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DNA methylation changes in plasticity genes accompany the formation and maintenance of memory

Abstract

The ability to form memories is a prerequisite for an organism's behavioral adaptation to environmental changes. At the molecular level, the acquisition and maintenance of memory requires changes in chromatin modifications. In an effort to unravel the epigenetic network underlying both short- and long-term memory, we examined chromatin modification changes in two distinct mouse brain regions, two cell types and three time points before and after contextual learning. We found that histone modifications predominantly changed during memory acquisition and correlated surprisingly little with changes in gene expression. Although long-lasting changes were almost exclusive to neurons, learning-related histone modification and DNA methylation changes also occurred in non-neuronal cell types, suggesting a functional role for non-neuronal cells in epigenetic learning. Finally, our data provide evidence for a molecular framework of memory acquisition and maintenance, wherein DNA methylation could alter the expression and splicing of genes involved in functional plasticity and synaptic wiring.

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Figure 1: High-resolution brain region– and cell type–specific chromatin modification data.
Figure 2: A high-quality, in vivo network of neuronal and non-neuronal gene and CRM activity.
Figure 3: Histone modifications display global and gene-specific changes during learning.
Figure 4: Transient and stable DNA methylation during memory acquisition and maintenance.
Figure 5: DNA methylation correlates strongly with the spatio-temporal location of associative memory.
Figure 6: DNA methylation changes are associated with the expression of functional and synaptic plasticity genes.

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References

  1. Guzman-Karlsson, M.C., Meadows, J.P., Gavin, C.F., Hablitz, J.J. & Sweatt, J.D. Transcriptional and epigenetic regulation of Hebbian and non-Hebbian plasticity. Neuropharmacology 80, 3–17 (2014).

    CAS  Article  Google Scholar 

  2. Gräff, J. & Tsai, L.-H. Histone acetylation: molecular mnemonics on the chromatin. Nat. Rev. Neurosci. 14, 97–111 (2013).

    Article  Google Scholar 

  3. Zovkic, I.B., Guzman-Karlsson, M.C. & Sweatt, J.D. Epigenetic regulation of memory formation and maintenance. Learn. Mem. 20, 61–74 (2013).

    CAS  Article  Google Scholar 

  4. Sweatt, J.D. The emerging field of neuroepigenetics. Neuron 80, 624–632 (2013).

    CAS  Article  Google Scholar 

  5. Lopez-Atalaya, J.P. & Barco, A. Can changes in histone acetylation contribute to memory formation? Trends Genet. 30, 529–539 (2014).

    CAS  Article  Google Scholar 

  6. Levenson, J.M. et al. Regulation of histone acetylation during memory formation in the hippocampus. J. Biol. Chem. 279, 40545–40559 (2004).

    CAS  Article  Google Scholar 

  7. Gupta, S. et al. Histone methylation regulates memory formation. J. Neurosci. 30, 3589–3599 (2010).

    CAS  Article  Google Scholar 

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

    CAS  Article  Google Scholar 

  9. Miller, C.A. et al. Cortical DNA methylation maintains remote memory. Nat. Neurosci. 13, 664–666 (2010).

    CAS  Article  Google Scholar 

  10. Strahl, B.D. & Allis, C.D. The language of covalent histone modifications. Nature 403, 41–45 (2000).

    CAS  Article  Google Scholar 

  11. Day, J.J. & Sweatt, J.D. Epigenetic mechanisms in cognition. Neuron 70, 813–829 (2011).

    CAS  Article  Google Scholar 

  12. Fischer, A. Epigenetic memory: the Lamarckian brain. EMBO J. 33, 945–967 (2014).

    CAS  Article  Google Scholar 

  13. Fanselow, M.S. Factors governing one-trial contextual conditioning. Anim. Learn. Behav. 18, 264–270 (1990).

    Article  Google Scholar 

  14. Kim, J.J. & Fanselow, M.S. Modality-specific retrograde amnesia of fear. Science 256, 675–677 (1992).

    CAS  Article  Google Scholar 

  15. Runyan, J.D., Moore, A.N. & Dash, P.K. A role for prefrontal cortex in memory storage for trace fear conditioning. J. Neurosci. 24, 1288–1295 (2004).

    CAS  Article  Google Scholar 

  16. Einarsson, E.O. & Nader, K. Involvement of the anterior cingulate cortex in formation, consolidation, and reconsolidation of recent and remote contextual fear memory. Learn. Mem. 19, 449–452 (2012).

