Locus-Specific DNA Methylation Assays to Study Glutamate Receptor Regulation

Recent findings indicate that glutamate receptors are regulated at the epigenetic level through the posttranslational modification of histones and through DNA methylation. Furthermore, dysregulation of these marks in the context of neurological disease has been shown to influence glutamate receptor function. Over the past two decades, an appreciation for the essential role epigenetic mechanisms play in nervous system function has led to the development of many methods and tools to map, quantitate, and manipulate these chromatin marks. Here we describe two popular methods used to quantitate DNA methylation levels at the gene or nucleotide level. The first, cloning-based bisulfite sequencing involves modification of DNA samples using the chemical sodium bisulfite (BS) , which deaminates all unmethylated cytosines to form uracil. Subsequent PCR amplification converts the uracils to thymine, leaving any cytosines in the PCR product representative of methylation. Fragments are then cloned and sequenced to quantitate the percentage of methylation at each cytosine. The second technique, methyl-binding domain capture (MBDCap), involves shearing the genomic DNA into fragments via sonication. Samples are then incubated with magnetic beads conjugated to methyl-binding domain (MBD) peptides to bind and enrich fragments containing methylated CpGs. Quantitation of DNA methylation levels are then measured indirectly using qRT-PCR with primers specific to the region of interest. Because these methods do not require advanced technical knowledge and can be performed with common laboratory equipment, they are great options for interrogating DNA methylation patterns at the level of the gene, the regulatory region, or in the case of bisulfite sequencing, the nucleotide.