SEARCH

SEARCH BY CITATION

References

  • 1
    Jones PA & Baylin SB (2002) The fundamental role of epigenetic events in cancer. Nat Rev Genet 3, 415428.
  • 2
    Klose RJ & Bird AP (2006) Genomic DNA methylation: the mark and its mediators. Trends Biochem Sci 31, 8997.
  • 3
    Jaenisch R & Bird A (2003) Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat Genet 33(Suppl), 245254.
  • 4
    Bird A (2002) DNA methylation patterns and epigenetic memory. Genes Dev 16, 621.
  • 5
    Jones PA & Takai D (2001) The role of DNA methylation in mammalian epigenetics. Science 293, 10681070.
  • 6
    Goll MG & Bestor TH (2005) Eukaryotic cytosine methyltransferases. Annu Rev Biochem 74, 481514.
  • 7
    Reik W (2007) Stability and flexibility of epigenetic gene regulation in mammalian development. Nature 447, 425432.
  • 8
    Futscher BW, Oshiro MM, Wozniak RJ, Holtan N, Hanigan CL, Duan H & Domann FE (2002) Role for DNA methylation in the control of cell type specific maspin expression. Nat Genet 31, 175179.
  • 9
    Ching TT, Maunakea AK, Jun P, Hong C, Zardo G, Pinkel D, Albertson DG, Fridlyand J, Mao JH, Shchors K et al. (2005) Epigenome analyses using BAC microarrays identify evolutionary conservation of tissue-specific methylation of SHANK3. Nat Genet 37, 645651.
  • 10
    Kankel MW, Ramsey DE, Stokes TL, Flowers SK, Haag JR, Jeddeloh JA, Riddle NC, Verbsky ML & Richards EJ (2003) Arabidopsis MET1 cytosine methyltransferase mutants. Genetics 163, 11091122.
  • 11
    Li E, Bestor TH & Jaenisch R (1992) Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 69, 915926.
  • 12
    Walsh CP & Bestor TH (1999) Cytosine methylation and mammalian development. Genes Dev 13, 2634.
  • 13
    Warnecke PM & Clark SJ (1999) DNA methylation profile of the mouse skeletal alpha-actin promoter during development and differentiation. Mol Cell Biol 19, 164172.
  • 14
    Jackson-Grusby L, Beard C, Possemato R, Tudor M, Fambrough D, Csankovszki G, Dausman J, Lee P, Wilson C, Lander E et al. (2001) Loss of genomic methylation causes p53-dependent apoptosis and epigenetic deregulation. Nat Genet 27, 3139.
  • 15
    Song F, Smith JF, Kimura MT, Morrow AD, Matsuyama T, Nagase H & Held WA (2005) Association of tissue-specific differentially methylated regions (TDMs) with differential gene expression. Proc Natl Acad Sci USA 102, 33363341.
  • 16
    Khulan B, Thompson RF, Ye K, Fazzari MJ, Suzuki M, Stasiek E, Figueroa ME, Glass JL, Chen Q, Montagna C et al. (2006) Comparative isoschizomer profiling of cytosine methylation: the HELP assay. Genome Res 16, 10461055.
  • 17
    Oakes CC, La SS, Smiraglia DJ, Robaire B & Trasler JM (2007) A unique configuration of genome-wide DNA methylation patterns in the testis. Proc Natl Acad Sci USA 104, 228233.
  • 18
    Kitamura E, Igarashi J, Morohashi A, Hida N, Oinuma T, Nemoto N, Song F, Ghosh S, Held WA, Yoshida-Noro C et al. (2007) Analysis of tissue-specific differentially methylated regions (TDMs) in humans. Genomics 89, 326337.
  • 19
    Weber M, Hellmann I, Stadler MB, Ramos L, Paabo S, Rebhan M & Schubeler D (2007) Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet 39, 457466.
  • 20
    Schilling E & Rehli M (2007) Global, comparative analysis of tissue-specific promoter CpG methylation. Genomics 90, 314323.
  • 21
    Maekita T, Nakazawa K, Mihara M, Nakajima T, Yanaoka K, Iguchi M, Arii K, Kaneda A, Tsukamoto T, Tatematsu M et al. (2006) High levels of aberrant DNA methylation in Helicobacter pylori-infected gastric mucosae and its possible association with gastric cancer risk. Clin Cancer Res 12, 989995.
  • 22
    Fraga MF, Ballestar E, Paz MF, Ropero S, Setien F, Ballestar ML, Heine-Suner D, Cigudosa JC, Urioste M, Benitez J et al. (2005) Epigenetic differences arise during the lifetime of monozygotic twins. Proc Natl Acad Sci USA 102, 1060410609.
  • 23
    Hayashizaki Y & Watanabe S (1997) Restriction Landmark Genomic Scanning (RLGS). Springer, Tokyo.
  • 24
    Costello JF, Fruhwald MC, Smiraglia DJ, Rush LJ, Robertson GP, Gao X, Wright FA, Feramisco JD, Peltomaki P, Lang JC et al. (2000) Aberrant CpG-island methylation has non-random and tumour-type-specific patterns. Nat Genet 24, 132138.
