Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Dnmt1 and Dnmt3a maintain DNA methylation and regulate synaptic function in adult forebrain neurons

Nature Neuroscience volume 13, pages 423–430 (2010)Cite this article

Subjects

Abstract

Dnmt1 and Dnmt3a are important DNA methyltransferases that are expressed in postmitotic neurons, but their function in the CNS is unclear. We generated conditional mutant mice that lack Dnmt1, Dnmt3a or both exclusively in forebrain excitatory neurons and found that only double knockout (DKO) mice showed abnormal long-term plasticity in the hippocampal CA1 region together with deficits in learning and memory. Although we found no neuronal loss, hippocampal neurons in DKO mice were smaller than in the wild type; furthermore, DKO neurons showed deregulated expression of genes, including the class I MHC genes and Stat1, that are known to contribute to synaptic plasticity. In addition, we observed a significant decrease in DNA methylation in DKO neurons. We conclude that Dnmt1 and Dnmt3a are required for synaptic plasticity, learning and memory through their overlapping roles in maintaining DNA methylation and modulating neuronal gene expression in adult CNS neurons.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on SpringerLink
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Mice with conditional deletion of Dnmt1 and Dnmt3a have small hippocampi without cell loss.
Figure 2: Impaired neural plasticity in DKO mice.
Figure 3: Impaired learning and memory in DKO mice.
Figure 4: Induction of immune genes in DKO mouse brain.
Figure 5: Stat1 protein increase in DKO mouse brain in conjunction with promoter demethylation in neuronal cells.
Figure 6: Gene ontology and bisulfite sequencing verification of MeDIP-chip analysis.

Similar content being viewed by others

Accession codes

Accessions

Gene Expression Omnibus

References

  1. Tsankova, N., Renthal, W., Kumar, A. & Nestler, E.J. Epigenetic regulation in psychiatric disorders. Nat. Rev. Neurosci. 8, 355–367 (2007).

    Article  CAS  Google Scholar 

  2. Martinowich, K. et al. DNA methylation-related chromatin remodeling in activity-dependent BDNF gene regulation. Science 302, 890–893 (2003).

    Article  CAS  Google Scholar 

  3. Chen, W.G. et al. Derepression of BDNF transcription involves calcium-dependent phosphorylation of MeCP2. Science 302, 885–889 (2003).

    Article  CAS  Google Scholar 

  4. Nelson, E.D., Kavalali, E.T. & Monteggia, L.M. Activity-dependent suppression of miniature neurotransmission through the regulation of DNA methylation. J. Neurosci. 28, 395–406 (2008).

    Article  CAS  Google Scholar 

  5. Feng, J., Fouse, S. & Fan, G. Epigenetic regulation of neural gene expression and neuronal function. Pediatr. Res. 61, 58R–63R (2007).

    Article  CAS  Google Scholar 

  6. Guan, J.S. et al. HDAC2 negatively regulates memory formation and synaptic plasticity. Nature 459, 55–60 (2009).

    Article  CAS  Google Scholar 

  7. Feng, J., Chang, H., Li, E. & Fan, G. Dynamic expression of de novo DNA methyltransferases Dnmt3a and Dnmt3b in the central nervous system. J. Neurosci. Res. 79, 734–746 (2005).

    Article  CAS  Google Scholar 

  8. Goto, K. et al. Expression of DNA methyltransferase gene in mature and immature neurons as well as proliferating cells in mice. Differentiation 56, 39–44 (1994).

    Article  CAS  Google Scholar 

  9. Okano, M., Bell, D.W., Haber, D.A. & Li, E. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 99, 247–257 (1999).

    Article  CAS  Google Scholar 

  10. Li, E., Bestor, T.H. & Jaenisch, R. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 69, 915–926 (1992).

    Article  CAS  Google Scholar 

  11. Fan, G. et al. DNA hypomethylation perturbs the function and survival of CNS neurons in postnatal animals. J. Neurosci. 21, 788–797 (2001).

    Article  CAS  Google Scholar 

  12. Golshani, P., Hutnick, L., Schweizer, F. & Fan, G. Conditional Dnmt1 deletion in dorsal forebrain disrupts development of somatosensory barrel cortex and thalamocortical long-term potentiation. Thalamus Relat. Syst. 3, 227–233 (2005).

