DNA methylation changes in plasticity genes accompany the formation and maintenance of memory (original) (raw)

• 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).
  Article CAS Google Scholar
• Gräff, J. & Tsai, L.-H. Histone acetylation: molecular mnemonics on the chromatin. Nat. Rev. Neurosci. 14, 97–111 (2013).
  Article Google Scholar
• Zovkic, I.B., Guzman-Karlsson, M.C. & Sweatt, J.D. Epigenetic regulation of memory formation and maintenance. Learn. Mem. 20, 61–74 (2013).
  Article CAS Google Scholar
• Sweatt, J.D. The emerging field of neuroepigenetics. Neuron 80, 624–632 (2013).
  Article CAS Google Scholar
• Lopez-Atalaya, J.P. & Barco, A. Can changes in histone acetylation contribute to memory formation? Trends Genet. 30, 529–539 (2014).
  Article CAS Google Scholar
• Levenson, J.M. et al. Regulation of histone acetylation during memory formation in the hippocampus. J. Biol. Chem. 279, 40545–40559 (2004).
  Article CAS Google Scholar
• Gupta, S. et al. Histone methylation regulates memory formation. J. Neurosci. 30, 3589–3599 (2010).
  Article CAS Google Scholar
• Miller, C.A. & Sweatt, J.D. Covalent modification of DNA regulates memory formation. Neuron 53, 857–869 (2007).
  Article CAS Google Scholar
• Miller, C.A. et al. Cortical DNA methylation maintains remote memory. Nat. Neurosci. 13, 664–666 (2010).
  Article CAS Google Scholar
• Strahl, B.D. & Allis, C.D. The language of covalent histone modifications. Nature 403, 41–45 (2000).
  Article CAS Google Scholar
• Day, J.J. & Sweatt, J.D. Epigenetic mechanisms in cognition. Neuron 70, 813–829 (2011).
  Article CAS Google Scholar
• Fischer, A. Epigenetic memory: the Lamarckian brain. EMBO J. 33, 945–967 (2014).
  Article CAS Google Scholar
• Fanselow, M.S. Factors governing one-trial contextual conditioning. Anim. Learn. Behav. 18, 264–270 (1990).
  Article Google Scholar
• Kim, J.J. & Fanselow, M.S. Modality-specific retrograde amnesia of fear. Science 256, 675–677 (1992).
  Article CAS Google Scholar
• 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).
  Article CAS Google Scholar
• 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
• 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).
  Article CAS Google Scholar
• Bonn, S. et al. Cell type-specific chromatin immunoprecipitation from multicellular complex samples using BiTS-ChIP. Nat. Protoc. 7, 978–994 (2012).
  Article CAS Google Scholar
• 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
• Peleg, S. et al. Altered histone acetylation is associated with age-dependent memory impairment in mice. Science 328, 753–756 (2010).
  Article CAS Google Scholar
• Barski, A. et al. High-resolution profiling of histone methylations in the human genome. Cell 129, 823–837 (2007).
  Article CAS Google Scholar
• 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
• 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).
  Article CAS Google Scholar
• 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).
  Article CAS Google Scholar
• Guo, J.U. et al. Neuronal activity modifies the DNA methylation landscape in the adult brain. Nat. Neurosci. 14, 1345–1351 (2011).
  Article CAS Google Scholar
• Guo, J.U. et al. Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brain. Nat. Neurosci. 17, 215–222 (2014).
  Article CAS Google Scholar
• Lister, R. et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462, 315–322 (2009).
  Article CAS Google Scholar
• Kim, T.-K. et al. Widespread transcription at neuronal activity-regulated enhancers. Nature 465, 182–187 (2010).
  Article CAS Google Scholar
• Malik, A.N. et al. Genome-wide identification and characterization of functional neuronal activity-dependent enhancers. Nat. Neurosci. 17, 1330–1339 (2014).
