DNA methylation has been traditionally viewed as a highly stable epigenetic mark in postmitotic cells. However, postnatal brains appear to show stimulus-induced methylation changes, at least in a few identified CpG dinucleotides. How extensively the neuronal DNA methylome is regulated by neuronal activity is unknown. Using a next-generation sequencing–based method for genome-wide analysis at single-nucleotide resolution, we quantitatively compared the CpG methylation landscape of adult mouse dentate granule neurons in vivo before and after synchronous neuronal activation. About 1.4% of 219,991 CpGs measured showed rapid active demethylation or de novo methylation. Some modifications remained stable for at least 24 h. These activity-modified CpGs showed a broad genomic distribution with significant enrichment in low-CpG density regions, and were associated with brain-specific genes related to neuronal plasticity. Our study implicates modification of the neuronal DNA methylome as a previously underappreciated mechanism for activity-dependent epigenetic regulation in the adult nervous system.
Subscribe to Journal
Get full journal access for 1 year
only $4.92 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Tax calculation will be finalised during checkout.
Rent or Buy article
Get time limited or full article access on ReadCube.
All prices are NET prices.
Gene Expression Omnibus
Reik, W. Stability and flexibility of epigenetic gene regulation in mammalian development. Nature 447, 425–432 (2007).
Suzuki, M.M. & Bird, A. DNA methylation landscapes: provocative insights from epigenomics. Nat. Rev. Genet. 9, 465–476 (2008).
Ma, D.K. et al. Epigenetic choreographers of neurogenesis in the adult mammalian brain. Nat. Neurosci. 13, 1338–1344 (2010).
Wu, S.C. & Zhang, Y. Active DNA demethylation: many roads lead to Rome. Nat. Rev. Mol. Cell Biol. 11, 607–620 (2010).
Zemach, A., McDaniel, I.E., Silva, P. & Zilberman, D. Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science 328, 916–919 (2010).
Hellman, A. & Chess, A. Gene body-specific methylation on the active X chromosome. Science 315, 1141–1143 (2007).
Ball, M.P. et al. Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nat. Biotechnol. 27, 361–368 (2009).
Wu, H. et al. Dnmt3a-dependent nonpromoter DNA methylation facilitates transcription of neurogenic genes. Science 329, 444–448 (2010).
Guo, J.U., Su, Y., Zhong, C., Ming, G.L. & Song, H. Emerging roles of TET proteins and 5-hydroxymethylcytosines in active DNA demethylation and beyond. Cell Cycle 10, 2662–2668 (2011).
Tsankova, N., Renthal, W., Kumar, A. & Nestler, E.J. Epigenetic regulation in psychiatric disorders. Nat. Rev. Neurosci. 8, 355–367 (2007).
Borrelli, E., Nestler, E.J., Allis, C.D. & Sassone-Corsi, P. Decoding the epigenetic language of neuronal plasticity. Neuron 60, 961–974 (2008).
Szyf, M., McGowan, P. & Meaney, M.J. The social environment and the epigenome. Environ. Mol. Mutagen. 49, 46–60 (2008).
Day, J.J. & Sweatt, J.D. DNA methylation and memory formation. Nat. Neurosci. 13, 1319–1323 (2010).
Guan, J.S. et al. HDAC2 negatively regulates memory formation and synaptic plasticity. Nature 459, 55–60 (2009).
Doi, M., Hirayama, J. & Sassone-Corsi, P. Circadian regulator CLOCK is a histone acetyltransferase. Cell 125, 497–508 (2006).
Maze, I. et al. Essential role of the histone methyltransferase G9a in cocaine-induced plasticity. Science 327, 213–216 (2010).
Ma, D.K. et al. Neuronal activity-induced Gadd45b promotes epigenetic DNA demethylation and adult neurogenesis. Science 323, 1074–1077 (2009).
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).
Miller, C.A. et al. Cortical DNA methylation maintains remote memory. Nat. Neurosci. 13, 664–666 (2010).
Feng, J. et al. Dnmt1 and Dnmt3a maintain DNA methylation and regulate synaptic function in adult forebrain neurons. Nat. Neurosci. 13, 423–430 (2010).
LaPlant, Q. et al. Dnmt3a regulates emotional behavior and spine plasticity in the nucleus accumbens. Nat. Neurosci. 13, 1137–1143 (2010).
Martinowich, K. et al. DNA methylation-related chromatin remodeling in activity-dependent BDNF gene regulation. Science 302, 890–893 (2003).
Weaver, I.C. et al. Epigenetic programming by maternal behavior. Nat. Neurosci. 7, 847–854 (2004).
Miller, C.A. & Sweatt, J.D. Covalent modification of DNA regulates memory formation. Neuron 53, 857–869 (2007).
Dong, E., Nelson, M., Grayson, D.R., Costa, E. & Guidotti, A. Clozapine and sulpiride but not haloperidol or olanzapine activate brain DNA demethylation. Proc. Natl. Acad. Sci. USA 105, 13614–13619 (2008).
Lubin, F.D., Roth, T.L. & Sweatt, J.D. Epigenetic regulation of BDNF gene transcription in the consolidation of fear memory. J. Neurosci. 28, 10576–10586 (2008).
Elliott, E., Ezra-Nevo, G., Regev, L., Neufeld-Cohen, A. & Chen, A. Resilience to social stress coincides with functional DNA methylation of the Crf gene in adult mice. Nat. Neurosci. 13, 1351–1353 (2010).
Murgatroyd, C. et al. Dynamic DNA methylation programs persistent adverse effects of early-life stress. Nat. Neurosci. 12, 1559–1566 (2009).
McGowan, P.O. et al. Epigenetic regulation of the glucocorticoid receptor in human brain associates with childhood abuse. Nat. Neurosci. 12, 342–348 (2009).
