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
Subscribe to this journal
Receive 12 print issues and online access
$209.00 per year
only $17.42 per issue
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
Similar content being viewed by others
References
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).
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).
Jones, P.L. et al. Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription. Nat. Genet. 19, 187–191 (1998).
Nan, X. et al. Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex. Nature 393, 386–389 (1998).
Bird, A.P. & Wolffe, A.P. Methylation-induced repression–belts, braces, and chromatin. Cell 99, 451–454 (1999).
Fuks, F. et al. The methyl-CpG-binding protein MeCP2 links DNA methylation to histone methylation. J. Biol. Chem. 278, 4035–4040 (2003).
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).
Narlikar, G.J., Fan, H.Y. & Kingston, R.E. Cooperation between complexes that regulate chromatin structure and transcription. Cell 108, 475–487 (2002).
Peterson, C.L. & Workman, J.L. Promoter targeting and chromatin remodeling by the SWI/SNF complex. Curr. Opin. Genet. Dev. 10, 187–192 (2000).
Wang, W. et al. Purification and biochemical heterogeneity of the mammalian SWI-SNF complex. EMBO J. 15, 5370–5382 (1996).
Wang, W. et al. Diversity and specialization of mammalian SWI/SNF complexes. Genes Dev. 10, 2117–2130 (1996).
Martens, J.A. & Winston, F. Evidence that Swi/Snf directly represses transcription in S. cerevisiae. Genes Dev. 16, 2231–2236 (2002).
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).
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).
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).
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).
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).
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).
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).
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).
Ballestar, E. et al. Methyl-CpG binding proteins identify novel sites of epigenetic inactivation in human cancer. EMBO J. 22, 6335–6345 (2003).
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).
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).
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).
Hannon, G.J. RNA interference. Nature 418, 244–251 (2002).
Jin, P. & Warren, S.T. Understanding the molecular basis of fragile X syndrome. Hum. Mol. Genet. 9, 901–908 (2000).
Oberle, I. et al. Instability of a 550-base pair DNA segment and abnormal methylation in fragile X syndrome. Science 252, 1097–1102 (1991).
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).
Verheij, C. et al. Characterization of FMR1 proteins isolated from different tissues. Hum. Mol. Genet. 4, 895–901 (1995).
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).
Battaglioli, E. et al. REST repression of neuronal genes requires components of the hSWI.SNF complex. J. Biol. Chem. 277, 41038–41045 (2002).
Kass, S.U., Landsberger, N. & Wolffe, A.P. DNA methylation directs a time-dependent repression of transcription initiation. Curr. Biol. 7, 157–165 (1997).
Flaus, A. & Owen-Hughes, T. Dynamic properties of nucleosomes during thermal and ATP-driven mobilization. Mol. Cell. Biol. 23, 7767–7779 (2003).
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).
Jones, P.A. & Laird, P.W. Cancer epigenetics comes of age. Nat. Genet. 21, 163–167 (1999).
Di, C.L. et al. Methyltransferase recruitment and DNA hypermethylation of target promoters by an oncogenic transcription factor. Science 295, 1079–1082 (2002).
Rhee, I. et al. DNMT1 and DNMT3b cooperate to silence genes in human cancer cells. Nature 416, 552–556 (2002).
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).
Sutcliffe, J.S. et al. DNA methylation represses FMR-1 transcription in fragile X syndrome. Hum. Mol. Genet. 1, 397–400 (1992).
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).
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).
Wade, P.A. et al. Mi-2 complex couples DNA methylation to chromatin remodelling and histone deacetylation. Nat. Genet. 23, 62–66 (1999).
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).
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).
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).
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).
Martens, J.A., Laprade, L. & Winston, F. Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene. Nature 429, 571–574 (2004).
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).
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).
El-Osta, A. & Wolffe, A.P. Analysis of chromatin-immunopurified MeCP2-associated fragments. Biochem. Biophys. Res. Commun. 289, 733–737 (2001).
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
Corresponding author
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
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
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/ng1516
This article is cited by
-
Smad linker region phosphorylation is a signalling pathway in its own right and not only a modulator of canonical TGF-β signalling
Cellular and Molecular Life Sciences (2020)
-
smarce1 mutants have a defective endocardium and an increased expression of cardiac transcription factors in zebrafish
Scientific Reports (2018)
-
Biological processes and signal transduction pathways regulated by the protein methyltransferase SETD7 and their significance in cancer
Signal Transduction and Targeted Therapy (2018)
-
Epigenetics in diabetic nephropathy, immunity and metabolism
Diabetologia (2018)
-
Transcriptional and Epigenetic Control of Mammalian Olfactory Epithelium Development
Molecular Neurobiology (2018)