Inhibition of Poly(ADP-Ribosyl)ation Allows DNA Hypermethylation

  • Anna Reale
  • Giuseppe Zardo
  • Maria Malanga
  • Jordanka Zlatanova
  • Paola Caiafa
Part of the Medical Intelligence Unit book series (MIUN)


This chapter emphasizes that along the chain of events that induce DNA methylation-dependent chromatin condensation, a post-synthetic modification other than histone acetylation, poly(ADP-ribosyl)ation, participates in the establishment and maintenance of methylation-free regions of chromatin. In fact, several lines of in vitro and in vivo evidence have shown that poly(ADP-ribosyl)ation is involved in the control of DNA methylation pattern, protecting genomic DNA from full methylation. More recent studies have provided some clues to the understanding of the molecular mechanism(s) connecting poly(ADP-ribosyl)ation with DNA methylation. We aim here to demonstrate the direct correlation existing between inhibition of poly(ADP-ribose) polymerases and DNA hypermethylation, and to describe some possible mechanisms underlying this molecular link. We will then present our hypothesis that the inhibition of the poly(ADP-ribosyl)ation process in the cell may be responsible for the anomalous hypermethylation of oncosuppressor gene promoters during tumorigenesis and to suggest the possibility that an active poly(ADP-ribosyl)ation process is also involved in maintaining the unmethylated state of CpG islands in normal cells.


Methylation Pattern Chromatin Fiber Linker Histone Demethylase Activity Full Methylation 
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  1. 1.
    Robertson KD, Jones PA. DNA methylation: Past, present and future directions. Carcinogenisis 2000; 21:461–467.CrossRefGoogle Scholar
  2. 2.
    Baylin SB, Herman JG. DNA methylation in tumorigenesis. Epigenetics joins genetics. Trends Genet 2000; 16:168–174.PubMedCrossRefGoogle Scholar
  3. 3.
    Costello JF, Plass C. Methylation matters. J Med Genet 2001; 38:285–303.PubMedCrossRefGoogle Scholar
  4. 4.
    Bird AP, Wolffe AP. Methylation-induced repression-belts, braces and chromatin. Cell 1999; 99:451–454.PubMedCrossRefGoogle Scholar
  5. 5.
    Bird A. DNA methylation patterns and epigenetic memory. Genes Dev 2002; 16:6–21PubMedCrossRefGoogle Scholar
  6. 6.
    Kass SU, Pruss D, Wolffe AP. How does methylation repress trnscription? Trends Genet 1997; 12:444–449.CrossRefGoogle Scholar
  7. 7.
    Razin A, Shemer R Epigenetic control of gene expression. Results Probl Cell Differ 1999; 25:189–204.PubMedGoogle Scholar
  8. 8.
    Szyf M. The role of DNA methyltransferase 1 in growth control. Front Biosci 2001; 6:599–609.Google Scholar
  9. 9.
    Cervoni N, Szyf M. Demethylase activity is directed by histone acetylation. J Biol Chem 2001; 276:40778–40787.PubMedCrossRefGoogle Scholar
  10. 10.
    Cervoni N, Detich N, Seo S-B et al. The oncoprotein Set/TAF-1b, an inhibitor of histone acetyltransferase, inhibits active demethylation of DNA, integrating DNA methylation and transcriptional silencing. J Biol Chem 2002; 277:25026–25031.PubMedCrossRefGoogle Scholar
  11. 11.
    Nan X, Ng H-H, Johnson CA et al. Transcriptional repression by the methyl-CpG binding protein MeCP2 involves a histone deacetylase complex. Nature 1998; 393:386–389.PubMedCrossRefGoogle Scholar
  12. 12.
    Jones PL, Veenstra GJC, Wade PA et al. Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription. Nat Genet 1998; 19:187–191.PubMedCrossRefGoogle Scholar
  13. 13.
    de Murcia G, Shall S, eds. From DNA damage and stress signaling to cell death Poly ADP-ribosylation reactions. Oxford University Press, 2000.Google Scholar
  14. 14.
    Alvarez-Gonzalez R, Althaus FR. Poly (ADP-ribose) catabolism in mammalian cells exposed to DNA-damaging agents. Mutation Res 1989; 218:67–74.PubMedGoogle Scholar
  15. 15.