    Article  CAS  Google Scholar 

  13. Hutnick, L.K. et al. DNA hypomethylation restricted to the murine forebrain induces cortical degeneration and impairs postnatal neuronal maturation. Hum. Mol. Genet. 18, 2875–2888 (2009).

    Article  CAS  Google Scholar 

  14. Nguyen, S., Meletis, K., Fu, D., Jhaveri, S. & Jaenisch, R. Ablation of de novo DNA methyltransferase Dnmt3a in the nervous system leads to neuromuscular defects and shortened lifespan. Dev. Dyn. 236, 1663–1676 (2007).

    Article  CAS  Google Scholar 

  15. Fan, G. et al. DNA methylation controls the timing of astrogliogenesis through regulation of JAK-STAT signaling. Development 132, 3345–3356 (2005).

    Article  CAS  Google Scholar 

  16. Endres, M., Fan, G., Meisel, A., Dirnagl, U. & Jaenisch, R. Effects of cerebral ischemia in mice lacking DNA methyltransferase 1 in post-mitotic neurons. Neuroreport 12, 3763–3766 (2001).

    Article  CAS  Google Scholar 

  17. Miller, C.A. & Sweatt, J.D. Covalent modification of DNA regulates memory formation. Neuron 53, 857–869 (2007).

    Article  CAS  Google Scholar 

  18. Levenson, J.M. et al. Evidence that DNA (cytosine-5) methyltransferase regulates synaptic plasticity in the hippocampus. J. Biol. Chem. 281, 15763–15773 (2006).

    Article  CAS  Google Scholar 

  19. Jüttermann, R., Li, E. & Jaenisch, R. Toxicity of 5-aza-2′-deoxycytidine to mammalian cells is mediated primarily by covalent trapping of DNA methyltransferase rather than DNA demethylation. Proc. Natl. Acad. Sci. USA 91, 11797–11801 (1994).

    Article  Google Scholar 

  20. Ooi, S.K. & Bestor, T.H. The colorful history of active DNA demethylation. Cell 133, 1145–1148 (2008).

    Article  CAS  Google Scholar 

  21. Weaver, I.C. et al. Epigenetic programming by maternal behavior. Nat. Neurosci. 7, 847–854 (2004).

    Article  CAS  Google Scholar 

  22. Weaver, I.C. et al. Reversal of maternal programming of stress responses in adult offspring through methyl supplementation: altering epigenetic marking later in life. J. Neurosci. 25, 11045–11054 (2005).

    Article  CAS  Google Scholar 

  23. Ma, D.K. et al. Neuronal activity-induced Gadd45b promotes epigenetic DNA demethylation and adult neurogenesis. Science 323, 1074–1077 (2009).

    Article  CAS  Google Scholar 

  24. Xu, G.L. et al. Chromosome instability and immunodeficiency syndrome caused by mutations in a DNA methyltransferase gene. Nature 402, 187–191 (1999).

    Article  CAS  Google Scholar 

  25. Ouimet, C.C., McGuinness, T.L. & Greengard, P. Immunocytochemical localization of calcium/calmodulin-dependent protein kinase II in rat brain. Proc. Natl. Acad. Sci. USA 81, 5604–5608 (1984).

    Article  CAS  Google Scholar 

  26. Huh, G.S. et al. Functional requirement for class I MHC in CNS development and plasticity. Science 290, 2155–2159 (2000).

    Article  CAS  Google Scholar 

  27. Stevens, B. et al. The classical complement cascade mediates CNS synapse elimination. Cell 131, 1164–1178 (2007).

    Article  CAS  Google Scholar 

  28. Tropea, D. et al. Gene expression changes and molecular pathways mediating activity-dependent plasticity in visual cortex. Nat. Neurosci. 9, 660–668 (2006).

    Article  CAS  Google Scholar 

  29. Neumann, H., Schmidt, H., Cavalie, A., Jenne, D. & Wekerle, H. Major histocompatibility complex (MHC) class I gene expression in single neurons of the central nervous system: differential regulation by interferon (IFN)-gamma and tumor necrosis factor (TNF)-alpha. J. Exp. Med. 185, 305–316 (1997).

