Skip to main content

DNA Methylation Patterns: Formation and Biological Functions

  • Chapter
DNA Methylation

Part of the book series: Springer Series in Molecular Biology ((SSMOL))

Abstract

It is now an established fact that the distribution of methylated bases along DNA form a distinct pattern that is characteristic of the cell in which this DNA is harbored. It is also becoming clear that the biological functions that are fulfilled by DNA methylation are dependent on these patterns. The relationship between DNA methylation patterns and the various biological functions that are associated with these patterns is discussed in other chapters in this volume. However, it is appropriate to mention one familiar, clear-cut example of how a pattern of methylation exerts its biological function. The biological function of the restriction-modification systems in bacteria is to protect the cell from invasion of foreign genetic material. This protection is achieved via degradation of foreign DNA by restriction enzymes that are sequence-specific endonucleases. The DNA cleavage activity of these endonucleases is refractory to methylation at their recognition sites (see Chapter 5). The methylation is carried out by sequence-specific modification enzymes, which can methylate efficiently the restriction enzyme recognition sites of the host DNA. Since this methylation must provide protection to all sites in the host DNA, the pattern of methylation obtained in this case is determined by the distribution of the restriction sites along the DNA.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

eBook
USD 16.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Adams RLP: The relationship between synthesis and methylation of DNA in mouse fibroblasts. Biochim Biophys Acta 1971; 254: 205–212.

    PubMed  CAS  Google Scholar 

  • Adams RLP, McKay EL, Craig LM, Burdon RH: Mouse DNA methylase: Methylation of native DNA. Biochim Biophys Acta 1979; 561: 345–357.

    PubMed  CAS  Google Scholar 

  • Ball DJ, Gross DS, Garrard WT: 5-methylcytosine is localized in nucleosomes that contain histone H1. Proc Natl Acad Sci (USA) 1983; 80: 5490–5494.

    Article  CAS  Google Scholar 

  • Bestor TH, Ingram VM: Two DNA methyltransferases from murine erythroleukemia cells: Purification sequence specificity and mode of interaction with DNA. Proc Nall Acad Sci (USA) 1983; 80: 5559–5563.

    Article  CAS  Google Scholar 

  • Billen D: Methylation of the bacterial chromosome: an event at the “replication point?” J Mol Biol 1968; 31: 477–486.

    Article  PubMed  CAS  Google Scholar 

  • Bird AP: Use of restriction enzymes to study eukaryotic DNA methylation. 2. The symmetry of methylated sites supports semi-conservative copying of the methylation pattern. J Mol Biol 1978; 118: 49–60.

    Article  PubMed  CAS  Google Scholar 

  • Bird AP, Southern EM: Use of restriction enzymes to study eukaryotic DNA methylation. 1. The methylation pattern in rDNA from Xenopus laevis. J Mol Biol 1978; 118: 27–47.

    Article  PubMed  CAS  Google Scholar 

  • Bird AP, Taggart MH, Smith BA: Methylated and unmethylated DNA compartments in the sea urchin genome. Cell 1979; 17: 889–901.

    Article  PubMed  CAS  Google Scholar 

  • Bird AP, Taggart MH: Variable patterns of total DNA and rDNA methylation in animals. Nucleic Acids Res 1980; 8: 1485–1497.

    Article  PubMed  CAS  Google Scholar 

  • Bird AP, Taggart MH, Macleod D: Loss of rDNA methylation accompanying the onset of ribosomal gene activity in early development of X. laevis. Cell 1981a; 26: 381–390.

    Article  PubMed  CAS  Google Scholar 

  • Bird AP, Taggart MH, Gehring CA: Methylated and unmethylated rRNA genes in the mouse. J Mol Biol 1981b; 152: 1–17.

    Article  PubMed  CAS  Google Scholar 

  • Bugler B, Bertaux O, Valencia R: Nucleic acids methylation of synchronized BHK21 HS5 fibroblasts during the mitotic phase. J Cell Phys 1980; 103: 149–157.

    Article  CAS  Google Scholar 

  • Cedar H, Solage A, Glaser G, Razin A: Direct detection of methylated cytosine in DNA by use of the restriction enzyme MspI. Nucleic Acids Res 1979; 6: 2125–2132.

