Secondary structure at a hot spot for DNA methylation in DNA from human breast cancers

Cancer Genomics and Proteomics

Volumn 5, Issue 5, 2008, Pages 241-252

  Clark, Jarrod ^a   Smith, Steven S ^a  

^a CITY OF HOPE NATIONAL MEDICAL CENTER   (United States)

Author keywords

Breast cancer; c Ha ras; DNA methylation; MspI site polymorphism; Secondary structure; VNTR

Indexed keywords

BISULFITE; CELL DNA; GENE PRODUCT; GENOMIC DNA; PROTEIN MSP1; SINGLE STRANDED DNA; UNCLASSIFIED DRUG;

ARTICLE; BREAST CANCER; BREAST CARCINOGENESIS; CONTROLLED STUDY; DNA CLEAVAGE; DNA METHYLATION; DNA MODIFICATION; DNA STRUCTURE; GENE MUTATION; GENETIC POLYMORPHISM; HUMAN; HUMAN TISSUE; LYMPHOCYTE; ONCOGENE C H RAS; PROTEIN SECONDARY STRUCTURE; SOUTHERN BLOTTING; VARIABLE NUMBER OF TANDEM REPEAT;

EID: 57149148425     PISSN: 11096535     EISSN: 17906245     Source Type: Journal    
DOI: None     Document Type: Article

References (48)

