DNA methylation analysis and identification of a novel antisense transcript in the Peg3 imprinted domain

Abstract

Genomic imprinting is a process that leads to the silencing of one allele of a gene in a parent of origin specific manner. Genes that are involved in this process are often regulated in clusters, one of which is the Peg3 (Paternally expressed gene 3) imprinted domain. We investigated this region for both CpG islands and long antisense transcripts, two common features of imprinted gene clusters. First, we performed a systematic survey of DNA methylation status of the CpG islands in this region of the mouse, cow, and human genomes. We identified two previously unreported differentially methylated regions (DMR): one in the promoter region of mouse Zim3 and another in the promoter region of human USP29. The PEG3-CpG island is the only DMR that is conserved among these three species. PEG3 has been implicated in several types of cancer, so we examined the methylation status of several CpG islands in this region using human tumor derived DNA. The CpG islands near PEG3 and USP29 both showed hypermethylation in DNA derived from breast and ovarian tumors. Second, we identified an antisense transcript to ZIM2 (zinc finger imprinted gene 2) called ZIM2as in the human, chimpanzee, and orangutan. In non-primate mammals, the 5’ side of the Peg3 imprinted domain is bounded by a cluster of olfactory receptor (OLFR) genes which may curtail the spread of imprinting. We report the presence of two previously unreported DMRs near the ZIM2as promoter region. The CpG island distal to ZIM2as was methylated allele-specifically in the human testis, while the CpG island proximal to the ZIM2as promoter showed a mosaic methylation pattern in the chimpanzee. Two CpG islands near the promoter region of ZIM2as showed different methylation patterns in these three species. Overall, this work provides a firm foundation for future studies of the Peg3 imprinted domain. It represents the first systematic study of DNA methylation in the Peg3 imprinted region. It also describes an antisense transcript that has formed in the great ape PEG3 imprinted domain which may control the extension of this imprinted domain.