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DNMT1 binds HDAC2 and a new co-repressor, DMAP1, to form a complex at replication foci

Abstract

DNA methylation can contribute to transcriptional silencing through several transcriptionally repressive complexes, which include methyl-CpG binding domain proteins (MBDs) and histone deacetylases (HDACs). We show here that the chief enzyme that maintains mammalian DNA methylation, DNMT1, can also establish a repressive transcription complex. The non-catalytic amino terminus of DNMT1 binds to HDAC2 and a new protein, DMAP1 (for DNMT1 associated protein), and can mediate transcriptional repression. DMAP1 has intrinsic transcription repressive activity, and binds to the transcriptional co-repressor TSG101. DMAP1 is targeted to replication foci through interaction with the far N terminus of DNMT1 throughout S phase, whereas HDAC2 joins DNMT1 and DMAP1 only during late S phase, providing a platform for how histones may become deacetylated in heterochromatin following replication. Thus, DNMT1 not only maintains DNA methylation, but also may directly target, in a heritable manner, transcriptionally repressive chromatin to the genome during DNA replication.

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Figure 1: The N terminus of DNMT1 represses transcription.
Figure 2: DNMT1 interacts with HDAC2.
Figure 3: Map and amino acid sequence of DMAP1.
Figure 4: DNMT1 interacts with DMAP1 in vitro and in vivo.
Figure 5: Functional characterization of DMAP1.
Figure 6: Immunofluorescent localization of DNMT1 and DMAP1 at replication foci.
Figure 7: Immunofluorescent co-localization of DNMT1 and HDAC2 at replication foci in late S phase.
Figure 8: Model for the participation of the DNMT1 complex in heritable transmission of chromatin states during early and late S phase DNA replication.

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References

  1. Lewin, B. The mystique of epigenetics. Cell 93, 301 –303 (1998).

    Article  CAS  Google Scholar 

  2. Jones, P.L. & Wolffe, A.P. Relationships between chromatin organization and DNA methylation in determining gene expression. Semin. Cancer Biol. 9, 339–347 (1999).

    Article  CAS  Google Scholar 

  3. Sadoni, N. et al. Nuclear organization of mammalian genomes. Polar chromosome territories build up functionally distinct higher order compartments. J. Cell Biol. 146, 1211–1226 ( 1999).

    Article  CAS  Google Scholar 

  4. Kass, S.U. & Wolffe, A.P. Histones, histone modifications, and the inheritance of chromatin structure. in Epigenetic Mechanisms of Gene Regulation (eds Russo, V.E.A., Martienssen, R.A. & Riggs, A.D.) 529–546 (Cold Spring Harbor Laboratory Press, New York, 1996).

    Google Scholar 

  5. Bird, A. The essentials of DNA methylation. Cell 70, 5–8 (1992).

    Article  CAS  Google Scholar 

  6. Eden, S. & Cedar, H. Role of DNA methylation in the regulation of transcription. Curr. Opin. Genet. Dev. 4, 255–259 (1994).

    Article  CAS  Google Scholar 

  7. Cameron, E.E., Bachman, K.E., Myohanen, S., Herman, J.G. & Baylin, S.B. Synergy of demethylation and histone deacetylase inhibition in the re-expression of genes silenced in cancer. Nature Genet. 21, 103–107 (1999).

    Article  CAS  Google Scholar 

  8. Selker, E.U. Trichostatin A causes selective loss of DNA methylation in Neurospora. Proc. Natl Acad. Sci. USA 95, 9430– 9435 (1998).

    Article  CAS  Google Scholar 

  9. Bird, A.P. & Wolffe, A.P. Methylation-induced repression-belts, braces, and chromatin. Cell 99, 451– 454 (1999).

    Article  CAS  Google Scholar 

  10. Jones, P.L. et al. Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription. Nature Genet. 19, 187– 191 (1998).

    Article  CAS  Google Scholar 

  11. Nan, X. et al. Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex. Nature 393, 386–389 (1998).

    Article  CAS  Google Scholar 

  12. Ng, H.H. et al. MBD2 is a transcriptional repressor belonging to the MeCP1 histone deacetylase complex. Nature Genet. 23, 58 –61 (1999).

    Article  CAS  Google Scholar 

  13. Wade, P.A. et al. Histone deacetylase directs the dominant silencing of transcription in chromatin: association with MeCP2 and the Mi-2 chromodomain SWI/SNF ATPase . Cold Spring Harb. Symp. Quant. Biol. 63, 435–445 (1998).

    Article  CAS  Google Scholar 

  14. Johnson, C.A. & Turner, B.M. Histone deacetylases: complex transducers of nuclear signals. Semin. Cell Dev. Biol. 10, 179–188 (1999).

