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Disruption of CTCF/cohesin-mediated high-order chromatin structures by DNA methylation downregulates PTGS2 expression

Oncogene volume 34, pages 5677–5684 (2015)Cite this article

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Abstract

The CCCTC-binding factor (CTCF)/cohesin complex regulates gene transcription via high-order chromatin organization of the genome. De novo methylation of CpG islands in the promoter region is an epigenetic hallmark of gene silencing in cancer. Although the CTCF/cohesin complex preferentially targets hypomethylated DNA, it remains unclear whether the CTCF/cohesin-mediated high-order chromatin structure is affected by DNA methylation during tumorigenesis. We found that DNA methylation downregulates the expression of prostaglandin-endoperoxide synthase 2 (PTGS2), which is an inducible, rate-limiting enzyme for prostaglandin synthesis, by disrupting CTCF/cohesin-mediated chromatin looping. We show that the CTCF/cohesin complex is enriched near a CpG island associated with PTGS2 and that the PTGS2 locus forms chromatin loops through methylation-sensitive binding of the CTCF/cohesin complex. DNA methylation abolishes the association of the CTCF/cohesin complex with the PTGS2 CpG island. Disruption of chromatin looping by DNA methylation abrogates the enrichment of transcriptional components, such as positive elongation factor b, at the transcriptional start site of the PTGS2 locus. These alterations result in the downregulation of PTGS2. Our results provide evidence that CTCF/cohesin-mediated chromatin looping of the PTGS2 locus is dynamically influenced by the DNA methylation status.

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Acknowledgements

The authors are grateful to all members of our group for their helpful advice. This research was supported by a grant from the National R&D Program for Cancer Control (MOHW, 0720540), the Basic Science Research Program (MOE, NRF-2011-0021123), the Mid-career Researcher Program (MSIP, NRF-2013R1A2A2A01009297) and the Korea Health Technology R&D Project (MOHW, HI14C1277), Republic of Korea.

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  1. J Y Kang and S H Song: These authors contributed equally to this work.

Authors and Affiliations

  1. Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea

    J Y Kang, S H Song, J Yun, M S Jeon, H P Kim, S W Han & T Y Kim

  2. Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University College of Medicine, Seoul, Republic of Korea

    J Y Kang, J Yun, M S Jeon & T Y Kim

  3. Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea

    S W Han & T Y Kim

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Kang, J., Song, S., Yun, J. et al. Disruption of CTCF/cohesin-mediated high-order chromatin structures by DNA methylation downregulates PTGS2 expression. Oncogene 34, 5677–5684 (2015). https://doi.org/10.1038/onc.2015.17

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