Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Brahma links the SWI/SNF chromatin-remodeling complex with MeCP2-dependent transcriptional silencing

Abstract

Transcriptional repression of methylated genes can be mediated by the methyl-CpG binding protein MeCP2. Here we show that human Brahma (Brm), a catalytic component of the SWI/SNF-related chromatin-remodeling complex, associates with MeCP2 in vivo and is functionally linked with repression. We used a number of different molecular approaches and chromatin immunoprecipitation strategies to show a unique cooperation between Brm, BAF57 and MeCP2. We show that Brm and MeCP2 assembly on chromatin occurs on methylated genes in cancer and the gene FMR1 in fragile X syndrome. These experimental findings identify a new role for SWI/SNF in gene repression by MeCP2.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Prices may be subject to local taxes which are calculated during checkout

Figure 1: MeCP2 associates with Brm in vivo.
Figure 2: High-resolution ChIP map of the ABCB1 promoter shows a similar distribution pattern for MeCP2 and Brm binding and movement in response to treatment with the epigenetic modifiers 5-azacytidine (5aC) and TSA.
Figure 3: Assembly of the MeCP2 and Brm corepressor complex on soluble chromatin, as shown by reciprocal ChIP-ReChIP analysis of the ABCB1 promoter.
Figure 4: Recruitment of the MeCP2 and Brm corepressor complex is specified by promoter methylation.
Figure 5: Somatic knockdown of Brm by siRNA reactivates silent ABCB1.
Figure 6: The applicability of the MeCP2-containing Brm corepressor complex on methylated gene silencing can be extended to FMR1.
Figure 7: Silent and active FMR1 assemble distinct complexes in normal and FRAXA cells.
Figure 8: Rendered model of MeCP2-Brm corepressor complex assembly on hypermethylated gene sequences.

Similar content being viewed by others

Accession codes

Accessions

GenBank/EMBL/DDBJ

References

  1. El-Osta, A. & Wolffe, A.P. DNA methylation and histone deacetylation in the control of gene expression: basic biochemistry to human development and disease. Gene Expr. 9, 63–75 (2000).

    Article  CAS  Google Scholar 

  2. Meehan, R.R., Lewis, J.D., Mckay, S., Kleiner, E.L. & Bird, A.P. Identification of a mammalian protein that binds specifically to DNA containing methylated CpGs. Cell 58, 499–507 (1989).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  4. 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 

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

    Article  CAS  Google Scholar 

  6. Fuks, F. et al. The methyl-CpG-binding protein MeCP2 links DNA methylation to histone methylation. J. Biol. Chem. 278, 4035–4040 (2003).

    Article  CAS  Google Scholar 

  7. Kimura, H. & Shiota, K. Methyl-CpG-binding protein, MeCP2, is a target molecule for maintenance DNA methyltransferase, Dnmt1. J. Biol. Chem. 278, 4806–4812 (2003).

    Article  CAS  Google Scholar 

  8. Narlikar, G.J., Fan, H.Y. & Kingston, R.E. Cooperation between complexes that regulate chromatin structure and transcription. Cell 108, 475–487 (2002).

    Article  CAS  Google Scholar 

  9. Peterson, C.L. & Workman, J.L. Promoter targeting and chromatin remodeling by the SWI/SNF complex. Curr. Opin. Genet. Dev. 10, 187–192 (2000).

    Article  CAS  Google Scholar 

  10. Wang, W. et al. Purification and biochemical heterogeneity of the mammalian SWI-SNF complex. EMBO J. 15, 5370–5382 (1996).

    Article  CAS  Google Scholar 

  11. Wang, W. et al. Diversity and specialization of mammalian SWI/SNF complexes. Genes Dev. 10, 2117–2130 (1996).

    Article  CAS  Google Scholar 

  12. Martens, J.A. & Winston, F. Evidence that Swi/Snf directly represses transcription in S. cerevisiae. Genes Dev. 16, 2231–2236 (2002).

    Article  CAS  Google Scholar 

  13. Tong, J.K., Hassig, C.A., Schnitzler, G.R., Kingston, R.E. & Schreiber, S.L. Chromatin deacetylation by an ATP-dependent nucleosome remodelling complex. Nature 395, 917–921 (1998).

    Article  CAS  Google Scholar 

  14. Sif, S., Saurin, A.J., Imbalzano, A.N. & Kingston, R.E. Purification and characterization of mSin3A-containing Brg1 and hBrm chromatin remodeling complexes. Genes Dev. 15, 603–618 (2001).

    Article  CAS  Google Scholar 

  15. Bowen, N.J., Fujita, N., Kajita, M. & Wade, P.A. Mi-2/NuRD: multiple complexes for many purposes. Biochim. Biophys. Acta 1677, 52–57 (2004).

