Rett syndrome, caused by mutations in the X-linked gene encoding methyl-CpG-binding protein 2 (MeCP2), is among the best characterized of the autism spectrum disorders. However, the biological function of MeCP2 and its pathogenic mechanisms remain unclear. Studies have implicated MeCP2 in transcription and gene expression, but further study of MeCP2-mediated gene regulation is complicated by the number of different cell types in the mammalian brain. This research utilizes a nucleic acid immunoprecipitation technique that will facilitate isolation of molecules integral to the transcription process, namely messenger RNA (mRNA) and micro RNA (miRNA). To determine gene expression profiles in distinct cell types, these 2 kinds of RNA will be isolated from glutamatergic and GABAergic neurons in the motor and cognitive areas of the mouse brain at 3 stages of postnatal development. Alterations in the gene expression profiles will be compared between wild type and MeCP2 mutant mice. Simultaneous analysis of mRNA and miRNA profiles will generate a comprehensive molecular portrait of the relevant cell types and their developmental trajectories, which can then be used to better understand Rett syndrome and the interaction of gene networks and neural networks.