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Experimental Neurology xxx (2014) xxxxxx
Experimental Neurology
journal homepage: www.elsevier.com/locate/yexnr
Review
a r t i c l e
i n f o
Article history:
Received 26 February 2014
Revised 26 April 2014
Accepted 2 May 2014
Available online xxxx
Keywords:
Epigenetics
Synaptic plasticity
Memory formation
Memory maintenance
a b s t r a c t
The formation of long-term memory involves a series of molecular and cellular changes, including gene transcription, protein synthesis and synaptic plasticity dynamics. Some of these changes arise during learning and are subsequently retained throughout life. Epigenetic regulation, which involves DNA methylation and histone
modications, plays a critical role in retaining long-term changes in post-mitotic cells. Accumulating evidence
suggests that the epigenetic machinery might regulate the formation and stabilization of long-term memory in
two ways: a gating role of the chromatin state to regulate activity-triggered gene expression; and a stabilizing
role of the chromatin state to maintain molecular and cellular changes induced by the memory-related event. The
neuronal activation regulates the dynamics of the chromatin status under precise timing, with subsequent alterations in the gene expression prole. This review summarizes the existing literature, focusing on the involvement
of epigenetic regulation in learning and memory. We propose that the identication of different epigenetic
regulators and signaling pathways involved in memory-related epigenetic regulations will provide mechanistic
insights into the formation of long-term memory.
2014 Elsevier Inc. All rights reserved.
Contents
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Epigenetic modications in memory formation . . . . . . . . . . . .
Gating mechanism of epigenetic regulation in memory formation . . . . . .
The stabilization mechanism of epigenetic regulation for long-term memory .
Summary and outlook . . . . . . . . . . . . . . . . . . . . . . . . . .
Acknowledgments . . . . . . . . . . . . . . . . . . . . . . . . . . .
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Introduction
Learning and the formation of new memories require the structural
and functional remodeling of synapses (Martin et al., 2000; Lamprecht
and LeDoux, 2004) through tightly regulated cellular and molecular regulation machines. In response to a specic pattern of neuronal activity,
synaptic strength undergoes long-lasting reduction or enhancement,
known as long-term depression (LTD) and long-term potentiation
(LTP), underlying the cellular mechanism of memory formation
(Martin et al., 2000; Cooper, 2005; Bliss and Collingridge, 1993). At
the molecular level, the neuronal activation triggers modication,
Corresponding author at: Medical School Building D206, School of Life Sciences,
Tsinghua University, Beijing 100084, China.
E-mail address: jsguan@mail.tsinghua.edu.cn (J.-S. Guan).
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http://dx.doi.org/10.1016/j.expneurol.2014.05.006
0014-4886/ 2014 Elsevier Inc. All rights reserved.
Please cite this article as: Guan, J.-S., et al., The role of epigenetic regulation in learning and memory, Exp. Neurol. (2014), http://dx.doi.org/
10.1016/j.expneurol.2014.05.006
regulation in synaptic plasticity and memory (Kaas et al., 2013; Liu et al.,
2009; Lubin et al., 2008; Rudenko et al., 2013; Stefanko et al., 2009; Sui
et al., 2012; Yu et al., 2011; Guan et al., 2009). The types of epigenetic
modiers and their metabolic dynamics are specically regulated in
particular brain regions (Baker-Andresen et al., 2013; Gupta-Agarwal
et al., 2012; Levenson et al., 2004, 2006; Mori et al., 2013; Miller et al.,
2008; Bousiges et al., 2013; Chwang et al., 2006). During learning, different epigenetic regulators work in concert to converge the upstream cascade signaling and manipulate downstream gene transcription with
precise timing. We propose that epigenetic regulation has two functions
in learning and memory formation: as a gating mechanism that
enables gene expression changes that are important for learning, and
a stabilizing mechanism, which enables the maintenance of gene
expression changes that is important for memory consolidation. We hypothesize that such dual roles of epigenetic regulation allow cellular
memory to form the basis of circuitry memory, where information
regarding different properties is stored in discrete neuronal cells
(Xie et al., 2014).
