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DNA demethylation in hormone-induced transcriptional derepression

Nature volume 461, pages 1007–1012 (2009)Cite this article

A Retraction to this article was published on 13 June 2012

A Corrigendum to this article was published on 26 October 2011

This article has been updated

Abstract

Epigenetic modifications at the histone level affect gene regulation in response to extracellular signals1,2. However, regulated epigenetic modifications at the DNA level, especially active DNA demethylation, in gene activation are not well understood3,4,5. Here we report that DNA methylation/demethylation is hormonally switched to control transcription of the cytochrome p450 27B1 (CYP27B1) gene. Reflecting vitamin-D-mediated transrepression of the CYP27B1 gene by the negative vitamin D response element (nVDRE)6,7, methylation of CpG sites (5mCpG) is induced by vitamin D in this gene promoter. Conversely, treatment with parathyroid hormone, a hormone known to activate the CYP27B1 gene8, induces active demethylation of the 5mCpG sites in this promoter. Biochemical purification of a complex associated with the nVDRE-binding protein (VDIR, also known as TCF3)6,7 identified two DNA methyltransferases, DNMT1 and DNMT3B, for methylation of CpG sites9, as well as a DNA glycosylase, MBD4 (ref. 10). Protein-kinase-C-phosphorylated MBD4 by parathyroid hormone stimulation promotes incision of methylated DNA through glycosylase activity11, and a base-excision repair process seems to complete DNA demethylation in the MBD4-bound promoter. Such parathyroid-hormone-induced DNA demethylation and subsequent transcriptional derepression are impaired in Mbd4-/- mice12. Thus, the present findings suggest that methylation switching at the DNA level contributes to the hormonal control of transcription.

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Figure 1: Hormonal control of DNA methylation/demethylation of the CYP27B1 gene promoter.
Figure 2: MBD4 is indispensable for PTH-induced DNA demethylation in the CYP27B1 promoter.
Figure 3: The DNA glycosylase activity of MBD4 is potentiated by PKC-phosphorylation.
Figure 4: MBD4-mediated DNA demethylation derepresses transcription of the vitamin D-transrepressed CYP27B1 gene.

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  • 26 October 2011

    Nature 461, 1007–1012 (2009) Several lanes of the ChIP analyses in this Letter were inadvertently duplicated or erroneously created during figure assembly. We now provide corrected figure panels for Figs 1f, 2c, 2f, 2g and 3h and Supplementary Figs S8, S9a, S9b, S11, S13b, S18 and S28. Our results and conclusions are not affected by these errors, but we apologise for the careless mistakes made.

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Acknowledgements

We thank A. Murayama, K. Saito and A. Matsukage for discussions, Y. Imai and R. Fujiki for technical assistance, K. Sugasawa for plasmids, and M. Yamaki and H. Yamazaki for preparing the manuscript. This work was supported in part by priority areas from the Ministry of Education, Culture, Sports, Science and Technology (to F.O. and S.K.).

Author Contributions M.-S.K., F.O. and S.K. designed the experiments. M.-S.K., S.F. and F.O. performed biochemical assays. M.-S.K., M.-Y.Y., Y.Y., Y.S. and I.Y. conducted the promoter analysis. T.K., S.T. and T.M. carried out the animal study. M.-S.K. and K.-I.T. were responsible for the data interpretation. M.-S.K. and S.K. wrote the manuscript. All authors discussed the results and commented on the manuscript.

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Authors and Affiliations

  1. ERATO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchisi, Saitama 332-0012, Japan ,

    Mi-Sun Kim, Takahiro Matsumoto, Sally Fujiyama, Yuko Shirode, Ikuko Yamaoka, Fumiaki Ohtake & Shigeaki Kato

  2. Institute of Molecular and Cellular Biosciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan ,

    Mi-Sun Kim, Takeshi Kondo, Ichiro Takada, Min-Young Youn, Yoko Yamamoto, Sayuri Takahashi, Takahiro Matsumoto, Sally Fujiyama, Yuko Shirode, Ikuko Yamaoka, Hirochika Kitagawa, Ken-Ichi Takeyama, Fumiaki Ohtake & Shigeaki Kato

  3. Department of Molecular Cell Biology, Medical Research Institute and School of Biomedical Science, Tokyo Medical and Dental University, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan,

    Mi-Sun Kim & Hiroshi Shibuya

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Correspondence to Shigeaki Kato.

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This file contains Supplementary Methods, Supplementary Figures S1-S29, Supplementary Tables SI-SII and Supplementary References. (PDF 3525 kb)

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Kim, MS., Kondo, T., Takada, I. et al. DNA demethylation in hormone-induced transcriptional derepression. Nature 461, 1007–1012 (2009). https://doi.org/10.1038/nature08456

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