    Article  CAS  Google Scholar 

  15. Grunstein, M. Yeast heterochromatin: regulation of its assembly and inheritance by histones . Cell 93, 325–328 (1998).

    Article  CAS  Google Scholar 

  16. Krude, T. Chromatin replication: finding the right connection. Curr. Biol. 9, 394–396 ( 1999).

    Article  Google Scholar 

  17. Bestor, T., Laudano, A., Mattaliano, R. & Ingram, V. Cloning and sequencing of a cDNA encoding DNA methyltransferase of mouse cells. The carboxyl-terminal domain of the mammalian enzymes is related to bacterial restriction methyltransferases. J. Mol. Biol. 203, 971–983 (1988).

    Article  CAS  Google Scholar 

  18. Yen, R.W. et al. Isolation and characterization of the cDNA encoding human DNA methyltransferase. Nucleic Acids Res. 20, 2287–2291 (1992).

    Article  CAS  Google Scholar 

  19. Li, E., Bestor, T.H. & Jaenisch, R. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 69, 915–926 (1992).

    Article  CAS  Google Scholar 

  20. Leonhardt, H., Page, A.W., Weier, H.U. & Bestor, T.H. A targeting sequence directs DNA methyltransferase to sites of DNA replication in mammalian nuclei . Cell 71, 865–873 (1992).

    Article  CAS  Google Scholar 

  21. Liu, Y., Oakeley, E.J., Sun, L. & Jost, J.P. Multiple domains are involved in the targeting of the mouse DNA methyltransferase to the DNA replication foci. Nucleic Acids Res. 26, 1038–1045 (1998).

    Article  CAS  Google Scholar 

  22. Chuang, L.S. et al. Human DNA-(cytosine-5) methyltransferase-PCNA complex as a target for p21WAF1. Science 277, 1996– 2000 (1997).

    Article  CAS  Google Scholar 

  23. Bestor, T.H. Activation of mammalian DNA methyltransferase by cleavage of a Zn-binding regulatory domain. EMBO J. 11, 2611– 2617 (1992).

    Article  CAS  Google Scholar 

  24. Leonhardt, H. & Bestor, T.H. Structure, function and regulation of mammalian DNA methyltransferase. EXS 64, 109–119 (1993).

    CAS  PubMed  Google Scholar 

  25. Hittelman, A.B., Burakov, D., Iniguez-Lluhi, J.A., Freedman, L.P. & Garabedian, M.J. Differential regulation of glucocorticoid receptor transcriptional activation via AF-1-associated proteins . EMBO J. 18, 5380–5388 (1999).

    Article  CAS  Google Scholar 

  26. Sun, Z., Pan, J., Hope, W.X., Cohen, S.N. & Balk, S.P. Tumor susceptibility gene 101 protein represses androgen receptor transactivation and interacts with p300. Cancer 86, 689–696 (1999).

    Article  CAS  Google Scholar 

  27. Watanabe, M. et al. A putative tumor suppressor, TSG101, acts as a transcriptional suppressor through its coiled-coil domain. Biochem. Biophys. Res. Commun. 245, 900–905 ( 1998).

    Article  CAS  Google Scholar 

  28. Fuks, F., Burgers, W.A., Brehm, A., Hughes-Davies, L. & Kouzarides, T. DNA methyltransferase Dnmt1 associates with histone deacetylase activity. Nature Genet. 24, 88–91 (2000).

    Article  CAS  Google Scholar 

  29. Yoder, J.A., Yen, R.W.C., Vertino, P.M., Bestor, T.H. & Baylin, S.B. New 5′ regions of the murine and human genes for DNA (cytosine-5)-methyltransferase. J. Biol. Chem. 271, 31092–31097 ( 1996).

    Article  CAS  Google Scholar 

  30. Tucker, K.L., Talbot, D., Lee, M.A., Leonhardt, H. & Jaenisch, R. Complementation of methylation deficiency in embryonic stem cells by a DNA methyltransferase minigene. Proc. Natl Acad. Sci. USA 93, 12920–12925 (1996).

    Article  CAS  Google Scholar 

  31. Li, L. & Cohen, S.N. TSG101: a novel tumor susceptibility gene isolated by controlled homozygous functional knockout of allelic loci in mammalian cells. Cell 85, 319– 329 (1996).

    Article  CAS  Google Scholar 

  32. O'Keefe, R.T., Henderson, S.C. & Spector, D.L. Dynamic organization of DNA replication in mammalian cell nuclei: spatially and temporally defined replication of chromosome-specific α-satellite DNA sequences. J. Cell Biol. 116, 1095– 1110 (1992).

