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Unmasking of epigenetically silenced candidate tumor suppressor genes by removal of methyl-CpG-binding domain proteins

Oncogene volume 27, pages 3556–3566 (2008)Cite this article

Abstract

Methyl-cytosine-phosphate-guanine (CpG)-binding domain (MBD) proteins are bound to hypermethylated promoter CpG islands of tumor suppressor genes in human cancer cells, although a direct causal relationship at the genome-wide level between MBD presence and gene silencing remains to be demonstrated. To this end, we have inhibited the expression of MBD proteins in HeLa cells by short hairpin RNAs; and studied the functional consequences of MBD depletion using microarray-based expression analysis in conjunction with extensive bisulfite genomic sequencing and chromatin immunoprecipitation. The removal of MBDs results in a release of gene silencing associated with a loss of MBD occupancy in 5′-CpG islands without any change in the DNA methylation pattern. Our results unveil new targets for epigenetic inactivation mediated by MBDs in transformed cells, such as the cell adhesion protein γ-parvin and the fibroblast growth factor 19, where we also demonstrate their bona fide tumor suppressor features. Our data support a fundamental role for MBD proteins in the direct maintenance of transcriptional repression of tumor suppressors and identify new candidate genes for epigenetic disruption in cancer cells.

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Acknowledgements

We are grateful to Professor Reinhard Fässler for providing us with the PARVG antibody. The work was supported by the Health (FIS01-04) and Education and Science (I+D+I MCYT08-03, FU2004-02073/BMC and Consolider MEC09-05) Departments of the Spanish Government, the European Grant Transfog LSHC-CT-2004-503438 and the Spanish Association Against Cancer (AECC). LL-S is a recipient of a BEFI predoctoral fellowship.

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Authors and Affiliations

  1. Cancer Epigenetics Laboratory, Spanish National Cancer Research Centre (CNIO), Madrid, Spain

    L Lopez-Serra, E Ballestar, S Ropero, F Setien, M F Fraga, P Lopez-Nieva & M Esteller

  2. Unité INSERM 590, Laboratoire d'Oncologie Moléculaire, Centre Léon Bérard, Lyon, France

    L-M Billard & R Dante

  3. Department of Histology, Granada University, Granada, Spain

    M Alaminos

  4. Fundación Hospital Clínico, Granada, Spain

    M Alaminos

  5. Centro de Investigación Biomédica, Servicio Navarro de Salud, Navarra, Spain

    D Guerrero

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  1. L Lopez-Serra
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  2. E Ballestar
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  3. S Ropero
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Correspondence to M Esteller.

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Supplementary Information accompanies the paper on the Oncogene website (http://www.nature.com/onc).

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Lopez-Serra, L., Ballestar, E., Ropero, S. et al. Unmasking of epigenetically silenced candidate tumor suppressor genes by removal of methyl-CpG-binding domain proteins. Oncogene 27, 3556–3566 (2008). https://doi.org/10.1038/sj.onc.1211022

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  • DOI: https://doi.org/10.1038/sj.onc.1211022

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