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Heterochromatin Formation: Role of Short RNAs and DNA Methylation

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Abstract

The role of small double-stranded RNAs is considered in formation of silent chromatin structure. Small RNAs are implicated in the regulation of individual gene transcription, suppression of transposon expression, and in maintaining functional structure of extended heterochromatic regions. Interrelations between short RNA-dependent gene silencing, histone modifications, and DNA methylation are discussed. Specific features of RNA-induced chromatin repression in various eucaryotes are also described.

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Abbreviations

dsRNA:

double-stranded RNA

RNAi:

RNA interference

RISC:

RNA-induced silencing complex

siRNA:

short interfering RNA

RdRp:

RNA-directed RNA polymerase

HMT:

histone methyltransferase

HDAC:

histone deacetylase

RITS:

RNA-induced initiation of transcriptional silencing

MBD:

methyl DNA binding domain

LTR:

long terminal repeats

REFERENCES

  1. Jenuwein, T., and Allis, C. D. (2001) Science, 293, 1074–1080.

    Article  PubMed  CAS  ISI  Google Scholar 

  2. Litt, M. D., Simpson, M., Gaszner, M., Allis, C. D., and Felsenfeld, G. (2001) Science, 293, 2453–2455.

    Article  PubMed  CAS  ISI  Google Scholar 

  3. Peters, A. H., O'Carroll, D., Scherthan, H., Mechtler, K., Sauer, S., Schofer, C., Weipoltshammer, K., Pagani, M., Lachner, M., Kohlmaier, A., Opravil, S., Doyle, M., Sibilia, M., and Jenuwein, T. (2001) Cell, 107, 323–337.

    Article  PubMed  CAS  ISI  Google Scholar 

  4. Nakayama, J., Rice, J. C., Strahl, B. D., Allis, C. D., and Grewal, S. I. (2001) Science, 292, 110–113.

    Article  PubMed  CAS  Google Scholar 

  5. Lachner, M., and Jenuwein, T. (2002) Curr. Opin. Cell. Biol., 14, 286–298.

    Article  PubMed  CAS  Google Scholar 

  6. Strahl, B. D., and Allis, C. D. (2000) Nature, 403, 41–45.

    PubMed  CAS  ISI  Google Scholar 

  7. Zhang, Y., and Reinberg, D. (2001) Genes Dev., 15, 2343–2360.

    PubMed  CAS  Google Scholar 

  8. Kouzarides, T. (2002) Curr. Opin. Genet. Dev., 12, 198–209.

    Article  PubMed  CAS  Google Scholar 

  9. Lachner, M., O'Sullivan, R. J., and Jenuwein, T. (2003) J. Cell Sci., 116, 2117–2124.

    Article  PubMed  CAS  Google Scholar 

  10. Bird, A. (2002) Genes Dev., 16, 6–21.

    Article  PubMed  CAS  Google Scholar 

  11. Tariq, M., and Paszkowski, J. (2004) Trends Genet., 20, 244–251.

    Article  PubMed  CAS  Google Scholar 

  12. Lyko, F. (2001) Trends Genet., 17, 169–172.

    Article  PubMed  CAS  Google Scholar 

  13. Pollard, T. D., and Ernshaw, W. C. (2002) in Cell Biology, Sanders, Philadelphia-London-N. Y., pp. 210, 805.

    Google Scholar 

  14. Akhtar, A. (2003) Curr. Opin. Genet. Dev., 13, 161–169.

    Article  PubMed  CAS  Google Scholar 

  15. Richards, E. J., and Elgin, S. C. (2002) Cell, 108, 489–500.

    Article  PubMed  CAS  ISI  Google Scholar 

  16. Lachner, M., O'Carroll, D., Rea, S., Mechtler, K., and Jenuwein, T. (2001) Nature, 410, 116–120.

    Article  PubMed  CAS  ISI  Google Scholar 

  17. Bannister, A. J., Zegerman, P., Partridge, J. F., Miska, E. A., Thomas, J. O., Allshire, R. C., and Kouzarides, T. (2001) Nature, 410, 120–124.

    Article  PubMed  CAS  ISI  Google Scholar 

  18. Andersen, A. A., and Panning, B. (2003) Curr. Opin. Cell. Biol., 15, 281–289.

    PubMed  CAS  Google Scholar 

  19. Kelley, R. L., and Kuroda, M. I. (2000) Cell, 103, 9–12.

    Article  PubMed  CAS  ISI  Google Scholar 

  20. Fire, A., Xu, S., Montgomery, M. K., Kostas, S. A., Driver, S. E., and Mello, C. C. (1998) Nature, 391, 806–811.

    Article  PubMed  CAS  ISI  Google Scholar 

  21. Hannon, G. J. (2002) Nature, 418, 244–251.

    Article  PubMed  CAS  ISI  Google Scholar 

  22. Aravin, A. A., Klenov, M. S., Vagin, V. V., Rozovsky, Ya. M., and Gvosdev, V. A. (2002) Mol. Biol. (Moscow), 36, 240–251.