    Article  CAS  Google Scholar 

  33. Krude, T. Mimosine arrests proliferating human cells before onset of DNA replication in a dose-dependent manner. Exp. Cell Res. 247, 148–159 (1999).

    Article  CAS  Google Scholar 

  34. Wu, J. et al. Expression of an exogenous eukaryotic DNA methyltransferase gene induces transformation of NIH 3T3 cells. Proc. Natl Acad. Sci. USA 90, 8891–8895 ( 1993).

    Article  CAS  Google Scholar 

  35. Bakin, A.V. & Curran, T. Role of DNA 5-methylcytosinetransferase in cell transformation by fos. Science 283, 387–390 (1999).

    Article  CAS  Google Scholar 

  36. Vertino, P.M., Yen, R.W., Gao, J. & Baylin, S.B. De novo methylation of CpG island sequences in human fibroblasts overexpressing DNA (cytosine-5-)-methyltransferase . Mol. Cell. Biol. 16, 4555– 4565 (1996).

    Article  CAS  Google Scholar 

  37. Gaudet, F., Talbot, D., Leonhardt, H. & Jaenisch, R. A short DNA methyltransferase isoform restores methylation in vivo. J. Biol. Chem. 273, 32725–32729 (1998).

    Article  CAS  Google Scholar 

  38. Mertineit, C. et al. Sex-specific exons control DNA methyltransferase in mammalian germ cells. Development 125, 889– 897 (1998).

    CAS  PubMed  Google Scholar 

  39. Shibahara, K. & Stillman, B. Replication-dependent marking of DNA by PCNA facilitates CAF-1-coupled inheritance of chromatin. Cell 96, 575–585 ( 1999).

    Article  CAS  Google Scholar 

  40. Taddei, A., Roche, D., Sibarita, J.B., Turner, B.M. & Almouzni, G. Duplication and maintenance of heterochromatin domains. J. Cell Biol. 147, 1153–1166 (1999).

    Article  CAS  Google Scholar 

  41. Rein, T., Kobayashi, T., Malott, M., Leffak, M. & DePamphilis, M.L. DNA methylation at mammalian replication origins. J. Biol. Chem. 274, 25792–25800 (1999).

    Article  CAS  Google Scholar 

  42. Collingwood, T.N., Urnov, F.D. & Wolffe, A.P. Nuclear receptors: coactivators, corepressors and chromatin remodeling in the control of transcription. J. Mol. Endocrinol. 23, 255–275 ( 1999).

    Article  CAS  Google Scholar 

  43. Zhong, Q., Chen, Y., Jones, D. & Lee, W.H. Perturbation of TSG101 protein affects cell cycle progression. Cancer Res. 58, 2699–2702 (1998).

    CAS  PubMed  Google Scholar 

  44. Sobel, R.E., Cook, R.G., Perry, C.A., Annunziato, A.T. & Allis, C.D. Conservation of deposition-related acetylation sites in newly synthesized histones H3 and H4. Proc. Natl Acad. Sci. USA 92, 1237–1241 ( 1995).

    Article  CAS  Google Scholar 

  45. Annunziato, A.T. & Seale, R.L. Histone deacetylation is required for the maturation of newly replicated chromatin. J. Biol. Chem. 258, 12675–12684 (1983).

    CAS  PubMed  Google Scholar 

  46. Li, E. The mojo of methylation. Nature Genet. 23, 5 –6 (1999).

    Article  Google Scholar 

  47. Hsieh, J.J., Zhou, S., Chen, L., Young, D.B. & Hayward, S.D. CIR, a corepressor linking the DNA binding factor CBF1 to the histone deacetylase complex. Proc. Natl Acad. Sci. USA 96, 23–28 ( 1999).

    Article  CAS  Google Scholar 

  48. Bar-Peled, M. & Raikhel, N.V. A method for isolation and purification of specific antibodies to a protein fused to the GST. Anal. Biochem. 241, 140–142 ( 1996).

    Article  CAS  Google Scholar 

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Acknowledgements

We thank R.-W.C. Yen, K. Wieman, E. Cameron, S. Myöhänen, R. Casero and J. Herman for technical support and advice; J. Boeke and M. Brasch for the Gene Quest yeast two-hybrid system and advice; D. Murphy and M. Delanoy for immunostaining and confocal microscopy advice; and D. Hayward and S. Zhou for the Flag-HDAC2 expression plasmid and Vero cells. This work was supported by National Institutes of Health-National Cancer Institute grants CA-43318 and CA-54396.

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Correspondence to Michael R. Rountree.

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Rountree, M., Bachman, K. & Baylin, S. DNMT1 binds HDAC2 and a new co-repressor, DMAP1, to form a complex at replication foci. Nat Genet 25, 269–277 (2000). https://doi.org/10.1038/77023

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