  • 25
    Plass C, Shibata H, Kalcheva I, Mullins L, Kotelevtseva N, Mullins J, Kato R, Sasaki H, Hirotsune S, Okazaki Y et al. (1996) Identification of Grf1 on mouse chromosome 9 as an imprinted gene by RLGS-M. Nat Genet 14, 106109.
  • 26
    Toyota M, Ahuja N, Ohe-Toyota M, Herman JG, Baylin SB & Issa JP (1999) CpG island methylator phenotype in colorectal cancer. Proc Natl Acad Sci USA 96, 86818686.
  • 27
    Plass C, Weichenhan D, Catanese J, Costello JF, Yu F, Yu L, Smiraglia D, Cavenee WK, Caligiuri MA, deJong P et al. (1997) An arrayed human NotI–EcoRV boundary library as a tool for RLGS spot analysis. DNA Res 4, 253255.
  • 28
    Zardo G, Tiirikainen MI, Hong C, Misra A, Feuerstein BG, Volik S, Collins CC, Lamborn KR, Bollen A, Pinkel D et al. (2002) Integrated genomic and epigenomic analyses pinpoint biallelic gene inactivation in tumors. Nat Genet 32, 453458.
  • 29
    Matsuyama T, Kimura MT, Koike K, Abe T, Nakano T, Asami T, Ebisuzaki T, Held WA, Yoshida S & Nagase H (2003) Global methylation screening in the Arabidopsis thaliana and Mus musculus genome: applications of virtual image restriction landmark genomic scanning (Vi-RLGS). Nucleic Acids Res 31, 44904496.
  • 30
    Rouillard JM, Erson AE, Kuick R, Asakawa J, Wimmer K, Muleris M, Petty EM & Hanash S (2001) Virtual genome scan: a tool for restriction landmark-based scanning of the human genome. Genome Res 11, 14531459.
  • 31
    Eckhardt F, Lewin J, Cortese R, Rakyan VK, Attwood J, Burger M, Burton J, Cox TV, Davies R, Down TA et al. (2006) DNA methylation profiling of human chromosomes 6, 20 and 22. Nat Genet 38, 13781385.
  • 32
    Sugahara Y, Akiyoshi S, Okazaki Y, Hayashizaki Y & Tanihata I (1998) An automatic image analysis system for RLGS films. Mamm Genome 9, 643651.
  • 33
    Takahashi K, Nakazawa M, Watanabe Y & Konagaya A (1998) Fully-automated spot recognition and matching algorithms for 2-D gel electrophoretogram of genomic DNA. Genome Inform Ser Workshop Genome Inform 9, 161172.
  • 34
    Ovcharenko I, Loots GG, Nobrega MA, Hardison RC, Miller W & Stubbs L (2005) Evolution and functional classification of vertebrate gene deserts. Genome Res 15, 137145.
  • 35
    Lorincz MC, Dickerson DR, Schmitt M & Groudine M (2004) Intragenic DNA methylation alters chromatin structure and elongation efficiency in mammalian cells. Nat Struct Mol Biol 11, 10681075.
  • 36
    Kochanek S, Renz D & Doerfler W (1993) DNA methylation in the Alu sequences of diploid and haploid primary human cells. EMBO J 12, 11411151.
  • 37
    Hellmann-Blumberg U, Hintz MF, Gatewood JM & Schmid CW (1993) Developmental differences in methylation of human Alu repeats. Mol Cell Biol 13, 45234530.
  • 38
    Rubin CM, VandeVoort CA, Teplitz RL & Schmid CW (1994) Alu repeated DNAs are differentially methylated in primate germ cells. Nucleic Acids Res 22, 51215127.
  • 39
    Betzl G, Brem G & Weidle UH (1996) Epigenetic modification of transgenes under the control of the mouse mammary tumor virus LTR: tissue-dependent influence on transcription of the transgenes. Biol Chem 377, 711719.
  • 40
    Weber B, Stresemann C, Brueckner B & Lyko F (2007) Methylation of human microRNA genes in normal and neoplastic cells. Cell Cycle 6, 10011005.
  • 41
    Carninci P & Hayashizaki Y (2007) Noncoding RNA transcription beyond annotated genes. Curr Opin Genet Dev 17, 139144.
  • 42
    Smiraglia DJ & Plass C (2002) The study of aberrant methylation in cancer via restriction landmark genomic scanning. Oncogene 21, 54145426.
  • 43
    Esteller M, Corn PG, Baylin SB & Herman JG (2001) A gene hypermethylation profile of human cancer. Cancer Res 61, 32253229.
  • 44
    Lin X, Tascilar M, Lee WH, Vles WJ, Lee BH, Veeraswamy R, Asgari K, Freije D, van Rees B, Gage WR et al. (2001) GSTP1 CpG island hypermethylation is responsible for the absence of GSTP1 expression in human prostate cancer cells. Am J Pathol 159, 18151826.
  • 45
    Jeronimo C, Usadel H, Henrique R, Silva C, Oliveira J, Lopes C & Sidransky D (2002) Quantitative GSTP1 hypermethylation in bodily fluids of patients with prostate cancer. Urology 60, 11311135.