    Article  Google Scholar 

  17. Bonn, S. et al. Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development. Nat. Genet. 44, 148–156 (2012).

    CAS  Article  Google Scholar 

  18. Bonn, S. et al. Cell type-specific chromatin immunoprecipitation from multicellular complex samples using BiTS-ChIP. Nat. Protoc. 7, 978–994 (2012).

    CAS  Article  Google Scholar 

  19. 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 

  20. Peleg, S. et al. Altered histone acetylation is associated with age-dependent memory impairment in mice. Science 328, 753–756 (2010).

    CAS  Article  Google Scholar 

  21. Barski, A. et al. High-resolution profiling of histone methylations in the human genome. Cell 129, 823–837 (2007).

    CAS  Article  Google Scholar 

  22. Zhou, V.W., Goren, A. & Bernstein, B.E. Charting histone modifications and the functional organization of mammalian genomes. Nat. Rev. Genet. 12, 7–18 (2010).

    Article  Google Scholar 

  23. Cahoy, J.D. et al. A transcriptome database for astrocytes, neurons, and oligodendrocytes: a new resource for understanding brain development and function. J. Neurosci. 28, 264–278 (2008).

    CAS  Article  Google Scholar 

  24. Ko, Y. et al. Cell type-specific genes show striking and distinct patterns of spatial expression in the mouse brain. Proc. Natl. Acad. Sci. USA 110, 3095–3100 (2013).

    CAS  Article  Google Scholar 

  25. Guo, J.U. et al. Neuronal activity modifies the DNA methylation landscape in the adult brain. Nat. Neurosci. 14, 1345–1351 (2011).

    CAS  Article  Google Scholar 

  26. Guo, J.U. et al. Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brain. Nat. Neurosci. 17, 215–222 (2014).

    CAS  Article  Google Scholar 

  27. Lister, R. et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462, 315–322 (2009).

    CAS  Article  Google Scholar 

  28. Kim, T.-K. et al. Widespread transcription at neuronal activity-regulated enhancers. Nature 465, 182–187 (2010).

    CAS  Article  Google Scholar 

  29. Malik, A.N. et al. Genome-wide identification and characterization of functional neuronal activity-dependent enhancers. Nat. Neurosci. 17, 1330–1339 (2014).

    CAS  Article  Google Scholar 

  30. Heintzman, N.D. et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459, 108–112 (2009).

    CAS  Article  Google Scholar 

  31. Lyons, G.E., Micales, B.K., Schwarz, J., Martin, J.F. & Olson, E.N. Expression of mef2 genes in the mouse central nervous system suggests a role in neuronal maturation. J. Neurosci. 15, 5727–5738 (1995).

    CAS  Article  Google Scholar 

  32. Gao, Z. et al. Neurod1 is essential for the survival and maturation of adult-born neurons. Nat. Neurosci. 12, 1090–1092 (2009).

    CAS  Article  Google Scholar 

  33. Nakayama, A. et al. Role for RFX transcription factors in non-neuronal cell-specific inactivation of the microtubule-associated protein MAP1A promoter. J. Biol. Chem. 278, 233–240 (2003).

    CAS  Article  Google Scholar 

  34. Reiprich, S. & Wegner, M. From CNS stem cells to neurons and glia: Sox for everyone. Cell Tissue Res. 359, 111–124 (2015).

    CAS  Article  Google Scholar 

  35. Lesburguères, E. et al. Early tagging of cortical networks is required for the formation of enduring associative memory. Science 331, 924–928 (2011).

    Article  Google Scholar 

  36. Reijmers, L.G., Perkins, B.L., Matsuo, N. & Mayford, M. Localization of a stable neural correlate of associative memory. Science 317, 1230–1233 (2007).

    CAS  Article  Google Scholar 

  37. Garner, A.R. et al. Generation of a synthetic memory trace. Science 335, 1513–1516 (2012).

    CAS  Article  Google Scholar 

  38. Silva, A.J., Zhou, Y., Rogerson, T., Shobe, J. & Balaji, J. Molecular and cellular approaches to memory allocation in neural circuits. Science 326, 391–395 (2009).

    CAS  Article  Google Scholar 

  39. Ramirez, S. et al. Creating a false memory in the hippocampus. Science 341, 387–391 (2013).

    CAS  Article  Google Scholar 

  40. Park, C.S., Rehrauer, H. & Mansuy, I.M. Genome-wide analysis of H4K5 acetylation associated with fear memory in mice. BMC Genomics 14, 539 (2013).

