Abstract
The pioneering data on base composition and pyrimidine sequences in DNA of pro-and eukaryotes are considered, and their significance for the origin of genosystematics is discussed. The modern views on specificity and functional role of enzymatic DNA methylation in eukaryotes are described. DNA methylation controls all genetic functions and is a mechanism of cellular differentiation and gene silencing. A model of regulation of DNA replication by methylation is suggested. Adenine DNA methylation in higher eukaryotes (higher plants) was first observed, and it was established that one and the same gene can be methylated at both cytosine and adenine moieties. Thus, there are at least two different and seemingly interdependent DNA methylation systems present in eukaryotic cells. The first eukaryotic adenine DNA-methyltransferase is isolated from wheat seedlings and described: the enzyme methylates DNA with formation of N6-methyladenine in the sequence TGATCA → TGm6ATCA. It is found that higher plants have endonucleases that are dependent on S-adenosyl-L-methionine (SAM) and sensitive to DNA methylation status. Therefore, as in bacteria, plants seem to have a restriction-modification (R-M) system. A system of conjugated up-and down-regulation of SAM-dependent endonucleases by SAM modulations is found in plants. Revelation of an essential role of DNA methylation in regulation of genetic processes is a fundament of materialization of epigenetics and epigenomics.
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Abbreviations
- m6A:
-
N6-methyladenine
- m5C:
-
5-methylcytosine
- SAH:
-
S-adenosyl-L-homocysteine
- SAM:
-
S-adenosyl-L-methionine
- SiBA:
-
S-isobutyladenosine
References
Spirin, A. S., Belozersky, A. N., Shugaeva, N. V., and Vanyushuin, B. F. (1957) Biokhimiya, 22, 744–754.
Barbu, E., Lee, K. Y., and Wahl, R. (1956) Ann. Inst. Pasteur, 91, 212–224.
Visher, E., and Chargaff, E. (1948) J. Biol. Chem., 176, 703–709.
Visher, E., Zamenhof, S., and Chargaff, E. (1949) J. Biol. Chem., 177, 429–535.
Chargaff, E. (1950) Experientia, 6, 201–209.
Magasanik, B., Visher, E., Doniger, R., Elson, D., and Chargaff, E. (1950) J. Biol. Chem., 186, 37–50.
Marmur, J., Falkow, S., and Mandel, M. (1963) Ann. Rev. Microbiol., 17, 329–372.
Aleksandrushkina, N. I., Komissarova, L. V., Gershanovich, V. N., and Vanyushin, B. F. (1974) Dokl. Akad. Nauk SSSR, 219, 738–741.
Vanyushin, B. F., Duda, V. I., and Dobritsa, S. V. (1972) Dokl. Akad. Nauk SSSR, 206, 1226–1229.
Vanyushin, B. F., and Belozersky, A. N. (1960) Dokl. Akad. Nauk SSSR, 135, 197–199.
Vanyushin, B. F., Kokurina, N. A., and Belozersky, A. N. (1964) Dokl. Akad. Nauk SSSR, 158, 722–724.
Chumakova, R. I., Vanyushin, B. F., Vanyushin, B. F., Kokurina, N. A., Vorobjeva, T. V., and Medvedev, S. E. (1972) Mikrobiologiya, 31, 613–620.
Vorobjeva, L. I., Vanyushin, B. F., Kokurina, N. A., and Prosvetova, N. K. (1965) Mikrobiologiya, 3, 1003–1007.
Aseeva, I. V., Dobritsa, A. P., Dobrovolskaya, T. G., and Vanyushin, B. F. (1972) Dokl. Akad. Nauk SSSR, 205, 473–476.
Kuo, T. T., Huang, T. C., and Teng, M. H. (1968) J. Mol. Biol., 34, 373–375.
Vanyushin, B. F., Belyaeva, N. N., Kokurina, N. A., Stelmashchyuk, V. Ya., and Tikhonenko, A. S. (1970) Mol. Biol. (Moscow), 4, 724–729.
