Identification of CpG islands hypermethylated in tumor and transformed cells by the methylation-sensitive arbitrarily primed polymerase chain reaction

Carcinogenesis is associated with hypermethylation of certain DNA regions, which can suppress transcription of the corresponding genes. With a version of methylation-sensitive arbitrarily primed polymerase chain reaction (MS- AP-PCR), three fragments were identified that are hypermethylated in human cervical carcinomas and transformed hamster cells expressing exogenous h-N- ras. The fragments were cloned, sequenced, and shown to possess properties characteristic of CpG islands. Of these, one was identified as a fragment o f the beta 3A-adaptin gene and two showed no homology to known sequences. M S PCR with specific primers showed that the CpG island of the beta 3A-adapt in gene was hypermethylated in four (15%) of 27 cervical carcinomas examine d. Southern blotting with the cloned hamster DNA fragment confirmed hyperme thylation of the corresponding CpG island in three hamster cell lines expre ssing N-ras. The method proved useful for identification of CpG islands, in cluding those hypermethylated in tumor and transformed cells.