    Althaus FR, Richter C. ADP-Ribosylation of proteins: Enzymology and Biological Significance. Berlin: Springer-Verlag, 1987.Google Scholar
  16. 16.
    D’Amours D, Desnoyers S, D’Silva I et al. Poly(ADP-ribosyl)ation reactions in the regulation of nuclear functions. Biochem J 1999; 342:242–268.Google Scholar
  17. 17.
    Mendoza-Alvarez H, Alvarez-Gonzalez R. Poly (ADP-ribose) polymerase is a catalytic dimer and the automodification reaction is intermolecular. J Biol Chem 1993; 268:22575–22580.PubMedGoogle Scholar
  18. 18.
    Alvarez-Gonzalez R, Jacobson MK. Characterization of polymers of adenosine diphosphate ribose generated in vitro and in vivo. Biochemistry 1987; 26:3218–3224.PubMedCrossRefGoogle Scholar
  19. 19.
    Kawaichi M, Ueda K, Hayaishi O. Multiple poly(ADP-ribosyl)ation of rat liver poly(ADP-ribose) synthetase. Mode of modification and properties of automodified synthetase. J Biol Chem 1981; 256:9483–9489.PubMedGoogle Scholar
  20. 20.
    Desmarais Y, Menard L, Lagueux J et al. Enzymological properties of poly(ADP-ribose)polymerase: characterization of automodification sites and NADase activity. Biochim Biophys Acta 1991; 1078:179–186.PubMedGoogle Scholar
  21. 21.
    Ferro AM, Higgins NP, Olivera BM. Poly (ADP-ribosylation) of a DNA topoisomerase. J Biol Chem 1983; 258:6000–6003.PubMedGoogle Scholar
  22. 22.
    Yoshihara K, Itaya A, Tanaka Y et al. Inhibition of DNA polymerase a, DNA polymerase b, terminal deoxynucleotidyl transferase, and DNA ligase II by poly(ADP-ribosyl)ation reaction in vitro. Biochem Biophys Res Commun 1985; 28:161–67.Google Scholar
  23. 23.
    Boulikas T. DNA str, breaks alter histone ADP-ribosylation. Proc Natl Acad Sci USA 1989; 86:3499–3503.PubMedCrossRefGoogle Scholar
  24. 24.
    Scovassi AI, Mariani C, Negroni M et al. ADP-ribosylation of nonhistone proteins in HeLa cells: Modification of topoisomerase II. Exp Cell Res 1993; 206:177–181.PubMedCrossRefGoogle Scholar
  25. 25.
    Ménissier-de Murcia J, Molinete M, Gradwohl G et al. Zinc-binding domain of poly(ADP-ribose) polymerase participates in the recognition of single strand breaks on DNA. J Mol Biol 1989; 210:229–233.PubMedCrossRefGoogle Scholar
  26. 26.
    Gradwohl G, de Murcia JM, Molinete M et al. The second zinc-finger domain of poly(ADP-ribose) polymerase determines specificity for single-stranded breaks in DNA. Proc Natl Acad Sci USA 1990; 87:2990–2994.PubMedCrossRefGoogle Scholar
  27. 27.
    Ikejma M, Noguchi S, Yameshita R et al. The zinc-fingers of human poly(ADP-ribose) polymerase are differentially required for the recognition of DNA breaks and nicks and the consequent enzyme activation. J Biol Chem 1990; 265:21907–21913.Google Scholar
  28. 28.
    de Murcia G, Ménissier-de Murcia J. Poly(ADP-ribose) polymerase: a molecular nick sensor. Trends Biochem Sci 1994; 19:172–176.PubMedCrossRefGoogle Scholar
  29. 29.
    de Murcia G, Jacobson M, Shall S. Regulation by ADP-ribosylation. Trends Cell Biol 1995; 5:78–81.PubMedCrossRefGoogle Scholar
  30. 30.
    Griesenbeck J, Oei SL, Mayer-Kuckuk P et al. Protein-protein interaction of the human poly(ADP-ribosyl)transferase depends on the functional state of the enzyme. Biochemistry 1997; 36:7297–7304.PubMedCrossRefGoogle Scholar
  31. 31.
