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Local epigenetic reprogramming induced by G-quadruplex ligands

Nature Chemistry volume 9, pages 1110–1117 (2017)Cite this article

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Abstract

DNA and histone modifications regulate transcriptional activity and thus represent valuable targets to reprogram the activity of genes. Current epigenetic therapies target the machinery that regulates these modifications, leading to global transcriptional reprogramming with the potential for extensive undesired effects. Epigenetic information can also be modified as a consequence of disrupting processive DNA replication. Here, we demonstrate that impeding replication by small-molecule-mediated stabilization of G-quadruplex nucleic acid secondary structures triggers local epigenetic plasticity. We report the use of the BU-1 locus of chicken DT40 cells to screen for small molecules able to induce G-quadruplex-dependent transcriptional reprogramming. Further characterization of the top hit compound revealed its ability to induce a dose-dependent inactivation of BU-1 expression in two steps: the loss of H3K4me3 and then subsequent DNA cytosine methylation, changes that were heritable across cell divisions even after the compound was removed. Targeting DNA secondary structures thus represents a potentially new approach for locus-specific epigenetic reprogramming.

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Figure 1: DT40 BU-1 gene expression as a sensitive screen for the in vivo activity of G4 ligands.
Figure 2: In vivo screen for new G4 quadruplex ligands.
Figure 3: G4- and PDC12-dependent induction of Bu-1 loss variants.
Figure 4: PDC12 reprograms histone marks leading to reduced mRNA expression.
Figure 5: PDC12 induces irreversible loss of BU-1 expression and subsequently CpG methylation.

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Acknowledgements

The authors thank M. Stankovic for help with genotyping PCR across BU-1 G4 and with the ChIP experiment, M. Daly, F. Zhang and V. Romashova in the LMB flow cytometry facility for cell sorting, J. Grimmett and T. Darling in LMB scientific computing for their help in sequencing analysis and C. Lowe for proofreading the manuscript. Work in the Sale group is supported by a central grant to the LMB by the MRC (U105178808). B.R. is supported by an LMB/AstraZeneca BlueSkies postdoctoral fellowship (BSF5). S.B. is a Wellcome Trust Senior Investigator (grant no. 099232/z/12/z). The Balasubramanian group is supported by a European Research Council Advanced Grant (no. 339778) and receives core funding (C14303/A17197) and programme funding (C9681/A18618) from Cancer Research UK.

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Author notes

  1. Guillaume Guilbaud and Pierre Murat: These authors contributed equally to this work.

Authors and Affiliations

  1. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK

    Guillaume Guilbaud, Bénédicte Recolin, Ahmed Maiter & Julian E. Sale

  2. Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK

    Pierre Murat, Beth C. Campbell & Shankar Balasubramanian

  3. Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK

    Pierre Murat & Shankar Balasubramanian

  4. School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0SP, UK

    Shankar Balasubramanian

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  1. Guillaume Guilbaud
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Contributions

G.G. and P.M. designed and performed the experiments. All authors analysed and interpreted the data. B.R. analysed the impact of PDC12 on the DNA damage response. B.C.C. and P.M. synthesized the G4 ligand library. A.M., with G.G., performed the first screen of the library. G.G., P.M. and J.E.S. wrote the manuscript with contributions from all authors. J.E.S. and S.B. supervised the project.

Corresponding authors

Correspondence to Julian E. Sale or Shankar Balasubramanian.

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The authors declare no competing financial interests.

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Guilbaud, G., Murat, P., Recolin, B. et al. Local epigenetic reprogramming induced by G-quadruplex ligands. Nature Chem 9, 1110–1117 (2017). https://doi.org/10.1038/nchem.2828

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