33745216678 scopus 로고    scopus 로고
    • The role and expression of the protocadherin-alpha clusters in the CNS
    • 10.1016/j.conb.2006.05.003, 16697637
    • Hirayama T, Yagi T. The role and expression of the protocadherin-alpha clusters in the CNS. Curr Opin Neurobiol 2006, 16:336-342. 10.1016/j.conb.2006.05.003, 16697637.
    • (2006) Curr Opin Neurobiol , vol.16 , pp. 336-342
    • Hirayama, T.1    Yagi, T.2
  • 53
    • 0025743208 scopus 로고
    • Long-term reconstitution of the mouse hematopoietic system by embryonic stem cell-derived fetal liver
    • 10.1073/pnas.88.17.7514, 52331, 1881890
    • Forrester LM, Bernstein A, Rossant J, Nagy A. Long-term reconstitution of the mouse hematopoietic system by embryonic stem cell-derived fetal liver. Proc Natl Acad Sci USA 1991, 88:7514-7517. 10.1073/pnas.88.17.7514, 52331, 1881890.
    • (1991) Proc Natl Acad Sci USA , vol.88 , pp. 7514-7517
    • Forrester, L.M.1    Bernstein, A.2    Rossant, J.3    Nagy, A.4
  • 56
    • 0034326859 scopus 로고    scopus 로고
    • Sequence and functional comparison in the Beckwith-Wiedemann region: implications for a novel imprinting centre and extended imprinting
    • 10.1093/hmg/9.18.2691, 11063728
    • Engemann S, Strodicke M, Paulsen M, Franck O, Reinhardt R, Lane N, Reik W, Walter J. Sequence and functional comparison in the Beckwith-Wiedemann region: implications for a novel imprinting centre and extended imprinting. Hum Mol Genet 2000, 9:2691-2706. 10.1093/hmg/9.18.2691, 11063728.
    • (2000) Hum Mol Genet , vol.9 , pp. 2691-2706
    • Engemann, S.1    Strodicke, M.2    Paulsen, M.3    Franck, O.4    Reinhardt, R.5    Lane, N.6    Reik, W.7    Walter, J.8
  • 57
    • 0027400888 scopus 로고
    • Maternal-specific methylation of the imprinted mouse lgf2r locus identifies the expressed locus as carrying the imprinting signal
    • 10.1016/0092-8674(93)90160-R, 8462104
    • Stoger R, Kubicka P, Liu C-G, Kafri T, Razin A, Cedar H, Barlow P. Maternal-specific methylation of the imprinted mouse lgf2r locus identifies the expressed locus as carrying the imprinting signal. Cell 1993, 73:61-71. 10.1016/0092-8674(93)90160-R, 8462104.
    • (1993) Cell , vol.73 , pp. 61-71
    • Stoger, R.1    Kubicka, P.2    Liu, C.-G.3    Kafri, T.4    Razin, A.5    Cedar, H.6    Barlow, P.7


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.