Epigenetic modications in memory formation
Nucleosomes, the basic units used by eukaryotic chromatin to pack
huge genomes into the cell nucleus, contain an octamer of histone proteins, which are two pairs of the core histones H2A, H2B, H3 and H4
surrounded by 147 bp of DNA. The protruding N-terminal tails of the
histone proteins, which are known to interact with nucleosomal DNA,
undergo post-translational modications (Jiang et al., 2008). As summarized in Fig. 1, various epigenetic modications change the status of
chromatin, thereby affecting gene transcription. Histone acetylation
usually enhances transcription, because the acetyl group on lysine releases compacted DNA to be accessible to the transcription machinery,
facilitating transcriptional initiation and elongation (Shahbazian and
Grunstein, 2007). The addition of the acetyl group is catalyzed by
histone acetyltransferases (HATs). The removal of the acetyl group is
Fig. 1. Illustration of epigenetic modication involved in learning and memory. (A) 146 bp of DNA coiled around histone octamers forms chromatin, which can be turned in to open state or
closed state by different combinations of histone modications. In an open state, transcriptional machinery is accessible to the chromatin, while in a closed state, the machinery is
prevented from binding to the gene region. (B) (C) Epigenetic modication enzymes catalyze the addition and removal of modication groups. HATs catalyze the addition of acetyl
group and HDACs remove it. HMTs and HDMs are responsible for the addition and removal of methyl group, respectively. The histone tail is phosphorylated by PPs and dephosphorylated
by PKs. Finally, the DNMTs add a methyl group to the cytosine base while the active DNA demethylation is conducted by TETs or through TDG-mediated base excision repair. CH3, methyl
group; Ac, acetyl group; P, phosphoryl group; RNAPII, RNA polymerase II; TF, transcription factor.
Please cite this article as: Guan, J.-S., et al., The role of epigenetic regulation in learning and memory, Exp. Neurol. (2014), http://dx.doi.org/
10.1016/j.expneurol.2014.05.006
Table 1
The implication of epigenetic regulators in learning and memory.
Classication
Regulator
Effect
Refs.
HATs
CBP/P300
HDACs
PCAF
HDAC1
HDAC2
Knockout of CBP in dorsal CA1 or p300 in supercial layers of the cortex and CA1 impairs long-term potentiation and long-term memory for contextual fear and object recognition. Intra-LA inhibition of CBP/P300
activity impairs fear memory consolidation and reconsolidation in the LA.
PCAF-KO mice show impaired learning and memory.
Overexpression of HDAC1 in the hippocampus affects the extinction of contextual fear memories.
Neuron-specic overexpression of HDAC2 decreased dendritic spine density, synapse number, synaptic
plasticity and memory formation; loss of HDAC2 increases synapse number, improves associative learning
and extinction rate of conditioned fear responses.
Genetic deletions and pharmacologic inhibition of Hdac3 in area CA1 of the dorsal hippocampus enhanced
long-term memory; Hdac3 deletion in nucleus accumbens enhance CPP acquisition; generally pharmacologic
inhibition of Hdac3 enhances extinction of an established CPP.
Selective deletion of Hdac4 in brain impairs long-term synaptic plasticity and hippocampal-dependent
learning and memory.
Loss of function of SIRT1 impairs memory and synaptic plasticity; Knockout of SIRT1 affects in both short and
long-term hippocampus-dependent memory.
Both short- and long-term courtship memories are impaired in EHMT mutant ies.
Inhibition of G9a/GLP in the EC enhances contextual fear conditioning.
Knockout of mll2/kmt2b gene in forebrain impairs hippocampus-dependent memory formation.
Dnmt1 and Dnmt3a double knockout mice show abnormal long-term plasticity in CA1 region and impaired
learning and memory.
Genetical inhibition of PP1 or nuclear pool of PP1 in hippocampal neurons enhances learning and memory.
