Benito E, Barco A. The neuronal activity-driven transcriptome. Mol Neurobiol. 2015;51:1071–88.

Article  CAS  PubMed  Google Scholar 

Yap EL, Greenberg ME. Activity-regulated transcription: bridging the gap between neural activity and behavior. Neuron. 2018;100:330–48.

Brito DVC, Kupke J, Karaca KG, Zeuch B, Oliveira AMM. Mimicking age-associated Gadd45γ dysregulation results in memory impairments in young adult mice. J Neurosci. 2020;40:1197–210.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Alberini CM. Transcription factors in long-term memory and synaptic plasticity. Physiol Rev. 2009;89:121–45.

Article  CAS  PubMed  Google Scholar 

Alberini CM, Kandel ER. The regulation of transcription in memory consolidation. Cold Spring Harb Perspect Biol. 2015;7:a021741.

Article  PubMed Central  Google Scholar 

Cholewa-Waclaw J, Bird A, von Schimmelmann M, Schaefer A, Yu H, Song H, et al. The role of epigenetic mechanisms in the regulation of gene expression in the nervous system. J Neurosci. 2016;36:11427–34.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Day JJ, Sweatt JD. Epigenetic mechanisms in cognition. Neuron. 2011;70:813–29.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Oliveira AMM. DNA methylation: a permissive mark in memory formation and maintenance. Learn Mem. 2016;23:587–93.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Medrano-Fernández A, Barco A. Nuclear organization and 3D chromatin architecture in cognition and neuropsychiatric disorders. Mol Brain. 2016;9:83.

Article  PubMed  PubMed Central  Google Scholar 

Suzuki MM, Bird A. DNA methylation landscapes: provocative insights from epigenomics. Nat Rev Genet. 2008;9:465–76.

Article  CAS  PubMed  Google Scholar 

Halder R, Hennion M, Vidal RO, Shomroni O, Rahman RU, Rajput A, et al. DNA methylation changes in plasticity genes accompany the formation and maintenance of memory. Nat Neurosci. 2015;19:102–10.

Article  PubMed  Google Scholar 

Guo JU, Ma DK, Mo H, Ball MP, Jang MH, Bonaguidi MA, et al. Neuronal activity modifies the DNA methylation landscape in the adult brain. Nat Neurosci. 2011;14:1345–51.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Miller CA, Sweatt JD. Covalent modification of DNA regulates memory formation. Neuron. 2007;53:857–69.

Article  CAS  PubMed  Google Scholar 

Mitchnick KA, Creighton S, O’Hara M, Kalisch BE, Winters BD. Differential contributions of de novo and maintenance DNA methyltransferases to object memory processing in the rat hippocampus and perirhinal cortex - a double dissociation. Eur J Neurosci. 2015;41:773–86.

Article  PubMed  Google Scholar 

Feng J, Zhou Y, Campbell SL, Le T, Li E, Sweatt JD, et al. Dnmt1 and Dnmt3a maintain DNA methylation and regulate synaptic function in adult forebrain neurons. Nat Neurosci. 2010;13:423–30.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Morris MJ, Adachi M, Na ES, Monteggia LM. Selective role for DNMT3a in learning and memory. Neurobiol Learn Mem. 2014;115:30–7.

Article  CAS  PubMed  Google Scholar 

Zocher S, Overall RW, Berdugo‐Vega G, Rund N, Karasinsky A, Adusumilli VS, et al. De novo DNA methylation controls neuronal maturation during adult hippocampal neurogenesis. EMBO J. 2021;40:e107100.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Tatton-Brown K, Zachariou A, Loveday C, Renwick A, Mahamdallie S, Aksglaede L, et al. The Tatton-Brown-Rahman syndrome: a clinical study of 55 individuals with de novo constitutive DNMT3A variants. Wellcome Open Res. 2018;3:46.

Article  PubMed  PubMed Central  Google Scholar 

Tatton-Brown K, Seal S, Ruark E, Harmer J, Ramsay E, del Vecchio Duarte S, et al. Mutations in the DNA methyltransferase gene DNMT3A cause an overgrowth syndrome with intellectual disability. Nat Genet. 2014;46:385–8.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chen T, Ueda Y, Xie S, Li E. A Novel Dnmt3a isoform produced from an alternative promoter localizes to euchromatin and its expression correlates with activede novo methylation. J Biol Chem. 2002;277:38746–54.

