DNA Methylation in Memory Formation: Emerging Insights

Abstract

The establishment of synaptic plasticity and long-term memory requires lasting cellular and molecular modifications that, as a whole, must endure despite the rapid turnover of their constituent parts. Such a molecular feat must be mediated by a stable, self-perpetuating, cellular information storage mechanism. DNA methylation, being the archetypal cellular information storage mechanism, has been heavily implicated as being necessary for stable activity-dependent transcriptional alterations within the CNS. This review details the foundational discoveries from both gene-targeted and whole-genome sequencing studies that have brought DNA methylation to our attention as a chief regulator of activity- and experience-dependent transcriptional alterations within the CNS. We present a hypothetical framework to resolve disparate experimental findings regarding distinct manipulations of DNA methylation and their effect on memory, taking into account the unique impact activity-dependent alterations in DNA methylation potentially have on both memory-promoting and memory-suppressing gene expression. And last, we discuss potential avenues for future inquiry into the role of DNA methylation during remote memory formation.

Keywords: DNA demethylation; DNA methylation; epigenetics; memory; synaptic plasticity.

Figure 1

General schematic of DNA methylation and its mechanisms of regulation. (A) Methylation of DNA involves covalent addition of a methyl group to the 5′ position of the cytosine pyrimidine ring by DNMTs. DNA methylation commonly occurs at genes enriched with cytosine-guanine nucleotides (CpG islands). De novo methyltransferases (e.g., DNMT3a) methylate CpG pairs for which neither CpG is methylated (e.g., CpG:GpC → DNMT3A/B → mCpG/GpC), where as the maintenance methyltransferase (i.e., DNMT1) methylates hemimethylated DNA strands (B) General mechanisms of DNA demethylation within the mammalian central nervous system. TET1 participates in sequential 5mC oxidation prior to 5caC being subject to base-excision-repair that results in the regeneration of C. Abbreviations: 5-hydroxymethylcytosine (5hmC); 5-formylcytosine (5fC); 5-carboxylcytosine (5caC).

Figure 2

A model depicting the manner by which experience-dependent stimuli have been proposed to differentially regulate the expression of memory-promoter genes and memory-suppressor genes. Environmental stimuli, which consist primarily of associative learning tasks in animal models, evoke neurotransmitter-induced activation of specific post-synaptic receptors. Receptor activation stimulates specific intracellular signaling cascades that lead to distinct epigenetic patterns and transcriptional regulation at the gene regulatory domain of memory promoters and suppressors. The net increase in memory-promoter gene expression facilitates the establishment of synaptic plasticity and memory formation. List of memory-promoters: Activity-regulated cytoskeletal-related protein (Arc), Brain-derived neurotrophic factor, exon IV (BDNFexIV), Reelin (Rln), Fibroblast growth factor, 1beta (Fgf-1b). List of memory-suppressors: Calcineurin (Ppp3ca), Protein phophatase 1, catalytic subunit, beta (Ppp1cb).

Figure 3

Hypothetical framework of basal versus activity-dependent gene expression for memory-promoters (screen left) and memory-suppressors (screen right). Numbers in green circles depict the order of events. A) Control mouse. 1) During basal conditions the memory-promoter (MP) gene Rln is transcriptionally silenced, whereas the memory-suppressor (MS) gene Ppp1cb is transcriptionally activated. 2) After neuronal activation and the promoter region of Rln is demethylated by TET1, whereas the promoter of Ppp1cb is methylated by DNMT3a. 3) The MP is now transcriptionally activated, whereas the MS is transcriptionally silenced. The net-memory promoter expression-load does is not outweighed by that of memory suppressor, therefore memory-promoting cellular processes are induced. 4) After sufficient time after the neuronal activating event has passed the MP’s promoter is re-methylated and gene expression is silenced, thus returned in the basal gene expression state, whereas the MS’s promoter is demethylated and gene expression is de-repressed, and thus returned to the basal gene expression state of transcriptional activation. B) DNMT1-inhibition/KO mouse. 1) During basal conditions the gene expression of memory-promoter (MP) gene Rln is silenced, whereas gene expression of the memory-suppressor (MS) gene Ppp1cb is activated. 2) After neuronal activation the promoter region of the MP’s gene is demethylated by TET1, whereas the MS’s gene promoter is not methylated due to the inhibition, or deletion, of DNMT3a. 3) The MP is now transcriptionally activated, whereas the MS is also transcriptional active. The net-memory promoter expression-load does not outweigh that of memory suppressor, therefore memory-suppressing cellular processes are maintained.

Figure 4

Hypothetical framework of basal versus activity-dependent gene expression for memory-promoters (screen left) and memory-suppressors (screen right). Numbers in green circles depict the order of events. A) Control mouse. 1) During basal conditions the memory-promoter (MP) gene Rln is transcriptionally silenced, whereas the memory-suppressor (MS) gene is transcriptionally activated. 2) After neuronal activation the MP’s gene promoter is demethylated by TET1, whereas the MS’s gene promoter is methylated by DNMT3a. 3) The MP is now transcriptionally activated, whereas the MS is transcriptionally silenced. The net-memory promoter expression-load is not outweighed by that of memory suppressor, therefore memory-promoting cellular processes are induced. 4) After sufficient time after the neuronal activating event has passed the MP promoter is remethylated and silenced, thus returning to the basal gene expression state, whereas the MS promoter is demethylated and gene expression is derepressed, and thus returned to the basal gene expression state of transcriptional activation. B) TET1KO mouse. 1) During basal conditions the memory-promoter (MP) gene Rln is transcriptionally silenced, whereas the memory-suppressor (MS) gene is transcriptionally activated. 2) After neuronal activation MP’s gene promoter remains methylated due to the lack of TET1 owing to TET1 deletion, whereas the MS’s gene promoter is methylated by DNMT3a. 3) The MP remains transcriptionally silenced, whereas the MS is also transcriptionally silenced. The net-memory promoter expression-load is not outweighed by that of memory suppressor, therefore memory-promoting cellular processes are induced. 4) After sufficient time after the neuronal activating event has passed the MP promoter remains hypermethylated and the gene expression of the MP remains silenced, yet the MS promoter also remains hypermethylated and the gene expression of the MP remains silenced, thus setting the stage for future memory promoting conditions. C) TET1OE mouse. 1) During basal conditions the memory-promoter (MP) gene Rln is transcriptionally silenced, whereas the memory-suppressor (MS) gene is transcriptionally activated. 2) After neuronal activation and the promoter region of the MP’s gene promoter is demethylated by an abundance of TET1 owing to TET1 overexpression, whereas the MS’s gene promoter is methylated by DNMT3a. 3) The MP is now transcriptionally activated, whereas the MS is transcriptionally silenced. 4) Due to the abundance of over-expressed TET1 the MS is rapidly demethylated thus reestablishing its transcriptional activativation. Even before the MP’s gene promoter is remethylated the net-memory promoter expression-load is outweighed by that of memory suppressor, therefore memory-suppressing cellular processes are maintained.