    Article  CAS  Google Scholar 

  16. El-Osta, A., Kantharidis, P., Zalcberg, J.R. & Wolffe, A.P. Precipitous release of methyl-CpG binding protein 2 and histone deacetylase 1 from the methylated human multidrug resistance gene (MDR1) on activation. Mol. Cell. Biol. 22, 1844–1857 (2002).

    Article  CAS  Google Scholar 

  17. 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. Nat. Genet. 21, 103–107 (1999).

    Article  CAS  Google Scholar 

  18. Coffee, B., Zhang, F., Warren, S.T. & Reines, D. Acetylated histones are associated with FMR1 in normal but not fragile X-syndrome cells. Nat. Genet. 22, 98–101 (1999).

    Article  CAS  Google Scholar 

  19. Magdinier, F. & Wolffe, A.P. Selective association of the methyl-CpG binding protein MBD2 with the silent p14/p16 locus in human neoplasia. Proc. Natl. Acad. Sci. USA 98, 4990–4995 (2001).

    Article  CAS  Google Scholar 

  20. Nguyen, C.T., Gonzales, F.A. & Jones, P.A. Altered chromatin structure associated with methylation-induced gene silencing in cancer cells: correlation of accessibility, methylation, MeCP2 binding and acetylation. Nucleic Acids Res. 29, 4598–4606 (2001).

    Article  CAS  Google Scholar 

  21. Ballestar, E. et al. Methyl-CpG binding proteins identify novel sites of epigenetic inactivation in human cancer. EMBO J. 22, 6335–6345 (2003).

    Article  CAS  Google Scholar 

  22. Pal, S. et al. mSin3A/histone deacetylase 2- and PRMT5-containing Brg1 complex is involved in transcriptional repression of the Myc target gene cad. Mol. Cell. Biol. 23, 7475–7487 (2003).

    Article  CAS  Google Scholar 

  23. El-Osta, A., Baker, E.K. & Wolffe, A.P. Profiling methyl-CpG specific determinants on transcriptionally silent chromatin. Mol. Biol. Rep. 28, 209–215 (2001).

    Article  CAS  Google Scholar 

  24. Li, Q., Ahuja, N., Burger, P.C. & Issa, J.P. Methylation and silencing of the Thrombospondin-1 promoter in human cancer. Oncogene 18, 3284–3289 (1999).

    Article  CAS  Google Scholar 

  25. Hannon, G.J. RNA interference. Nature 418, 244–251 (2002).

    Article  CAS  Google Scholar 

  26. Jin, P. & Warren, S.T. Understanding the molecular basis of fragile X syndrome. Hum. Mol. Genet. 9, 901–908 (2000).

    Article  CAS  Google Scholar 

  27. Oberle, I. et al. Instability of a 550-base pair DNA segment and abnormal methylation in fragile X syndrome. Science 252, 1097–1102 (1991).

    Article  CAS  Google Scholar 

  28. Kremer, E.J. et al. Mapping of DNA instability at the fragile X to a trinucleotide repeat sequence p(CCG)n. Science 252, 1711–1714 (1991).

    Article  CAS  Google Scholar 

  29. Verheij, C. et al. Characterization of FMR1 proteins isolated from different tissues. Hum. Mol. Genet. 4, 895–901 (1995).

    Article  CAS  Google Scholar 

  30. Klose, R.J. & Bird, A.P. MeCP2 behaves as an elongated monomer that does not stably associate with the Sin3a chromatin remodeling complex. J. Biol. Chem. 279, 46490–46496 (2004).

    Article  CAS  Google Scholar 

  31. Battaglioli, E. et al. REST repression of neuronal genes requires components of the hSWI.SNF complex. J. Biol. Chem. 277, 41038–41045 (2002).

    Article  CAS  Google Scholar 

  32. Kass, S.U., Landsberger, N. & Wolffe, A.P. DNA methylation directs a time-dependent repression of transcription initiation. Curr. Biol. 7, 157–165 (1997).

    Article  CAS  Google Scholar 

  33. Flaus, A. & Owen-Hughes, T. Dynamic properties of nucleosomes during thermal and ATP-driven mobilization. Mol. Cell. Biol. 23, 7767–7779 (2003).

    Article  CAS  Google Scholar 

  34. Fyodorov, D.V., Blower, M.D., Karpen, G.H. & Kadonaga, J.T. Acf1 confers unique activities to ACF/CHRAC and promotes the formation rather than disruption of chromatin in vivo. Genes Dev. 18, 170–183 (2004).

    Article  CAS  Google Scholar 

  35. Jones, P.A. & Laird, P.W. Cancer epigenetics comes of age. Nat. Genet. 21, 163–167 (1999).

    Article  CAS  Google Scholar 

  36. Di, C.L. et al. Methyltransferase recruitment and DNA hypermethylation of target promoters by an oncogenic transcription factor. Science 295, 1079–1082 (2002).

