DNA methylation and its implications and accessibility for neuropsychiatric therapeutics

Abstract

In this review, we discuss the potential pharmacological targeting of a set of powerful epigenetic mechanisms: DNA methylation control systems in the central nervous system (CNS). Specifically, we focus on the possible use of these targets for novel future treatments for learning and memory disorders. We first describe several unique pharmacological attributes of epigenetic mechanisms, especially DNA cytosine methylation, as potential drug targets. We then present an overview of the existing literature regarding DNA methylation control pathways and enzymes in the nervous system, particularly as related to synaptic function, plasticity, learning and memory. Lastly, we speculate upon potential categories of CNS cognitive disorders that might be amenable to methylomic targeting.

Keywords: DNMT; Tet oxidase; cognitive disorders; cognitive enhancement; cytosine methylation; demethylation; epigenetics; learning; memory; neuropharmacology.

Figure 1

Cytosine is methylated in vivo by DNMTs, which use SAM as an electrophilic methyl source, to produce mC at CpG sites in double-stranded DNA. Maintenance DNMTs may then methylate the complimentary cytosine to produce double-stranded CpG methylation. An otherwise stable epigenetic mark, mC can be oxidized by the α-KG-dependent Tet family of dioxygenases to yield hmC, which is the first step in removing the methyl as an epigenetic mark. Abbreviations: α-KG, α-ketoglutarate; CpG, cytosine-phosphate-guanine; DNMT, DNA methyltransferase; hmC, 5-hydroxymethylcytosine; mC, 5-methylcytosine; SAM, S-adenosyl methionine; Tet, ten-eleven translocation.

Figure 2

DNA methyl (orange) addition, recognition, and oxidation. (top) Crystal structures of DNMT1, MeCP2, and TET2 bound to DNA. (a) Mouse DNMT1 (teal) trapped by double-stranded DNA containing 5-fluorocytosine to reveal active site catalysis and means of detecting hemimethylation (19). The coproduct SAH is shown in white. (b) Human MeCP2 (yellow) bound to methylated DNA (20). Hydrogen bond contacts showcase CpG recognition. (c) Human Tet2 (red) is bound to methylated DNA with a water-Fe complex rather than oxygen (26). α-KG is shown in white. Abbreviations: α-KG, α-ketoglutarate; CpG, cytosine-phosphate-guanine; DNMT, DNA methyltransferase; MeCP2, methyl CpG–binding protein 2; SAH, S-adenosyl-l-homocysteine; Tet, ten-eleven translocation.

Figure 3

Current and future pharmacological and genetic approaches to manipulating DNA methylation. (a) Current tools include ➊ traditional gene knockout transgenic mouse lines that lack a specific component of DNA methylation machinery; ❷ virally mediated knockdown or ❸ overexpression of DNA methylation components; ❹ small-molecule inhibitors such as RG108 that block the active site on DNMTs; ❺ direct infusion, injection, or dietary supplementation of the methyl group donor SAM; and ❻ nucleoside analogue DNMT inhibitors that incorporate into DNA and trap DNMT enzymes. Unfortunately, the approaches exhibit poor temporal control over DNA methylation and create changes that are genetically and cellularly global. (b) New approaches include spherical nucleic acids and antisense oligonucleotides, which can be used to selectively and robustly inhibit translation of DNA methylation components. Specific changes in DNA methylation at target genes can be accomplished using TALEs, which selectively bind a specific DNA sequence and serve as an anchor for DNA methylation enzymes such as DNMTs or methylcytosine hydroxylases. This system can also be adapted for use with optogenetic tools. For example, a sequence-specific TALE construct could be fused to CRY2, which changes conformation in the presence of blue light, causing it to recruit its binding partner CIB1. Thus, fusion of an effector enzyme such as a DNMT to CIB1 could generate DNA methylation changes with both genetic and temporal specificity. Abbreviations: C, C terminus; CIB1, cryptochrome-interacting basic-helix-loop-helix 1; CRY2, cryptochrome 2; DNMT, de novo DNA methyltransferase; epiTALE, epigenetically modified TALE; GADD45b, growth arrest and DNA damage-inducible protein 45; hmC, 5-hydroxymethylcytosine; mC, 5-methylcytosine; N, N terminus; opto-epiTALE, optogenetic epiTALE; RNAi, RNA interference; SAH, S-adenosyl-l-homocysteine; SAM, S-adenosyl methionine; shRNA, small hairpin RNA; TALE, transcriptional activator–like effector; Tet, ten-eleven translocation.