Evolutionary changes in CpG and methylation levels in the genome of vertebrates

Gene

Volumn 205, Issue 1-2, 1997, Pages 109-118

  Jabbari, Kamel ^a   Cacciò, Simone ^a,c   Païs De Barros, Jean Paul ^b   Desgrès, Jean ^b   Bernardi, Giorgio ^a  

^a INSTITUT JACQUES MONOD   (France)

^b UNIVERSITÉ DE BOURGOGNE   (France)

^c ISTITUTO SUPERIORE DI SANITÀ   (Italy)

Author keywords

CpG dinucleotide; Isochore; Vertebrate evolution

Indexed keywords

5 METHYLCYTOSINE; DINUCLEOTIDE; DNA; REPETITIVE DNA;

ANIMAL TISSUE; CONFERENCE PAPER; CPG ISLAND; DNA METHYLATION; EVOLUTION; GENOME; HUMAN; HUMAN TISSUE; ISOCHORE; NONHUMAN; PRIORITY JOURNAL; VERTEBRATE;

ANIMALS; CPG ISLANDS; DNA; DNA METHYLATION; EVOLUTION, MOLECULAR; GENOME; HUMANS; REPETITIVE SEQUENCES, NUCLEIC ACID; SPECIES SPECIFICITY; VERTEBRATES;

AMPHIBIA; ANIMALIA; AVES; MAMMALIA; PISCES; REPTILIA; VERTEBRATA;

EID: 0031593251     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0378-1119(97)00475-7     Document Type: Conference Paper

References (69)

