Bading, H., 2013. Nuclear calcium signalling in the regulation of brain function. Nat Rev Neurosci 14, 593–608. https://doi.org/10.1038/nrn3531
Bito, H., Deisseroth, K., Tsien, R.W., 1996. CREB Phosphorylation and Dephosphorylation: A Ca2+- and Stimulus Duration–Dependent Switch for Hippocampal Gene Expression. Cell 87, 1203–1214. https://doi.org/10.1016/S0092-8674(00)81816-4
Borrelli, E., Nestler, E.J., Allis, C.D., Sassone-Corsi, P., 2008. Decoding the Epigenetic Language of Neuronal Plasticity. Neuron 60, 961–974. https://doi.org/10.1016/j.neuron.2008.10.012
Brami-Cherrier, K., Lavaur, J., Pagès, C., Arthur, J.S.C., Caboche, J., 2006. Glutamate induces histone H3 phosphorylation but not acetylation in striatal neurons: role of mitogen- and stress-activated kinase-1: MSK1 and nucleosomal response in neurons. Journal of Neurochemistry 101, 697–708. https://doi.org/10.1111/j.1471-4159.2006.04352.x
Chen, C.-C., Wada, K., Jarvis, E.D., 2012. Radioactive in situ Hybridization for Detecting Diverse Gene Expression Patterns in Tissue. JoVE 3764. https://doi.org/10.3791/3764
Chen, L.-F., Zhou, A.S., West, A.E., 2017. Transcribing the connectome: roles for transcription factors and chromatin regulators in activity-dependent synapse development. Journal of Neurophysiology 118, 755–770. https://doi.org/10.1152/jn.00067.2017
Deal, R.B., Henikoff, J.G., Henikoff, S., 2010. Genome-Wide Kinetics of Nucleosome Turnover Determined by Metabolic Labeling of Histones. Science 328, 1161–1164. https://doi.org/10.1126/science.1186777
Deaton, A.M., Gómez-Rodríguez, M., Mieczkowski, J., Tolstorukov, M.Y., Kundu, S., Sadreyev, R.I., Jansen, L.E., Kingston, R.E., 2016. Enhancer regions show high histone H3.3 turnover that changes during differentiation. eLife 5, e15316. https://doi.org/10.7554/eLife.15316
Dominski, Z., Marzluff, W.F., 1999. Formation of the 3′ end of histone mRNA. Gene 239, 1–14. https://doi.org/10.1016/S0378-1119(99)00367-4
Goldberg, A.D., Banaszynski, L.A., Noh, K.-M., Lewis, P.W., Elsaesser, S.J., Stadler, S., Dewell, S., Law, M., Guo, X., Li, X., Wen, D., Chapgier, A., DeKelver, R.C., Miller, J.C., Lee, Y.-L., Boydston, E.A., Holmes, M.C., Gregory, P.D., Greally, J.M., Rafii, S., Yang, C., Scambler, P.J., Garrick, D., Gibbons, R.J., Higgs, D.R., Cristea, I.M., Urnov, F.D., Zheng, D., Allis, C.D., 2010. Distinct Factors Control Histone Variant H3.3 Localization at Specific Genomic Regions. Cell 140, 678–691. https://doi.org/10.1016/j.cell.2010.01.003
Greer, P.L., Greenberg, M.E., 2008. From Synapse to Nucleus: Calcium- Dependent Gene Transcription in the Control of Synapse Development and Function. Neuron 59, 846–860. https://doi.org/10.1016/j.neuron.2008.09.002
Hamilton, A.M., Oh, W.C., Vega-Ramirez, H., Stein, I.S., Hell, J.W., Patrick, G.N., Zito, K., 2012. Activity-Dependent Growth of New Dendritic Spines Is Regulated by the Proteasome. Neuron 74, 1023–1030. https://doi.org/10.1016/j.neuron.2012.04.031
Hammond, C.M., Strømme, C.B., Huang, H., Patel, D.J., Groth, A., 2017. Histone chaperone networks shaping chromatin function. Nat Rev Mol Cell Biol 18, 141–158. https://doi.org/10.1038/nrm.2016.159
Harada, A., Okada, S., Konno, D., Odawara, J., Yoshimi, T., Yoshimura, S., Kumamaru, H., Saiwai, H., Tsubota, T., Kurumizaka, H., Akashi, K., Tachibana, T., Imbalzano, A.N., Ohkawa, Y., 2012. Chd2 interacts with H3.3 to determine myogenic cell fate: Chd2 incorporates H3.3 to mark myogenic genes. The EMBO Journal 31, 2994–3007. https://doi.org/10.1038/emboj.2012.136
Hardingham, G.E., Arnold, F.J.L., Bading, H., 2001. Nuclear calcium signaling controls CREB-mediated gene expression triggered by synaptic activity. Nat Neurosci 4, 261–267. https://doi.org/10.1038/85109