HDAC3
HDAC4
SIRT1
HMTs
DNMTs
EHMT
G9a/GLP
Mll
DNMT1/DNMT3a
PPs
PP1
Others
TET1
Gadd45b
(Vecsey et al., 2007; Yeh et al., 2004; Alarcon et al., 2004; Barrett et al.,
2011). It has been found that HDAC2 is one of the major regulators
involved in the regulation of long-term memory. Specically, mice
over-expressing HDAC2 showed impaired LTP and memory, while
HDAC2-knockout mice showed enhanced synaptic plasticity (Guan
et al., 2009). Other HDACs might also be involved in this process. The inhibition of HDAC3 enhanced behavior performance in fear memory formation and the extinction of drug-seeking behavior (Rogge et al., 2013;
Malvaez et al., 2013; McQuown et al., 2011). In contrast to HDAC2- and
HDAC3-decient mice, mice with brain-specic knockout of HDAC4
showed signicant memory decits (Kim et al., 2012). The inhibition
or knockout of SIRT1, the class III HDAC, led to the decits in both
short-term memory and long-term memory (Michan et al., 2010; Gao
et al., 2010). Therefore, the HDAC regulation on memory is typespecic, suggesting that the specicity of epigenetic processes on different genomic loci resulting from various regulatory processes might have
different impacts. In addition to HDACs, HATs such as the CREB-binding
protein (CBP) and E1A-binding protein (p300) are also known to regulate long-term memory. Importantly, the disruptions of those epigenetic
regulators have been associated with the pathogenesis of Alzheimer's
disease (Caccamo et al., 2010; Duclot et al., 2010; Maddox et al., 2013).
Histone methylation is another modication tightly associated
with learning and memory. Forebrain-specic knockout of the histone methyltransferase myeloid/lymphoid or mixed-lineage leukemia 2 (mll2/kmt2b) gene, which specically regulates H3K4 di- and
tri-methylation, led to impaired learning function (Kerimoglu et al.,
2013). Another methyltransferase, Ehmt, which catalyzes H3K9
dimethylation, has been reported to regulate courtship memory in
Drosophila (Kramer et al., 2011). Additionally, the inhibition of the
G9a/GLP complex in the hippocampus affected long-term memory formation in mice, while the inhibition of G9a in the entorhinal cortex (EC)
interfered with memory consolidation (Gupta-Agarwal et al., 2012).
Therefore, both histone methylation and acetylation are critical regulators of memory formation.
In addition to histone modications, DNA methylation has also been
associated with memory formation and maintenance. The inhibition of
DNA methyltransferases resulted in memory suppression and impaired
memory consolidation (Lubin et al., 2008; Miller et al., 2008; Miller and
Sweatt, 2007). Additionally, Dnmt1 and Dnmt3a double-knockout mice
Please cite this article as: Guan, J.-S., et al., The role of epigenetic regulation in learning and memory, Exp. Neurol. (2014), http://dx.doi.org/
10.1016/j.expneurol.2014.05.006
Fig. 2. (A) A model for epigenetic gating of neuronal activity induced transcription in learning and memory. Task induced activation of specic post-synaptic receptor activates downstream signal cascades, which lead to the epigenetic modication changes in memory-related gene region. The open epigenetic status allows the neuronal activity to trigger long-term
potentiation (LTP), synaptic and structural plasticity. (B) A model for stabilization shows that specic neuron population is activated by environmental stimuli, transformed from the
initial state to tagged state, with different epigenetic markers on plasticity-related genes. The tagged neurons showed different cellular properties from the initial state, such as the
potential of plastic changes, protecting the intact circuit of specic memory traces from disruption by subsequent events. These long-lasting epigenetic modications maintain the
stabilization of long-term memory.
Please cite this article as: Guan, J.-S., et al., The role of epigenetic regulation in learning and memory, Exp. Neurol. (2014), http://dx.doi.org/
10.1016/j.expneurol.2014.05.006
and led to a hyperacetylation-related increase of gene expression in cultured neurons (Nott et al., 2008). Therefore, neuronal activation, as the
trigger of new memory formation, is tightly associated with gene transcription and post-transcriptional regulation on epigenetic regulators.
