To promote memory formation, changes in DNA methylation must be selective, potentially even at the single-nucleotide level. The neuron cannot risk dedifferentiation, so plastic sites must be compartmentalized from maintenance sites, from sites involved in the perpetuation of cellular phenotype. At present the upstream mechanisms that regulate this process are very mysterious, and it is unclear how one specific site or gene region is targeted for methylation or demethylation in any cell type42
. However, recent discoveries are already suggesting neuron-specific mechanisms. For example, hydroxymethylcytosine (OH-MeC) has been found at high levels in neural tissue43, 44
. Although the function of OH-MeC is not known, it is noteworthy that it possesses a lower affinity for proteins with methyl binding domains such as MeCP2 than does MeC45
. Thus, it is possible that OH-MeC could be a chemical precursor to target sites for active demethylation or may even constitute a plastic mechanism to reversibly negate the effects of methylation.
How might selective modifications of specific C–G dinucleotides within an entire genome be attained? Recent findings indicate that one component of specificity in altering DNA methylation profiles may be conferred by via histone modifications that encourage the binding of DNMTs to DNA. For example, the de novo methyltransferase DNMT3a binds to DNA with more efficiency when lysine 9 on H3 is trimethylated than when lysine 4 on H3 is trimethylated46
. Conversely, entire stretches of non-methylated CpGs may be preserved despite global DNMT activity by proteins such as Cfp1, which bind selectively to non-methylated CpG islands and may assist in the perpetuation of this state via interactions with H3K4 methylation47
. Thus, DNA methylation may be specifically guided by some chromatin modifications and permanently inhibited by others, resulting in a multi-layered regulation of methylation patterns.
Changes in DNA methylation may therefore affect neuronal activity in many ways, most of which are only beginning to be understood. Although DNA methylation was once mainly associated with transcriptional repression, it is also possible that DNA methylation may also result in transcriptional activation in the CNS48, 49
. Given this, a final consideration is what the gene products are that may be targeted for epigenetic modification, that in turn result in changes in synaptic strength or the capacity for synaptic plasticity? The answer to this question is essentially completely unknown at present. However, alterations in DNA methylation or in the proteins that bind to methylated DNA produce robust changes in the expression patterns of several genes that have been implicated in synaptic plasticity, including bdnf, calcineurin, PP1
, and reelin12, 19, 30, 34, 50
. Likewise, inhibition of DNA methylation disrupts long-term potentiation within the hippocampus, providing additional evidence of its role in neuronal plasticity16
. Thus, DNA methylation could potentially play multiple roles in neuronal change, all of which may also be regionally, temporally, and even neuronally specific. In fact, understanding how epigenetic mechanisms contribute to functional change in diverse neuronal populations is an especially important issue that will come with its own challenges. Since unique sets of cells perform specific functions within a neuronal circuit, and each cell within this set maintains its own epigenome, discovering which epigenetic mechanisms are used by specific neuronal phenotypes will be critical for relating epigenetic changes to neuronal function. Adding to this difficulty is the fact that discrete neuronal populations often physically overlap within the same brain region, making it harder to assay the epigenetic status of any given neuronal phenotype.
It is clear that we have not yet begun to determine in a comprehensive fashion how
DNA methylation at the cellular level gets translated into altered circuit and behavioral function. Thus far most studies have been restricted to using a candidate target gene approach to identify specific sites of methylation changes. However, these data only allow the assessment of a small subset of changes in DNA methylation. It is not yet possible to try to mechanistically tie these specific changes at single gene exons to complex multicellular, multicomponent processes like LTP, hippocampal circuit stabilization, and behavioral memory at this point, because of the limitation that the molecular approaches are sampling such a small subset of genes. Thus, a future challenge for neuroepigenetics researchers will be to expand the level of analysis by incorporating sophisticated epigenome-wide screens into the technical repertoire17
, potentially revealing a myriad of functional effector genes subjected to epigenetic control and perhaps identify novel mnemogenic molecules.
In summary, all of these considerations imply the existence in neurons of specialized epigenetic biochemical machinery and processes that may not exist in other cell types. Regardless of the nomenclature, future studies will hopefully yield increasing understanding of the processes subserving the epigenetic code operating in memory formation, as well as other long-lasting forms of behavioral change.