    Realini C, Althaus FR. Histone shuttling by poly (ADP-ribosylation). J Biol Chem 1992; 267:18858–188621.PubMedGoogle Scholar
  32. 32.
    Panzeter PL, Realini CA, Althaus FR. Noncovalent interactions of poly(adenosine diphosphate ribose) with histones. Biochemistry 1992; 31:1379–1385.PubMedCrossRefGoogle Scholar
  33. 33.
    Panzeter PL, Zweifel B, Malanga M et al. Targeting of histone tails by poly(ADP-ribose). J Biol Chem 1993; 268:17662–17664.PubMedGoogle Scholar
  34. 34.
    Malanga M, Atorino L, Tramontano F et al. Poly(ADP-ribose) binding properties of histone H1 variants. Biochim Biophys Acta 1998; 1399:154–160.PubMedGoogle Scholar
  35. 35.
    Reale A, Malanga M, Zardo G et al. In vitro induction of H1-H1 histone cross-linking by adenosine diphosphate-ribose polymers. Biochemistry 2000; 39:10413–10418.PubMedCrossRefGoogle Scholar
  36. 36.
    Pleschke JM, Kleczkowska HE, Strom M et al. Poly(ADP-ribose) binds to specific domains in DNA damage checkpoint proteins. J Biol Chem 2000; 275:40974–40980.PubMedCrossRefGoogle Scholar
  37. 37.
    Mayer-Kuckuk P, Ullrich O, Ziegler M et al. Functional interaction of poly(ADP-ribose) with the 20S proteasome in vitro. Biochem Biophys Res Commun 1999; 259:576–581.PubMedCrossRefGoogle Scholar
  38. 38.
    Germain M, Affair EB, D’Amours D et al. Cleavage of automodified poly(ADP-ribose) polymerase during apoptosis. J Biol Chem 1999; 274:28379–28384.PubMedCrossRefGoogle Scholar
  39. 39.
    Malanga M, Pleschke JM, Kleczkowska HE et al. Poly(ADP-ribose) binds to specific domains of p53 and alters its DNA binding functions. J Biol Chem 1998; 273:11839–11843.PubMedCrossRefGoogle Scholar
  40. 40.
    Shall S, de Murcia G. Poly(ADP-ribose) polymerase-1: what have we learned from the deficient mouse model? Mutation Res 2000; 460:1–15.PubMedGoogle Scholar
  41. 41.
    Schreiber V, Amé JC, Dollé P et al. Poly(ADP-ribose) polymerase-2 (PARP-2) is required for efficient base excision DNA repair in association with PARP-1 and XRCC1. J Biol Chem 2002; 277:23028–23036.PubMedCrossRefGoogle Scholar
  42. 42.
    Althaus FR, Kleczkowska HE, Malanga M et al. Poly ADP-ribosylation: A DNA break signal mechanism. Mol Cell Biochem 1999; 193:5–11.PubMedCrossRefGoogle Scholar
  43. 43.
    Zardo G, D’Erme M, Reale A et al. Does poly(ADP-ribosyl)ation regulate the DNA methylation pattern? Biochemistry 1997; 36:7937–7943.PubMedCrossRefGoogle Scholar
  44. 44.
    Zardo G, Caiafa P The unmethylated state of CpG islands in mouse fibroblasts depends on the poly(ADP-ribosyl)ation process J Biol Chem 1998; 273:16517–16520.PubMedCrossRefGoogle Scholar
  45. 45.
    de Capoa A, Febbo Giovannelli FR, Niveleau A et al. Reduced levels of poly(ADP-ribosyl)ation result in chromatin compaction and hypermethylation as shown by cell-by-cell computer assisted quantitative analysis. FASEB J 1999; 13:89–93.PubMedGoogle Scholar
  46. 46.
    Zardo G, Marenzi S, Perilli M et al. I. nhibition of poly(ADP-ribosyl)ation introduces an anomalous methylation pattern in transfected foreign DNA. FASEB J 1999; 13:1518–1522.PubMedGoogle Scholar
  47. 47.
    Bird AP. CpG islands as gene markers in the vertebrate nucleus. Trends Genet 1987; 3:342–347.CrossRefGoogle Scholar
  48. 48.
