Article

Tet3 regulates synaptic transmission and homeostatic plasticity via DNA oxidation and repair

  • Nature Neuroscience volume 18, pages 836843 (2015)
  • doi:10.1038/nn.4008
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Abstract

Contrary to the long-held belief that DNA methylation of terminally differentiated cells is permanent and essentially immutable, post-mitotic neurons exhibit extensive DNA demethylation. The cellular function of active DNA demethylation in neurons, however, remains largely unknown. Tet family proteins oxidize 5-methylcytosine to initiate active DNA demethylation through the base-excision repair (BER) pathway. We found that synaptic activity bi-directionally regulates neuronal Tet3 expression. Functionally, knockdown of Tet or inhibition of BER in hippocampal neurons elevated excitatory glutamatergic synaptic transmission, whereas overexpressing Tet3 or Tet1 catalytic domain decreased it. Furthermore, dysregulation of Tet3 signaling prevented homeostatic synaptic plasticity. Mechanistically, Tet3 dictated neuronal surface GluR1 levels. RNA-seq analyses further revealed a pivotal role of Tet3 in regulating gene expression in response to global synaptic activity changes. Thus, Tet3 serves as a synaptic activity sensor to epigenetically regulate fundamental properties and meta-plasticity of neurons via active DNA demethylation.

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Acknowledgements

We thank R. Huganir, P. Worley, G.C. Turrigiano and L. Chen for suggestions, members of the Ming and Song laboratories for help and critical comments, G.L. Xu for Tet3 antibodies, and L. Liu, Q. Hussaini and Y. Cai for technical support. This work was supported by the US National Institutes of Health (NS047344 to H.S., NS048271 and MH105128 to G.-l.M., NS062691 to G.C. and D.H.G.), a grant from the Simons Foundation (SFARI240011 to H.S.), the Brain and Behavior Research Foundation (H.S., G.-l.M. and Y.S.), Maryland Stem Cell Research Foundation (G.-l.M. and H.S.), and by the Dr. Miriam and Sheldon G. Adelson Medical Research Foundation (G.-l.M., D.H.G. and G.C.). J.S. was supported by a Samsung fellowship.

Author information

Author notes

    • Junjie U Guo

    Present address: Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA.

Affiliations

  1. Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.

    • Huimei Yu
    • , Yijing Su
    • , Jaehoon Shin
    • , Chun Zhong
    • , Junjie U Guo
    • , Yi-Lan Weng
    • , Guo-li Ming
    •  & Hongjun Song
  2. Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.

    • Huimei Yu
    • , Yijing Su
    • , Chun Zhong
    • , Junjie U Guo
    • , Yi-Lan Weng
    • , Guo-li Ming
    •  & Hongjun Song
  3. Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA.

    • Fuying Gao
    • , Daniel H Geschwind
    •  & Giovanni Coppola
  4. Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA.

    • Fuying Gao
    • , Daniel H Geschwind
    •  & Giovanni Coppola
  5. Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA.

    • Fuying Gao
    • , Daniel H Geschwind
    •  & Giovanni Coppola
  6. Department of Psychiatry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA.

    • Fuying Gao
    • , Daniel H Geschwind
    •  & Giovanni Coppola
  7. Graduate Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.

    • Jaehoon Shin
    • , Guo-li Ming
    •  & Hongjun Song
  8. The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.

    • Guo-li Ming
    •  & Hongjun Song
  9. Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.

    • Guo-li Ming

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Contributions

H.Y. performed electrophysiological analyses. Y.S. performed biochemical and DNA methylation analyses. J.S. and J.U.G. performed bioinformatics analysis. C.Z. and Y.-L.W. generated AAV. F.G., D.H.G. and G.C. performed RNA-seq. G.-l.M. and H.S. designed the project and wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Hongjun Song.

Integrated supplementary information

Supplementary information

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  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–11

  2. 2.

    Supplementary Methods Checklist

Excel files

  1. 1.

    Supplementary Table 1

    Summary of shRNA and primer sequences used in the current study. (a) Primer sequences used for qPCR analysis; (b) shRNA sequences; (c) Primer sequences for bisulfite sequencing analysis; (d) Primer sequences for ChIP-PCR analyses.

  2. 2.

    Supplementary Table 2

    Summary of RNA-seq analysis. (a) RNA-seq run and mapping information; (b) Gene list and information on differentially expressed genes upon Tet3 knockdown. (c-d) Gene lists and information on bicuculline-regulated genes in neurons expressing sh-control (c) and those expressing sh-Tet3-2 (d). (e-f) Gene lists and information on TTX-regulated genes in neurons expressing shRNA-control (e) and those expressing sh-Tet3-2 (f). (g) KEGG pathway analysis.