    CAS  Google Scholar 

  23. Meister, G., and Tuschl, T. (2004) Nature, 431, 343–349.

    Article  PubMed  CAS  ISI  Google Scholar 

  24. Tuschl, T., Zamore, P. D., Lehmann, R., Bartel, D. P., and Sharp, P. A. (1999) Genes Dev., 13, 3191–3197.

    Article  PubMed  CAS  Google Scholar 

  25. Zamore, P. D., Tuschl, T., Sharp, P. A., and Bartel, D. P. (2000) Cell, 101, 25–33.

    Article  PubMed  CAS  ISI  Google Scholar 

  26. Hammond, S. M., Bernstein, E., Beach, D., and Hannon, G. J. (2000) Nature, 404, 293–296.

    PubMed  CAS  ISI  Google Scholar 

  27. Bernstein, E., Caudy, A. A., Hammond, S. M., and Hannon, G. J. (2001) Nature, 409, 363–366.

    Article  PubMed  CAS  ISI  Google Scholar 

  28. Elbashir, S. M., Lendeckel, W., and Tuschl, T. (2001) Genes Dev., 15, 188–200.

    Article  PubMed  CAS  Google Scholar 

  29. Elbashir, S. M., Harborth, J., Lendeckel, W., Yalcin, A., Weber, K., and Tuschl, T. (2001) Nature, 411, 494–498.

    Article  PubMed  CAS  ISI  Google Scholar 

  30. Martinez, J., Patkaniowska, A., Urlaub, H., Luhrmann, R., and Tuschl, T. (2002) Cell, 110, 563–574.

    Article  PubMed  CAS  ISI  Google Scholar 

  31. Chiu, Y. L., and Rana, T. M. (2002) Mol. Cell, 10, 549–561.

    PubMed  CAS  Google Scholar 

  32. Schwarz, D. S., Hutvagner, G., Du, T., Xu, Z., Aronin, N., and Zamore, P. D. (2003) Cell, 115, 199–208.

    Article  PubMed  CAS  ISI  Google Scholar 

  33. Olsen, P. H., and Ambros, V. (1999) Dev. Biol., 216, 671–680.

    Article  PubMed  CAS  Google Scholar 

  34. Saxena, S., Jonsson, Z. O., and Dutta, A. (2003) J. Biol. Chem., 278, 44312–44319.

    PubMed  CAS  Google Scholar 

  35. Hammond, S. M., Boettcher, S., Caudy, A. A., Kobayashi, R., and Hannon, G. J. (2001) Science, 293, 1146–1150.

    Article  PubMed  CAS  ISI  Google Scholar 

  36. Martinez, J., and Tuschl, T. (2004) Genes Dev., 18, 975–980.

    Article  PubMed  CAS  Google Scholar 

  37. Liu, J., Carmell, M. A., Rivas, F. V., Marsden, C. G., Thomson, J. M., Song, J. J., Hammond, S. M., Joshua-Tor, L., and Hannon, G. J. (2004) Science, 305, 1437–1441.

    PubMed  CAS  ISI  Google Scholar 

  38. Cerutti, L., Mian, N., and Bateman, A. (2000) Trends Biochem. Sci., 25, 481–482.

    Article  PubMed  CAS  Google Scholar 

  39. Song, J. J., Liu, J., Tolia, N. H., Schneiderman, J., Smith, S. K., Martienssen, R. A., Hannon, G. J., and Joshua-Tor, L. (2003) Nat. Struct. Biol., 10, 1026–1032.

    Article  PubMed  CAS  Google Scholar 

  40. Lingel, A., Simon, B., Izaurralde, E., and Sattler, M. (2004) Nat. Struct. Mol. Biol., 11, 576–577.

    Article  PubMed  CAS  Google Scholar 

  41. Ma, J. B., Ye, K., and Patel, D. J. (2004) Nature, 429, 318–322.

    Article  PubMed  CAS  ISI  Google Scholar 

  42. Song, J. J., Smith, S. K., Hannon, G. J., and Joshua-Tor, L. (2004) Science, 305, 1434–1437.

    Article  PubMed  CAS  ISI  Google Scholar 

  43. Tabara, H., Sarkissian, M., Kelly, W. G., Fleenor, J., Grishok, A., Timmons, L., Fire, A., and Mello, C. C. (1999) Cell, 99, 123–132.

