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Transient cyclical methylation of promoter DNA


Methylation of CpG dinucleotides is generally associated with epigenetic silencing of transcription and is maintained through cellular division1,2,3. Multiple CpG sequences are rare in mammalian genomes, but frequently occur at the transcriptional start site of active genes, with most clusters of CpGs being hypomethylated4. We reported previously that the proximal region of the trefoil factor 1 (TFF1, also known as pS2) and oestrogen receptor α (ERα) promoters could be partially methylated by treatment with deacetylase inhibitors5, suggesting the possibility of dynamic changes in DNA methylation. Here we show that cyclical methylation and demethylation of CpG dinucleotides, with a periodicity of around 100 min, is characteristic for five selected promoters, including the oestrogen (E2)-responsive pS2 gene, in human cells. When the pS2 gene is actively transcribed, DNA methylation occurs after the cyclical occupancy of ERα and RNA polymerase II (polII). Moreover, we report conditions that provoke methylation cycling of the pS2 promoter in cell lines in which pS2 expression is quiescent and the proximal promoter is methylated. This coincides with a low-level re-expression of ERα and of pS2 transcripts.

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Figure 1: The methylation status of the pS2 promoter cycles on release from synchronization.
Figure 2: Cyclical changes in methylation status occur on promoters of several genes.
Figure 4: ERα and pS2 are re-expressed at low levels after transitory treatment with doxorubicin.
Figure 3: Doxorubicin induces cyclical changes in the methylation status of transcriptionally inactive promoters.

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Primary accessions

Gene Expression Omnibus

Data deposits

The gene expression data set reported has been deposited in the NCBI Gene Expression Omnibus (GEO, under accession number GSE10145.


  1. Jones, P. A. & Takai, D. The role of DNA methylation in mammalian epigenetics. Science 293, 1068–1070 (2001)

    CAS  Article  Google Scholar 

  2. Li, E. Chromatin modification and epigenetic reprogramming in mammalian development. Nature Rev. Genet. 3, 662–673 (2002)

    CAS  Article  Google Scholar 

  3. Siegfried, Z. et al. DNA methylation represses transcription in vivo. Nature Genet. 22, 203–206 (1999)

    CAS  Article  Google Scholar 

  4. Costello, J. F. & Plass, C. Methylation matters. J. Med. Genet. 38, 285–303 (2001)

    CAS  Article  Google Scholar 

  5. Reid, G. et al. Multiple mechanisms induce transcriptional silencing of a subset of genes, including oestrogen receptor α, in response to deacetylase inhibition by valproic acid and trichostatin A. Oncogene 24, 4894–4907 (2005)

    CAS  Article  Google Scholar 

  6. Ng, H. H. & Bird, A. DNA methylation and chromatin modification. Curr. Opin. Genet. Dev. 9, 158–163 (1999)

    CAS  Article  Google Scholar 

  7. Duncan, B. K. & Miller, J. H. Mutagenic deamination of cytosine residues in DNA. Nature 287, 560–561 (1980)

    ADS  CAS  Article  Google Scholar 

  8. Shang, Y. et al. Cofactor dynamics and sufficiency in estrogen receptor-regulated transcription. Cell 103, 843–852 (2000)

    CAS  Article  Google Scholar 

  9. Reid, G. et al. Cyclic, proteasome-mediated turnover of unliganded and liganded ERα on responsive promoters is an integral feature of estrogen signaling. Mol. Cell 11, 695–707 (2003)

    CAS  Article  Google Scholar 

  10. Metivier, R. et al. Estrogen receptor-α directs ordered, cyclical, and combinatorial recruitment of cofactors on a natural target promoter. Cell 115, 751–763 (2003)

    CAS  Article  Google Scholar 

  11. Gewirtz, D. A. A critical evaluation of the mechanisms of action proposed for the antitumor effects of the anthracycline antibiotics adriamycin and daunorubicin. Biochem. Pharmacol. 57, 727–741 (1999)

