International Journal of Molecular Sciences Review Epigenetic Mechanisms of Learning and Memory: Implications for Aging 1 1 2 1,2, , Samantha D. Creighton , Gilda Stefanelli , Anas Reda and Iva B. Zovkic * y 1 Department of Psychology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada; [email protected] (S.D.C.); [email protected] (G.S.) 2 Department of Cell & Systems Biology, University of Toronto, Toronto, ON M5S, Canada; [email protected] * Correspondence: [email protected] Assistant Professor, Canada Research Chair in Behavioural Epigenetics, University of Toronto Mississauga, y Mississauga, ON L5L 1C6, Canada. Received: 28 August 2020; Accepted: 17 September 2020; Published: 21 September 2020 Abstract: The neuronal epigenome is highly sensitive to external events and its function is vital for producing stable behavioral outcomes, such as the formation of long-lasting memories. The importance of epigenetic regulation in memory is now well established and growing evidence points to altered epigenome function in the aging brain as a contributing factor to age-related memory decline. In this review, we first summarize the typical role of epigenetic factors in memory processing in a healthy young brain, then discuss the aspects of this system that are altered with aging. There is general agreement that many epigenetic marks are modified with aging, but there are still substantial inconsistencies in the precise nature of these changes and their link with memory decline. Here, we discuss the potential source of age-related changes in the epigenome and their implications for therapeutic intervention in age-related cognitive decline. Keywords: epigenetics; aging; memory; brain 1. Introduction Memory formation is a core feature of neuroplasticity that allows transient events to produce long-lasting changes in the brain and behavior. The establishment of long-lasting memories requires extensive cellular and molecular changes in brain regions associated with memory formation and maintenance. Some of the best understood molecular markers of memory involve changes in protein synthesis and gene expression [1,2], but their transient nature has initiated a search for more stable molecular markers that can persist for the duration of the memory, particularly epigenetics. Epigenetic mechanisms in general and DNA methylation in particular, have long been studied as self-perpetuating mechanisms for maintaining cellular identity over cycles of cell division and as such, epigenetics was hypothesized to represent a way for our brain to store memories over time [3–6]. In this review, we describe the evolving understanding of epigenetics in memory by exploring the complementary role these mechanisms play in transient adaptation to changing environmental stimuli, as well as stable changes involved in memory maintenance. Furthermore, we discuss how epigenetic factors are altered with aging and their emerging role as therapeutic targets for age-related cognitive decline. Int. J. Mol. Sci. 2020, 21, 6918; doi:10.3390/ijms21186918 www.mdpi.com/journal/ijms Int. J. Mol. Sci. 2020, 21, 6918 2 of 28 2. A Brief Review of Epigenetic Modifications 2.1. Chromatin Structure Int. J. DNAMol. Sci. is 2020 packaged, 21, x FOR into PEER the REVIEW nucleus by wrapping in 147 base pair segments around a complex2 of of29 eight histone proteins from four histone families: two each of histones H2A, H2B, H3, and H4 [7,8]. histone–DNA complex forms nucleosomes, which serve as building blocks of chromatin that create a This histone–DNA complex forms nucleosomes, which serve as building blocks of chromatin that create physical barrier to transcriptional machinery. The effect of chromatin on transcription is influenced by a physical barrier to transcriptional machinery. The effect of chromatin on transcription is influenced enzymes that write, read, and erase various epigenetic modifications to either promote or repress by enzymes that write, read, and erase various epigenetic modifications to either promote or repress transcription, thus conferring a vital regulatory function for gene transcription. Specifically, “writer” transcription, thus conferring a vital regulatory function for gene transcription. Specifically, “writer” enzymes catalyze the addition of epigenetic marks on histone tails or DNA, whereas “eraser” enzymes enzymes catalyze the addition of epigenetic marks on histone tails or DNA, whereas “eraser” enzymes remove these epigenetic marks. In contrast, “reader” proteins interact with the already established remove these epigenetic marks. In contrast, “reader” proteins interact with the already established epigenetic marks to initiate downstream effects by recruiting diverse interaction partners, or epigenetic marks to initiate downstream effects by recruiting diverse interaction partners, or chromatin chromatin remodeling machinery that further regulates chromatin structure and function [9,10]. remodeling machinery that further regulates chromatin structure and function [9,10]. 