Activity-dependent regulation of DNA methylation in the adult brain

DNA methylation is the most prevalent covalent modification of the metazoan genomic DNA. Besides its well-established role in animal development, accumulating evidence suggests important roles of DNA methylation in postnatal brain functions. Recent studies have shown DNA methylation in post-mitotic neurons can be modified in a region-specific manner by neuronal activity. However, a comprehensive genome-wide view of how extensively the neuronal methylome is modified by neuronal activity is lacking. In addition, little is known on the enzymatic mechanism underlying active DNA demethylation in post-mitotic cells.;The first part of the thesis describes the comprehensive characterization of how neuronal activity modifies the neuronal methylome, using a single-base resolution genome-wide DNA methylation profiling method. It was found that a single trial of neuronal activation modified >1% of all CpG dinucleotides in the genome. Bioinformatic analysis showed that these activity-modified CpGs are widely distributed with the preference of low CpG density, intergenic regions and neuronal genes and pathways.;The second part of the thesis addresses the enzymatic mechanism underlying active DNA demethylation in mammalian cells including neurons in vivo. TET protein-catalyzed conversion of 5-methylcytosines (5mCs) to 5-hydroxymethylcytosines (5hmCs) was found to play a direct and critical role in promoting active DNA demethylation both in human cell lines and in the adult mouse brain. Biochemical properties of the 5hmC demethylation activity were also characterized.;In summary, these studies challenge the traditional view of DNA methylation as a static modification of the mammalian genomic DNA in post-mitotic cells, and implicate active modifications of DNA methylation as a previously underappreciated mechanism in neuronal plasticity.