    Article  PubMed  CAS  Google Scholar 

  • Cedar H, Stein R, Gruenbaum Y, Naveh-Many T, Sciaky-Gallili N, Razin A: Effect of DNA methylation on gene expression. Cold Spring Harbor Symposia Quant Biol 1982; 47: 605–609.

    CAS  Google Scholar 

  • Cooper DN, Taggart MH, Bird AP: Unmethylated domains in vertebrate DNA. Nucleic Acids Res 1983; 11: 647–657.

    Article  PubMed  CAS  Google Scholar 

  • Creusot F, Acs G, Christman JK: Inhibition of DNA methyltransferase and induction of Friend erythroleukemia cell differentiation by 5-azacytidine and 5-aza-2’-deoxycytidine. J Biol Chem 1982; 257: 2041–2048.

    PubMed  CAS  Google Scholar 

  • Doerfler W: DNA methylation and gene activity. Ann Rev Biochem 1983; 52: 93–124.

    Article  PubMed  CAS  Google Scholar 

  • Drahovsky D, Morris NR: Mechanism of action of rat liver DNA methylase. 2 Interactions with single-stranded methyl-acceptor DNA. J Mol Biol 1971; 61: 343–356.

    Article  PubMed  CAS  Google Scholar 

  • Ehrlich M, Gama-Sosa MA, Huang LH, Midgett RM, Kuo KC, McCune RA, Gehrke C: Amount and distribution of 5-methylcytosine in human DNA from different types of tissues or cells. Nucleic Acids Res 1982; 10: 2709–2721.

    Article  PubMed  CAS  Google Scholar 

  • Fradin A, Manley JL, Prives CL: Methylation of simian virus 40 HpaII site affects late, but not early, viral gene expression. Proc Natl Acad Sci (USA) 1982; 79: 5142–5146.

    Article  CAS  Google Scholar 

  • Garovsky MA, Hattman S, Pleger GL: [6N] methyladenine in the nuclear DNA of a eucaryote. Tetrahymena pyriformis. J Cell Biol 1973; 56: 697–701.

    Article  Google Scholar 

  • Gjerset RA, Martin DW: Presence of a DNA demethylating activity in the nucleus of murine erythroleukemia cells. J Biol Chem 1982; 257: 8581–8583.

    PubMed  CAS  Google Scholar 

  • Gruenbaum Y, Naveh-Many T, Cedar H, Razin, A: Sequence specificity of methylations in higher plant DNA. Nature 1981a; 292: 860–862.

    Article  PubMed  CAS  Google Scholar 

  • Gruenbaum Y, Cedar H, Razin A: Restriction enzyme digestion of hemimethylated DNA. Nucleic Acids Res 1981b; 11: 2509–2515.

    Article  Google Scholar 

  • Gruenbaum Y, Cedar H, Razin A: Substrate and sequence specificity of a eukaryotic DNA methylase Nature 1982; 295: 620–622.

    Article  PubMed  CAS  Google Scholar 

  • Gruenbaum Y, Szyf M, Cedar H, Razin, A: Methylation of replicating and post- replicated mouse L-cell DNA. Proc Natl Acad Sci (USA) 1983; 80: 4919–4921.

    Article  CAS  Google Scholar 

  • Harbers K, Harbers B, Spencer JH: Nucleotide clusters in deoxyribonucleic acids. 12 The distribution of 5-methylcytosine in pyrimidine oligonucleotides of mouse L-cells satellite DNA and main band DNA. Biochem Biophys Res Commun 1975; 66: 738–746.

    Article  PubMed  CAS  Google Scholar 

  • Harland RM: Inheritance of DNA methylation in microinjected eggs of Xenopus laevis. Proc Natl Acad Sci (USA) 1982; 79: 2323–2327.

    Article  CAS  Google Scholar 

  • Holliday R, Pugh JE: DNA modification mechanisms and gene activity during development. Science 1975; 187: 226–232.

    Article  PubMed  CAS  Google Scholar 

  • Jähner D, Stuhlmann H, Stewart CL, Harbers K, Loehler J, Simon I, Jaenisch R: De novo methylation and expression of retroviral genomes during mouse embryogenesis. Nature 1982; 298: 623–628.