Kirnos, M. D., Khudyakov, I. Y., Alexandrushkina, N. I., and Vanyushin, B. F. (1977) Nature, 270, 369–370.
Vanyushin, B. F., Belozersky, A. N., and Bogdanova, S. L. (1960) Dokl. Akad. Nauk SSSR, 134, 1222–1225.
Uryson, S. O., and Belozersky, A. N. (1960) Dokl. Akad. Nauk SSSR, 132, 703–705.
Uryson, S. O., and Belozersky, A. N. (1959) Dokl. Akad. Nauk SSSR, 125, 1144–1147.
Vanyushin, B. F., and Belozersky, A. N. (1959) Dokl. Akad. Nauk SSSR, 129, 944–946.
Antonov, A. S., and Belozersky, A. N. (1961) Dokl. Akad. Nauk SSSR, 138, 1216–1219.
Antonov, A. S. (1965) Usp. Sovrem. Biol., 60, 161–168.
Vanyushin, B. F., Tkacheva, S. G., and Belozersky, A. N. (1970) Nature, 225, 948–949.
Burton, K., and Petersen, G. B. (1960) Biochem. J., 75, 17–27.
Mazin, A. L., and Vanyushin, B. F. (1967) Biokhimiya, 32, 377–387.
Vanyushin, B. F., and Buryanov, Ya. I. (1969) Biokhimiya, 34, 546–555.
Vanyushin, B. F., and Buryanov, Ya. I. (1969) Biokhimiya, 34, 718–728.
Vanyushin, B. F., Buryanov, Ya. I., and Belozersky, A. N. (1971) Nature, New Biology, 230, 25–27.
Mazin, A. L., Vanyushin, B. F., and Sulimova, G. E. (1969) Biokhimiya, 34, 1202–1208.
Mazin, A. L., and Vanyushin, B. F. (1969) Mol. Biol. (Moscow), 3, 846–855.
Guseinov, V. A., Mazin, A. L., Vanyushin, B. F., and Belozersky, A. N. (1972) Biokhimiya, 37, 381–388.
Guseinov, V. A., and Vanyushin, B. F. (1975) Biochim. Biophys. Acta, 395, 229–238.
Hotchkiss, R. D. (1948) J. Biol. Chem., 175, 315–332.
Wyatt, G. R. (1950) Nature, 166, 237.
Dunn, D. B., and Smith, J. D. (1958) Biochem. J., 68, 627–636.
Mazin, A. L., and Vanyushin, B. F. (1988) Mol. Biol. (Moscow), 22, 1399–1404.
Mazin, A. L., Mukhovatova, L. M., Shuppe, N. G., and Vanyushin, B. F. (1984) Dokl. Akad. Nauk SSSR, 276, 760–762.
Gowher, H., Leismann, O., and Jeltsch, A. (2000) EMBO J., 19, 6918–6923.
Lyko, F., Ramsahoye, B. H., and Jaenisch, R. (2000) Nature, 408, 538–540.
Ashapkin, V.V., Antoniv, T.T., and Vanyushin, B. F. (1995) Gene, 157, 273–277.
Jaenisch, R., and Bird, A. (2003) Nature Genetics, 33, 245–252.
Bird, A., and Wolffe, A. P. (1999) Cell, 99, 451–454.
Mazin, A. L., Gimadutdinov, O. A., Turkin, S. I., Burtseva, N. N., and Vanyushin, B. F. (1985) Mol. Biol. (Moscow), 19, 903–914.
Vanyushin, B. F., and Dobritsa, A. P. (1975) Biochim. Biophys. Acta, 407, 61–72.
Vanyushin, B. F., Belozersky, A. N., Kokurina, N. A., and Kadirova, D. X. (1968) Nature, 218, 1066–1067.
Dobritsa, S. V., Dobritsa, A. P., and Vanyushin, B. F. (1976) Dokl. Akad. Nauk SSSR, 227, 995–998.