    CAS  Article  Google Scholar 

  12. Yokochi, T. & Roberson, K. D. Doxorubicin inhibits DNMT1, resulting in conditional apoptosis. Mol. Pharmacol. 66, 1415–1420 (2004)

    CAS  Article  Google Scholar 

  13. Métivier, R. et al. Cyclical DNA methylation of a transcriptionally active promoter. Nature doi: 10.1038/nature06544 (this issue)

  14. Metivier, R., Reid, G. & Gannon, F. Transcription in four dimensions: nuclear receptor-directed initiation of gene expression. EMBO Rep. 7, 161–167 (2006)

    CAS  Article  Google Scholar 

  15. Spector, D. L. The dynamics of chromosome organization and gene regulation. Annu. Rev. Biochem. 72, 573–608 (2003)

    CAS  Article  Google Scholar 

  16. Khorasanizadeh, S. The nucleosome: from genomic organization to genomic regulation. Cell 116, 259–272 (2004)

    CAS  Article  Google Scholar 

  17. Dillon, N. Gene regulation and large-scale chromatin organization in the nucleus. Chromosome Res. 14, 117–126 (2006)

    CAS  Article  Google Scholar 

  18. Mellor, J. Dynamic nucleosomes and gene transcription. Trends Genet. 22, 320–329 (2006)

    CAS  Article  Google Scholar 

  19. Jenuwein, T. & Allis, C. D. Translating the histone code. Science 293, 1074–1080 (2001)

    CAS  Article  Google Scholar 

  20. Kress, C., Thomassin, H. & Grange, T. Active cytosine demethylation triggered by a nuclear receptor involves DNA strand breaks. Proc. Natl Acad. Sci. USA 103, 11112–11117 (2006)

    ADS  CAS  Article  Google Scholar 

  21. Nelson, J. E. & Krawetz, S. A. Purification of cloned and genomic DNA by guanidine thiocyanate/isobutyl alcohol fractionation. Anal. Biochem. 207, 197–201 (1992)

    CAS  Article  Google Scholar 

  22. Metivier, R. et al. Transcriptional complexes engaged by apo-estrogen receptor-α isoforms have divergent outcomes. EMBO J. 23, 3653–3666 (2004)

    CAS  Article  Google Scholar 

  23. Nan, X. & Meehan, R. R. Dissection of the methyl-CpG binding domain from the chromosomal protein MecP2. Nucleic Acids Res. 21, 4886–4892 (1993)

    CAS  Article  Google Scholar 

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The authors thank L. Cortesi, S. Denger and J. Lewis for their critical reading of this manuscript, and J. Blake for his assistance in expression array analysis. This work was supported by the EC 6th framework programme grant CRESCENDO and by the European Molecular Biology Organisation (EMBO).

Author Contributions G.R. and F.G. conceived the study, designed the experimental strategy and analysed data; S.K., B.S. and R.M. contributed to the experimental design. S.K. and B.S. prepared the GST–MBD fusion protein, validated the pull-down method, performed the MBD pull-downs and RT–PCR, and prepared DNA and chromatin for methylation analysis and for ChIP. R.M. performed restriction-sensitive methylation analysis and ChIP. M.P.-S. generated RNA for expression analysis and conducted the western blot studies. D.I., R.P.C. and V.B. produced the bisulphite sequencing results and expression array data from material provided by S.K., B.S. and M.P.-S. G.R., R.M. and F.G. wrote the paper, S.K. prepared the Supplementary Information, and all authors discussed the results and commented on the manuscript. F.G. and G.R. are joint senior authors.

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Correspondence to George Reid.

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Supplementary Information

The file contains Supplementary Notes, Supplementary Methods and additional references, followed by Supplementary Table 1 and Supplementary Figures S1-S5 with Legends. (PDF 5170 kb)

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Kangaspeska, S., Stride, B., Métivier, R. et al. Transient cyclical methylation of promoter DNA. Nature 452, 112–115 (2008).

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