Abstract
In the brain, neuronal gene expression is dynamically changed in response to neuronal activity. In particular, the expression of immediate-early genes (IEGs) such as egr-1, c-fos, and Arc is rapidly and selectively upregulated in subsets of neurons in specific brain regions associated with learning and memory formation. IEG expression has therefore been widely used as a molecular marker for neuronal populations that undergo plastic changes underlying formation of long-term memory. In recent years, optogenetic and pharmacogenetic studies of neurons expressing c-fos or Arc have revealed that, during learning, IEG-positive neurons encode and store information that is required for memory recall, suggesting that they may be involved in formation of the memory trace. However, despite accumulating evidence for the role of IEGs in synaptic plasticity, the molecular and cellular mechanisms associated with this process remain unclear. In this review, we first summarize recent literature concerning the role of IEG-expressing neuronal ensembles in organizing the memory trace. We then focus on the physiological significance of IEGs, especially Arc, in synaptic plasticity, and describe our hypotheses about the importance of Arc expression in various types of input-specific circuit reorganization. Finally, we offer perspectives on Arc function that would unveil the role of IEG-expressing neurons in the formation of memory traces in the hippocampus and other brain areas.
Introduction
Optogenetics and pharmacogenetics have become indispensable techniques to interrogate neuronal populations and circuits that underlie specific physiological functions and behavior (; Urban and Roth, 2015). In particular, combination of these techniques with cellular labeling/tagging specific to active neuronal ensembles has allowed elucidation of the physiological significance of neuronal ensembles in memory formation, storage, and recall. This review aims to provide an overview of recent understanding of memory traces in the brain and to help understand the molecular and cellular mechanisms underlying the memory trace by discussing two major topics: (I) immediate-early gene (IEG)-expressing neuronal ensembles as memory traces, and (II) the roles of Arc in synaptic plasticity and memory formation. Below, we begin with a brief background describing relationships between memory, synaptic plasticity, and IEGs.
Long-lasting forms of synaptic plasticity such as long-term potentiation (LTP) and long-term depression (LTD) are fundamental cellular mechanisms underlying learning and memory (). Induction of LTP occurs concomitantly with learning in the hippocampus of freely moving animals and is known to preclude subsequent electrical induction of LTP in the hippocampus (Whitlock et al., 2006). Conversely, prior massive induction of hippocampal LTP is also known to interfere with spatial memory formation (). A recent study has demonstrated that in vivo artificial induction of LTD impaired recall of associative memory, which was restored by subsequent LTP induction (Nabavi et al., 2014). Taken together, these findings suggest that a causal relationship exists between long-term synaptic plasticity and memory processes.
The molecular mechanisms underlying LTP have also been extensively investigated. Following plasticity-inducing synaptic input, Ca2+ entry through N-methyl-D-aspartate (NMDA)-type receptors (NMDARs) plays a critical role in the onset of LTP via facilitation of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic (AMPA) receptor (AMPAR) recruitment to the potentiated post-synaptic sites (; ). Furthermore, NMDAR-associated Ca2+ influx influences stabilization of LTP through activation of intracellular signaling cascades that subsequently promote mRNA and protein synthesis (). The blockade of these pathways using NMDAR antagonists (e.g., APV) or protein synthesis inhibitors (e.g., anisomycin) results in failure of the establishment of persistent LTP and impairment in formation of long-term memory (LTM; ; Redondo and Morris, 2011). Although these studies suggest that specific genes, induced during LTP, encode plasticity-related proteins (PRPs) required for LTP maintenance and memory formation, the identity of these genes remains unknown. A subset of plasticity-evoked, stimuli-induced genes, known as IEGs, has been implicated in the above events because of their rapid and transient responsiveness to synaptic activation (Okuno, 2011). For example, expression of IEGs such as egr-1 (zif268/krox-24), c-fos, and Arc (arg3.1), is rapidly upregulated after neuronal activation associated with pharmacologically induced convulsive and sensory stimuli (Morgan et al., 1987; Saffen et al., 1988; ; ). Behavioral tasks also induce IEG expression in neurons; such IEG-expressing neurons are distributed across a wide variety of brain regions (Rosen et al., 1998; ; Vann et al., 2000; ; Ramirez-Amaya et al., 2005). In the following sections, we describe studies analyzing the behavioral-induced IEG expression related to memory trace formation in more detail.
