Investigation of MECP2/MeCP2 expression and function in neurodevelopmental disorders has been the focus of intensive research. However, despite the critical importance of precisely controlled levels of MeCP2 expression in the brain, the underlying regulatory mechanisms have been understudied. Here, we report the correlation between the expression of Mecp2 isoforms and DNA methylation patterns at the Mecp2 REs at different stages of NSC differentiation. Further, we demonstrate the effect of dynamic changes in DNA methylation induced by exposure and withdrawal of decitabine on the expression of Mecp2/MeCP2 isoforms.