Structure of Dnmt3a bound to Dnmt3L suggests a model for de novo DNA methylation (original) (raw)

• Feil, R. & Berger, F. Convergent evolution of genomic imprinting in plants and mammals. Trends Genet. 23, 192–199 (2007)
  Article CAS Google Scholar
• Ooi, S. K. T. et al. DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. Nature 448, 714–717 (2007)
  Article ADS CAS Google Scholar
• Ferguson-Smith, A. C. & Surani, M. A. Imprinting and the epigenetic asymmetry between parental genomes. Science 293, 1086–1089 (2001)
  Article CAS Google Scholar
• Okano, M., Bell, D. W., Haber, D. A. & Li, E. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 99, 247–257 (1999)
  Article CAS Google Scholar
• Bourc’his, D., Xu, G. L., Lin, C. S., Bollman, B. & Bestor, T. H. Dnmt3L and the establishment of maternal genomic imprints. Science 294, 2536–2539 (2001)
  Article ADS Google Scholar
• Kaneda, M. et al. Essential role for de novo DNA methyltransferase Dnmt3a in paternal and maternal imprinting. Nature 429, 900–903 (2004)
  Article ADS CAS Google Scholar
• Bourc’his, D. & Bestor, T. H. Meiotic catastrophe and retrotransposon reactivation in male germ cells lacking Dnmt3L. Nature 431, 96–99 (2004)
  Article ADS Google Scholar
• Chen, T., Ueda, Y., Xie, S. & Li, E. A novel Dnmt3a isoform produced from an alternative promoter localizes to euchromatin and its expression correlates with active de novo methylation. J. Biol. Chem. 277, 38746–38754 (2002)
  Article CAS Google Scholar
• Gowher, H., Liebert, K., Hermann, A., Xu, G. & Jeltsch, A. Mechanism of stimulation of catalytic activity of Dnmt3A and Dnmt3B DNA-(cytosine-C5)-methyltransferases by Dnmt3L. J. Biol. Chem. 280, 13341–13348 (2005)
  Article CAS Google Scholar
• Schubert, H. L., Blumenthal, R. M. & Cheng, X. Many paths to methyltransfer: a chronicle of convergence. Trends Biochem. Sci. 28, 329–335 (2003)
  Article CAS Google Scholar
• Gowher, H. et al. Mutational analysis of the catalytic domain of the murine Dnmt3a DNA-(cytosine C5)-methyltransferase. J. Mol. Biol. 357, 928–941 (2006)
  Article CAS Google Scholar
• Chedin, F., Lieber, M. R. & Hsieh, C. L. The DNA methyltransferase-like protein DNMT3L stimulates de novo methylation by Dnmt3a. Proc. Natl Acad. Sci. USA 99, 16916–16921 (2002)
  Article ADS CAS Google Scholar
• Suetake, I., Shinozaki, F., Miyagawa, J., Takeshima, H. & Tajima, S. DNMT3L stimulates the DNA methylation activity of Dnmt3a and Dnmt3b through a direct interaction. J. Biol. Chem. 279, 27816–27823 (2004)
  Article CAS Google Scholar
• Kareta, M. S., Botello, Z. M., Ennis, J. J., Chou, C. & Chedin, F. Reconstitution and mechanism of the stimulation of de novo methylation by human DNMT3L. J. Biol. Chem. 281, 25893–25902 (2006)
  Article CAS Google Scholar
• Klimasauskas, S., Kumar, S., Roberts, R. J. & Cheng, X. HhaI methyltransferase flips its target base out of the DNA helix. Cell 76, 357–369 (1994)
  Article CAS Google Scholar
• Gowher, H. & Jeltsch, A. Molecular enzymology of the catalytic domains of the Dnmt3a and Dnmt3b DNA methyltransferases. J. Biol. Chem. 277, 20409–20414 (2002)
  Article CAS Google Scholar
• Kobayashi, H. et al. Bisulfite sequencing and dinucleotide content analysis of 15 imprinted mouse differentially methylated regions (DMRs): paternally methylated DMRs contain less CpGs than maternally methylated DMRs. Cytogenet. Genome Res. 113, 130–137 (2006)
  Article CAS Google Scholar
• Webster, K. E. et al. Meiotic and epigenetic defects in Dnmt3L-knockout mouse spermatogenesis. Proc. Natl Acad. Sci. USA 102, 4068–4073 (2005)
  Article ADS CAS Google Scholar
• Aravin, A. A., Sachidanandam, R., Girard, A., Fejes-Toth, K. & Hannon, G. J. Developmentally regulated piRNA clusters implicate MILI in transposon control. Science 316, 744–747 (2007)
  Article ADS CAS Google Scholar
• Delaval, K. et al. Differential histone modifications mark mouse imprinting control regions during spermatogenesis. EMBO J. 26, 720–729 (2007)
  Article CAS Google Scholar
• Fournier, C. et al. Allele-specific histone lysine methylation marks regulatory regions at imprinted mouse genes. EMBO J. 21, 6560–6570 (2002)
  Article CAS Google Scholar
• Yamasaki, Y. et al. Neuron-specific relaxation of Igf2r imprinting is associated with neuron-specific histone modifications and lack of its antisense transcript Air. Hum. Mol. Genet. 14, 2511–2520 (2005)
  Article CAS Google Scholar
• Vu, T. H., Li, T. & Hoffman, A. R. Promoter-restricted histone code, not the differentially methylated DNA regions or antisense transcripts, marks the imprinting status of IGF2R in human and mouse. Hum. Mol. Genet. 13, 2233–2245 (2004)
  Article CAS Google Scholar
• Studier, F. W. Protein production by auto-induction in high density shaking cultures. Protein Expr. Purif. 41, 207–234 (2005)
  Article CAS Google Scholar
• Frommer, M. et al. A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc. Natl Acad. Sci. USA 89, 1827–1831 (1992)
  Article ADS CAS Google Scholar
• Clark, S. J., Harrison, J., Paul, C. L. & Frommer, M. High sensitivity mapping of methylated cytosines. Nucleic Acids Res. 22, 2990–2997 (1994)
  Article CAS Google Scholar
• Flaus, A. & Richmond, T. J. Positioning and stability of nucleosomes on MMTV 3′LTR sequences. J. Mol. Biol. 275, 427–441 (1998)
  Article CAS Google Scholar
• McCoy, A. J. Solving structures of protein complexes by molecular replacement with Phaser. Acta Crystallogr. D 63, 32–41 (2007)
  Article CAS Google Scholar
• Terwilliger, T. C. SOLVE and RESOLVE: automated structure solution and density modification. Methods Enzymol. 374, 22–37 (2003)
  Article CAS Google Scholar
• Brunger, A. T. et al. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905–921 (1998)
  Article CAS Google Scholar