  Article CAS Google Scholar
• Heintzman, N.D. et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459, 108–112 (2009).
  Article CAS Google Scholar
• 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).
  Article CAS Google Scholar
• Gao, Z. et al. Neurod1 is essential for the survival and maturation of adult-born neurons. Nat. Neurosci. 12, 1090–1092 (2009).
  Article CAS Google Scholar
• 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).
  Article CAS Google Scholar
• Reiprich, S. & Wegner, M. From CNS stem cells to neurons and glia: Sox for everyone. Cell Tissue Res. 359, 111–124 (2015).
  Article CAS Google Scholar
• 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
• Reijmers, L.G., Perkins, B.L., Matsuo, N. & Mayford, M. Localization of a stable neural correlate of associative memory. Science 317, 1230–1233 (2007).
  Article CAS Google Scholar
• Garner, A.R. et al. Generation of a synthetic memory trace. Science 335, 1513–1516 (2012).
  Article CAS Google Scholar
• 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).
  Article CAS Google Scholar
• Ramirez, S. et al. Creating a false memory in the hippocampus. Science 341, 387–391 (2013).
  Article CAS Google Scholar
• 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).
  Article CAS Google Scholar
• Bero, A.W. et al. Early remodeling of the neocortex upon episodic memory encoding. Proc. Natl. Acad. Sci. USA 111, 11852–11857 (2014).
  Article CAS Google Scholar
• Heyward, F.D. & Sweatt, J.D. DNA methylation in memory formation: emerging insights. Neuroscientist 21, 475–489 (2015).
  Article CAS Google Scholar
• Shukla, S. et al. CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing. Nature 479, 74–79 (2011).
  Article CAS Google Scholar
• Fosque, B.F. et al. Neural circuits. Labeling of active neural circuits in vivo with designed calcium integrators. Science 347, 755–760 (2015).
  Article CAS Google Scholar
• Peng, X. et al. Statistical implications of pooling RNA samples for microarray experiments. BMC Bioinformatics 4, 26 (2003).
  Article Google Scholar
• 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).
  Article CAS Google Scholar
• Kendziorski, C.M., Zhang, Y., Lan, H. & Attie, A.D. The efficiency of pooling mRNA in microarray experiments. Biostatistics 4, 465–477 (2003).
  Article CAS Google Scholar
• Egelhofer, T.A. et al. An assessment of histone-modification antibody quality. Nat. Struct. Mol. Biol. 18, 91–93 (2011).
  Article CAS Google Scholar
• 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).
  Article CAS Google Scholar
• 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).
  Article CAS Google Scholar
• 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).
  Article CAS Google Scholar
• Andrews, S. FastQC A quality control tool for high throughput sequence data http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ (2010).
• Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
  Article Google Scholar
• 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).
  Article CAS Google Scholar
• Capece, V. et al. Oasis: online analysis of small RNA deep sequencing data. Bioinformatics 31, 2205–2207 (2015).
  Article CAS Google Scholar
• Landt, S.G. et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res. 22, 1813–1831 (2012).
  Article CAS Google Scholar
• Salzberg, S.L. & Langmead, B. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
  Article Google Scholar
• Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).
  Article CAS Google Scholar
• 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
• 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
• 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
• Rajagopal, N. et al. RFECS: a random-forest based algorithm for enhancer identification from chromatin state. PLoS Comput. Biol. 9, e1002968 (2013).
  Article CAS Google Scholar
• Quinlan, A.R. & Hall, I.M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).
  Article CAS Google Scholar
• Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).
  Article Google Scholar
• Song, Q. & Smith, A.D. Identifying dispersed epigenomic domains from ChIP-Seq data. Bioinformatics 27, 870–871 (2011).
  Article CAS Google Scholar
• Anders, S., Reyes, A. & Huber, W. Detecting differential usage of exons from RNA-seq data. Genome Res. 22, 2008–2017 (2012).
  Article CAS Google Scholar