DNA Methylation

Overview

DNA methylation is the addition of a methyl group to cytosine residues, most commonly at cytosine-guanine dyads (CpG sites). It plays a pivotal role in cell differentiation, genomic imprinting, and X chromosome inactivation. Compared to histone modifications, DNA methylation is considered a more stable epigenetic change.

Mechanism

5-methylcytosine (5mC): Addition of methyl group to C5 position of cytosine. At gene promoters, generally represses transcription — either by blocking transcription factor binding or by recruiting methyl-CpG-binding proteins that recruit transcriptional co-repressors.
Writers: DNA methyltransferases (DNMTs):
- DNMT1 — maintenance methylation (copies patterns after DNA replication)
- DNMT3a, DNMT3b — de novo methylation
Erasers (demethylation):
- TET proteins oxidize 5mC → 5-hydroxymethylcytosine (5hmC) → 5-formylcytosine → 5-carboxylcytosine → eventual demethylation via base excision repair
- GADD45 family proteins implicated in active demethylation
- Enzymatic basis of demethylation remains incompletely understood

5mC vs. 5hmC — A Critical Distinction

5hmC is enriched in neurons relative to other cell types
Unlike 5mC (repressive), 5hmC correlates with gene activation
Most studies of DNA methylation in psychiatric disorders have not distinguished between 5mC and 5hmC — a major limitation acknowledged by the field
Requires different assays (e.g., TET-assisted bisulfite sequencing vs. standard bisulfite)

Non-CpG Methylation

A significant portion of DNA methylation occurs at non-CpG sites in neurons. Its role is less understood but increasingly recognized. Standard bisulfite sequencing cannot distinguish CpG from non-CpG methylation context without additional analysis.

Relevance to Psychiatric Disorders

Depression

Chronic social defeat stress increases Dnmt3a expression in NAc
- Overexpressing Dnmt3a increases depression-like behavior
- Intra-NAc DNMT inhibitor (RG108) exerts antidepressant effects
DNMT expression altered in limbic regions and brainstem of depressed suicide completers
Crf (corticotropin releasing factor) promoter methylation in PVN decreases in susceptible mice → increased CRF → HPA hyperactivation; restored by imipramine
Early life adversity: persistent hypermethylation at Nr3c1 (glucocorticoid receptor), BDNF, Reelin, Gad1 promoters following prenatal stress or maternal separation

Schizophrenia

RELN promoter hypermethylated in PFC; associated with elevated DNMT1 expression
SOX10 hypermethylated in PFC
GAD1 hypermethylated in PFC
Genome-wide DNA methylation maps in SCZ brain are limited; PsychENCODE consortium ongoing

Bipolar Disorder

HLA9 shows methylation differences in brain, blood, and sperm — mechanism unknown
GAD1 altered methylation in hippocampus
Overlap with SCZ at many promoters in postmortem studies

Status: Confirmed vs. Hypothesized

Claim	Status
DNMT3a upregulation in NAc drives depression susceptibility	Established in rodents; not confirmed in humans
RELN promoter hypermethylation in SCZ PFC	Established: replicated postmortem
HPA axis CRF methylation changes mediate stress susceptibility	Established in animals; human data limited
Nr3c1 methylation encodes early-life adversity	Strong evidence across rodents and humans
5hmC has distinct functional role from 5mC in brain	Established as distinct mark; psychiatric relevance being investigated
Peripheral DNA methylation reflects brain methylation	Contested — see Debates