Preventing such changes in the epigenetic markers and gene expression
leads to the failure of circuit modication and memory formation.
Importantly, such epigenetic regulation in memory is precisely regulated in a time-sensitive window. Histone H3 only showed increased
acetylation 1 h after contextual fear conditioning, and not 24 h later. A
similar phenomenon was reported for H3K9me2 (Gupta-Agarwal
et al., 2012; Levenson et al., 2004). Such precise timing of epigenetic regulation during learning appears to be critical for memory formation. The
inhibition of DMNT impaired fear memory only if infused immediately
after training. The HDACi only improves memory retrieval at day 30 if
applied during early exposure (Lubin et al., 2008; Miller et al., 2008;
Lesburgueres et al., 2011). Similarly, the effect of DNMT inhibition and
HDACi on memory consolidation is observed only if infusion is conducted 60 min after memory reactivation, but not 6 h after the reactivation
(Maddox and Schafe, 2011). In general, epigenetic changes are required
at specic time points to encode or modify the memory traces.
The stabilization mechanism of epigenetic regulation for
long-term memory
Learning-induced protein synthesis is transient, while memories
stored in our brain usually last for months or years, or even a lifetime.
Owing to the rapid turnover of proteins, the newly synthesized proteins
might not underlie the long-lasting character of long-term memory. In
fact, epigenetic regulation might also take on the role of stabilization
for long-term memory, in which specic epigenetic markers might
maintain the important gene expression changes for memory consolidation. These markers that achieve the role of stabilization are different
from those that perform the role of gating. Different epigenetic regulatory machines and marker dynamics are employed in those two conditions. Recent work showed that contextual fear conditioning induced
rapid and transient increases in DNMT expression in the hippocampus
within 24 h (Miller et al., 2008; Gupta et al., 2010). Surprisingly, a
long-lasting increase of DNA methylation in the specic gene promoter
region in the medial prefrontal cortex (mPFC) was observed 30 days
after fear conditioning, while the administration of a DNMT inhibitor
on day 30 in the mPFC impaired memory recall (Miller et al., 2010). Additionally, DNA demethylation is required for memory extinction. TET1
knockout mice showed impaired memory extinction, and the lack of
TET1 in the hippocampus blocked memory recall (Rudenko et al.,
2013). These results implicated that keeping the marker of DNA methylation changes could be essential for the proper recall of long-term
memory. However, those reports need to be further validated by other
research groups, and the cellular mechanism by which DNA methylation regulates long-term memory is still waiting to be revealed.
In addition to DNA methylation, histone modications might also be
involved in the maintenance of long-term memory. DNA methylation
and histone markers showed intensive cross-talk to maintain memory
status. The administration of a DNMT inhibitor, which prevented the reinstatement of old memories before extinction (Maddox and Schafe,
2011; Wang et al., 2010; Lattal et al., 2007), affects not only DNA methylation but also the decrease of H3 and H4 acetylation (Sui et al., 2012).
Similarly, HDACis could also prevent the reinstatement of past memories when administered before extinction. HDACis not only increases
the histone acetylation, but also reduces DNMT1 expression through
the suppression of the ERK pathway (Sarkar et al., 2011). Consistently,
HDACis rescued the impairment of memory reconsolidation and the
retrieval-induced H3 acetylation by inhibiting the expression of DNMT
(Maddox and Schafe, 2011). The various modications on the histone
tail showed intensive cross-talk as well. The administration of HDACi
in the hippocampus leads to an increase in H3K4me3 but a decrease
in H3K9me2 (Gupta et al., 2010). Such crosstalk between various
Please cite this article as: Guan, J.-S., et al., The role of epigenetic regulation in learning and memory, Exp. Neurol. (2014), http://dx.doi.org/
10.1016/j.expneurol.2014.05.006
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Please cite this article as: Guan, J.-S., et al., The role of epigenetic regulation in learning and memory, Exp. Neurol. (2014), http://dx.doi.org/
10.1016/j.expneurol.2014.05.006