    CAS  Article  Google Scholar 

  41. Bero, A.W. et al. Early remodeling of the neocortex upon episodic memory encoding. Proc. Natl. Acad. Sci. USA 111, 11852–11857 (2014).

    CAS  Article  Google Scholar 

  42. Heyward, F.D. & Sweatt, J.D. DNA methylation in memory formation: emerging insights. Neuroscientist 21, 475–489 (2015).

    CAS  Article  Google Scholar 

  43. Shukla, S. et al. CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing. Nature 479, 74–79 (2011).

    CAS  Article  Google Scholar 

  44. Fosque, B.F. et al. Neural circuits. Labeling of active neural circuits in vivo with designed calcium integrators. Science 347, 755–760 (2015).

    CAS  Article  Google Scholar 

  45. Peng, X. et al. Statistical implications of pooling RNA samples for microarray experiments. BMC Bioinformatics 4, 26 (2003).

    Article  Google Scholar 

  46. Kendziorski, C., Irizarry, R.A., Chen, K.S., Haag, J.D. & Gould, M.N. On the utility of pooling biological samples in microarray experiments. Proc. Natl. Acad. Sci. USA 102, 4252–4257 (2005).

    CAS  Article  Google Scholar 

  47. Kendziorski, C.M., Zhang, Y., Lan, H. & Attie, A.D. The efficiency of pooling mRNA in microarray experiments. Biostatistics 4, 465–477 (2003).

    CAS  Article  Google Scholar 

  48. Egelhofer, T.A. et al. An assessment of histone-modification antibody quality. Nat. Struct. Mol. Biol. 18, 91–93 (2011).

    CAS  Article  Google Scholar 

  49. Proudhon, C. et al. Protection against de novo methylation is instrumental in maintaining parent-of-origin methylation inherited from the gametes. Mol. Cell 47, 909–920 (2012).

    CAS  Article  Google Scholar 

  50. Bessa, J. et al. Zebrafish enhancer detection (ZED) vector: a new tool to facilitate transgenesis and the functional analysis of cis-regulatory regions in zebrafish. Dev. Dyn. 238, 2409–2417 (2009).

    CAS  Article  Google Scholar 

  51. Kimmel, C.B., Ballard, W.W., Kimmel, S.R., Ullmann, B. & Schilling, T.F. Stages of embryonic development of the zebrafish. Dev. Dyn. 203, 253–310 (1995).

    CAS  Article  Google Scholar 

  52. Andrews, S. FastQC A quality control tool for high throughput sequence data http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ (2010).

  53. Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).

    Article  Google Scholar 

  54. Lienhard, M., Grimm, C., Morkel, M., Herwig, R. & Chavez, L. MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments. Bioinformatics 30, 284–286 (2014).

    CAS  Article  Google Scholar 

  55. Capece, V. et al. Oasis: online analysis of small RNA deep sequencing data. Bioinformatics 31, 2205–2207 (2015).

    CAS  Article  Google Scholar 

  56. Landt, S.G. et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res. 22, 1813–1831 (2012).

    CAS  Article  Google Scholar 

  57. Salzberg, S.L. & Langmead, B. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).

    Article  Google Scholar 

  58. Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).

    CAS  Article  Google Scholar 

  59. Shen, L., Shao, N., Liu, X. & Nestler, E. ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases. BMC Genomics 15, 284 (2014).

    Article  Google Scholar 

  60. Love, M.I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).

    Article  Google Scholar 

  61. Wang, J., Duncan, D., Shi, Z. & Zhang, B. WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013. Nucleic Acids Res. 41, W77–W83 (2013).

    Article  Google Scholar 

  62. Rajagopal, N. et al. RFECS: a random-forest based algorithm for enhancer identification from chromatin state. PLoS Comput. Biol. 9, e1002968 (2013).

    CAS  Article  Google Scholar 

  63. Quinlan, A.R. & Hall, I.M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).

    CAS  Article  Google Scholar 

  64. Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).

    Article  Google Scholar 

  65. Song, Q. & Smith, A.D. Identifying dispersed epigenomic domains from ChIP-Seq data. Bioinformatics 27, 870–871 (2011).