IEG-Expressing Neuronal Ensembles as Memory Traces
Induction of IEG Expression in Cell Ensembles Related to Cognitive Information Processing
Immediate-early genes such as Arc, c-fos, and egr-1 are induced in specific brain regions during neuronal activity associated with behavioral tasks. In the hippocampus, a center of declarative memory formation, rapid transcription of IEGs occurs during hippocampal-dependent learning paradigms including Morris water maze, novel environment exposure, and contextual fear conditioning (CFC; , ; Vann et al., 2000; ; Ramirez-Amaya et al., 2005; ). Arc transcription is activated in a constant population (about 40%) of CA1 neurons following exposure to a novel environment (, ; Vazdarjanova et al., 2002). This proportion is similar to the percentage of activated neurons mapped using electrophysiology (), suggestive of a strong correlation between neuronal activity and Arc expression. In addition to the hippocampus, other brain regions also contain IEG-positive neurons activated during learning and memory. Fear conditioning results in rapid IEG expression in the lateral amygdala (Rosen et al., 1998; ; Reijmers et al., 2007; Ploski et al., 2008), suggesting that these IEG-expressing neurons may be associated with emotional memory formation (Ploski et al., 2008; ).
The RNA transcripts of several IEGs, including Arc, egr-1 and homer1a, first appear in the nucleus minutes after neuronal activation and are subsequently transferred to the cytoplasm (). This temporally distinctive localization of IEG mRNA permits the differential labeling of activated neurons at different time points. This labeling method, known as cellular compartment analysis of temporal activity by fluorescent in situ hybridization (catFISH), has shown that sequential exposure to different environments induces IEG mRNA expression in distinct neuronal ensembles within the hippocampus, while sequential exposure to identical environments induces IEG mRNA in the same ensembles, indicating that activity-dependent IEG expression reflects spatial information processing in the hippocampus ().
Neuronal Ensembles with IEG Expression are Part of the Memory Trace
Our understanding of the role of IEG-expressing neuronal ensembles in fear memory formation has been dramatically enhanced by recent studies using optogenetic and pharmacogenetic manipulation of neuronal activity in these ensembles. The CFC paradigm is designed to create an association between a neutral conditioned stimulus (e.g., chamber exposure) and an aversive unconditioned stimulus (e.g., foot shock; ). If an animal forms a fear memory through conditioning, freezing behavior is observed when the animal is re-exposed to the conditioned stimulus alone. Activated neurons during CFC transiently express IEGs (; ). Moreover, expression of light-gated ion channels such as Channelrhodopsin 2 (ChR2) and Archaerhodopsin (Arch-T) or ligand-gated G-protein-coupled receptors such as designer receptors exclusively activated by designer drugs (DREADDs) in neurons under the control of IEG promoters permits manipulation of the activity of IEG-expressing neurons responding to specific training experiences (Figure 1; Neves et al., 2008). Figure 2 summarizes recent evidence concerning optogenetic and pharmacogenetic manipulation of IEG-expressing neurons. The seminal study by that demonstrated involvement of IEG-expressing neurons in the memory trace used two transgene components, c-fos-tTA transgenic (tg) mice and TRE-ChR2 adeno-associated viral (AAV) vectors, by which ChR2 was expressed via a c-fos promoter only during an off-doxycycline (off-Dox) phase (). These mice were subjected to CFC training in a conditioning chamber (context A) without Dox to label c-fos-positive ensembles with ChR2. After 24 h, activation of ChR2-expressing c-fos ensembles using blue light illumination under a distinct neutral context (context B) elicited freezing responses only during illumination, suggesting that reactivation of c-fos ensembles formed during CFC training was sufficient for the retrieval of the fear memory (Figure 1B). Inactivation of c-fos-positive ensembles in the dorsal CA1 region of the hippocampus expressing Arch-T has also been shown to impair memory recall (Tanaka et al., 2014). Similar to c-fos studies, optogenetic suppression of neuronal activity of Arc-positive neurons in hippocampal CA3 or dentate gyrus (DG), labeled with Arch-T during CFC training (context A), significantly impaired memory retrieval during re-exposure to the identical context (Figure 1C; ). Conversely, mice showed intact memory retrieval during suppression of Arc-positive ensembles responding to context B, supporting the concept of specificity in Arc-expressing ensembles (). These studies indicate that reactivation of IEG ensembles represents a critical event underlying retrieval of fear memories.
