ABCG2 is a ubiquitous ATP-binding cassette transmembrane protein that is important in clinical drug resistance. Little is known about the mechanism(s) regulating the expression of ABCG2. We hypothesized that DNA methylation could play a role in the epigenetic regulation of ABCG2 gene expression. The promoter methylation status of three renal carcinoma cell lines was assessed with restriction enzyme digestion-coupled PCR and bisulfite genomic sequencing. Both UOK121 and UOK143, with known methylation of the VHL promoter, showed induction of ABCG2 expression after 5-aza-2-deoxycytidine (5-aza-dC) treatment, suggesting that aberrant methylation of the ABCG2 gene was associated with gene silencing. In vitro methylation of the ABCG2 promoter-driven luciferase reporter vector resulted in a significant inhibition of transcription. Our data suggested that the ABCG2 gene is regulated coordinately at both histone and DNA levels. A chromatin immunoprecipitation assay demonstrated that the methylated promoter in UOK121 and UOK143, but not the unmethylated one in UOK181, is associated with the methyl CpG binding domain proteins (MBDs), MBD2 and MeCP2. Histone deacetylase 1 and a corepressor, mSin3A, were identified binding to the promoter region containing the CpG island, thereby suppressing ABCG2 transcription. Reactivation of ABCG2 was achieved by treatment with 5-aza-dC, a demethylating agent, concomitant with the release of MBDs from the promoter. Furthermore, the association of methylated lysine 9 on histone H3, a hallmark of promoter methylation, with the promoter was reduced following 5-aza-dC treatment. These data suggest that DNA methylation-dependent formation of a repressor complex in the CpG island contributes to inactivation of ABCG2.ABCG2 (previously named BCRP, MXR, or ABCP) is an ATP-binding cassette half-transporter, originally identified as a multidrug resistance transporter (2, 15, 39). It is highly expressed in many normal tissues, including the epithelium of the small intestine and the liver canalicular membrane (36). In addition to conferring resistance in cancer cells to chemotherapeutic agents such as mitoxantrone, topotecan, and methotrexate (14, 56), ABCG2 has been shown to mediate apically directed drug transport and to play a significant role in absorption, distribution, and elimination of its substrates (8,55).To date, little is known about the molecular mechanisms controlling ABCG2 expression. Characterization of the ABCG2 gene promoter revealed that it is a TATA-less promoter with several Sp1, AP1, and AP2 sites and a CCAAT box downstream from a putative CpG island. Both positive and negative cis-regulatory elements have been suggested in the ABCG2 promoter (4). Although the role of these cis-elements in ABCG2 transcription has not been assessed, recent studies have demonstrated functional hormone (16) and hypoxia (32) response elements in the ABCG2 promoter. Early observations in our laboratory revealed that ABCG2 expression in some renal clear cell carcinoma (RCC) cell lines could be upregula...