Hardingham, G.E., Pruunsild, P., Greenberg, M.E., Bading, H., 2018. Lineage divergence of activity-driven transcription and evolution of cognitive ability. Nat Rev Neurosci 19, 9–15. https://doi.org/10.1038/nrn.2017.138
Henikoff, S., Smith, M.M., 2015. Histone Variants and Epigenetics. Cold Spring Harb Perspect Biol 7, a019364. https://doi.org/10.1101/cshperspect.a019364
Hong, E.J., McCord, A.E., Greenberg, M.E., 2008. A Biological Function for the Neuronal Activity-Dependent Component of Bdnf Transcription in the Development of Cortical Inhibition. Neuron 60, 610–624. https://doi.org/10.1016/j.neuron.2008.09.024
Horita, H., Kobayashi, M., Liu, W., Oka, K., Jarvis, E.D., Wada, K., 2012. Specialized Motor-Driven dusp1 Expression in the Song Systems of Multiple Lineages of Vocal Learning Birds. PLoS ONE 7, e42173. https://doi.org/10.1371/journal.pone.0042173
Horita, H., Wada, K., Rivas, M., Hara, E., Jarvis, E.D., 2010. The dusp1 immediate early gene is regulated by natural stimuli predominantly in sensory input neurons. J. Comp. Neurol. NA-NA. https://doi.org/10.1002/cne.22370
Impey, S., Fong, A.L., Wang, Y., Cardinaux, J.-R., Fass, D.M., Obrietan, K., Wayman, G.A., Storm, D.R., Soderling, T.R., Goodman, R.H., 2002. Phosphorylation of CBP Mediates Transcriptional Activation by Neural Activity and CaM Kinase IV. Neuron 34, 235–244. https://doi.org/10.1016/S0896- 6273(02)00654-2
Kaech, S., Banker, G., 2006. Culturing hippocampal neurons. Nat Protoc 1, 2406–2415. https://doi.org/10.1038/nprot.2006.356
Kobor et al_2004_A Protein Complex Containing the Conserved Swi2-Snf2- Related ATPase Swr1p.pdf, n.d.
Kornhauser, J.M., Cowan, C.W., Shaywitz, A.J., Dolmetsch, R.E., Griffith, E.C., Hu, L.S., Haddad, C., Xia, Z., Greenberg, M.E., 2002. CREB
Transcriptional Activity in Neurons Is Regulated by Multiple, Calcium-Specific Phosphorylation Events. Neuron 34, 221–233. https://doi.org/10.1016/S0896-6273(02)00655-4
Lyons, S.M., Cunningham, C.H., Welch, J.D., Groh, B., Guo, A.Y., Wei, B., Whitfield, M.L., Xiong, Y., Marzluff, W.F., 2016. A subset of replication- dependent histone mRNAs are expressed as polyadenylated RNAs in terminally differentiated tissues. Nucleic Acids Res gkw620. https://doi.org/10.1093/nar/gkw620
Ma et al_2009_Neuronal Activity-Induced Gadd45b Promotes Epigenetic DNA Demethylation and.pdf, n.d.
Malgaroli 1992 -Glutamate-induced long-term potentiation of the frequency of miniature synaptic currents in cultured hippocampal neurons, n.d.
Martire, S., Banaszynski, L.A., 2020. The roles of histone variants in fine- tuning chromatin organization and function. Nat Rev Mol Cell Biol 21, 522–541. https://doi.org/10.1038/s41580-020-0262-8
Marzluff, W.F., Gongidi, P., Woods, K.R., Jin, J., Maltais, L.J., 2002. The Human and Mouse Replication-Dependent Histone Genes. Genomics 80, 487–498. https://doi.org/10.1006/geno.2002.6850
Marzluff, W.F., Wagner, E.J., Duronio, R.J., 2008. Metabolism and regulation of canonical histone mRNAs: life without a poly(A) tail. Nat Rev Genet 9, 843– 854. https://doi.org/10.1038/nrg2438
Maze, I., Wenderski, W., Noh, K.-M., Bagot, R.C., Tzavaras, N., Purushothaman, I., Elsässer, S.J., Guo, Y., Ionete, C., Hurd, Y.L., Tamminga, C.A., Halene, T., Farrelly, L., Soshnev, A.A., Wen, D., Rafii, S., Birtwistle, M.R., Akbarian, S., Buchholz, B.A., Blitzer, R.D., Nestler, E.J., Yuan, Z.-F., Garcia, B.A., Shen, L., Molina, H., Allis, C.D., 2015. Critical Role of Histone Turnover in Neuronal Transcription and Plasticity. Neuron 87, 77–94. https://doi.org/10.1016/j.neuron.2015.06.014
Meshorer, E., Yellajoshula, D., George, E., Scambler, P.J., Brown, D.T., Misteli, T., 2006. Hyperdynamic Plasticity of Chromatin Proteins in Pluripotent Embryonic Stem Cells. Developmental Cell 10, 105–116. https://doi.org/10.1016/j.devcel.2005.10.017
