AIM: The aim of the present study was to examine DNA methylation and histone 
modification changes in hepatocellular carcinomas (HCC).
METHODS: DNA methylation in the P16, RASSF1a, progesterone receptor (PGR) and 
estrogen receptor alpha (ERalpha) promoters was determined by quantitative 
bisulfite-pyrosequencing technique in HCC patients. Histone H3-lysine (K) 4, 
H3-K9 and H3-K27 modifications in all these four genes were examined by 
chromatin immunoprecipitation (ChIP) assay in HCC cell lines. Expression of two 
DNA methyltransferases (DNMT1 and DNMT3b) and three histone methyltransferases 
(SUV39H1, G9a and EZH2) in HCC patients was measured by real-time polymerase 
chain reaction.
RESULTS: Aberrant DNA methylation was detected in all the HCC. Patients with DNA 
methylation in the RASSF1a, PGR andERalpha promoters in cancers also had 
substantial DNA methylation in their non-cancerous liver tissues, whereas DNA 
methylation in the P16 promoter was cancer specific. Epigenetic states in HCC 
cell lines showed that silencing of P16 and RASSF1a depended on DNA methylation 
and histone H3-K9 methylation. However, silencing of the PGR and ERalpha genes 
was more closely related to H3-K27 methylation rather than DNA methylation. 
Consistent with the alteration of histone status, higher expression of G9a and 
EZH2 was found in HCC than in non-cancerous liver tissues (P < 0.01).
CONCLUSION: These data suggest that multiple epigenetic silencing mechanisms are 
inappropriately active in HCC cells.