Original Article | Published:

DNA methylation reactivates GAD1 expression in cancer by preventing CTCF-mediated polycomb repressive complex 2 recruitment

Oncogene volume 35, pages 39954008 (28 July 2016) | Download Citation

  • A Corrigendum to this article was published on 27 June 2016

This article has been updated

Abstract

Levels of γ-aminobutyric acid (GABA) and glutamic acid decarboxylase 1 (GAD1), the enzyme that synthesizes GABA, are significantly increased in neoplastic tissues. However, the mechanism underlying this increase remains elusive. Instead of silencing gene transcription, we showed that the GAD1 promoter was hypermethylated in both colon and liver cancer cells, leading to the production of high levels of GAD1. GAD1 is a target gene that is silenced by H3K27me3. The key locus responsible for GAD1 reactivation was mapped to a DNA methylation-sensitive CTCF-binding site (CTCF-BS3) within the third intron of GAD1. Chromosome configuration capture (3C) analysis indicated that an intrachromosomal loop was formed by CTCF self-dimerisation in normal cells (CTCF binds to both unmethylated CTCF-BS3 and CTCF-BS2). The CTCF dimer then interacted with suppressor of zeste 12 homologue (SUZ12), which is a domain of Polycomb repressive complex 2 (PRC2), promoting the methylation of H3K27 and the silencing of GAD1 expression. This silencing was shown to be inhibited by DNA methylation in cancer cells. These findings strongly suggest that GAD1 is reactivated by DNA methylation, which provided a model for DNA methylation and the active orchestration of oncogenic gene expression by CTCF in cancer cells.

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Change history

  • 28 July 2016

    This article has been corrected since Advance Online Publication and a corrigendum is also printed in this issue

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Acknowledgements

This work was supported by grants from the National Natural Science Foundation of China (grants no. 81071680, 81272280, 81172307) Shanghai Pujiang Outstanding Young Scientist Project.

Author contributions

Conception and design: Hongli Yan, Shuhan SUN, Anmei Deng. Development of methodology: Hongli Yan, Guannan Tang, Hao Wang, Tianlin He, Xiaobo Sun. Analysis and interpretation of data (for example, statistical analysis, biostatistics, computational analysis): Hongli Yan, Hao Wang, Liqiang Hao, Anmei Deng. Writing, review of the manuscript: Hongli Yan, Shuhan SUN, Anmei Deng. Conception and design: Hongli Yan, Shuhan SUN, Anmei Deng. Development of methodology: Hongli Yan, Guannan Tang, Hao Wang, Tianlin He, Xiaobo Sun. Analysis and interpretation of data (for example, statistical analysis, biostatistics, computational analysis): Hongli Yan, Hao Wang, Liqiang Hao, Anmei Deng. Writing, review of the manuscript: Hongli Yan, Shuhan SUN, Anmei Dengonception and design: Hongli Yan, Shuhan SUN, Anmei Deng.

Author information

Author notes

    • H Yan
    • , G Tang
    • , H Wang
    •  & L Hao

    These authors contributed equally to this work

Affiliations

  1. Department of Laboratory Medicine, Changhai Hospital, The Second Military Medical University, Shanghai, China

    • H Yan
    • , X Sun
    •  & A Deng
  2. Institute of Genetics, Second Military Medical University, Shanghai, China

    • G Tang
    •  & S Sun
  3. Department of Colorectal Surgery, Changhai Hospital, Second Military Medical University, Shanghai, China

    • H Wang
    •  & L Hao
  4. Division of Hepatopancreatobiliary Surgery, Changhai Hospital, Second Military Medical University, Shanghai, China

    • T He
  5. Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA

    • A H Ting

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The authors declare no conflict of interest.

Corresponding authors

Correspondence to H Yan or A Deng or S Sun.

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DOI

https://doi.org/10.1038/onc.2015.423

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

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