Abstract Advances in human genetics have led to the identification of a large number of genes associated with autism spectrum disorder (ASD), intellectual disability (ID), and related neurodevelopmental diseases. A critical new challenge is to understand the molecular pathways these genes contribute to in neurons and to dissect how their disruption alters nervous system function. Methylation of cytosines in DNA classically occurs only at CG dinucleotides, but recent studies have also uncovered functions for unique non-CpG DNA methylation in neurons (which occur largely at CA dinucleotides, mCA). We have discovered that the methyl-DNA-binding protein MeCP2, which is critical for proper nervous system function, binds to mCA within the transcribed regions of genes in neurons to downregulate their expression. New studies have identified mutations in DNMT3A, the DNA methyltransferase required for the deposition of mCA in the brain, in individuals with ID and ASD. These findings support the hypothesis that disruption of gene regulation mediated by mCA contributes to disorders caused by mutation of DNMT3A. Our proposed studies will test this hypothesis by pursuing three specific aims: Aim 1 will use in vitro cell culture systems to determine how disease-associated mutations in DNMT3A affect enzyme function and alter deposition of mCA in neurons. Aim 2 will employ newly-generated transgenic mice carrying heterozygous mutations in DNMT3A to determine the effects of this disruption on neuronal DNA methylation, chromatin structure, transcription and cellular functions. Aim 3 will interrogate the mechanisms by which mCA and MeCP2 directly regulate transcription in neurons, testing the hypothesis that these components interact with novel gene-regulatory sites to control transcription. Together these studies will determine the molecular mechanisms by which mCA regulates gene expression in neurons, and define a site of molecular pathology in ASD and ID.