    Article  CAS  Google Scholar 

  30. Fouse, S.D. et al. Promoter CpG methylation contributes to ES cell gene regulation in parallel with Oct4/Nanog, PcG complex, and histone H3 K4/K27 trimethylation. Cell Stem Cell 2, 160–169 (2008).

    Article  CAS  Google Scholar 

  31. Rhee, I. et al. DNMT1 and DNMT3b cooperate to silence genes in human cancer cells. Nature 416, 552–556 (2002).

    Article  CAS  Google Scholar 

  32. Chen, T., Ueda, Y., Dodge, J.E., Wang, Z. & Li, E. Establishment and maintenance of genomic methylation patterns in mouse embryonic stem cells by Dnmt3a and Dnmt3b. Mol. Cell. Biol. 23, 5594–5605 (2003).

    Article  CAS  Google Scholar 

  33. Liang, G. et al. Cooperativity between DNA methyltransferases in the maintenance methylation of repetitive elements. Mol. Cell. Biol. 22, 480–491 (2002).

    Article  CAS  Google Scholar 

  34. Bachman, K.E., Rountree, M.R. & Baylin, S.B. Dnmt3a and Dnmt3b are transcriptional repressors that exhibit unique localization properties to heterochromatin. J. Biol. Chem. 276, 32282–32287 (2001).

    Article  CAS  Google Scholar 

  35. Boulanger, L.M. & Shatz, C.J. Immune signaling in neural development, synaptic plasticity and disease. Nat. Rev. Neurosci. 5, 521–531 (2004).

    Article  CAS  Google Scholar 

  36. Perry, V.H. & O'Connor, V. C1q: the perfect complement for a synaptic feast? Nat. Rev. Neurosci. 9, 807–811 (2008).

    Article  CAS  Google Scholar 

  37. Jackson-Grusby, L. et al. Loss of genomic methylation causes p53-dependent apoptosis and epigenetic deregulation. Nat. Genet. 27, 31–39 (2001).

    Article  CAS  Google Scholar 

  38. Bhattacharya, S.K., Ramchandani, S., Cervoni, N. & Szyf, M. A mammalian protein with specific demethylase activity for mCpG DNA. Nature 397, 579–583 (1999).

    Article  CAS  Google Scholar 

  39. Barreto, G. et al. Gadd45a promotes epigenetic gene activation by repair-mediated DNA demethylation. Nature 445, 671–675 (2007).

    Article  CAS  Google Scholar 

  40. Brooks, P.J., Marietta, C. & Goldman, D. DNA mismatch repair and DNA methylation in adult brain neurons. J. Neurosci. 16, 939–945 (1996).

    Article  CAS  Google Scholar 

  41. Kriaucionis, S. & Heintz, N. The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science 324, 929–930 (2009).

    Article  CAS  Google Scholar 

  42. Tahiliani, M. et al. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324, 930–935 (2009).

    Article  CAS  Google Scholar 

  43. Dodge, J.E. et al. Inactivation of Dnmt3b in mouse embryonic fibroblasts results in DNA hypomethylation, chromosomal instability, and spontaneous immortalization. J. Biol. Chem. 280, 17986–17991 (2005).

    Article  CAS  Google Scholar 

  44. Han, Y.G. et al. Hedgehog signaling and primary cilia are required for the formation of adult neural stem cells. Nat. Neurosci. 11, 277–284 (2008).

    Article  CAS  Google Scholar 

  45. Lu, X.H. et al. Bacterial artificial chromosome transgenic mice expressing a truncated mutant parkin exhibit age-dependent hypokinetic motor deficits, dopaminergic neuron degeneration, and accumulation of proteinase K-resistant alpha-synuclein. J. Neurosci. 29, 1962–1976 (2009).

    Article  Google Scholar 

  46. Cui, L. et al. Transcriptional repression of PGC-1alpha by mutant huntingtin leads to mitochondrial dysfunction and neurodegeneration. Cell 127, 59–69 (2006).

