In the mammalian genome, DNA methylation is an epigenetic mechanism involving the transfer of a methyl group onto the C5 position of the cytosine to form 5-methylcytosine. DNA methylation regulates gene expression by recruiting proteins involved in gene repression or by inhibiting the binding of transcription factor(s) to DNA. During development, the pattern of DNA methylation in the genome changes as a result of a dynamic process involving both de novo DNA methylation and demethylation. As a consequence, differentiated cells develop a stable and unique DNA methylation pattern that regulates tissue-specific gene transcription. In this chapter, we will review the process of DNA methylation and demethylation in the nervous system. We will describe the DNA (de)methylation machinery and its association with other epigenetic mechanisms such as histone modifications and noncoding RNAs. Intriguingly, postmitotic neurons still express DNA methyltransferases and components involved in DNA demethylation. Moreover, neuronal activity can modulate their pattern of DNA methylation in response to physiological and environmental stimuli. The precise regulation of DNA methylation is essential for normal cognitive function. Indeed, when DNA methylation is altered as a result of developmental mutations or environmental risk factors, such as drug exposure and neural injury, mental impairment is a common side effect. The investigation into DNA methylation continues to show a rich and complex picture about epigenetic gene regulation in the central nervous system and provides possible therapeutic targets for the treatment of neuropsychiatric disorders. Although these methods can quantify 5hmC and identify DNA sequences with which it is associated, single base-pair resolution has not been attained. In order to clarify the genomic distribution and the epigenetic role of 5hmC in the brain, a locus-specific method of identifying 5hmC will need to be developed.

As other high-throughput techniques, including RNA and chromatin immunoprecipitation (ChIP) sequencing, become more accessible to researchers, there is a growing need to integrate high-throughput data. Currently, DNA methylation, histone modification, and miRNA are studied in relative isolation. In order to fully understand how gene expression is regulated within the nervous system, future research must consider the epigenome as a whole. By dissecting the biological mechanisms that mediate crosstalk among these biological mechanisms and integrating high-throughput data, we can begin to study the epigenome as a whole. Finally, for a complete understanding of how the epigenome regulates gene expression, future research will have to uncover the biological mechanisms that mediate activity-dependent changes in the epigenomic landscape of the mammalian brain. Aberrant DNA methylation patterns are observed in a wide variety of psychiatric and neurological illnesses. With declining costs and the ability to perform genome-wide methylation analysis on limited tissue quantities, it will soon be possible to map-out genome-wide DNA methylation patterns from distinct brain regions from patients with neurological and psychiatric disorders. The analysis of neural tissue from psychiatric patients will lead to new insights into the etiology of psychiatric illness and open up new avenues of drug discovery and targeted therapies.

Although current protocols enable scientists to precisely quantify DNA methylation at single-nucleotide resolution using progressively smaller tissue quantities, many of the most commonly used methods for profiling and quantification of DNA methylation, such as bisulfite sequencing and methylation-sensitive enzyme-based assays, are unable to distinguish between 5hmC and 5mC 

One extremely rare neurodegenerative disease illustrates the importance of proper DNMT activity in the adult brain. Patients with hereditary sensory and autonomic neuropathy type 1 (HSAN1) develop dementia and hearing loss in adulthood that result from an autosomal-dominant mutation in the N-terminal regulatory domain of DNMT1. This mutation results in misfolding, impaired nuclear localization, and early degradation of DNMT1. However, the mutation does not affect the targeting of DNMT1 to the replication foci during cellular replication, but the DNMT1 association with heterochromatin beyond S phase is disrupted. This association may affect the maintenance of DNA methylation within these regions. Although there is only a modest 8% reduction of global DNA methylation level, neurodegeneration does result. The involvement of DNMT1 in the pathogenic mechanism of HSAN1 supports the necessity of DNMT1 in the adult brain. Improper methylation of a single gene or a single allele can have drastic consequences within the brain. Fragile X Syndrome is caused by abnormal methylation of a trinucleotide repeat expansion in the FMR1 gene on the X chromosome and is a common form of mental retardation