Estrogens play a critical role in brain development by acting on areas that 
express estrogen receptors. In the rodent cortex, estrogen receptor alpha (ER 
alpha) mRNA expression is high early in postnatal development but declines 
starting at postnatal day (PND) 10 and is virtually absent in the adult cortex. 
The mechanisms controlling this regulation are largely unknown. Methylation is 
important for gene silencing during development in many tissues, including the 
brain. In the present study, we examined the methylation status of ER alpha 5' 
untranslated exons during early postnatal development in male and female mice 
using methylation-specific PCR and pyrosequencing. Several regions of ER alpha 
promoter displayed a significant increase in methylation at PND 18 and 25 
compared with PND 4. DNA methyltransferases (DNMT) are important for the 
initiation and maintenance of methylation. Real-time PCR showed that DNMT3A, the 
de novo DNMT peaked at PND 10 and was decreased by PND 25. DNMT1, which is 
important for maintenance of methylation, increased across development and 
stayed high in adult cortex. The methyl-CpG-binding protein 2 (MeCP2) is also 
important for stabilization of methylation. A chromatin immunoprecipitation 
assay showed a correlation between association of MeCP2 with ER alpha promoter 
and the increase in methylation and decrease in ER alpha expression after PND 
10. In mice containing a mutant MeCP2 protein, ER alpha mRNA expression and 
promoter methylation patterns across development were different compared with 
wild-type mice. These data suggest that methylation of ER alpha promoters 
regulates ER alpha mRNA expression in the cortex during postnatal development in 
a MeCP2-dependent fashion.