    Bird AP. CpG-rich islands and the function of DNA methylation. Nature 1986; 321:209–213.PubMedCrossRefGoogle Scholar
  49. 49.
    Frommer M, McDonald IE, Millar DS et al. A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc Natl Acad Sci USA 1992; 89:1827–1831.PubMedCrossRefGoogle Scholar
  50. 50.
    Buschhausen G, Wittig B, Graessmann M et al. Chromatin structure is required to block transcription of the methylated herpes simplex virus thymidine kinase gene. Proc Natl Acad Sci USA 1987; 84:1177–1181.PubMedCrossRefGoogle Scholar
  51. 51.
    Kass SU, Landsberger N, Wolffe AP. DNA methylation directs a time-dependent repression of transcription initiation. Curr Biol 1997; 7 157–165.PubMedCrossRefGoogle Scholar
  52. 52.
    Kass SU, Goddard JP, Adams RLP. Inactive chromatin spreads from a focus of methylation. Mol Cell Biol 1993; 13:7372–7379.PubMedGoogle Scholar
  53. 53.
    Zardo G, Marenzi S, Caiafa P. Correlation between DNA methylation and poly(ADP-ribosylation) process. Gene Therapy Mol Biol 1998; 1:661–679.Google Scholar
  54. 54.
    Karymov MA, Tomschik M, Leuba SH et al. DNA methylation-dependent chromatin fiber compaction in vivo and in vitro: Requirement for linker histone. FASEB J 2001; 15:2631–2641.PubMedCrossRefGoogle Scholar
  55. 55.
    Simpson RT, Thoma F, Brubaker JM. Chromatin reconstituted from tandemly repeated cloned DNA fragments and core histones; a model for study of higher order structure. Cell 1985; 42:799–808.PubMedCrossRefGoogle Scholar
  56. 56.
    Antequera F, Bird A. CpG islands as genomic footprints of promoters that are associated with replication origins. Curr Biol 1999; 9:661–667.CrossRefGoogle Scholar
  57. 57.
    Keshet I, Ysraeli J, Cedar H. Effect of regional DNA methylation on gene expression. Proc Natl Acad Sci USA 1985; 82:2560–2564.PubMedCrossRefGoogle Scholar
  58. 58.
    Szyf M, Tanigawa G, McCarthy PL Jr. A DNA signal from the Thy-1 gene defines de novo methylation patterns in embryonic stem cells. Mol Cell Biol 1990; 10:4396–4400.PubMedGoogle Scholar
  59. 59.
    Tollefsbol TO, Hutchinson III CA. Control of methylation spreading in synthetic DNA sequences by the murine DNA methyltransferase. J Mol Biol 1997; 269:494–504.PubMedCrossRefGoogle Scholar
  60. 60.
    Szyf M. DNA methylation patterns: an additional level of information? Biochem Cell Biol 1991; 69:764–767.PubMedCrossRefGoogle Scholar
  61. 61.
    Mummaneni P, Bishop PL, Turker MS A cis-acting element accounts for a conserved methylation pattern upstream of the mouse adenine phosphoribosyltransferase gene. J Biol Chem 1993; 268:552–558.PubMedGoogle Scholar
  62. 62.
    Brandeis M, Frank D, Keshet I et al. Spl elements protect a CpG island from de novo methylation. Nature 1994; 371:435–438.PubMedCrossRefGoogle Scholar
  63. 63.
    Hasse A, Schulz WA. Enhancement of reporter gene de novo methylation by DNA fragments from the alpha-fetoprotein control region. J Biol Chem 1994; 269:1821–1826.PubMedGoogle Scholar
  64. 64.
    MacLeod D, Charlton J, Mullins J et al. Sp1 sites in the mouse aprt gene promoter are required to prevent methylation of the CpG island. Genes Dev 1994; 8:2282–2292.PubMedGoogle Scholar
  65. 65.
    Magewu AN, Jones PA. Ubiquitous and tenacesous methylation of the CpG sites in codon 248 of the p53 gene may explain its frequent appearance as a mutational hot spot in human cancer. Mol Cell Biol 1994; 14:4225–4232.PubMedGoogle Scholar
  66. 66.
    Mummaneni P, Walker KA, Bishop PL et al. Epigenetic gene inactivation induced by a cis-acting methylation center. J Biol Chem 1995; 270:788–792.PubMedCrossRefGoogle Scholar
  67. 67.