1. Akman SA, Lingeman RG, Doroshow JH and Smith SS: Quadruplex DNA formation in a region of the tRNA gene supF associated with hydrogen peroxide mediated mutations. Biochemistry 30: 8648-8653, 1991.
2. Smith SS, Laayoun A, Lingeman RG, Baker DJ and Riley J: Hypermethylation of telomere-like foldbacks at codon 12 of the human c-Ha-ras gene and the trinucleotide repeat of the FMR-1 gene of fragile X. J Mol Biol 243: 143-151, 1994.
3. Smith SS, Baker DJ and Jardines LA: A G4-DNA/B-DNA junction at codon 12 of c-Ha-ras is actively and asymmetrically methylated by DNA(cytosine-5)methyltransferase. Biochem Biophys Res Commun 160: 1397-1402, 1989.
4. Chen X, Mariappan SV, Catasti P, Ratliff R, Moyzis RK, Laayoun A, Smith SS, Bradbury EM and Gupta G: Hairpins are formed by the single DNA strands of the fragile X triplet repeats: structure and biological implications. Proc Natl Acad Sci USA 92: 5199-5203, 1995.
5. Gacy AM, Goellner G, Juranic N, Macura S and McMurray CT: Trinucleotide repeats that expand in human disease form hairpin structures in vitro. Cell 81: 533-540, 1995.
6. Raghavan SC, Swanson PC, Wu X, Hsieh CL and Lieber MR: A non-B-DNA structure at the Bcl-2 major breakpoint region is cleaved by the RAG complex. Nature 428: 88-93, 2004.
7. Catasti P, Gupta G, Garcia AE, Ratliff R, Hong L, Yau P, Moyzis RK and Bradbury EM: Unusual structures of the tandem repetitive DNA sequences located at human centromeres. Biochemistry 33: 3819-3830, 1994.
8. Rhodes D: In: de Lange T, Lundblad, V. and Blackburn, E. (eds.), Telomeres, 2nd Ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, pp. 317-343, 2006.
9. Sun D, Guo K, Rusche JJ and Hurley LH: Facilitation of a structural transition in the polypurine/polypyrimidine tract within the proximal promoter region of the human VEGF gene by the presence of potassium and G-quadruplex-interactive agents. Nucleic Acids Res 33: 6070-6080, 2005.
10. Lew A, Rutter WJ and Kennedy GC: Unusual DNA structure of the diabetes susceptibility locus IDDM2 and its effect on transcription by the insulin promoter factor Pur-1/MAZ. Proc Natl Acad Sci USA 97: 12508-12512, 2000.
11. Haga K, Fujita H, Nomoto M, Sazawa A, Nakagawa K, Harabayashi T, Shinohara N, Takimoto M, Nonomura K and Kuzumaki N: Gelsolin gene silencing involving unusual hypersensitivities to dimethylsulfate and KMnO4 in vivo footprinting on its promoter region. Int J Cancer 111: 973-990, 2004.
12. Ackerman SL, Minden AG and Yeung CY: The minimal self-sufficient element in a murine G+C-rich promoter is a large element with imperfect dyad symmetry. Proc Natl Acad Sci USA 90: 11865-11869, 1993.
13. Simonsson T, Pecinka P and Kubista M: DNA tetraplex formation in the control region of c-myc. Nucleic Acids Res 26: 1167-1172, 1998.
14. Catasti P, Chen X, Moyzis RK, Bradbury EM and Gupta G: Structure-function correlations of the insulin-linked polymorphic region. J Mol Biol 264: 534-545, 1996.
15. Litz CE, Vos JA and Copenhaver CM: Aberrant methylation of the major breakpoint cluster region in chronic myeloid leukemia. Blood 88: 2241-2249, 1996.
16. Haiman CA, Brown M, Hankinson SE, Spiegelman D, Colditz GA, Willett WC, Kantoff PW and Hunter DJ: The androgen receptor CAG repeat polymorphism and risk of breast cancer in the Nurses' Health Study. Cancer Res 62: 1045-1049, 2002.
17. Liede A, Zhang W, De Leon Matsuda ML, Tan A and Narod SA: Androgen receptor gene polymorpbism and breast cancer susceptibility in The Philippines. Cancer Epidemiol Biomarkers Prev 12: 848-852, 2003.
18. Oberle I, Rousseau F, Heitz D, Kretz C, Devys D, Hanauer A, Boue J, Bertheas MF and Mandel JL: Instability of a 550-base pair DNA segment and abnormal methylation in fragile X syndrome. Science 252: 1097-1102, 1991.
19. de Bustros A, Nelkin BD, Silverman A, Ehrlich G, Poiesz B and Baylin SB: The short arm of chromosome 11 is a "hot spot" for hypermethylation in human neoplasia. Proc Natl Acad Sci USA 85: 5693-5697, 1988.
20. Langdon JA and Armour JA: Evolution and population genetics of the H-ras minisatellite and cancer predisposition. Hum Mol Genet 12: 891-900, 2003.
21. Shevchuk T, Kretzner L, Munson K, Axume J, Clark J, Dyachenko OV, Caudill M, Buryanov Y and Smith SS: Transgene-induced CCWGG methylation does not alter CG methylation patterning in human kidney cells. Nucleic Acids Res 33: 6124-6136, 2005.