    Article  PubMed  Google Scholar 

  • Jones PA, Taylor SM: Hemimethylated duplex DNAs prepared from 5-azacytidine-treated cells. Nucleic Acids Res 1981; 9: 2933–2947.

    Article  PubMed  CAS  Google Scholar 

  • Kappler JW: The kinetics of DNA methylation in cultures of a mouse adrenal cell line. J Cell Physiol 1970; 75: 21–32.

    Article  PubMed  CAS  Google Scholar 

  • Kappler JW: The 5-methylcytosine content of DNA: tissue specificity. J Cell Physiol 1971; 78: 33–36.

    Article  PubMed  CAS  Google Scholar 

  • Kunnath L, Locker J: Variable methylation of the rRNA genes of the rat. Nucleic Acids Res 1982; 10: 3877–3892.

    Article  PubMed  CAS  Google Scholar 

  • Lark C: Studies on the in vivo methylation of DNA in Escherichia coli 15T-. J Mol Biol 1968; 31: 389–399.

    Article  PubMed  CAS  Google Scholar 

  • Mandel JL, Chambon P: DNA methylation: organ specific variations in the methylation pattern within and around ovalbumin and other chicken genes. Nucleic Acids Res 1979; 7: 2081–2090.

    Article  PubMed  CAS  Google Scholar 

  • Marinus MG, Morris NR: Pleiotropic effects of a DNA adenine methylation mutation (dam-3) in Escherichia coli K-12. Mutat Res 1975; 28: 15–26.

    Article  PubMed  CAS  Google Scholar 

  • Miller OJ, Schnedl W, Allen J, Erlanger BF: 5-methylcytosine localized in mammalian constitutive heterochromatin. Nature 1974; 251: 636–637.

    Article  PubMed  CAS  Google Scholar 

  • Modrich P: Studies of sequence and recognition by type 2 restriction and modification enzymes. CRC Crit Rev Biochem 1983; 13: 287–323.

    Article  Google Scholar 

  • Naveh-Many T, Cedar H: Topographical distribution of 5-methylcytosine in animal and plant DNA. Mol Cell Biol 1982; 2: 758–762.

    PubMed  CAS  Google Scholar 

  • Nesterenko VF, Buryanov YaI, Baev AA: Isolation and properties of DNA-cytosine methylase 1 from Escherichia coli MRE600. Biochimiya 1979; 44: 130–141.

    CAS  Google Scholar 

  • Niwa O, Yokota Y, Ishida H, Sugahara, T: Independent mechanisms involved in suppression of the Moloney Leukemia virus genome during differentiation of murine teratocarcinoma cells. Cell 1983; 32: 1105–1113.

    Article  PubMed  CAS  Google Scholar 

  • Pfeifer GP, Grunwald S, Bohem TLS, Drahovsky, D: Isolation and characterization of DNA cytosine 5-methyltransferase from human placenta. Biochim Biophys. Acta 1983; 740: 323–330.

    PubMed  CAS  Google Scholar 

  • Pollack Y, Stein R, Razin A, Cedar, H: Methylation of foreign DNA sequences in eukaryotic cells. Proc Natl Acad Sci (USA) 1980; 77: 6463–6467.

    Article  CAS  Google Scholar 

  • Rae PMM, Steele RE: Modified bases in the DNAs of unicellular eukaryotes: an examination of distributions and possible roles with emphasis on OH methyl uracil in Dinoflagellates. Biosystems 1978; 10: 37–53.

    Article  PubMed  CAS  Google Scholar 

  • Razin A, Cedar H: Distribution of 5-methylcytosine in chromatin. Proc Nall Acad Sci (USA) 1977; 74: 2725–2728.

    Article  CAS  Google Scholar 

  • Razin A, Riggs AD: DNA methylation and gene function. Science 1980; 210: 604–610.

    Article  PubMed  CAS  Google Scholar 

  • Razin A, Urieli S, Pollack Y, Gruenbaum Y, Glaser, G: Studies on the biological role of DNA methylation: 4. Mode of methylation of DNA in E. coli cells. Nucleic Acids Res 1980; 8: 1783–1792.

    Article  PubMed  CAS  Google Scholar 

  • Razin A, Friedman J: DNA methylation and its possible biological roles. Prog Nucleic Acids Res Mol Biol 1981; 25: 33–52.