FIGURE 1
FIGURE 2

A compendium of the current literature investigating the role of IEG-expressing neurons in memory formation. Driver transgenes promote the expression of the effector proteins that can manipulate neuronal activity. Labeling events induce effector protein expression via the driver transgenes. During activity manipulation events, IEG-expressing neurons are activated or inactivated by applying the trigger (e.g., light or clozapine-N-oxide; CNO). Tg, transgenic animal; AAV, adeno-associated virus; LV, lentivirus; tTA, tetracycline transactivator; tetO, tetracycline operator; TRE, tetracycline response element; ChEF, channelrhodopsin chimeric variant; Ctx, context; US, unconditioned stimulus (e.g., electrical foot shock); FLEX, flip-excision (double floxed system); TeNT, tetanus toxin.
Optogenetic or pharmacogenetic activation of c-fos-positive neurons related to the neutral context B during fear memory training in context A interfere with memory encoding by generating a hybrid contextual fear memory (
Several studies attempted to associate memory traces in the hippocampus and basolateral amygdala (BLA) by optogenetic neuronal activation. Simultaneous optogenetic co-activation of c-fos ensembles in the BLA (responding to a fear experience) with c-fos-expressing CA1 neurons (encoding a neutral context) generated a new fear memory associated with the neutral context (Ohkawa et al., 2015). Similarly, c-fos ensembles in the DG encoding a rewarding context can be changed to a fear memory trace via optical reactivation of the DG reward-related ensemble during fear conditioning (Redondo et al., 2014). These data suggest that IEG-expressing ensembles in brain regions such as the hippocampus and amygdala integrate to create associative fear memory. Consistent with this theory, a recent study demonstrated a critical role of the hippocampal-neocortical network formed by IEG-expressing neurons (
These hippocampal-cortical memory trace interactions at the early phase of memory formation and maintenance may stimulate reconsideration of a conventional view of system consolidation that assumes a slow, sequential involvement of cortical areas in memory trace formation (
c-fos Memory Trace Largely Overlaps with Other IEG-Expressing Ensembles
The majority of studies concerning memory trace have focused on cell ensembles expressing c-fos (Figure 2). Do c-fos-expressing ensembles also express other IEGs? Surprisingly, little information is available regarding how and to what extent c-fos-expressing neuronal ensembles overlap with neuronal ensembles expressing other IEGs during memory encoding, although the individual expression patterns of each IEG have been well documented. Double in situ hybridization (ISH) analysis on the same section indicated most neurons in the cortical regions coexpressed IEGs including c-fos, Arc, and Nr4a1 after monocular stimulation or sleep deprivation (Thompson et al., 2010; Nakagami et al., 2013). In the hippocampal CA1 and CA3, Arc-expressing neurons responding to a context exposure were more largely overlapped with Homer1a-expressing ensembles responding to the same context exposure than to a different context exposure (Vazdarjanova and Guzowski, 2004). Immunofluorescence analysis of fear-conditioned brain sections revealed that most DG neurons coexpressed Arc and Egr-1 regardless of their differential expression time courses (
Functional Characteristics of IEG-Expressing Neurons
Recent studies have investigated the characteristics of IEG-expressing neurons when compared to non-expressing neurons. In cortical regions, increased spontaneous firing rates have been observed in somatosensory neurons expressing c-fos or Arc (Yassin et al., 2010), and Arc-expressing neurons in the frontal cortex exhibit persistent firing after motor learning (Ren et al., 2014). Fear conditioning has been shown to increase surface expression of calcium-permeable AMPARs (i.e., GluA1 subunit-containing AMPA receptors) within c-fos-expressing cortical neurons (
The Roles of Arc in Synaptic Plasticity and Memory Formation
Although optogenetic and pharmacogenetic interventional approaches have suggested an important involvement of IEG-expressing neurons in memory formation, it remains unclear how IEG expression during learning participates in incorporation of IEG-expressing ensembles into the memory trace. In contrast to studies of memory traces encoded by c-fos-positive ensembles, little is known concerning the biological and physiological effects of c-fos on synaptic plasticity and neuronal circuit reorganization, in part because c-fos encodes a transcription factor composing the AP-1 complex, whose target genes in neurons have yet to be fully characterized. In contrast to c-fos, several IEGs including BDNF, narp, homer1a, and Arc are known to encode synaptic or secretory proteins directly affecting synaptic properties (
