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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.

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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.

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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.

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Correspondence to Assam El-Osta.

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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)

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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

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