    Article  PubMed  CAS  ISI  Google Scholar 

  44. Fagard, M., Boutet, S., Morel, J. B., Bellini, C., and Vaucheret, H. (2000) Proc. Natl. Acad. Sci. USA, 97, 11650–11654.

    Article  PubMed  CAS  Google Scholar 

  45. Williams, R. W., and Rubin, G. M. (2002) Proc. Natl. Acad. Sci. USA, 99, 6889–6894.

    PubMed  CAS  Google Scholar 

  46. Carmell, M. A., Xuan, Z., Zhang, M. Q., and Hannon, G. J. (2002) Genes Dev., 16, 2733–2742.

    Article  PubMed  CAS  Google Scholar 

  47. Catalanotto, C., Azzalin, G., Macino, G., and Cogoni, C. (2002) Genes Dev., 16, 790–795.

    Article  PubMed  CAS  Google Scholar 

  48. Volpe, T. A., Kidner, C., Hall, I. M., Teng, G., Grewal, S. I., and Martienssen, R. A. (2002) Science, 297, 1833–1837.

    Article  PubMed  CAS  ISI  Google Scholar 

  49. Mochizuki, K., Fine, N. A., Fujisawa, T., and Gorovsky, M. A. (2002) Cell, 110, 689–699.

    Article  PubMed  CAS  ISI  Google Scholar 

  50. Shi, H., Djikeng, A., Tschudi, C., and Ullu, E. (2004) Mol. Cell. Biol., 24, 420–427.

    PubMed  CAS  Google Scholar 

  51. Bartel, D. P. (2004) Cell, 116, 281–297.

    Article  PubMed  CAS  ISI  Google Scholar 

  52. Hutvagner, G., and Zamore, P. D. (2002) Science, 297, 2056–2060.

    Article  PubMed  CAS  ISI  Google Scholar 

  53. Schramke, V., and Allshire, R. (2003) Science, 301, 1069–1074.

    Article  PubMed  CAS  ISI  Google Scholar 

  54. Zilberman, D., Cao, X., and Jacobsen, S. E. (2003) Science, 299, 716–719.

    Article  PubMed  CAS  ISI  Google Scholar 

  55. Kawasaki, H., and Taira, K. (2004) Nature, 431, 211–217.

    PubMed  CAS  ISI  Google Scholar 

  56. Mette, M. F., Aufsatz, W., van der Winden, J., Matzke, M. A., and Matzke, A. J. (2000) EMBO J., 19, 5194–5201.

    Article  PubMed  CAS  Google Scholar 

  57. Morris, K. V., Chan, S. W., Jacobsen, S. E., and Looney, D. J. (2004) Science, 305, 1289–1292.

    PubMed  CAS  ISI  Google Scholar 

  58. Pal-Bhadra, M., Leibovitch, B. A., Gandhi, S. G., Rao, M., Bhadra, U., Birchler, J. A., and Elgin, S. C. (2004) Science, 303, 669–672.

    Article  PubMed  CAS  ISI  Google Scholar 

  59. Okamura, K., Ishizuka, A., Siomi, H., and Siomi, M. C. (2004) Genes Dev., 18, 1655–1666.

    Article  PubMed  CAS  Google Scholar 

  60. Sigova, A., Rhind, N., and Zamore, P. D. (2004) Genes Dev., 18, 2359–2367.

    Article  PubMed  CAS  Google Scholar 

  61. Verdel, A., Jia, S., Gerber, S., Sugiyama, T., Gygi, S., Grewal, S. I., and Moazed, D. (2004) Science, 303, 672–676.

    Article  PubMed  CAS  ISI  Google Scholar 

  62. Grishok, A., Pasquinelli, A. E., Conte, D., Li, N., Parrish, S., Ha, I., Baillie, D. L., Fire, A., Ruvkun, G., and Mello, C. C. (2001) Cell, 106, 23–34.

    Article  PubMed  CAS  ISI  Google Scholar 

  63. Grewal, S. I. (2000) J. Cell Physiol., 184, 311–318.

    Article  PubMed  CAS  Google Scholar 

  64. Reinhart, B. J., and Bartel, D. P. (2002) Science, 297, 1831.

    Article  PubMed  CAS  ISI  Google Scholar 

  65. Motamedi, M. R., Verdel, A., Colmenares, S. U., Gerber, S. A., Gygi, S. P., and Moazed, D. (2004) Cell, 119, 789–802.

    Article  PubMed  CAS  ISI  Google Scholar 

  66. Sugiyama, T., Cam, H., Verdel, A., Moazed, D., and Grewal, S. I. (2005) Proc. Natl. Acad. Sci. USA, 102, 152–157.

    Article  PubMed  CAS  Google Scholar 

  67. Bernard, P., Maure, J. F., Partridge, J. F., Genier, S., Javerzat, J. P., and Allshire, R. C. (2001) Science, 294, 2539–2542.

