Aberrant methylation of promoter cytosine guanine dinucleotide (CpG) islands is known to be responsible for the alteration and silencing of cancer genes. The data presented here show that most methylations of Estrogen Receptorα (ERα) and ERβ are found at or near the transcriptional factor binding sites in the breast cancer tissues.

Fifty archival breast cancer tissues and twenty-five normal tissues were selected and the status of the methylation and the transcription were investigated by bisulfite genomic sequencing and reverse transcription (RT) PCR.

Consequently, the hypermethylation of ERα and ERβ genes was found in 66.0% and 50.0% of 50 breast cancers, respectively. In particular, the methylation sites were frequently located near the CCAAT box (-363 and -375) for the ERα gene, and at or adjacent to binding sites of GATA (-217, -302) and Sp1 (+224, +227, +160) for the ERβ gene. The methylations at or near the binding sites were observed in most of the methylated cancers (ERα 87.9%, and ERβ 84.0%). The methylated cases were negatively correlated with the expression of ERα and ERβ RNA (P<0.01). In particular, tumors with CpG methylation of ERα and ERβ at or near the binding sites did not express mRNA, whereas those CpG methylation outside the sites showed moderate expression. Four tumors with methylated ERα genes at sites unrelated to the binding sites showed higher levels of protein expression than those with methylation at or near the sites (P=0.01).

Although the number of samples was relatively small, our results suggest that DNA methylation in ERα and ERβ appears to take significant effect on transcriptional silencing and is most often present in the CpG sites at or near the putative transcriptional factor binding sites. We believe this finding offers a clue to the initiation or spread pattern of CpG methylation in human breast cancer.