DNA methylation of the promoter region at the CREB1 binding site is a mechanism for the epigenetic regulation of brain-specific PKM zeta

Abstract

Protein kinase M zeta, PKM?, is a brain enriched kinase with a well characterized role in Long-Term Potentiation (LTP), the activity-dependent strengthening of synapses involved in long-term memory formation. However, little is known about the molecular mechanisms that maintain the tissue specificity of this kinase. Here, we characterized the epigenetic factors, mainly DNA methylation, regulating PKM?expression in the human brain. The PRKCZ gene has an upstream promoter regulating Protein kinase C ? (PKC?), and an internal promoter driving PKM?expression. A demethylated region, including a canonical CREB binding site, situated at the in-ternal promoter was only observed in human CNS tissues. The induction of site-specific hypermethylation of this region resulted in decreased CREB1 binding and downregulation of PKM?expression. Noteworthy, CREB binding sites were absent in the upstream promoter of PRKCZ locus, suggesting a specific mechanism for regulating PKM? expression. These observations were validated using a system of human neuronal differentiation from induced pluripotent stem cells (iPSCs). CREB1 binding at the internal promoter was detected only in differentiated neurons, where PKM?is expressed. The same epigenetic mechanism in the context of CREB binding site was identified in other genes involved in neuronal differentiation and LTP. Additionally, aberrant DNA hyper-methylation at the internal promoter was observed in cases of Alzheimer's disease, correlating with decreased expression of PKM?in patient brains. Altogether, we present a conserved epigenetic mechanism regulating PKM? expression and other genes enhanced in the CNS with possible implications in neuronal differentiation and Alzheimer's disease.