    Article  PubMed  CAS  ISI  Google Scholar 

  68. Hall, I. M., Noma, K., and Grewal, S. I. (2003) Proc. Natl. Acad. Sci. USA, 100, 193–198.

    PubMed  CAS  Google Scholar 

  69. Volpe, T., Schramke, V., Hamilton, G. L., White, S. A., Teng, G., Martienssen, R. A., and Allshire, R. C. (2003) Chromosome Res., 11, 137–146.

    Article  PubMed  CAS  Google Scholar 

  70. Hall, I. M., Shankaranarayana, G. D., Noma, K., Ayoub, N., Cohen, A., and Grewal, S. I. (2002) Science, 297, 2232–2237.

    Article  PubMed  CAS  ISI  Google Scholar 

  71. Hansen, K. R., Burns, G., Mata, J., Volpe, T. A., Martienssen, R. A., Bahler, J., and Thon, G. (2005) Mol. Cell. Biol., 25, 590–601.

    Article  PubMed  CAS  Google Scholar 

  72. Sijen, T., Vijn, I., Rebocho, A., van Blokland, R., Roelofs, D., Mol, J. N., and Kooter, J. M. (2001) Curr. Biol., 11, 436–440.

    Article  PubMed  CAS  Google Scholar 

  73. Dalmay, T., Hamilton, A., Rudd, S., Angell, S., and Baulcombe, D. C. (2000) Cell, 101, 543–553.

    Article  PubMed  CAS  ISI  Google Scholar 

  74. Xie, Z., Johansen, L. K., Gustafson, A. M., Kasschau, K. D., Lellis, A. D., Zilberman, D., Jacobsen, S. E., and Carrington, J. C. (2004) PLoS Biol., 2, E104.

    Article  PubMed  Google Scholar 

  75. Chan, S. W., Zilberman, D., Xie, Z., Johansen, L. K., Carrington, J. C., and Jacobsen, S. E. (2004) Science, 303, 1336.

    PubMed  CAS  ISI  Google Scholar 

  76. Zilberman, D., Cao, X., Johansen, L. K., Xie, Z., Carrington, J. C., and Jacobsen, S. E. (2004) Curr. Biol., 14, 1214–1220.

    Article  PubMed  CAS  Google Scholar 

  77. Baulcombe, D. (2004) Nature, 431, 356–363.

    Article  PubMed  CAS  ISI  Google Scholar 

  78. Bao, N., Lye, K. W., and Barton, M. K. (2004) Dev. Cell, 7, 653–662.

    Article  PubMed  CAS  Google Scholar 

  79. Hunter, C., Sun, H., and Poethig, R. S. (2003) Curr. Biol., 13, 1734–1739.

    Article  PubMed  CAS  Google Scholar 

  80. Hamilton, A., Voinnet, O., Chappell, L., and Baulcombe, D. (2002) EMBO J., 21, 4671–4679.

    Article  PubMed  CAS  Google Scholar 

  81. Tang, G., Reinhart, B. J., Bartel, D. P., and Zamore, P. D. (2003) Genes Dev., 17, 49–63.

    Article  PubMed  CAS  Google Scholar 

  82. Mallory, A. C., Mlotshwa, S., Bowman, L. H., and Vance, V. B. (2003) Plant J., 35, 82–92.

    Article  PubMed  CAS  Google Scholar 

  83. Voinnet, O., and Baulcombe, D. C. (1997) Nature, 389, 553.

    Article  PubMed  CAS  ISI  Google Scholar 

  84. Cogoni, C., and Macino, G. (1999) Curr. Opin. Microbiol., 2, 657–662.

    Article  PubMed  CAS  Google Scholar 

  85. Pickford, A. S., Catalanotto, C., Cogoni, C., and Macino, G. (2002) Adv. Genet., 46, 277–303.

    PubMed  CAS  Google Scholar 

  86. Tijsterman, M., Ketting, R. F., and Plasterk, R. H. (2002) Annu. Rev. Genet., 36, 489–519.

    Article  PubMed  CAS  Google Scholar 

  87. Napoli, C., Lemieux, C., and Jorgensen, R. (1990) Plant Cell, 2, 279–289.

    Article  PubMed  CAS  ISI  Google Scholar 

  88. Van der Krol, A. R., Mur, L. A., Beld, M., Mol, J. N., and Stuitje, A. R. (1990) Plant Cell, 2, 291–299.

    PubMed  Google Scholar 

  89. Ingelbrecht, I., van Houdt, H., van Montagu, M., and Depicker, A. (1994) Proc. Natl. Acad. Sci. USA, 91, 10502–10506.