    Article  Google Scholar 

  37. Rhee, I. et al. DNMT1 and DNMT3b cooperate to silence genes in human cancer cells. Nature 416, 552–556 (2002).

    Article  CAS  Google Scholar 

  38. Godde, J.S., Kass, S.U., Hirst, M.C. & Wolffe, A.P. Nucleosome assembly on methylated CGG triplet repeats in the fragile X mental retardation gene 1 promoter. J. Biol. Chem. 271, 24325–24328 (1996).

    Article  CAS  Google Scholar 

  39. Sutcliffe, J.S. et al. DNA methylation represses FMR-1 transcription in fragile X syndrome. Hum. Mol. Genet. 1, 397–400 (1992).

    Article  CAS  Google Scholar 

  40. Coffee, B., Zhang, F., Ceman, S., Warren, S.T. & Reines, D. Histone modifications depict an aberrantly heterochromatinized FMR1 gene in fragile x syndrome. Am. J. Hum. Genet. 71, 923–932 (2002).

    Article  Google Scholar 

  41. Hendrich, B., Guy, J., Ramsahoye, B., Wilson, V.A. & Bird, A. Closely related proteins MBD2 and MBD3 play distinctive but interacting roles in mouse development. Genes Dev. 15, 710–723 (2001).

    Article  CAS  Google Scholar 

  42. Wade, P.A. et al. Mi-2 complex couples DNA methylation to chromatin remodelling and histone deacetylation. Nat. Genet. 23, 62–66 (1999).

    Article  CAS  Google Scholar 

  43. Zhang, Y. et al. Analysis of the NuRD subunits reveals a histone deacetylase core complex and a connection with DNA methylation. Genes Dev. 13, 1924–1935 (1999).

    Article  CAS  Google Scholar 

  44. Damelin, M. et al. The genome-wide localization of Rsc9, a component of the RSC chromatin-remodeling complex, changes in response to stress. Mol. Cell 9, 563–573 (2002).

    Article  CAS  Google Scholar 

  45. Ng, H.H., Robert, F., Young, R.A. & Struhl, K. Genome-wide location and regulated recruitment of the RSC nucleosome-remodeling complex. Genes Dev. 16, 806–819 (2002).

    Article  CAS  Google Scholar 

  46. Goldmark, J.P., Fazzio, T.G., Estep, P.W., Church, G.M. & Tsukiyama, T. The Isw2 chromatin remodeling complex represses early meiotic genes upon recruitment by Ume6p. Cell 103, 423–433 (2000).

    Article  CAS  Google Scholar 

  47. Martens, J.A., Laprade, L. & Winston, F. Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene. Nature 429, 571–574 (2004).

    Article  CAS  Google Scholar 

  48. Valerius, O., Brendel, C., Duvel, K. & Braus, G.H. Multiple factors prevent transcriptional interference at the yeast ARO4-HIS7 locus. J. Biol. Chem. 277, 21440–21445 (2002).

    Article  CAS  Google Scholar 

  49. Wheatley, S.P., Carvalho, A., Vagnarelli, P. & Earnshaw, W.C. INCENP is required for proper targeting of Survivin to the centromeres and the anaphase spindle during mitosis. Curr. Biol. 11, 886–890 (2001).

    Article  CAS  Google Scholar 

  50. El-Osta, A. & Wolffe, A.P. Analysis of chromatin-immunopurified MeCP2-associated fragments. Biochem. Biophys. Res. Commun. 289, 733–737 (2001).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank P.A. Wade for anti-ISWI antibody and comments, A.T. Hoogeveen for fragile X cell lines and M.E. Cooper and G.L. Jennings for encouragement and support of the research. This work was supported by a grant from the Fragile X Research Foundation, by the National Health and Medical Research Council of Australia and in part by a Conquer Fragile X Foundation Research Grant. A Research Fellowship with the Fragile X Research Foundation supported A.E.-O. The University of Melbourne Postgraduate Scholarship supports M.C., and E.K.B. is a recipient of the Joanna Middows Fellowship. The American Cancer Society and The Sidney Kimmel Foundation supported research in the laboratory of S.S. A.E.-O. dedicates this work to the late A.P. Wolffe, who was a good friend and an inspirational leader. His enthusiasm and curiosity was the motivation behind this study to unravel the mechanisms behind chromatin remodeling and transcriptional activity.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Assam El-Osta.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Fig. 1

The hBrm complex is quantitatively released from the MDR1 promoter following 5aC-induced demethylation. (PDF 527 kb)

Supplementary Fig. 2

Schematic representations of the silent and active MDR1 genes. (PDF 507 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

K N, H., Chow, M., Baker, E. et al. Brahma links the SWI/SNF chromatin-remodeling complex with MeCP2-dependent transcriptional silencing. Nat Genet 37, 254–264 (2005). https://doi.org/10.1038/ng1516

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/ng1516

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing