The landscape of the genomic imprinting and DNA methylation at the bovine SGCE/PEG10 locus
Genomic imprinting is a epigenetic regulation in mammals in which a small subset of genes is monoallelically expressed dependent on their parental origin. Imprinted genes are critical for fetal and placental development, metabolism and neuronal function. A large imprinted domain, SGCE/PEG10 locus, was located in human chromosome 7q21s and mouse proximal chromosome 6. However, genomic imprinting of bovine SGCE/PEG10 cluster had not been systematically studied. In this study, we investigated allele expression of 14 genes (CALCR, TFPI2, GNG11, GNGT1, BET1, COL1A2, CASD1, SGCE, PEG10, PPP1R9A, PON1, PON3, PON2, and ASB4) of SGCE/PEG10 locus in bovine somatic tissues and term placenta using single nucleotide polymorphism (SNP)-based sequencing method. Except for SGCE and PEG10, two conserved paternally expressed genes in human and mice, five other paternally expressed genes (TFPI2, GNG11, ASB4, PON1, and PON3) were found. TFPI2, GNG11 and ASB4 were paternally expressed in tissues and placenta. PON1 showed paternal expression only in placenta. PON3 exhibited tissue-specific monoallelic expression. Three genes, BET1, COL1A2, and CASD1, exhibited tissue-specific monoallelic expression. CALCR showed monoallelic expression in tissues but biallelic expression in the placenta. Three genes, GNGT1, PPP1R9A, and PON2, escaped genomic imprinting and showed biallelic expression both in tissues and placentas. In addition, the DNA methylation of the ten CpG rich regions was characterized using bisulfite sequencing polymerase chain reaction (PCR) analyses, which associated with TFPI2, CASD1, SGCE/PEG10, PON3, ASB4, CALCR, GNG11, BET1, COL1A2, and PON1 genes. Five differentially methylated regions (DMRs) were found to be associated with the allelic expression of TFPI2, COL1A2, SGCE-PEG10, PON3, and ASB4 genes, respectively. The SGCE/PEG10 DMR is a maternally hypermethylated germline DMR (gDMR), but TFPI2, COL1A2, PON3, and ASB4 DMRs are secondary DMRs (sDMRs). We identified five novel bovine imprinted genes (GNG11, BET1, COL1A2, CASD1, and PON1) and four sDMRs were in SGCE/PEG10 locus. Compared to humans and mice, the genomic imprinting of bovine SGCE/PEG10 locus seems to more diverse.