    PubMed  CAS  Google Scholar 

  90. Van Eldik, G. J., Litiere, K., Jacobs, J. J., van Montagu, M., and Cornelissen, M. (1998) Nucleic Acids Res., 26, 5176–5181.

    PubMed  Google Scholar 

  91. Jones, L., Hamilton, A. J., Voinnet, O., Thomas, C. L., Maule, A. J., and Baulcombe, D. C. (1999) Plant Cell, 11, 2291–2301.

    Article  PubMed  CAS  ISI  Google Scholar 

  92. Holtorf, H., Schob, H., Kunz, C., Waldvogel, R., and Meins, F., Jr. (1999) Plant Cell, 11, 471–484.

    Article  PubMed  CAS  ISI  Google Scholar 

  93. Hamilton, A. J., and Baulcombe, D. C. (1999) Science, 286, 950–952.

    Article  PubMed  CAS  ISI  Google Scholar 

  94. Mourrain, P., Beclin, C., Elmayan, T., Feuerbach, F., Godon, C., Morel, J. B., Jouette, D., Lacombe, A. M., Nikic, S., Picault, N., Remoue, K., Sanial, M., Vo, T. A., and Vaucheret, H. (2000) Cell, 101, 533–542.

    Article  PubMed  CAS  ISI  Google Scholar 

  95. Vaistij, F. E., Jones, L., and Baulcombe, D. C. (2002) Plant Cell, 14, 857–867.

    Article  PubMed  CAS  ISI  Google Scholar 

  96. Vaucheret, H., Nussaume, L., Palauqui, J. C., Quillere, I., and Elmayan, T. (1997) Plant Cell, 9, 1495–1504.

    Article  PubMed  CAS  ISI  Google Scholar 

  97. Que, Q., Wang, H. Y., English, J. J., and Jorgensen, R. A. (1997) Plant Cell, 9, 1357–1368.

    Article  PubMed  CAS  ISI  Google Scholar 

  98. Gazzani, S., Lawrenson, T., Woodward, C., Headon, D., and Sablowski, R. (2004) Science, 306, 1046–1048.

    Article  PubMed  CAS  ISI  Google Scholar 

  99. Wassenegger, M., Heimes, S., Riedel, L., and Sanger, H. L. (1994) Cell, 76, 567–576.

    Article  PubMed  CAS  ISI  Google Scholar 

  100. Ruiz, M. T., Voinnet, O., and Baulcombe, D. C. (1998) Plant Cell, 10, 937–946.

    Article  PubMed  CAS  ISI  Google Scholar 

  101. Jones, L., Hamilton, A. J., Voinnet, O., Thomas, C. L., Maule, A. J., and Baulcombe, D. C. (1999) Plant Cell, 11, 2291–2301.

    Article  PubMed  CAS  ISI  Google Scholar 

  102. English, J. J., Mueller, E., and Baulcombe, D. C. (1996) Plant Cell, 8, 179–188.

    Article  PubMed  CAS  ISI  Google Scholar 

  103. Angell, S. M., and Baulcombe, D. C. (1997) EMBO J., 16, 3675–3684.

    Article  PubMed  CAS  Google Scholar 

  104. Marathe, R., Anandalakshmi, R., Smith, T. H., Pruss, G. J., and Vance, V. B. (2000) Plant Mol. Biol., 43, 295–306.

    Article  PubMed  CAS  Google Scholar 

  105. Matzke, M. A., Aufsatz, W., Kanno, T., Mette, M. F., and Matzke, A. J. (2002) Adv. Genet., 46, 235–275.

    PubMed  CAS  Google Scholar 

  106. Martienssen, R. A., and Colot, V. (2001) Science, 293, 1070–1074.

    Article  PubMed  CAS  ISI  Google Scholar 

  107. Finnegan, E. J., and Kovac, K. A. (2000) Plant Mol. Biol., 43, 189–201.

    Article  PubMed  CAS  Google Scholar 

  108. Aufsatz, W., Mette, M. F., Matzke, A. J., and Matzke, M. (2004) Plant Mol. Biol., 54, 793–804.

    Article  PubMed  CAS  Google Scholar 

  109. Kankel, M. W., Ramsey, D. E., Stokes, T. L., Flowers, S. K., Haag, J. R., Jeddeloh, J. A., Riddle, N. C., Verbsky, M. L., and Richards, E. J. (2003) Genetics, 163, 1109–1022.

    PubMed  CAS  ISI  Google Scholar 

  110. Saze, H., Scheid, O. M., and Paszkowski, J. (2003) Nat. Genet., 34, 65–69.

    Article  PubMed  CAS  Google Scholar 

  111. Cao, X., Aufsatz, W., Zilberman, D., Mette, M. F., Huang, M. S., Matzke, M., and Jacobsen, S. E. (2003) Curr. Biol., 13, 2212–2217.

