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Neuronal activity modifies the DNA methylation landscape in the adult brain

Abstract

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.

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Figure 1: Modification of DNA methylation landscape in the adult dentate gyrus by neuronal activity.
Figure 2: Persistence of activity-induced CpG modifications.
Figure 3: Biological properties of activity-induced CpG methylation changes in the adult dentate gyrus.
Figure 4: Voluntary exercise–induced CpG methylation changes in dentate granule cells of the adult mouse hippocampus.
Figure 5: Genomic characteristics of activity-modified CpGs.
Figure 6: Correlation between changes in CpG methylation and gene expression, and enrichment of activity-modified CpGs in brain-specific genes and neuronal pathways.

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Acknowledgements

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.

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Authors

Contributions

J.U.G., D.K.M., G.M., Y.G. and H.S. designed the project. J.U.G. led and was involved in all aspect of the project. H.M. performed sequence mapping and methylation calculation. M.P.B. constructed libraries and performed initial methylation analysis. M.-H.J. assisted in BrdU analysis, irradiation and drug infusion procedures. M.A.B. performed FACS purification. J.A.B. wrote the gene mapping program. H.L.E. adapted MOM for the current project. B.X. and H.M. performed Illumina sequencing. E.F. contributed to irradiation studies. K.Z. contributed to data processing. J.U.G., G.M., Y.G. and H.S. wrote the paper.

Corresponding authors

Correspondence to Yuan Gao or Hongjun Song.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–22 and Supplementary Table 1 (PDF 3117 kb)

Supplementary Table 2

Primer sets used for bisulfite sequencing analysis of selected CpGs (XLS 32 kb)

Supplementary Table 3

Primer sets used for HpaII-qPCR analysis of selected CpGs (XLS 33 kb)

Supplementary Table 4

MSCC results for all MSCC30+ sites (XLS 10842 kb)

Supplementary Table 5

List of repetitive sequences examined for CpG methylation changes (XLS 63 kb)

Supplementary Table 6

Mouse exon array expression profiles of dentate granule cells at E0 and E4 (XLS 3410 kb)

Supplementary Table 7

Expression profiles of genes associated with activity-modified CpGs (XLS 680 kb)

Supplementary Table 8

Primer sets and results of q-PCR analysis of promoter CpG changes-associated genes (XLS 34 kb)

Supplementary Table 9

Functional pathways that contain activity-modified CpGs (XLS 8485 kb)

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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

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