2.2. DNA Methylation and Demethylation DNA methylationmethylation is the additionaddition of aa methylmethyl groupgroup fromfrom S-adenosylS-adenosyl methioninemethionine (SAM) to thethe 5′position of a cytosine ring, typically adjacent to a guanine (CpG), to form 5-Methylcytosine (5mC) 50position of a cytosine ring, typically adjacent to a guanine (CpG), to form 5-Methylcytosine (5mC) [11]. However,[11]. However, recent recent evidence evidence has shown has shown that methylationthat methylation is not is restrictednot restricted to CpGs to CpGs and and can can also also occur occur on cytosineson cytosines adjacent adjacent to otherto other nucleotides, nucleotides, particularly particular inly tissuesin tissues with with low low cellular cellular turnover turnover rates, rates, such such as theas the brain brain [12 [12].]. DNA DNA methylation methylation is is catalyzed catalyzed by by DNA DNA methyltransferases methyltransferases (DNMTs),(DNMTs), enzymesenzymes thatthat belong toto a conceptual category of epigenetic “writers”“writers” that establish or lay downdown epigeneticepigenetic marksmarks [[13]13] (Figure(Figure1 1).). WhereasWhereas dede novonovo DNMTsDNMTs (DNMT (DNMT 3a 3a and and 3b) 3b) establish establish new new methyl methyl marks, marks, maintenance maintenance DNMTs (DNMT1) methylate methylate the the complementary complementary DNA DNA stra strandnd in dividing in dividing cells cellsto perpetuate to perpetuate the mark the markacross across cell divisions, cell divisions, thus underlying thus underlying one form one formof cellular of cellular memory memory [13]. DNA [13]. DNA methylation methylation has been has beenmost mostclosely closely associated associated with transcriptional with transcriptional repression repression through throughthe recruitment the recruitment of chromatin of chromatinregulators regulatorsthat promote that a closed promote chromatin a closed state, chromatin as well state, as steric as wellinterference as steric with interference transcription with factor transcription binding factor[14,15]. binding Although [14 some,15]. Althoughevidence points some to evidence a potent pointsially permissive to a potentially role of permissive5mC on transcription role of 5mC when on transcriptionit occurs in specific when genomic it occurs loci in specific[16], it is genomicstill predominantly loci [16], it associated is still predominantly with negative associated transcriptional with negativeregulation transcriptional [17]. regulation [17]. Figure 1. Schematic representation of methylation and de-methylation. Cytosines in the 50 position areFigure methylated 1. Schematic by DNA representation methyltransferases of methylation (DNMTs) and to producede-methylation. 5mC. Ten-eleven Cytosines translocation in the 5′ position (TET) enzymesare methylated mediate by severalDNA methyltransferases oxidation steps to (DNMTs) produce to 5hmC, produce 5fC 5mC. and 5caC, Ten-eleven which translocation can undergo (TET) base excisionenzymes repair mediate (BER), several in which oxidation modified steps cytosine to prod isuce replaced 5hmC, by 5fC an and unmethylated 5caC, which cytosine, can undergo resulting base in activeexcision de-methylation. repair (BER), in which modified cytosine is replaced by an unmethylated cytosine, resulting in active de-methylation. Based on evidence that DNA methylation is reversible in the brain [18], there has been extensive effortBased to identify on evidence mechanisms that DNA of DNA methylation de-methylation. is revers Inible 2009, in ten-eleventhe brain [18], translocation there has (TET)been extensive enzymes wereeffort identifiedto identify as mechanisms enzymes that of DNA bind methylatedde-methylati cytosineson. In 2009, (5mC) ten-eleven and catalyze translocation their conversion (TET) enzymes into hydroxymethylcytosinewere identified as enzymes (5hmC), that bind which methylated can be further cytosines deaminated (5mC) and to catalyze 5-hydroxymethyluracil their conversion andinto convertedhydroxymethylcytosine back to an unmethylated (5hmC), wh cytosineich can via be glycolysis-dependent further deaminated nucleotide to 5-hydroxymethyluracil excision repair [19 ,and20] converted back to an unmethylated cytosine via glycolysis-dependent nucleotide excision repair [19,20] (Figure 1). Both TETs and DNMTs are particularly abundant in neurons, where active methylation and de-methylation occurs during learning [21]. Although a majority of early studies focused on 5mC,