    Article  PubMed  CAS  Google Scholar 

  112. Cao, X., and Jacobsen, S. E. (2002) Curr. Biol., 12, 1138–1144.

    Article  PubMed  CAS  Google Scholar 

  113. Bartee, L., Malagnac, F., and Bender, J. (2001) Genes Dev., 15, 1753–1758.

    Article  PubMed  CAS  Google Scholar 

  114. Cao, X., and Jacobsen, S. E. (2002) Proc. Natl. Acad. Sci. USA, 99, 16491–16498.

    Article  PubMed  CAS  Google Scholar 

  115. Jeddeloh, J. A., Stokes, T. L., and Richards, E. J. (1999) Nat. Genet., 22, 94–97.

    PubMed  CAS  Google Scholar 

  116. Vignali, M., Hassan, A. H., Neely, K. E., and Workman, J. L. (2000) Mol. Cell. Biol., 20, 1899–1910.

    Article  PubMed  CAS  Google Scholar 

  117. Tamaru, H., and Selker, E. U. (2001) Nature, 414, 277–283.

    Article  PubMed  CAS  ISI  Google Scholar 

  118. Tamaru, H., Zhang, X., McMillen, D., Singh, P. B., Nakayama, J., Grewal, S. I., Allis, C. D., Cheng, X., and Selker, E. U. (2003) Nat. Genet., 34, 75–79.

    Article  PubMed  CAS  Google Scholar 

  119. Kouzminova, E., and Selker, E. U. (2001) EMBO J., 20, 4309–4323.

    Article  PubMed  CAS  Google Scholar 

  120. Freitag, M., Hickey, P. C., Khlafallah, T. K., Read, N. D., and Selker, E. U. (2004) Mol. Cell, 13, 427–434.

    Article  PubMed  CAS  Google Scholar 

  121. Johnson, L., Cao, X., and Jacobsen, S. (2002) Curr. Biol., 12, 1360–1367.

    PubMed  CAS  Google Scholar 

  122. Soppe, W. 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.

    Article  PubMed  CAS  Google Scholar 

  123. Tariq, M., Saze, H., Probst, A. V., Lichota, J., Habu, Y., and Paszkowski, J. (2003) Proc. Natl. Acad. Sci. USA, 100, 8823–8827.

    Article  PubMed  CAS  Google Scholar 

  124. Jackson, J. P., Lindroth, A. M., Cao, X., and Jacobsen, S. E. (2002) Nature, 416, 556–560.

    Article  PubMed  CAS  ISI  Google Scholar 

  125. Malagnac, F., Bartee, L., and Bender, J. (2002) EMBO J., 21, 6842–6852.

    Article  PubMed  CAS  Google Scholar 

  126. Chicas, A., Cogoni, C., and Macino, G. (2004) Nucleic Acids Res., 32, 4237–4243.

    Article  PubMed  CAS  Google Scholar 

  127. Freitag, M., Lee, D. W., Kothe, G. O., Pratt, R. J., Aramayo, R., and Selker, E. U. (2004) Science, 304, 1939.

    Article  PubMed  CAS  ISI  Google Scholar 

  128. Lippman, Z., May, B., Yordan, C., Singer, T., and Martienssen, R. (2003) PLoS Biol., 1, E67.

    Article  PubMed  Google Scholar 

  129. Lippman, Z., Gendrel, A. V., Black, M., Vaughn, M. W., Dedhia, N., McCombie, W. R., Lavine, K., Mittal, V., May, B., Kasschau, K. D., Carrington, J. C., Doerge, R. W., Colot, V., and Martienssen, R. (2004) Nature, 430, 471–476.

    Article  PubMed  CAS  ISI  Google Scholar 

  130. Soppe, W. J., Jacobsen, S. E., Alonso-Blanco, C., Jackson, J. P., Kakutani, T., Koornneef, M., and Peeters, A. J. (2000) Mol. Cell, 6, 791–802.