    Article  CAS  Google Scholar 

  • Razin A, Webb C, Szyf M, Yisraeli J, Rosenthal A, Naveh-Many T, Sciaky-Gallili N, Cedar H: Variations in DNA methylation during mouse cell differentiation in vivo and in vitro. Proc Natl Acad Sci (USA) 1984; 81: 2275–2279.

    Article  CAS  Google Scholar 

  • Reilly JG, Thomas CA Jr, Lundell MJ: Methylation of mouse ribosomal DNA genes. DNA 1982; 1: 259–266.

    Article  PubMed  CAS  Google Scholar 

  • Riggs AD: X inactivation, differentiation and DNA methylation. Cytogenet Cell Genet 1975; 14: 9–11.

    Article  PubMed  CAS  Google Scholar 

  • Roy PH, Weissbach A: DNA methylases from Hela cells nuclei. Nucleic Acids Res 1975; 2: 1669–1684.

    Article  PubMed  CAS  Google Scholar 

  • Rubin RA, Modrich P: EcoRI methylase: physical and catalytic properties of the homogeneous enzyme. J Biol Chem 1977; 252: 7265–7272.

    PubMed  CAS  Google Scholar 

  • Saenundsen AK, Perlmann C, Klein G: Intracellular Epstein-Barr Virus DNA is methylated in and around the EcoRI-J fragment in both producer and non-producer cell lines. Virology 1983; 126: 701–706.

    Article  Google Scholar 

  • Salomon R, Kaye AM, Hertzberg M: Mouse nuclear satellite DNA: 5-methylcytosine content, pyrimidine isoplith distribution and electron microscopic appearance. J Mol Biol 1969; 43: 581–592.

    Article  PubMed  CAS  Google Scholar 

  • Simon D, Grunert F, von Acken U, Döring HP, Kröger, H: DNA methylase from regenerating rat liver: purification and characterization. Nucleic Acids Res 1978; 5: 2153–2167.

    Article  PubMed  CAS  Google Scholar 

  • Simon D, Stuhlmann A, Jahner D, Wagner H, Werner E, Jaenisch R: Retrovirus genomes methylated by mammalian but not bacterial methylase are noninfectious. Nature 1983; 304: 275–277.

    Article  PubMed  CAS  Google Scholar 

  • Sims MA, Doering JL, Hoyle HD: DNA methylation patterns in the 5S DNAs of Xenopus laevis. Nucleic Acids Res 1983; 11: 277–290.

    Article  PubMed  CAS  Google Scholar 

  • Sneider TW, Teague WM, Rogachevsky LM: S-adenosylmethionine dependent DNA-cytosine 5-methyltransferase from a Novikoff hepatoma cell line. Nucleic Acids Res 1975; 2: 1685–1700.

    Article  CAS  Google Scholar 

  • Solage A, Cedar H: Organization of 5-methylcytosine in chromosome DNA. Biochemistry 1978; 17: 2934–2938.

    Article  PubMed  CAS  Google Scholar 

  • Stein R, Gruenbaum Y, Pollack Y, Razin A, Cedar H: Clonal inheritance of the pattern of DNA methylation in mouse cells. Proc Natl Acad Sci (USA) 1982; 79: 61–65.

    Article  CAS  Google Scholar 

  • Stein R, Sciaky-Gallili N, Razin A, Cedar H: Pattern of methylation of two genes coding for housekeeping functions. Proc Natl Acad Sci (USA) 1983; 80: 2422–2426.

    Article  CAS  Google Scholar 

  • Sturm KS, Taylor JH: Distribution of 5-methylcytosine in the DNA of somatic and germ line cells from bovine tissues. Nucleic Acids Res 1981; 9: 4537–4546.

    Article  PubMed  CAS  Google Scholar 

  • Subramanian KN: Sites on gene expression in a genome functioning autonomously in a vertebrate host. Nucleic Acids Res 1982; 10: 3475–3486.

    Article  PubMed  CAS  Google Scholar 

  • Sutter D, Doerfler W: Methylation of integrated adenovirus type 12 DNA sequences in transformed cells is inversely correlated with viral gene expression. Proc Natl Acad Sci 1980; 77: 253–256.