Article  CAS  PubMed  Google Scholar 

Manzo M, Wirz J, Ambrosi C, Villaseñor R, Roschitzki B, Baubec T. Isoform‐specific localization of DNMT3A regulates DNA methylation fidelity at bivalent CpG islands. EMBO J. 2017;36:3421–34.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bayraktar G, Yuanxiang PA, Confettura AD, Gomes GM, Raza SA, Stork O, et al. Synaptic control of DNA methylation involves activity-dependent degradation of DNMT3A1 in the nucleus. Neuropsychopharmacology. 2020;45:2120–30.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Oliveira AMM, Hemstedt TJ, Bading H. Rescue of aging-associated decline in Dnmt3a2 expression restores cognitive abilities. Nat Neurosci. 2012;15:1111–3.

Article  CAS  PubMed  Google Scholar 

Oliveira AMM, Hemstedt TJ, Freitag HE, Bading H. Dnmt3a2: a hub for enhancing cognitive functions. Mol Psychiatry. 2016;21:1130–6.

Article  CAS  PubMed  Google Scholar 

Gulmez Karaca K, Kupke J, Brito DVC, Zeuch B, Thome C, Weichenhan D, et al. Neuronal ensemble-specific DNA methylation strengthens engram stability. Nat Commun. 2020;11:639.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Feng J, Chang H, Li E, Fan G. Dynamic expression of de novo DNA methyltransferases Dnmt3a and Dnmt3b in the central nervous system. J Neurosci Res. 2005;79:734–46.

Article  CAS  PubMed  Google Scholar 

Guo JU, Szulwach KE, Su Y, Li Y, Yao B, Xu Z, et al. Genome-wide antagonism between 5-hydroxymethylcytosine and DNA methylation in the adult mouse brain. Front Biol. 2014;9:66–74.

Article  CAS  Google Scholar 

Gu T, Hao D, Woo J, Huang TW, Guo L, Lin X, et al. The disordered N-terminal domain of DNMT3A recognizes H2AK119ub and is required for postnatal development. Nat Genet. 2022;54:625–36.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Oliveira AM, Litke C, Paldy E, Hagenston AM, Lu J, Kuner R, et al. Epigenetic control of hypersensitivity in chronic inflammatory pain by the de novo DNA methyltransferase Dnmt3a2. Mol Pain. 2019;15:174480691982746.

Article  Google Scholar 

Cannella N, Oliveira AMM, Hemstedt T, Lissek T, Buechler E, Bading H, et al. Dnmt3a2 in the nucleus accumbens shell is required for reinstatement of cocaine seeking. J Neurosci. 2018;38:7516–28.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Carulli D, de Winter F, Verhaagen J. Semaphorins in adult nervous system plasticity and disease. Front Synaptic Neurosci. 2021;13:672891.

Pasterkamp RJ. Getting neural circuits into shape with semaphorins. Nat Rev Neurosci. 2012;13:605–18.

Article  CAS  PubMed  Google Scholar 

Gulmez Karaca K, Brito DVC, Kupke J, Zeuch B, Oliveira AMM. Engram reactivation during memory retrieval predicts long-term memory performance in aged mice. Neurobiol Aging. 2021;101:256–61.

Article  PubMed  Google Scholar 

Stegmeier F, Hu G, Rickles RJ, Hannon GJ, Elledge SJ. A lentiviral microRNA-based system for single-copy polymerase II-regulated RNA interference in mammalian cells. Proc Natl Acad Sci USA. 2005;102:13212–7.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zhang Z, Ferretti V, Güntan I, Moro A, Steinberg EA, Ye Z, et al. Neuronal ensembles sufficient for recovery sleep and the sedative actions of α 2 adrenergic agonists. Nat Neurosci. 2015;18:553–61.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Brito DVC, Gulmez Karaca K, Kupke J, Frank L, Oliveira AMM. MeCP2 gates spatial learning-induced alternative splicing events in the mouse hippocampus. Mol Brain. 2020;13:156.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bray NL, Pimentel H, Melsted P, Pachter L. Near-optimal probabilistic RNA-seq quantification. Nat Biotechnol. 2016;34:525–7.

Article  CAS  PubMed  Google Scholar 

Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, et al. Limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43:e47.