1. Aïssani, B., Bernardi, G., 1991a. CpG islands: features and distribution in the genome of vertebrates. Gene 106, 173-183.
2. Aïssani, B., Bernardi, G., 1991b. CpG islands, genes, isochores in the genome of vertebrates. Gene 106, 185-195.
3. Bachmann, K., 1972. Genome size in mammals. Chromosoma 37, 85-93.
4. Bernardi, G., 1985. The organization of the vertebrate genome and the problem of the CpG shortage. In: Cantoni, G.L., Razin, A. (Eds.), Chemistry, Biochemistry and Biology of DNA Methylation. Alan Liss, New York, NY, pp. 3-10.
5. Bernardi, G., 1993. Genome organization and species formation in vertebrates. J. Mol. Evol. 37, 331-337.
6. Bernardi, G., 1995. The human genome organization and evolutionary history. Annu. Rev. Genet. 29, 445-476.
7. Bernardi, G., Bernardi, G., 1986. Compositional constraints and genome evolution. J. Mol. Evol. 24, 1-11.
8. Bernardi, G., Bernardi, G., 1990. Compositional patterns in the nuclear genomes of cold-blooded vertebrates. J. Mol. Evol. 31, 265-281.
9. Bernardi, G., Olofsson, B., Filipski, J., Zerial, M., Salinas, J., Cuny, G., Meunier-Rotival, M., Rodier, F., 1985. The mosaic genome of warm-blooded vertebrates. Science 228, 953-958.
10. Bird, A., 1987. CpG islands as gene markers in the vertebrate nucleus. Trends Genet. 12, 342-347.
11. Brenner, S., Elgar, G., Sandford, R., Macrae, A., Venkatesh, B., Aparicio, S., 1993. Characterization of the pufferfish (Fugu) genome as a compact model vertebrate genome. Nature 366, 265-268.
12. Bush, G.L., Case, S.M., Wilson, A.C., Patton, J.L., 1977. Rapid speciation and chromosomal evolution in mammals. Proc. Natl. Acad. Sci. USA 74, 3942-3946.
13. Cacciò, S., Jabbari, K., Matassi, G., Gamonprez, F., Desgrès, J., Bernardi, G., 1997. Methylation patterns in the isochores of vertebrate genomes. Gene, in press.
14. Clark, S.J., Harrison, J., Frommer, M., 1995. CpNpG methylation in mammalian cells. Nature Genet. 10, 20-27.
15. Clay, O., Cacció, S., Zoubak, S., Mouchiroud, D., Bernardi, G., 1996. Human coding and noncoding DNA: compositional correlations. Mol. Phyl. Evol. 5, 2-12.
16. Cooper, D.N., Krawczak, M., 1989. Cytosine methylation and the fate of CpG dinucleotides in vertebrate genomes. Hum. Genet. 83, 181-188.
17. Cooper, D.N., Krawczak, M., 1996. Mutational processes in pathology and evolution. In: Jackson, M., Strachan, T., Dover, G. (Eds.), Human Genome Evolution, pp. 1-33.
18. 4/3,6 bis (acetato-mercurimethyl) dioxane density gradient. Eur. J. Biochem. 76, 13-19.
19. Coulondre, C., Miller, J.H., Farabaugh, P.J., Gilbert, W., 1978. Molecular basis of base substitution hotspots in Escherichia coli. Nature 274, 775-780.
20. Cuny, G., Soriano, P., Macaya, G., Bernardi, G., 1981. The major components of the mouse and human genomes: preparation, basic properties and compositional heterogeneity. Eur. J. Biochem. 111, 227-233.
21. Desgrès, J., Keith, G., Kuo, K.C., Gehrke, C.W., 1989. Presence of phosphorylated O-ribosyl-adenosine in T-y-stem of yeast methionine initiator tRNA. Nucleic Acids Res. 17, 865-882.
22. Doskocil, J., Sorm, F., 1962. Distribution of 5-methylcytosine in pyrimidine sequences of deoxyribonucleic acids. Biochim. Biophys. Acta 55, 953
23. Ehrlich, M., Gama-Sosa, M.A., Huang, L.H., Midgett, R.M., Kuo, K.C., McCune, R.A., Gehrke, C., 1982. Amount and distribution of 5-methylcytosine in human DNA from different types of tissues of cells. Nucleic Acids Res. 10, 2709-2721.
24. + density gradient centrifugation. J. Mol. Biol. 80, 177-197.
25. Forget, B.G., Cavalesco, C., De Riel, J.K., Tuan, D., Biro, A.P., Wilson, J.T., Wilson, L.B., Weismann, S.M., 1979. Structure of the human globin genes. J. Supramol. Struct. Suppl. 3, 44
26. Gama-Sosa, M.A., Midgett, R., Slagel, V.A., Githens, S., Kuo, K.C., Gehrke, C.W., Ehrlich, M., 1983a. Tissue-specific differences in DNA methylation in various mammals. Biochim. Biophys. Acta 740, 212-219.
27. Gama-Sosa, M.A., Wang, R., Kuo, K.C., Gehrke, C.W., Ehrlich, M., 1983b. The 5-methylcytosine content of highly repeated sequences in human DNA. Nucleic Acids Res. 11, 3087-3095.
28. Gehrke, C.W., MacCune, R.A., Gama-Sosa, M., Ehrlich, M., Kuo, K.C., 1984. Quantitative reverse phase high performance liquid chromatography of major and modified nucleosides in DNA. J. Chromatogr. 301, 199-219.
29. Ginatulin, A.A., 1984. Structure, Organization, Evolution of Vertebrate Genome. Nauka, Moscow.
30. Grippo, P., Iaccarino, M., Parisi, E., Scarano, E., 1968. Methylation of DNA in developing sea urchin embryos. J. Mol. Biol. 36, 195-208.
31. Gruenbaum, Y., Stein, R., Cedar, H., Razin, A., 1981. Methylation of CpG sequences in eukaryotic DNA. FEBS Lett. 124, 67-71.
32. Josse, J., Kaiser, A.D., Kornberg, A., 1961. Enzymatic synthesis of deoxyribonucleic acid. VIII. Frequencies of nearest neighbor base sequences in deoxyribonucleic acid. J. Biol. Chem. 236, 864-875.
33. Kadi, F., Mouchiroud, D., Sabeur, G., Bernardi, G., 1993. The compositional patterns of the aviain genomes and their evolutionary implications. J. Mol. Evol. 37, 544-551.
34. Karlin, S., Doerfler, W., Cardon, L.R., 1994. Why is CpG suppressed in the genomes of virtually all eukaryotic viruses but not in those of large eukaryotic viruses? J. Virol. 68, 2889-2897.
35. Kopecka, H., Macaya, G., Cortadas, J., Thiery, J.P., Bernardi, G., 1978. Restriction enzyme analysis of satellite DNA components from the bovine genome. Eur. J. Biochem. 84, 189-195.
