Cell type-specific DNA methylation analysis in neurons and glia

Abstract

The brain is a highly heterogeneous tissue with many types of neuronal and glial cells. Each brain cell type is expected to contain distinctive epigenetic profiles, which contribute to the complex regulation of gene expression. Within the fields of neuroscience, biological psychiatry and neurology, many studies based on postmortem human brains have suggested altered epigenetic status in patients with neuropsychiatric disorders. However, because most of these studies were performed using bulk brain tissue, interpretation of the reported data is quite difficult and often inconsistent across studies. To overcome this problem, several groups have performed epigenetic analyses using isolated neuronal and nonneuronal nuclei. Their work has successfully revealed cell type-specific epigenetic profiles. Here we describe a detailed method for isolation of neuronal and nonneuronal, which involves extracting nuclei from frozen brain tissue, staining them with fluorescence-labeled anti-NeuN antibody, and isolating NeuN + (neuronal) and NeuN + (nonneuronal) nuclei by flow cytometry.