    CAS  Article  Google Scholar 

  66. Anders, S., Reyes, A. & Huber, W. Detecting differential usage of exons from RNA-seq data. Genome Res. 22, 2008–2017 (2012).

    CAS  Article  Google Scholar 

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Acknowledgements

We would like to thank M. Boroomandi for help with the behavioral experiments. We would like to thank E.E. Furlong, A.G. Ladurner, C. Margulies, R.P. Zinzen and W. Jackson for critical reading of the manuscript. This work was supported by the DFG (BO4224/4-1) (S. Bonn), the Network of Centres of Excellence in Neurodegeneration (CoEN) initiative (S. Bonn and A.F.), iMed – the Helmholtz Initiative on Personalized Medicine (S. Bonn and A.F.), the EURYI Award of the ESF (A.F.), the Hans and Ilse Breuer Foundation (A.F.), and by the European Research Council under the European Union's Seventh Framework Program (FP7/2007–2013)/ ERC Grant Agreement No. 321366-Amyloid (advanced grant to C.H.).

Author information

Authors and Affiliations

Authors

Contributions

S. Bonn initiated the study and designed the experiments with A.F., R.H., M.H. and R.O.V. S. Burkhardt, M.N.S., R.H. and S.B.J. performed the behavioral experiments. F.v.B., C.H. and B.S. performed the zebrafish experiments. A.-L.S., S. Burkhardt, R.H. and M.H. were responsible for the library generation and sequencing of the samples. M.H., R.H., A.R. and E.B. conducted all other experiments and analyzed the data. R.O.V., O.S., R.-U.R., T.P.C., J.C.G.V., V.C., S. Bonn, R.H. and M.H. were responsible for the computational analysis of the data. S. Bonn, M.H. and R.O.V. wrote the manuscript. All of the authors read and approved the final manuscript.

Corresponding authors

Correspondence to Andre Fischer or Stefan Bonn.

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Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–30 (PDF 9692 kb)

Supplementary Methods Checklist (PDF 383 kb)

Supplementary Table 1: ChIP- and MeDIP-seq antibodies.

Detailed information on the antibodies used for ChIP- and MeDIP-seq experiments and their usage. (XLS 29 kb)

Supplementary Table 2: DEGs and DEEs.

Overview over all DEGs and DEEs for the different time-points, learning comparisons, and brain areas. Additional information on in vitro DEGs after KCl stimulation. (XLS 13418 kb)

Supplementary Table 3: Sequencing samples and quality.

Summarization of ChIP-, MeDIP-, and RNA-seq samples and their corresponding quality metrics. (XLS 88 kb)

Supplementary Table 4: Known cell type-specific genes.

Table containing the genes that were categorized as neuron- or glia-specific based on published information. (XLS 44 kb)

Supplementary Table 5: Predicted cell type-specific genes.

Table of the predicted cell-type specific genes in the CA1 and ACC, in neurons and non-neurons. (XLS 125 kb)

Supplementary Table 6: Predicted CRMs.

Table of the predicted cell-type specific CRMs in the CA1 and ACC, in neurons and non-neurons. (XLS 11301 kb)

Supplementary Table 7: Validated CRMs.

Detailed information on the CRMs that cloned and validated in Danio rerio enhancer assays. (XLS 53 kb)

Supplementary Table 8: Differential HPTMs.

Lists of genes containing DHPTMs for the in vivo and in vitro data and summary information. (XLS 158 kb)

Supplementary Table 9: Primer.

Table summarizing information of the ChIP, expression, and MeDIP qPCR primers used. (XLS 39 kb)

Supplementary Table 10: DHPTM-DEG overview.

Information on DHPTM-DEG comparisons for the different histone modifications, learning comparisons, and cell types. (XLS 57 kb)

Supplementary Table 11: DMRs and DMGs.

Overview over all DMRs for the different time-points, learning comparisons, brain areas, and cell types. (XLS 23253 kb)

Supplementary Table 12: DMG-DEG-DEE overview.

Information on DMG-DEG and DMG-DEE comparisons for the different time-points, learning comparisons, brain areas, and cell types. (XLS 430 kb)

Supplementary Data Set

Interactive Enrichment Files (ZIP 6838 kb)

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Halder, R., Hennion, M., Vidal, R. et al. DNA methylation changes in plasticity genes accompany the formation and maintenance of memory. Nat Neurosci 19, 102–110 (2016). https://doi.org/10.1038/nn.4194

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