The landscape of allelic expression and DNA methylation at the bovine SGCE/PEG10 locus.

Genomic imprinting is an epigenetic regulation in mammals in which a small subset of genes is monoallelically expressed dependent on their parental origin. A large imprinted domain, SGCE/PEG10 locus, is located on human chromosome 7q21s and mouse proximal chromosome 6. However, genomic imprinting of bovine SGCE/PEG10 cluster has not been systematically studied. In this study, we investigated allele expression of 14 genes of the SGCE/PEG10 locus in bovine somatic tissues and term placenta using a single nucleotide polymorphism (SNP)-based sequencing method. In addition to SGCE and PEG10, two conserved paternally expressed genes in human and mice, five other genes (TFPI2, GNG11, ASB4, PON1, and PON3) were paternally expressed. 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, showed biallelic expression in cattle. 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, but TFPI2, COL1A2, PON3, and ASB4 DMRs are secondary DMRs. In summary, we identified five novel bovine imprinted genes (GNG11, BET1, COL1A2, CASD1, and PON1) and four secondary DMRs at the SGCE/PEG10 locus.

PMM2 and NARFL are paternally imprinted genes in bovines.

In mammals, imprinted genes are required for both fetal development and postnatal growth. A novel candidate imprinted locus was found on human chromosome 16, and maternal uniparental disomy of this locus can cause a lethal developmental lung disease in human newborns. The PMM2 and NARFL genes are located in this region and its homologous region in cattle is on chromosome 25. Currently, there is no report on the genomic imprinting of the PMM2 and NARFL genes. In this study, we demonstrated that PMM2 and NARFL are two paternally imprinted genes in bovines using an SNP-based method. In addition, two differentially methylated regions of paternal methylation were found in the promoter region and the third intron of the bovine NARFL gene, which may be involved in regulating its imprinted expression. However, we did not find differential methylation in the promoter region or the seventh intron of the bovine PMM2 gene.

IMPACT and OSBPL1A are two isoform-specific imprinted genes in bovines.

The epigenetic process of genomic imprinting results in the monoallelic expression of genes based on their parental origin. Comparative analysis of imprinted genes between species is useful for investigating the biological significance and regulatory mechanisms of genomic imprinting. Mouse Impact is an imprinted gene, but its human ortholog IMPACT escapes genomic imprinting. Hrh4 and Osbpl1a are the two nearest neighbors of the Impact located in distal and proximal regions, respectively. This study aims to assess the allelic expression of bovine IMPACT, OSBPL1A and HRH4 genes and examine the differentially methylated regions (DMRs) associated with these three genes. Based on an expressed single-nucleotide polymorphism (SNP) approach, we found that both the IMPACT and OSBPL1A genes exhibit isoform-specific monoallelic expression in bovine adult tissues. In the seven detected bovine IMPACT transcripts, only one transcript variant (X6) is monoallelically expressed in bovine adult tissues and paternally expressed in the placenta. However, no DMR was found in the promoter region of the IMPACT gene. We obtained five transcript variants (V1-V5) of the bovine OSBPL1A gene of different lengths that start transcription from distinct alternative promoters by RT-PCR. Only the longest variant V1 was found to be expressed monoallelically in bovine adult tissues and a DMR was identified in its promoter region using the bisulfite sequencing method. Thus, the DMR in OSBPL1A V1 promoter region may contribute to its isoform-specific monoallelic expression. The bovine HRH4 gene is expressed biallelically. Hypermethylation was observed in brains without HRH4 expression, while hypomethylation was found in the spleens with HRH4 expression, so and the level of DNA methylation in the promoter seemed to be related to its expression in tissues.

Genomic imprinting of the IGF2R/AIR locus is conserved between bovines and mice.

Genomic imprinting is an epigenetic phenomenon that leads to genes monoallelically expressed in a parent-of-origin-specific manner and plays an important role in the embryonic development and postnatal growth of mammals. Imprinted genes usually occur in clusters in a chromosomal region and are regulated by a cis-acting imprinting control region that involves differential DNA methylation modification. Igf2r, Slc22a2 and Slc22a3 are three maternally expressed genes on mouse chromosome 17. The paternally expressed long noncoding RNA (lncRNA) Air and the nonimprinted gene Slc22a1 are also located in the imprinted region. Comparative characterization of imprinted clusters between species is useful for us to understand the biological significance and epigenetic regulating mechanism of genomic imprinting. The aim of this study was to analyze the allelic expression pattern of AIR and SLC22A1-3 genes in cattle and to determine the role of DNA methylation in regulating gene expression. Allelic expression analysis was performed in bovine adult tissues and term placenta using an SNP-based approach. We found that IGF2R, AIR and SLC22A3 were monoallelically expressed in all detected bovine somatic tissues, including heart, liver, spleen, lung, kidney, muscle, fat and brain. In bovine placenta, IGF2R and SLC22A3 are maternally expressed; however, the AIR gene is paternally expressed. Tissue-specific monoallelic expression of SLC22A2 is detected in bovines, with monoallelic expression in the spleen and brain but biallelic expression in kidney tissues. SLC22A1 is only detected in bovine liver and kidney tissues and is biallelicly expressed, which is consistent with the imprint expression in mice. To determine the possible role of DNA methylation in regulating the monoallelic/imprinted expression of bovine IGF2R, AIR, SLC22A2, and SLC22A3 genes, we analyzed the DNA methylation status of CpG islands in the first exon of SLC22A2, the promoter region of SLC22A3 and region 2 in the second intron of the IGF2R gene by bisulfite sequencing. Two differentially methylated regions (DMRs) were detected in the first exon of bovine SLC22A3 and the common regions of IGF2R and AIR. This suggests that DNA methylation is involved in the regulation of monoallelic/imprinted expression of IGF2R, AIR and SLC22A3 genes in cattle.

Conservation of Imprinting and Methylation of MKRN3, MAGEL2 and NDN Genes in Cattle.

Genomic imprinting is the epigenetic mechanism of transcriptional regulation that involves differential DNA methylation modification. Comparative analysis of imprinted genes between species can help us to investigate the biological significance and regulatory mechanisms of genomic imprinting. MKRN3, MAGEL2 and NDN are three maternally imprinted genes identified in the human PWS/AS imprinted locus. This study aimed to assess the allelic expression of MKRN3, MAGEL2 and NDN and to examine the differentially methylated regions (DMRs) of bovine PWS/AS imprinted domains. An expressed single-nucleotide polymorphism (SNP)-based approach was used to investigate the allelic expression of MKRN3, MAGEL2 and NDN genes in bovine adult tissues and placenta. Consistent with the expression in humans and mice, we found that the MKRN3, MAGEL2 and NDN genes exhibit monoallelic expression in bovine somatic tissues and the paternal allele expressed in the bovine placenta. Three DMRs, PWS-IC, MKRN3 and NDN DMR, were identified in the bovine PWS/AS imprinted region by analysis of the DNA methylation status in bovine tissues using the bisulfite sequencing method and were located in the promoter and exon 1 of the SNRPN gene, NDN promoter and 5' untranslated region (5'UTR) of MKRN3 gene, respectively. The PWS-IC DMR is a primary DMR inherited from the male or female gamete, but NDN and MKRN3 DMR are secondary DMRs that occurred after fertilization by examining the methylation status in gametes.