OBJECTIVES: Methyl-CpG binding protein 2 (MeCP2) is a ubiquitous epigenetic 
factor that represses gene expression by modifying chromatin. Mutations in the 
MeCP2 gene cause Rett syndrome, a progressive neurodevelopmental disorder. 
Recent studies also have shown that MeCP2 plays a role in carcinogenesis. 
Specifically, functional ablation of MeCP2 suppresses cell growth and leads to 
the proliferation of cancer cells. However, MeCP2's function in adult tissues 
remains poorly understood. We utilized a weight matrix-based comparison software 
to identify transcription factor binding site (TFBS) of MeCP2-regulated genes, 
which were recognized by cDNA microarray analysis.
METHODS: MeCP2 expression was silenced using annealed siRNA in HEK293 cells, and 
then a cDNA microarray analysis was performed. Functional analysis was carried 
out, and transcriptional levels in target genes regulated by MeCP2 were 
investigated. TFBS analysis was done within genes selected by the cDNA 
microarray analysis, using a weight matrix-based program and the TRANSFAC 6.0 
database.
RESULTS: Among the differentially expressed genes with a change in expression 
greater than two-fold, 189 genes were up-regulated and 91 genes were 
down-regulated. Genes related to apoptosis and cell proliferation (JUN, FOSL2, 
CYR61, SKIL, ATF3, BMABI, BMPR2, RERE, and FALZ) were highly up-regulated. Genes 
with anti-apoptotic and anti-proliferative functions (HNRPA0, HIS1, and FOXC1) 
were down-regulated. Using TFBS analysis within putative promoters of novel 
candidate target genes of MeCP2, disease-related transcription factors were 
identified.
CONCLUSIONS: The present results provide insights into the new target genes 
regulated by MeCP2 under epigenetic control. This information will be valuable 
for further studies aimed at clarifying the pathogenesis of Rett syndrome and 
neoplastic diseases.