22. Tolberg ME and Smith SS: Methylation of a middle repetitive DNA sequence class during differentiation in Friend erythroleukemia cells. FEBS Lett 176: 250-253, 1984.
23. Reed KC and Mann DA: Rapid transfer of DNA from agarose gels to nylon membranes. Nucleic Acids Res 13: 7207-7221, 1985.
24. Tautz D and Renz M: An optimized freeze-squeeze method for the recovery of DNA fragments from agarose gels. Anal Biochem 132: 14-19, 1983.
25. Feinberg AP and Vogelstein B: A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal Biochem 132: 6-13, 1983.
26. Feinberg AP and Vogelstein B: Hypomethylation of ras oncogenes in primary human cancers. Biochem Biophys Res Commun 111: 47-54, 1983.
27. Krontiris TG, DiMartino NA, Colb M and Pakinson DR: Unique Allelic Restiction Fragments of the Himan Ha-ras locus in Leukocytes and Leukocytes of Cancer Patients. Nature 313: 369, 1985.
28. McClelland M and Nelson M: The Effect of Site-Specific DNA Methylation on Restriciton Endonucleases and DNA Modification Methyltransferases. Gene 74: 291-304, 1988.
29. Hayatsu H, Wataya Y, Kai K and lida S: Reaction of sodium bisulfite with uracil, cytosine, and their derivatives. Biochemistry 9: 2858-2865, 1970.
30. Herman JG, Graff JR, Myohanen S, Nelkin BD and Baylin SB: Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands. Proc Natl Acad Sci USA 93: 9821-9826, 1996.
31. Feinberg AP and Vogelstein B: Hypomethylation distinguishes genes of some human cancers from their normal counterparts. Nature 301: 89-92, 1983.
32. Bestor T: Supercoiling-dependent sequence specificity of mammalian DNA methyltransferase. Nucleic Acids Res 15: 3835-3843, 1987,
33. Smith SS, Hardy TA and Baker DJ: Human DNA (cytosine-5) methyltransferase selectively methylates duplex DNA containing mispairs. Nucleic Acids Res 15: 6899-6916, 1987.
34. Smith SS, Kan JL, Baker DJ, Kaplan BE and Dembek P: Recognition of unusual DNA structures by human DNA (cytosine-5)methyltransferase. J Mol Biol 217: 39-51, 1991.
35. Smith SS: Biological implications of the mechanism of action of human DNA (cytosine-5)methyltransferase. Prog Nucleic Acid Res Mol Biol 49: 65-111, 1994.
36. Smith SS: Gilbert's conjecture: the search for DNA (cytosine-5) demethylases and the emergence of new functions for eukaryotic DNA (cytosine-5) methyltransferases. J Mol Biol 302: 1-7, 2000.
37. Bird A: DNA methylation patterns and epigenetic memory. Genes Dev 16: 6-21, 2002.
38. Buryanov YI and Shevchuk TV: DNA methyltransferases and structural-functional specificity of eukaryotic DNA modification. Biochemistry (Mosc) 70: 730-742, 2005.
39. Christman JK, Sheikhnejad G, Marasco CJ and Suffin JR: 5-Methyl-2′-deoxycytidine in single-stranded DNA can act in cis to signal de novo DNA methylation. Proc Natl Acad Sci USA 92: 7347-7351, 1995.
40. Guy J, Gan J, Selfridge J, Cobb S and Bird A: Reversal of neurological defects in a mouse model of Rett syndrome. Science 315: 1143-1147, 2007.
41. Galvao TC and Thomas JO: Structure-specific binding of MeCP2 to four-way junction DNA through its methyl CpG-binding domain. Nucleic Acids Res 33: 6603-6609, 2005.
42. Jair KW, Bachman KE, Suzuki H, Ting AH, Rhee I, Yen RW, Baylin SB and Schuebel KE: De novo CpG island methylation in human cancer cells. Cancer Res 66: 682-692, 2006.
43. Ting AH, Jair KW, Schuebel KE and Baylin SB: Differential requirement for DNA methyltransferase 1 in maintaining human cancer cell gene promoter hypermethylation. Cancer Res 66: 729-735, 2006.
44. Tsumagari K, Qi L, Jackson K, Shao C, Lacey M, Sowden J, Tawil R, Vedanarayanan V and Ehrlich M: Epigenetics of a tandem DNA repeat: chromatin DNaseI sensitivity and opposite methylation changes in cancers. Nucleic Acids Res 36: 2196-2207, 2008.
45. Kho MR, Baker DJ, Laayoun A and Smith SS: Stalling of human DNA (cytosine-5) methyltransferase at single-strand conformers from a site of dynamic mutation. J Mol Biol 275: 67-79, 1998.
46. Smith SS and Crocitto L: DNA methylation in eukaryotic chromosome stability revisited: DNA methyltransferase in the management of DNA conformation space. Mol Carcinog 26: 1-9, 1999.
47. Smith SS: Stalling of DNA methyltransferase in chromosome stability and chromosome remodelling (Review). International Journal of Molecular Medicine 1: 147-156, 1998.
48. Tolberg ME and Smith SS: Methylation of a middle repetitive DNA sequence class during differentiation in Friend erythroleukemia cells. FEBS Lett 176: 250-254, 1984.