Vanyushin, B. F., Kokurina, N. A., and Belozersky, A. N. (1970) Dokl. Akad. Nauk SSSR, 193, 215–218.
Kirnos, M. D., Aleksandrushkina, N. I., and Vanyushin, B. F. (1981) Biokhimiya, 46, 1458–1474.
Gruenbaum, Y., Naveh-Many, T., Cedar, H., and Razin, A. (1981) Nature, 292, 860–862.
Wassenegger, M., Heimes, S., Riedel, L., and Sanger, H. L. (1994) Cell, 76, 567–576.
Finnegan, E. J., and Kovac, K. A. (2000) Plant Mol. Biol., 43, 189–210.
Finnegan, E. J., Peacock, W. J., and Dennis, E. S. (2000) Curr. Opin. Genet. Devel., 10, 217–223.
Vanyushin, B. F., Tkacheva, S. G., and Belozersky, A. N. (1970) Nature, 225, 948–949.
Drozhdenyuk, A. P., Sulimova, G. E., and Vanyushin, B. F. (1977) Biokhimiya, 42, 1439–1444.
Cooney, C., and Lawren, B. (1999) Methyl Magic, Andrews McMeel Publishing, Kansas City, USA, Preface XV, pp. 124, 182.
Berdyshev, G. D., Korotaev, G. K., Boyarskikh, G. V., and Vanyushin, B. F. (1967) Biokhimiya, 32, 988–993.
Zin’kovskaya, G. G., Berdyshev, G. D., and Vanyushin, B. F. (1978) Biokhimiya, 43, 1883–1892.
Romanov, G. A., Zin’kovskaya, G. G., Berdyshev, G. D., and Vanyushin, B. F. (1979) Biokhimiya, 44, 1576–1581.
Vanyushin, B. F., Zin’kovskaya, G. G., and Berdyshev, G. D. (1980) Mol. Biol. (Moscow), 14, 857–866.
Romanov, G. A., and Vanyushin, B. F. (1981) Biochim. Biophys. Acta, 653, 204–218.
Vanyushin, B. F., Nemirovsky, L. E., Klimenko, V. V., Vasiliev, V. K., and Belozersky, A. N. (1973) Gerontologia (Basel), 19, 138–152.
Kudryashova, I. B., and Vanyushin, B. F. (1976) Biokhimiya, 41, 1106–1115.
Vanyushin, B. F., and Romanenko, E. B. (1979) Biokhimiya, 44, 78–85.
Vanyushin, B. F., Mazin, A. L., Vasiliev, V. K., and Belozersky, A. N. (1973) Biochim. Biophys. Acta, 299, 397–403.
Vanyushin, B. F., and Kirnos, M. D. (1974) FEBS Lett., 39, 195–199.
Vanyushin, B. F., and Kirnos, M. D. (1977) Biochim. Biophys. Acta, 475, 323–336.
Kudryashova, I. B., Kirnos, M. D., and Vanyushin, B. F. (1976) Biokhimiya, 41, 1968–1977.
Kudryashova, I. B., and Vanyushin, B. F. (1976) Biokhimiya, 41, 215–222.
Vanyushin, B. F. (2005) Biochemistry (Moscow), 70, 488–499.
Vanyushin, B. F. (2005) Mol. Biol. (Moscow), 39, 557–566.
Vanyushin, B. F. (2006) Current Topics Microbiol. Immunol., 301, 67–122.
Vanyushin, B. F. (2006) Genetika, 42, 1–14.
Romanov, G. A., Kiryanov, G. I., Dvorkin, V. M., and Vanyushin, B. F. (1976) Biokhimiya, 41, 1038–1043.
Smirnov, V. G., Romanov, G. A., and Vanyushin, B. F. (1977) Dokl. Akad. Nauk SSSR, 232, 961–963.
Vanyushin, B. F., Tushmalova, N. A., and Guskova, L. V. (1974) Dokl. Akad. Nauk SSSR, 219, 742–744.
Vanyushin, B. F., Tushmalova, N. A., Guskova, L. V., Demidkina, N. P., and Nikandrova, L. R. (1977) Mol. Biol. (Moscow), 11, 181–187.