Long-Term Memory Formation Requires Arc Induction
Arc expression is required for LTM consolidation, but not for learning or short-term memory formation (STM; Plath et al., 2006). Arc knockout (KO) mice exhibit impaired consolidation of spatial and fear memories (Plath et al., 2006; Peebles et al., 2010; Yamada et al., 2011). Transient inhibition of Arc expression following infusion of Arc antisense oligodeoxynucleotides (ODNs) into the hippocampus, lateral amygdala, or anterior cingulate cortex inhibits memory consolidation (
Synaptic Localization of Arc
One unique characteristic of Arc is that its mRNA and protein can be targeted to dendritic compartments of neurons. Within minutes of neuronal activation triggered by behavioral events, Arc mRNA is expressed in the nucleus and subsequently transported through the cytoplasm into the dendrites (Wallace et al., 1998;
Roles of Arc in Synaptic Scaling and Synaptic Plasticity
Neurons possess the ability to maintain their excitability within a certain dynamic range by modifying surface AMPAR expression on synapses in response to changes in synaptic input, without affecting the relative balance between strong and weak synapses. These cellular changes have been termed “homeostatic” plasticity (Turrigiano, 2008), and induction of Arc by neuronal activation and synaptic AMPAR endocytosis provide this IEG with a function in this process. Arc KO neurons in culture lack homeostatic AMPAR scaling (Shepherd et al., 2006) and Arc KO mice exhibit a deficit of synaptic scaling in response to sensory deprivation (
Arc-dependent AMPAR endocytosis is also involved in induction of LTD (Plath et al., 2006; Park et al., 2008). Activation of metabotropic glutamate receptors (mGluRs) rapidly induces Arc translation, which is necessary for expression of mGluR-dependent LTD (Park et al., 2008) and suggests that Arc protein plays an important role in both input-specific synaptic plasticity and cell-wide synaptic scaling. Synaptic AMPAR downregulation by Arc appears irreconcilable with increases in Arc expression reported to occur following LTP-inducing stimulus and the transport of Arc mRNA and protein into activated dendrites. However, recent observations that Arc protein is preferentially transported to inactive dendritic spines by binding with the inactive form of CaMKIIβ and that AMPAR is selectively decreased in inactive spines in which Arc is accumulated (Okuno et al., 2012), may help explain this apparent incongruity. This Arc-dependent downregulation of AMPAR in inactive synapses, termed “inverse synaptic tagging,” likely functions to increase the contrast of synaptic strength between active and inactive synapses following synaptic potentiation (Figure 3A). Taken together, consolidation of synaptic plastic changes responding to neuronal activity is achieved, in part, via regulation of the expression and localization of Arc protein, which is in turn involved in surface AMPAR endocytosis.
FIGURE 3

Models of Arc mRNA and protein dynamics in inverse tagging (A), behavioral tagging (B), and LTD priming (C) processes.(A)Arc protein is synthesized in the soma following neuronal activation (left) and transported to an activated dendrite (right). Arc preferentially binds to the inactive form of CaMKII and promotes AMPAR endocytosis in the inactive synapse, resulting in the increasing synaptic strength of the activated synapse. (B) A novel exploration task induces Arc protein expression (left). Arc protein diffuses throughout the dendrite, decreases AMPAR in the non-tagged synapse, and serves to maintain the enhanced synaptic strength of synapses transiently potentiated by a weak training (right). (C) Other types of behavioral experiences promote Arc mRNA synthesis in the nucleus and transport to nearby synaptic sites, but its translation is suspended (left). Subsequent mGluR activation promotes Arc translation from dendritically localized Arc mRNA, resulting in AMPAR internalization and LTD of the mGluR-activated synapse. (D)Arc expression plays a permissive role in inducing synapse-specific plastic changes to organize a new memory trace following a new behavior/experience. Arrow and arrowhead indicate LTD-primed and behavioral-tagged synapses, respectively.