    Baylin SB. Tying it all together: epigenetics, genetics, cell cycle and cancer. Science 1997; 277:1948–1949.PubMedCrossRefGoogle Scholar
  68. 68.
    Pradhan S, Kim GD. The retinoblastoma gene product interacts with maintenance human DNA (cytosine-5) methyltransferase and modulates its activity. EMBO J 2002; 21:1–10.CrossRefGoogle Scholar
  69. 69.
    Di Croce L, Raker VA, Corsaro M et al. Methyltransferase recruitment and DNA hypermethylation of target promoters by an oncogenic transcription factor. Science 2002; 295:1079–1082.PubMedCrossRefGoogle Scholar
  70. 70.
    Szyf M, Bozivic V, Tanigawa G. Growth regulation of mouse DNA methyltransferase gene expression. J Biol Chem 1991; 266:10027–10030.PubMedGoogle Scholar
  71. 71.
    Robertson KD, Keyomarsi K, Gonzales FA et al. Differential mRNA expression of the human DNA methyltransferase (DNMTs) 1, 3a and 3b during the G0/G1 to S phase transition in normal and tumor cells. Nucleic Acids Res 2000; 28:2108–2113.PubMedCrossRefGoogle Scholar
  72. 72.
    Chuang LS, Ian HI, Koh TW et al. Human DNA-(cytosine-5) methyltransferase-PCNA complex as a target for p21 WAF1. Science 1997; 26:1996–2000.CrossRefGoogle Scholar
  73. 73.
    Zardo G, Reale A, Passananti C et al. Inhibition of poly(ADP-ribosyl)ation induces DNA hypermethylation: A possible molecular mechanism. FASEB J 2002; 21:1319–1321.Google Scholar
  74. 74.
    Goldman MA, Holmquist GP, Gray MC et al. Replication timing of genes and middle repetitive sequences. Science 1984; 224:686–692.PubMedCrossRefGoogle Scholar
  75. 75.
    Selig S, Okumura K, Ward DC et al. Delineation of DNA replication time zones by fluorescence in situ hybridization. EMBO J 1992; 11:1217–1225.PubMedGoogle Scholar
  76. 76.
    Simbulan-Rosenthal CM, Rosenthal DS, Boulares AH et al. Regulation of the expression or recruitment of components of the DNA synthesome by poly(ADP-ribose) polymerase. Biochemistry 1998; 37:9363–9370.PubMedCrossRefGoogle Scholar
  77. 77.
    Zardo G, Marenzi S, Caiafa P. H1 histone as a trans-acting factor involved in protecting genomic DNA from full methylation. Biol Chem 1998; 353:647–654.Google Scholar
  78. 78.
    Meisterernst M, Stelzer G, Roeder RG. Poly(ADP-ribose) polymerase enhances activator-dependent transcription in vitro. Proc Natl Acad Sci USA 1997; 94:2261–2265.PubMedCrossRefGoogle Scholar
  79. 79.
    Oei SL, Griesenbeck J, Schweiger M et al. Regulation of RNA polymerase II-dependent transcription by poly(ADP-ribosyl)ation of transcription factors. J Biol Chem 1998; 273:31644–31647.PubMedCrossRefGoogle Scholar
  80. 80.
    Oei SL, Griesenbeck J, Ziegler M et al. A novel function of poly(ADP-ribosyl)ation: silencing of RNA polymerase II-dependent transcription. Biochemistry 1998; 37:1465–1469.PubMedCrossRefGoogle Scholar

Copyright information

© and Kluwer Academic/Plenum Publishers 2005

Authors and Affiliations

  • Anna Reale
    • 1
  • Giuseppe Zardo
    • 1
  • Maria Malanga
    • 2
  • Jordanka Zlatanova
    • 3
  • Paola Caiafa
    • 1
  1. 1.Department of Cellular Biotechnologies and HaematologyUniversite di Roma “La Sapienza”RomeItaly
  2. 2.Department of Biological ChemistryUniversity “Federico II” of NaplesNaplesItaly
  3. 3.Department of Chemistry and Chemical EngineeringPolytechnic UniversityBrooklynUSA

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