Michod, D., Bartesaghi, S., Khelifi, A., Bellodi, C., Berliocchi, L., Nicotera, P., Salomoni, P., 2012. Calcium-Dependent Dephosphorylation of the Histone Chaperone DAXX Regulates H3.3 Loading and Transcription upon Neuronal Activation. Neuron 74, 122–135. https://doi.org/10.1016/j.neuron.2012.02.021
Pandey, N.B., Chodchoy, N., Liu, T.-J., Marzluff, W.F., 1990. Introns in histone genes alter the distribution of 3′ ends. Nucl Acids Res 18, 3161–3170. https://doi.org/10.1093/nar/18.11.3161
Piña, B., Suau, P., 1987. Changes in histones H2A and H3 variant composition in differentiating and mature rat brain cortical neurons. Developmental Biology 123, 51–58. https://doi.org/10.1016/0012-1606(87)90426-X
Ray-Gallet, D., Quivy, J.-P., Scamps, C., Martini, E.M.-D., Lipinski, M., Almouzni, G., 2002. HIRA Is Critical for a Nucleosome Assembly Pathway Independent of DNA Synthesis. Molecular Cell 9, 1091–1100. https://doi.org/10.1016/S1097-2765(02)00526-9
Santoro, S.W., Dulac, C., 2012. The activity-dependent histone variant H2BE modulates the life span of olfactory neurons. eLife 1, e00070. https://doi.org/10.7554/eLife.00070
Tachiwana, H., Kagawa, W., Osakabe, A., Kawaguchi, K., Shiga, T., Hayashi- Takanaka, Y., Kimura, H., Kurumizaka, H., 2010. Structural basis of instability of the nucleosome containing a testis-specific histone variant, human H3T. Proceedings of the National Academy of Sciences 107, 10454–10459. https://doi.org/10.1073/pnas.1003064107
Tagami, H., Ray-Gallet, D., Almouzni, G., Nakatani, Y., 2004. Histone H3.1 and H3.3 Complexes Mediate Nucleosome Assembly Pathways Dependent or Independent of DNA Synthesis. Cell 116, 51–61. https://doi.org/10.1016/S0092- 8674(03)01064-X
Talbert, P.B., Ahmad, K., Almouzni, G., Ausió, J., Berger, F., Bhalla, P.L., Bonner, W.M., Cande, W., Chadwick, B.P., Chan, S.W.L., Cross, G.A.M., Cui, L., Dimitrov, S.I., Doenecke, D., Eirin-López, J.M., Gorovsky, M.A., Hake, S.B., Hamkalo, B.A., Holec, S., Jacobsen, S.E., Kamieniarz, K., Khochbin, S., Ladurner, A.G., Landsman, D., Latham, J.A., Loppin, B., Malik, H.S., Marzluff, W.F., Pehrson, J.R., Postberg, J., Schneider, R., Singh, M.B., Smith, M., Thompson, E., Torres-Padilla, M.-E., Tremethick, D., Turner, B.M., Waterborg, J., Wollmann, H., Yelagandula, R., Zhu, B., Henikoff, S., 2012. A unified phylogeny- based nomenclature for histone variants. Epigenetics & Chromatin 5, 7. https://doi.org/10.1186/1756-8935-5-7
Tropberger, P., Pott, S., Keller, C., Kamieniarz-Gdula, K., Caron, M., Richter, F., Li, G., Mittler, G., Liu, E.T., Bühler, M., Margueron, R., Schneider, R., 2013. Regulation of Transcription through Acetylation of H3K122 on the Lateral Surface of the Histone Octamer. Cell 152, 859–872. https://doi.org/10.1016/j.cell.2013.01.032
Tvardovskiy, A., Schwämmle, V., Kempf, S.J., Rogowska-Wrzesinska, A., Jensen, O.N., 2017. Accumulation of histone variant H3.3 with age is associated with profound changes in the histone methylation landscape. Nucleic Acids Research 45, 9272–9289. https://doi.org/10.1093/nar/gkx696
West, A.E., Greenberg, M.E., 2011. Neuronal Activity-Regulated Gene Transcription in Synapse Development and Cognitive Function. Cold Spring Harbor Perspectives in Biology 3, a005744–a005744. https://doi.org/10.1101/cshperspect.a005744
Wright, W.E., Shay, J.W., 2006. Inexpensive low-oxygen incubators. Nat Protoc 1, 2088–2090. https://doi.org/10.1038/nprot.2006.374
Yamasu’, K., 1990. Units of H3 and H4 Histones. J. Biochem. 107, 6.
Yap, E.-L., Greenberg, M.E., 2018. Activity-Regulated Transcription: Bridging the Gap between Neural Activity and Behavior. Neuron 100, 330–348. https://doi.org/10.1016/j.neuron.2018.10.013
Zovkic, I.B., Paulukaitis, B.S., Day, J.J., Etikala, D.M., Sweatt, J.D., 2014. Histone H2A.Z subunit exchange controls consolidation of recent and remote memory. Nature 515, 582–586. https://doi.org/10.1038/nature13707