Metaplastic Changes of Arc-Expressing Neurons
While it has been well documented that Arc expression is robustly induced throughout the rodent brain following exposure to a novel environment, the significance and consequence of its upregulation remain unclear. Several studies have revealed that Arc induction is associated with alteration of neuronal network properties, thereby facilitating consolidation of otherwise labile memories. For example, Arc-expressing neurons responding to novel environment exposure are preferentially reactivated during subsequent spontaneous hippocampal ripples, which are crucial for memory consolidation (Mizunuma et al., 2014). Arc may also be involved in a specific type of memory facilitating process called “behavioral tagging” (
Conclusion and Future Directions
In this review, we characterized the role of IEG-expressing neurons in memory formation and storage. Neurons activated during cognitive tasks induce IEGs and organize the memory trace (Figures 1 and 2). During memory formation and recall, hippocampal IEG-positive cells are co-activated alongside IEG-positive neurons in other brain areas, including the amygdala and neocortex, suggesting that IEG-positive neurons are preferentially connected with each other across brain regions. Furthermore, IEG-positive neurons exhibit functional synaptic changes that may underlie memory formation. We also summarized evidence for the role of Arc in synaptic plasticity and memory formation. Taken together, the literature suggests that continued characterization of the functional changes in Arc-expressing neurons will elucidate novel molecular mechanisms underlying memory formation and/or storage.
The expression of IEGs is dynamically regulated in response to neuronal activity in the brain; while many neurons only express IEG at basal levels, some neurons display rapid induction of IEG expression surpassing the basal level after learning (Rosen et al., 1998;
Recently, visualization of dynamic changes in IEG expression in vivo using fluorescent reporters under the control of the IEG promoter has been achieved (
Furthermore, it is widely believed that dysregulation of neuronal activity and synaptic functions cause various types of cognitive disorders including autism, schizophrenia, and dementia, as these diseases are related to mutations in genes associated with activity-dependent gene expression and synaptic maturation (West and Greenberg, 2011; Purcell et al., 2014). Future studies analyzing the roles of activity- and/or behavioral-dependent expression of Arc and other IEGs in synaptic plasticity may enhance our understanding of the pathogenesis and treatment of specific psychiatric and neurological disorders.
Statements
Author contributions
KM, conceived the content and wrote the manuscript; MA, provided the ideas and discussions; HO, conceived the content, wrote the manuscript, and supervised the work.
Acknowledgments
We apologize to the many authors we could not mention due to space limitations. We thank the members of SK project and Okuno lab for their support. This work was supported in part by research funds from Shionogi & CO., LTD; by Grants-in-Aid for Scientific Research (KAKENHI 15H04258) from the Ministry of Education, Culture, Sports, Science and Technology of Japan; and by a research grant from Brain Science Foundation.
Conflict of interest
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
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Summary
Keywords
immediate-early gene, c-fos, Arc, synaptic plasticity, neuronal ensemble, memory trace
Citation
Minatohara K, Akiyoshi M and Okuno H (2016) Role of Immediate-Early Genes in Synaptic Plasticity and Neuronal Ensembles Underlying the Memory Trace. Front. Mol. Neurosci. 8:78. doi: 10.3389/fnmol.2015.00078
Received
14 October 2015
Accepted
03 December 2015
Published
05 January 2016
Volume
8 - 2015
Edited by
Peter K. Giese, King’s College London, UK
Reviewed by
Naoki Matsuo, Osaka University, Japan; Marco Peters, Dart NeuroScience LLC, USA
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© 2016 Minatohara, Akiyoshi and Okuno.
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*Correspondence: Hiroyuki Okuno, okuno@sk.med.kyoto-u.ac.jp
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