Lisanby, S.H. Electroconvulsive therapy for depression. N. Engl. J. Med. 357, 1939–1945 (2007).
Shock, L.S., Thakkar, P.V., Peterson, E.J., Moran, R.G. & Taylor, S.M. DNA methyltransferase 1, cytosine methylation, and cytosine hydroxymethylation in mammalian mitochondria. Proc. Natl. Acad. Sci. USA 108, 3630–3635 (2011).
Nass, M.M. Differential methylation of mitochondrial and nuclear DNA in cultured mouse, hamster and virus-transformed hamster cells. In vivo and in vitro methylation. J. Mol. Biol. 80, 155–175 (1973).
Laurent, L. et al. Dynamic changes in the human methylome during differentiation. Genome Res. 20, 320–331 (2010).
Lister, R. et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462, 315–322 (2009).
Stresemann, C., Brueckner, B., Musch, T., Stopper, H. & Lyko, F. Functional diversity of DNA methyltransferase inhibitors in human cancer cell lines. Cancer Res. 66, 2794–2800 (2006).
Ma, D.K., Guo, J.U., Ming, G.L. & Song, H. DNA excision repair proteins and Gadd45 as molecular players for active DNA demethylation. Cell Cycle 8, 1526–1531 (2009).
Ford, E.C. et al. Localized CT-guided irradiation inhibits neurogenesis in specific regions of the adult mouse brain. Radiat. Res. 175, 774–783 (2011).
Illingworth, R.S. et al. Orphan CpG islands identify numerous conserved promoters in the mammalian genome. PLoS Genet. 6, e1001134 (2010).
Meissner, A. et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454, 766–770 (2008).
Muotri, A.R. et al. Somatic mosaicism in neuronal precursor cells mediated by L1 retrotransposition. Nature 435, 903–910 (2005).
Kim, T.K. et al. Widespread transcription at neuronal activity-regulated enhancers. Nature 465, 182–187 (2010).
Weber, M. et al. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat. Genet. 39, 457–466 (2007).
Klug, M. et al. Active DNA demethylation in human postmitotic cells correlates with activating histone modifications, but not transcription levels. Genome Biol. 11, R63 (2010).
Pierfelice, T., Alberi, L. & Gaiano, N. Notch in the vertebrate nervous system: an old dog with new tricks. Neuron 69, 840–855 (2011).
Irizarry, R.A. et al. The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat. Genet. 41, 178–186 (2009).
Herman, J.G. & Baylin, S.B. Gene silencing in cancer in association with promoter hypermethylation. N. Engl. J. Med. 349, 2042–2054 (2003).
Thompson, R.F. et al. Tissue-specific dysregulation of DNA methylation in aging. Aging Cell 9, 506–518 (2010).
Guo, J.U., Su, Y., Zhong, C., Ming, G.L. & Song, H. Hydroxylation of 5-methylcytosine by TET1 promotes active DNA demethylation in the adult brain. Cell 145, 423–434 (2011).
Simonsson, S. & Gurdon, J. DNA demethylation is necessary for the epigenetic reprogramming of somatic cell nuclei. Nat. Cell Biol. 6, 984–990 (2004).
Eaves, H.L. & Gao, Y. MOM: maximum oligonucleotide mapping. Bioinformatics 25, 969–970 (2009).
We thank G. Church, S. Baylin, D. Ginty and K. Christian for comments and suggestions; G. Sun for help with FACS; and W.Y. Kim (Johns Hopkins University) for breeding Gadd45b knockout mice. This work was supported by US National Institutes of Health (NIH; AG024984, NS047344), McKnight Scholar Award and NARSAD (Brain and Behavior Research Fund) to H.S.; by NIH (HD069184, NS048271), Johns Hopkins Brain Science Institute, Dr. Miriam and Sheldon G. Adelson Medical Research Foundation, and NARSAD grants to G.-l.M.; and Lieber Institute start-up funds to Y.G. J.U.G. was a FARMS (Foundation for Advanced Research in Medical Sciences) fellow. M.H.J. was supported by a US National Institute of Mental Health K99 award (MH090115). M.A.B. was partially supported by a fellowship from Maryland Stem Cell Research Fund (MSCRF); M.P.B. was supported by grants from the NIH to G. Church.
The authors declare no competing financial interests.
Supplementary Figures 1–22 and Supplementary Table 1 (PDF 3117 kb)
Primer sets used for bisulfite sequencing analysis of selected CpGs (XLS 32 kb)
Primer sets used for HpaII-qPCR analysis of selected CpGs (XLS 33 kb)
MSCC results for all MSCC30+ sites (XLS 10842 kb)
List of repetitive sequences examined for CpG methylation changes (XLS 63 kb)
Mouse exon array expression profiles of dentate granule cells at E0 and E4 (XLS 3410 kb)
Expression profiles of genes associated with activity-modified CpGs (XLS 680 kb)
Primer sets and results of q-PCR analysis of promoter CpG changes-associated genes (XLS 34 kb)
Functional pathways that contain activity-modified CpGs (XLS 8485 kb)
About this article
Cite this article
Guo, J., Ma, D., Mo, H. et al. Neuronal activity modifies the DNA methylation landscape in the adult brain. Nat Neurosci 14, 1345–1351 (2011). https://doi.org/10.1038/nn.2900
Developmental Biology (2021)
DNA Methyltransferase 1 (DNMT1) Shapes Neuronal Activity of Human iPSC-Derived Glutamatergic Cortical Neurons
International Journal of Molecular Sciences (2021)
Drug Metabolism Reviews (2021)
Free Radical Biology and Medicine (2021)
Molecular Psychiatry (2021)