Guskova, L. V., Burtseva, N. N., Tushmalova, N. A., and Vanyushin, B. F. (1977) Dokl. Akad. Nauk SSSR, 233, 993–996.
Sulimova, G. E., Drozhdenyuk, A. P., and Vanyushin, B. F. (1978) Mol. Biol. (Moscow), 12, 496–504.
Chvojka, L. A., Sulimova, G. E., Bulgakov, R., Bashkite, E. A., and Vanyushin, B. F. (1978) Biokhimiya, 43, 996–1000.
Burtseva, N. N., Azizov, Yu. M., Itkin, B. Z., and Vanyushin, B. F. (1977) Biokhimiya, 42, 1690–1696.
Burtseva, N. N., Demidkina, N. P., Azizov, Yu. M., and Vanyushin, B. F. (1978) Biokhimiya, 43, 2082–2091.
Burtseva, N. N., Azizov, Yu. M., and Vanyushin, B. F. (1979) Biokhimiya, 44, 1296–1302.
Burtseva, N. N., Romanov, G. A., Azizov, Yu. M., and Vanyushin, B. F. (1979) Biokhimiya, 44, 2006–2072.
Burtseva, N. N., Romanov, G. A., Gimadutdinov, O. A., and Vanyushin, B. F. (1983) Dokl. Akad. Nauk SSSR, 268, 1251–1255.
Burtseva, N. N., Gimadutdinov, O. A., and Vanyushin, B. F. (1987) Biokhimiya, 52, 290–301.
Lopatina, N. G., Vanyushin, B. F., Cronin, G. M., and Poirier, L. A. (1998) Carcinogenesis, 19, 1777–1781.
Vanyushin, B. F., Lopatina, N. G., Wise, C. K., Fullerton, F. R., and Poirier, L. A. (1998) Eur. J. Biochem., 256, 518–527.
Zhavoronkova, E. N., and Vanyushin, B. F. (1987) Biokhimiya, 52, 870–877.
Bashkite, E. A., Kirnos, M. D., Kiryanov, G. I., Aleksandrushkina, N. I., and Vanyushin, B. F. (1980) Biokhimiya, 45, 1448–1456.
Vanyushin, B. F., Bashkite, E. A., and Chvojka, L. A. (1981) Biokhimiya, 46, 47–54.
Vanyushin, B. F., and Kirnos, M. D. (1988) Gene, 74, 117–121.
Vanyushin, B. F. (1984) Current Topics Microbiol. Immunol., 108, 99–114.
Kiryanov, G. I., Kirnos, M. D., Demidkina, N. P., Alexandrushkina, N. I., and Vanyushin, B. F. (1980) FEBS Lett., 112, 225–228.
Kiryanov, G. I., Isaeva, L. V., Kirnos, M. D., Ganicheva, N. I., and Vanyushin, B. F. (1982) Biokhimiya, 47, 153–161.
Kirnos, M. D., Aleksandrushkina, N. I., Kutueva, L. I., and Vanyushin, B. F. (1988) Biokhimiya, 53, 1397–1406.
Kirnos, M. D., Aleksandrushkina, N. I., and Vanyushin, B. F. (1988) Biokhimiya, 53, 1667–1678.
Kirnos, M. D., Artyukhovskaya, N. A., Aleksandrushkina, N. I., Ashapkin, V. V., and Vanyushin, B. F. (1986) Biokhimiya, 51, 1875–1885.
Kirnos, M. D., Aleksandrushkina, N. I., Kutueva, L. I., Artyukhovskaya, N. A., and Vanyushin, B. F. (1987) Biokhimiya, 52, 625–637.
Kirnos, M. D., Aleksandrushkina, N. I., Kutueva, L. I., and Vanyushin, B. F. (1988) Biokhimiya, 53, 355–367.
Vanyushin, B. F., Sevostyanova S. S., Kirnos, M. D., and Saidova, N. S. (1990) Izv. Akad. Nauk SSSR, Ser. Biol., 1, 75–83.