    Article  PubMed  CAS  Google Scholar 

  131. Kanno, T., Mette, M. F., Kreil, D. P., Aufsatz, W., Matzke, M., and Matzke, A. J. (2004) Curr. Biol., 14, 801–805.

    Article  PubMed  CAS  Google Scholar 

  132. Aufsatz, W., Mette, M. F., van der Winden, J., Matzke, M., and Matzke, A. J. (2002) EMBO J., 21, 6832–6841.

    Article  PubMed  CAS  Google Scholar 

  133. Herr, A. J., Jensen, M. B., Dalmay, T., and Baulcombe, D. C. (2005) Science, 308, 118–120.

    Article  PubMed  CAS  ISI  Google Scholar 

  134. Onodera, Y., Haag, J. R., Ream, T., Nunes, P. C., Pontes, O., and Pikaard, C. S. (2005) Cell, 120, 613–622.

    Article  PubMed  CAS  ISI  Google Scholar 

  135. Djikeng, A., Shi, H., Tschudi, C., and Ullu, E. (2001) RNA, 7, 1522–1530.

    PubMed  CAS  ISI  Google Scholar 

  136. Llave, C., Kasschau, K. D., Rector, M. A., and Carrington, J. C. (2002) Plant Cell, 14, 1605–1619.

    Article  PubMed  CAS  ISI  Google Scholar 

  137. Ambros, V., Lee, R. C., Lavanway, A., Williams, P. T., and Jewell, D. (2003) Curr. Biol., 13, 807–818.

    Article  PubMed  CAS  Google Scholar 

  138. Sijen, T., and Plasterk, R. H. (2003) Nature, 426, 310–314.

    Article  PubMed  CAS  ISI  Google Scholar 

  139. Aravin, A. A., Lagos-Quintana, M., Yalcin, A., Zavolan, M., Marks, D., Snyder, B., Gaasterland, T., Meyer, J., and Tuschl, T. (2003) Dev. Cell, 5, 337–350.

    Article  PubMed  CAS  Google Scholar 

  140. Sarot, E., Payen-Groschene, G., Bucheton, A., and Pelisson, A. (2004) Genetics, 166, 1313–1321.

    Article  PubMed  CAS  ISI  Google Scholar 

  141. Lankenau, S., Corces, V., and Lankenau, D. (1994) Mol. Cell. Biol., 14, 1764–1775.

    PubMed  CAS  Google Scholar 

  142. Gvozdev, V. A. (2003) Genetika, 39, 151–156.

    PubMed  CAS  Google Scholar 

  143. Ketting, R. F., Haverkamp, T. H., van Luenen, H. G., and Plasterk, R. H. (1999) Cell, 99, 133–141.

    Article  PubMed  CAS  ISI  Google Scholar 

  144. Stapleton, W., Das, S., and McKee, B. D. (2001) Chromosoma, 110, 228–240.

    PubMed  CAS  ISI  Google Scholar 

  145. Aravin, A. A., Naumova, N. M., Tulin, A. V., Vagin, V. V., Rozovsky, Y. M., and Gvozdev, V. A. (2001) Curr. Biol., 11, 1017–1027.

    Article  PubMed  CAS  Google Scholar 

  146. Svoboda, P., Stein, P., Anger, M., Bernstein, E., Hannon, G. J., and Schultz, R. M. (2004) Dev. Biol., 269, 276–285.

    Article  PubMed  CAS  Google Scholar 

  147. Vagin, V. V., Klenov, M. S., Kalmykova, A. I., Stolyarenko, A. D., Kotelnikov, R. N., and Gvozdev, V. A. (2004) RNA Biol., 1, 51–55.

    Google Scholar 

  148. Kalmykova, A. I., Klenov, M. S., and Gvozdev, V. A. (2005) Nucleic Acids Res., in press.

  149. Wu-Scharf, D., Jeong, B., Zhang, C., and Cerutti, H. (2000) Science, 290, 1159–1162.

    Article  PubMed  CAS  ISI  Google Scholar 

  150. Hirochika, H., Okamoto, H., and Kakutani, T. (2000) Plant Cell, 12, 357–369.

    Article  PubMed  CAS  ISI  Google Scholar 

  151. Gendrel, A. V., Lippman, Z., Yordan, C., Colot, V., and Martienssen, R. A. (2002) Science, 297, 1871–1873.

    Article  PubMed  CAS  ISI  Google Scholar 

  152. Kinoshita, T., Miura, A., Choi, Y., Kinoshita, Y., Cao, X., Jacobsen, S. E., Fischer, R. L., and Kakutani, T. (2004) Science, 303, 521–523.

    Article  PubMed  CAS  ISI  Google Scholar 

  153. Melquist, S., and Bender, J. (2003) Genes Dev., 17, 2036–2047.

    Article  PubMed  CAS  Google Scholar 

  154. Melquist, S., Luff, B., and Bender, J. (1999) Genetics, 153, 401–413.

    PubMed  CAS  ISI  Google Scholar 

  155. Lyko, F., Ramsahoye, B. H., and Jaenisch, R. (2000) Nature, 408, 538–540.

    PubMed  CAS  ISI  Google Scholar 

  156. Gowher, H., Leismann, O., and Jeltsch, A. (2000) EMBO J., 19, 6918–6923.

    Article  PubMed  CAS  Google Scholar 

  157. Ivanov, A. I., Rovescalli, A. C., Pozzi, P., Yoo, S., Mozer, B., Li, H. P., Yu, S. H., Higashida, H., Guo, V., Spencer, M., and Nirenberg, M. (2004) Proc. Natl. Acad. Sci. USA, 101, 16216–16221.