36. Kramer, B., Kramer, W., Fritz, H.J., 1984. Different base/base mismatches are corrected with different efficiencies by the methyl-directed DNA mismatch repair system of E. coli. Cell 38, 879-887.
37. Kunnath, L., Locker, J., 1982. Characterization of DNA methylation in the rat. Biochim. Biophys. Acta 699, 264-271.
38. Lennon, G.G., Fraser, N.W., 1983. CpG frequency in large DNA segments. J. Mol. Evol. 19, 286-288.
39. Macaya, G., Cortadas, J., Bernardi, G., 1978. An analysis of the bovine genome by density gradient centrifugation. Eur. J. Biochem. 84, 179-188.
40. Matassi, G., Melis, R., Kuo, K.C., Macaya, G., Gehrke, C.W., Bernardi, G., 1992. Large-scale methylation patterns in the nuclear genomes of plants. Gene 122, 239-245.
41. McGeoch, D.J., 1970. Some base sequence characteristics of deoxyribonucleic acid. PhD thesis, Institute of Biochemistry, University of Glasgow.
42. Montero, L.M., Filipski, J., Gil, P., Capel, J., Martinez-Zapater, J.M., Salinas, J., 1992. The distribution of 5-methylcytosine in the nuclear genome of plants. Nucleic Acids Res. 20, 3207-3210.
43. Olmo, E., Capriglione, T., Odierna, G., 1989. Genome size evolution in vertebrates: trends and constraints. Comp. Biochem. Physiol. 73B, 739-745.
44. Olofsson, B., Bernardi, G., 1983. Organization of nucleotide sequences in the chicken genome. Eur. J. Biochem. 130, 241-245.
45. Pizon, V., Cuny, G., Bernardi, G., 1984. Nucleotide sequence organization in the very small genome of a tetraodontid fish Arothron diadematus. Eur. J. Biochem. 140, 25-30.
46. Pollock Jr., J.M., Swihart, M., Taylor, J.H., 1978. Methylation of DNA in early development: 5-methyl cytosine content of DNA in sea urchin sperm and embryos. Nucleic Acids Res. 5, 4855-4861.
47. Romanov, G.A., Vanyushin, B.F., 1981. Methylation of reiterated sequences in mammalian DNAs. Effects of the tissue type, age, malignancy and hormonal induction. Biochim. Biophys. Acta 653, 204-218.
48. Russell, G.J., 1974. Characterization of Deoxyribonucleic Acids by Doublet Frequency Analysis. Ph.D. Thesis, University of Glasgow, Glasgow.
49. Russell, G.J., Subak-Sharpe, J.H., 1977. Similarity of the general designs of protochordates and invertebrates. Nature 266, 533-536.
50. Russell, G.J., Walker, P.M.B., Elton, R.A., Subak-Sharpe, J.H., 1976. Doublet frequency analysis of fractionated vertebrate nuclear DNA. J. Mol. Biol. 108, 1-23.
51. Sabeur, G., Macaya, G., Kadi, F., Bernardi, G., 1993. The isochore patterns of mammalian genomes and their phylogenetic implications. J. Mol. Evol. 37, 93-108.
52. Salser, W., 1977. Globin mRNA sequences: analysis of base pairing and evolutionary implications. Cold Spring Harbor Symp. Quant. Biol. 40, 985-1002.
53. Serrano, J., Kuehl, D.W., Naumann, S., Analytical procedure and quality assurance criteria for the determination of major and minor deoxynucleosides in fish tissue DNA by liquid chromatography-ul-traviolet spectroscopy and liquid chromatography-thermo. 1993. J. Chromatogr. 615, 203-213.
54. Shen, J.C., Rideout, W.M., Jones, P.A., 1994. The rate of hydrolytic deamination of 5-methylcytosine in double-stranded DNA. Nucleic Acids Res. 22, 972-976.
55. Siegfried, Z., Cedar, H., 1997. DNA methylation: a molecular lock. Curr. Biol. 7, R305-R307.
56. Sinsheimer, R.L., 1955. The action of pancreatic deoxyribonuclease II. Isomeric dinucleotides,. J. Biol. Chem. 215, 579
57. Skalka, A., Audree, V.F., Hurwitz, G., 1966. The effect of histones on the enzymatic synthesis of ribonucleic acid. J. Biol. Chem. 241, 588-596.
58. Soriano, P., Macaya, G., Bernardi, G., 1981. The major components of the mouse and human genomes: reassociation kinetics. Eur. J. Biochem. 115, 235-239.
59. Subak-Sharpe, J.H., 1967. Doublet patterns and evolution of viruses. Brish Med. Bull. 23, 161-168.
60. Subak-Sharpe, H., Burk, R.R., Crowford, L.V., Morrisson, J.M., Hay, J., Keir, A.M., 1966. An approach to evolutionary relationship of mammalian DNA viruses through analysis of the pattern of nearest neighbor base sequence. Cold Spring Harbor Symp. Quant. Biol. 31, 737-738.
61. Subak-Sharpe, J.H., Elton, R.A., Russell, G.J., 1974. Evolutionary implications of doublet analysis. Symp. Soc. Gen. Microbiol. 24, 131-150.
62. Swartz, M.N., Trautner, T.A., Kornberg, A., 1962. Further studies on nearest neighbor base sequences in deoxyribonucleic acids. J. Biol. Chem. 237, 1961-1967.
63. Thiery, J.P., Macaya, G., Bernardi, G., 1976. An analysis of eukaryotic genomes by density gradient centrifugation. J. Mol. Biol. 108, 219-235.
64. Van der Ploeg, L.H.T., Flavell, R.A., 1980. DNA methylation in the human β-globin locus in erythroid and non-erythroid tissues. Cell 19, 947-958.
65. Vanyushin, B.F., Mazin, A.L., Vasilyev, V.K., Belozersky, A.N., 1973. The content of 5-methylcytosine in animal DNA: the species and tissue specificity. Biochim. Biophys. Acta 299, 397-403.
66. Vanyushin, B.F., Tkacheva, S.G., Belozersky, A.N., 1970. Rare bases in animal DNA. Nature 225, 948-949.
67. Venturini, G., Raffaella, D., Ernest, C., 1986. Size and structure of the bird genome-I DNA content of 48 species of neognathae. Comp. Biochem. Physiol. 85B, 61-65.
68. Woodcock, D.M., Crowther, P.J., Diver, W.P., 1987. The majority of methylated deoxycytosines in human DNA are not in the CpG dinucleotide. Biochim. Biophys. Res. Commun. 145, 888-894.
69. Yang, A.S., Gonzalgo, M.L., Zingg, J.M., Millar, R.P., Buckley, J.D., Jones, P.A., 1996. The rate of CpG mutation in Alu repetitive elements within the p53 tumor suppressor gene in the primate germline. J. Mol. Biol. 258, 240-250.