Project Summary: Mutations in transcriptional regulatory proteins have been identified as a major cause of neurodevelopmental disorders such as autism and intellectual disability. To understand how these proteins drive disease pathology, we need to first develop a mechanistic understanding of how these regulators contribute to normal neurodevelopment. Alterations in methyl-CpG binding protein 2 (MeCP2) results in Rett Syndrome (RTT), a severe neurodevelopmental disorder, and MeCP2 Duplication Syndrome, an autism spectrum disorder. MeCP2 has been shown to bind both methylated CG dinucleotides and a neuron-enriched form of methylation at cytosines in non-CpG contexts (mCA). Loss of MeCP2 leads to increased expression of long neuronal genes (>100kb) that are enriched for mCA within their gene body. Interestingly, mCA and MeCP2 have been shown to regulate gene expression in a cell-type specific manner. The long-term goal of our lab is to understand the function of MeCP2 and mCA transcriptional regulation in the nervous system and how their dysfunction results in neurological disorders. This proposal will determine how MeCP2 and mCA control cell-type specific gene expression programs through control of regulatory elements and in cooperation with genome topology. In Aim 1, I will test the hypothesis that MeCP2 regulates cell-type specific enhancers to drive gene expression programs in individual neurons. In Aim 2, I will further understand this regulatory mechanism by analyzing how chromatin architecture drives cell-type specific mCA patterns. The results from these experiments will provide important insights into the mechanism and function of MeCP2 and mCA and how they produce pathology when disrupted.