    PubMed  CAS  Google Scholar 

  158. Kuttenkeuler, D., and Boutros, M. (2004) Brief. Funct. Genomic Proteomic, 3, 168–176.

    PubMed  CAS  Google Scholar 

  159. Pal-Bhadra, M., Bhadra, U., and Birchler, J. A. (1997) Cell, 90, 479–490.

    PubMed  CAS  Google Scholar 

  160. Gvozdev, V. A., Aravin, A. A., Abramov, Y. A., Klenov, M. S., Kogan, G. L., Lavrov, S. A., Naumova, N. M., Olenkina, O. M., Tulin, A. V., and Vagin, V. V. (2003) Genetika, 117, 239–245.

    CAS  Google Scholar 

  161. Aravin, A. A., Klenov, M. S., Vagin, V. V., Bantignies, F., Cavalli, G., and Gvozdev, V. A. (2004) Mol. Cell. Biol., 24, 6742–6750.

    Article  PubMed  CAS  Google Scholar 

  162. Fukagawa, T., Nogami, M., Yoshikawa, M., Ikeno, M., Okazaki, T., Takami, Y., Nakayama, T., and Oshimura, M. (2004) Nat. Cell Biol., 6, 784–791.

    Article  PubMed  CAS  Google Scholar 

  163. Bernstein, E., Kim, S. Y., Carmell, M. A., Murchison, E. P., Alcorn, H., Li, M. Z., Mills, A. A., Elledge, S. J., Anderson, K. V., and Hannon, G. J. (2003) Nat. Genet., 35, 215–217.

    Article  PubMed  CAS  Google Scholar 

  164. Kanellopoulou, C., Muljo, S. A., Kung, A. L., Ganesan, S., Drapkin, R., Jenuwein, T., Livingston, D. M., and Rajewsky, K. (2005) Genes Dev., 19, 489–501.

    Article  PubMed  CAS  Google Scholar 

  165. Gillespie, D. E., and Berg, C. A. (1995) Genes Dev., 9, 2495–2508.

    PubMed  CAS  Google Scholar 

  166. Wilson, J. E., Connell, J. E., and Macdonald, P. M. (1996) Development, 122, 1631–1639.

    PubMed  CAS  ISI  Google Scholar 

  167. Tomancak, P., Guichet, A., Zavorszky, P., and Ephrussi, A. (1998) Development, 125, 1723–1732.

    PubMed  CAS  ISI  Google Scholar 

  168. Cook, H. A., Koppetsch, B. S., Wu, J., and Theurkauf, W. E. (2004) Cell, 116, 817–829.

    Article  PubMed  CAS  ISI  Google Scholar 

  169. Chen, J., Sun, M., Kent, W. J., Huang, X., Xie, H., Wang, W., Zhou, G., Shi, R. Z., and Rowley, J. D. (2004) Nucleic Acids Res., 32, 4812–4820.

    PubMed  CAS  Google Scholar 

  170. Maison, C., Bailly, D., Peters, A. H., Quivy, J. P., Roche, D., Taddei, A., Lachner, M., Jenuwein, T., and Almouzni, G. (2002) Nat. Genet., 30, 329–334.

    Article  PubMed  Google Scholar 

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  1. Institute of Molecular Genetics, Russian Academy of Sciences, pl. Kurchatova 2, 123182, Moscow, Russia

    M. S. Klenov & V. A. Gvozdev

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  1. M. S. Klenov
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  2. V. A. Gvozdev
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Correspondence to M. S. Klenov.

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__________

Translated from Biokhimiya, Vol. 70, No. 11, 2005, pp. 1445–1458.

Original Russian Text Copyright © 2005 by Klenov, Gvozdev.

Originally published in Biochemistry (Moscow) On-Line Papers in Press, as Manuscript BM05-053, July 3, 2005.

This paper was written in honor of the anniversary of B. F. Vanyushin (see special issue of Biochemistry (Moscow) (2005) 70, No. 5), a pioneer in studies on DNA methylation. In the 1960–1970s, he found variations in DNA methylation during development and also association of this process with tumorigenesis.

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Klenov, M.S., Gvozdev, V.A. Heterochromatin Formation: Role of Short RNAs and DNA Methylation. Biochemistry (Moscow) 70, 1187–1198 (2005). https://doi.org/10.1007/s10541-005-0247-4

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