Vanyushin, B. F., Kadyrova, D. Kh., Karimov, Kh. Kh., and Belozersky, A. N. (1971) Biokhimiya, 36, 1251–1258.
Buryanov, Ya. I., Eroshina, N. V., Vagabova, L. M., and Il’in, A. V. (1972) Dokl. Akad. Nauk SSSR, 206, 992–994.
Vanyushin, B. F., Alexandrushkina, N. I., and Kirnos, M. D. (1988) FEBS Lett., 233, 397–399.
Kirnos, M. D., Aleksandrushkina, N. I., Shorning, B. Yu., Bubenshchikova, S. N., and Vanyushin, B. F. (1997) Biochemistry (Moscow), 62, 1348–1357.
Kirnos, M. D., Alexandrushkina, N. I., Zagorskaya, G. Ya., Kireev, I. I., and Vanyushin, B. F. (1992) FEBS Lett., 298, 109–112.
Kirnos, M. D., Aleksandrushkina, N. I., Goremykin, V. V., Kudryashova, I. B., and Vanyushin, B. F. (1992) Biokhimiya, 57, 1566–1573.
Kirnos, M. D., Bakeeva, L. E., Volkova, S. A., Ganicheva, N. I., and Vanyushin, B. F. (1983) Biokhimiya, 48, 1505–1512.
Bakeeva, L. E., Kirnos, M. D., Aleksandrushkina, N. I., Kazimirchyuk, S. B., Shorning, B. Yu., Zamyatnin, V. A., Yaguzhinsky, L. S., and Vanyushin, B. F. (1999) FEBS Lett., 457, 122–125.
Shorning, B. Yu., and Vanyushin, B. F. (2001) Biochemistry (Moscow), 66, 753–762.
Fedoreyeva, L. I., and Vanyushin, B. F. (2002) FEBS Lett., 514, 305–308.
Ashapkin, V. V., Kutueva, L. I., and Vanyushin, B. F. (2002) FEBS Lett., 532, 367–372.
Kudryashova, I. B., and Vanyushin, B. F. (1986) Biokhimiya, 51, 321–327.
Mazin, A. L., and Vanyushin, B. F. (1986) Izv. Akad. Nauk SSSR, Ser. Biol., 1, 122–124.
Fedoreyeva, L. I., Sobolev, D. E., and Vanyushin, B. F. (2007) Epigenetics, 2, 50–53.
Jenuwein, T., and Allis, C. D. (2001) Science, 293, 1074–1080.
Tamaru, H., and Selker, E. U. (2001) Nature, 414, 277–283.
Soppe, W. J. J., Jasencakova, Z., Houben, A., Kakutani, T., Meister, A., Huang, M. S., Jacobsen, S. E., Schubert, I., and Fransz, P. F. (2002) EMBO J., 21, 6549–6559.
Nan, X., Ng, H. H., Johnson, C. A., Laherty, C. D., Turner, B. M., Eisenman, R. N., and Bird, A. (1998) Nature, 393, 386–389.
Jones, P. L., Veenstra, G. J., Wade, P. A., Vermaak, D., Kass, S. U., Landsberger, N., Stroubouli, J., and Wolffe, A. P. (1998) Nature Genetics, 19, 187–191.
Bestor, T. H. (1998) Nature, 393, 311–312.
Matzke, M., Aufsatz, W., Kanno, T., Daxinger, L., Papp, I., Mette, M. F., and Matzke, A. J. M. (2004) Biochim. Biophys. Acta, 1677, 129–141.
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Published in Russian in Biokhimiya, 2007, Vol. 72, No. 12, pp. 1583–1593.
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Vanyushin, B.F. A view of an elemental naturalist at the DNA world (Base composition, sequences, methylation). Biochemistry Moscow 72, 1289–1298 (2007). https://doi.org/10.1134/S0006297907120036
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DOI: https://doi.org/10.1134/S0006297907120036