    Article  CAS  Google Scholar 

  47. Ethell, I.M. et al. EphB/syndecan-2 signaling in dendritic spine morphogenesis. Neuron 31, 1001–1013 (2001).

    Article  CAS  Google Scholar 

  48. Jiang, Y., Matevossian, A., Huang, H.S., Straubhaar, J. & Akbarian, S. Isolation of neuronal chromatin from brain tissue. BMC Neurosci. 9, 42 (2008).

    Article  Google Scholar 

  49. Crain, P.F. Preparation and enzymatic hydrolysis of DNA and RNA for mass spectrometry. Methods Enzymol. 193, 782–790 (1990).

    Article  CAS  Google Scholar 

  50. Song, L.J.S., Kazim, L. & Karpf, A.R. Specific method for the determination of genomic DNA methylation by liquid chromatography-electrospray ionization tandem mass spectrometry. Anal. Chem. 77, 504–510 (2005).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank X.-H. Lu and X.W. Yang for help with stereology analysis, T. Chailangkarn and S. Fouse for technical support and P. Golshani for critical reading of the paper. We also thank all members of the Fan laboratory for help and advice. Funding was provided by grants from the US National Institutes of Health to G.F. (RO1 NS051411), A.J.S. (P50-MH0779720) and J.D.S. (AG031722, MH57014 and NS057098). G.F. is a Carol Moss Spivak Scholar in Neuroscience.

Author information

Author notes

  1. Yu Zhou

    Present address: Present address: Department of Physiology, Medical College of Qingdao University, Qingdao, China.,

Authors and Affiliations

  1. Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA

    Jian Feng, Thuc Le & Guoping Fan

  2. Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA

    Yu Zhou & Alcino J Silva

  3. Department of Neurobiology, University of Alabama at Birmingham, Birmingham, Alabama, USA

    Susan L Campbell & J David Sweatt

  4. Interdepartmental Neuroscience Program, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA

    Thuc Le

  5. Epigenetics Program, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA

    En Li

Authors
  1. Jian Feng
    View author publications

    You can also search for this author inPubMed Google Scholar

  2. Yu Zhou
    View author publications

    You can also search for this author inPubMed Google Scholar

  3. Susan L Campbell
    View author publications

    You can also search for this author inPubMed Google Scholar

  4. Thuc Le
    View author publications

    You can also search for this author inPubMed Google Scholar

  5. En Li
    View author publications

    You can also search for this author inPubMed Google Scholar

  6. J David Sweatt
    View author publications

    You can also search for this author inPubMed Google Scholar

  7. Alcino J Silva
    View author publications

    You can also search for this author inPubMed Google Scholar

  8. Guoping Fan
    View author publications

    You can also search for this author inPubMed Google Scholar

Contributions

The studies were directed by G.F. and conceived and designed by J.F. and G.F. G.F., A.J.S. and J.D.S. coordinated the project. J.F. performed the behavioral tests, morphology analysis, gene expression and DNA methylation analysis. Y.Z. performed the fear-conditioning test, LTD and synaptic transmission experiments. S.L.C. performed the LTP experiments. T.L. carried out DNA hydrolysis/LC-ESI-MS/MS experiments and contributed to the DNA methylation analysis. E.L. contributed Dnmt3a2lox/2lox mice. The paper was written by J.F. and G.F. and was commented on by all the authors.

Corresponding author

Correspondence to Guoping Fan.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–10 and Supplementary Tables 1–3 (PDF 5773 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Feng, J., Zhou, Y., Campbell, S. et al. Dnmt1 and Dnmt3a maintain DNA methylation and regulate synaptic function in adult forebrain neurons. Nat Neurosci 13, 423–430 (2010). https://doi.org/10.1038/nn.2514

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nn.2514

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing
pFad - Phonifier reborn

Pfad - The Proxy pFad of © 2024 Garber Painting. All rights reserved.

Note: This service is not intended for secure transactions such as banking, social media, email, or purchasing. Use at your own risk. We assume no liability whatsoever for broken pages.


Alternative Proxies:

Alternative Proxy

pFad Proxy

pFad v3 Proxy

pFad v4 Proxy