    Article  PubMed  CAS  Google Scholar 

  • Szyf M, Gruenbaum Y, Urieli-Shoval S, Razin A: Studies on the biological role of DNA methylation: 5. The pattern of E. coli DNA methylation. Nucleic Acids Res 1982; 10: 7247–7259.

    CAS  Google Scholar 

  • Szyf M, Avraham-Haezni K, Reifman A, Shlomai J, Kaplan F, Oppenheim A, Razin A: A DNA methylation pattern is determined by the intracellular level of the methylase. Proc Nat Acad Sci (USA) 1984; 81: 3278–3282.

    Article  CAS  Google Scholar 

  • Tantravahi U, Guntaka R, Erlanger BF, Miller OJ: Amplified ribosomal RNA genes in a rat hepatoma cell line are enriched in 5-methylcytosine. Proc Natl Acad Sci (USA) 1981; 78: 489–493.

    Article  CAS  Google Scholar 

  • Taylor SM, Jones PA: Mechanism of action of eukaryotic DNA methyltransferase. Use of 5-azacytosine-containing DNA. J Mol Biol 1982; 162: 679–692.

    Article  PubMed  CAS  Google Scholar 

  • Turnbull JF, Adams RLP: DNA methylase: purification from ascites cells and the effect of various DNA substrates on its activity. Nucleic Acids Res 1976; 3: 677–695.

    PubMed  CAS  Google Scholar 

  • Urieli-Shoval S, Gruenbaum Y, Sedat J, Razin A: The absence of detectable methylated bases in Drosophila melanogaster DNA. FEBS Lett 1982; 146: 148–152.

    Article  PubMed  CAS  Google Scholar 

  • Urieli-Shoval S, Gruenbaum Y, Razin A: Sequence and substrate specificity of isolated DNA methylases from Escherichia coli C. J Bacteriol 1983; 153: 274–280.

    CAS  Google Scholar 

  • Vardimon L, Kressmann A, Cedar H, Maechler M, Doerfler W: The expression of a cloned adenovirus gene is inhibited by in vitro methylation. Proc Nall Acad Sci (USA) 1982; 79: 1075–1077.

    Google Scholar 

  • Vovis GF, Horiuchi K, Hartman N, Zinder ND: Restriction endonuclease B and fl heteroduplex DNA. Nature New Biol 1973; 246: 13–16.

    PubMed  CAS  Google Scholar 

  • Vovis GF, Horiuchi K, Zinder D: Kinetics of methylation by a restriction endonuclease from E. coli B. Proc Nall Acad Sci (USA) 1974; 71: 3810–3813.

    Article  CAS  Google Scholar 

  • Wettstein FO, Stevens JG: Shope Papilloma Virus DNA is extensively methylated in Non-Virus-Producing Neoplasms. Virology 1983; 126: 493–504.

    Article  PubMed  CAS  Google Scholar 

  • Whittaker PA, McLachlan A, Hardman N: Sequence organization in nuclear DNA from Physarum polycephalum: methylation of repetitive sequences. Nucleic Acids Res 1981; 9: 801–814.

    Article  PubMed  CAS  Google Scholar 

  • Wigler M, Levy D, Perucho M: The somatic replication of DNA methylation. Cell 1981; 24: 33–40.

    Article  PubMed  CAS  Google Scholar 

  • Wilson VL, Jones PA: DNA methylation decreases in aging but not in immortal cells. Science 1983; 220: 1055–1057.

    Article  PubMed  CAS  Google Scholar 

  • Woodcock DM, Adams JK, Allan RG, Cooper IA: Effect of several inhibitors of enzymatic DNA methylation on the in vivo methylation of different classes of DNA sequences in a cultured cell line. Nucleic Acids Res 1983; 11: 489–499.

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 1984 Springer-Verlag New York Inc.

About this chapter

Cite this chapter

Razin, A. (1984). DNA Methylation Patterns: Formation and Biological Functions. In: Razin, A., Cedar, H., Riggs, A.D. (eds) DNA Methylation. Springer Series in Molecular Biology. Springer, New York, NY. https://doi.org/10.1007/978-1-4613-8519-6_7

Download citation

  • DOI: https://doi.org/10.1007/978-1-4613-8519-6_7

  • Publisher Name: Springer, New York, NY

  • Print ISBN: 978-1-4613-8521-9

  • Online ISBN: 978-1-4613-8519-6

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics