Yinjiao Zhang, Cui Zhang, Weina Chen, Haonan Huo, Shujing Li, Wenli Yu, Lanjie Jin, Kun Wang, Shijie Li
{"title":"牛 SGCE/PEG10 基因座的等位基因表达和 DNA 甲基化状况","authors":"Yinjiao Zhang, Cui Zhang, Weina Chen, Haonan Huo, Shujing Li, Wenli Yu, Lanjie Jin, Kun Wang, Shijie Li","doi":"10.1111/age.13429","DOIUrl":null,"url":null,"abstract":"<p>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, <i>SGCE/PEG10</i> locus, is located on human chromosome 7q21s and mouse proximal chromosome 6. However, genomic imprinting of bovine <i>SGCE/PEG10</i> cluster has not been systematically studied. In this study, we investigated allele expression of 14 genes of the <i>SGCE/PEG10</i> locus in bovine somatic tissues and term placenta using a single nucleotide polymorphism (SNP)-based sequencing method. In addition to <i>SGCE</i> and <i>PEG10</i>, two conserved paternally expressed genes in human and mice, five other genes (<i>TFPI2</i>, <i>GNG11</i>, <i>ASB4</i>, <i>PON1</i>, and <i>PON3</i>) were paternally expressed. Three genes, <i>BET1</i>, <i>COL1A2</i>, and <i>CASD1</i>, exhibited tissue-specific monoallelic expression. <i>CALCR</i> showed monoallelic expression in tissues but biallelic expression in the placenta. Three genes, <i>GNGT1</i>, <i>PPP1R9A</i>, and <i>PON2</i>, showed biallelic expression in cattle. Five differentially methylated regions (DMRs) were found to be associated with the allelic expression of <i>TFPI2</i>, <i>COL1A2</i>, <i>SGCE/PEG10</i>, <i>PON3</i>, and <i>ASB4</i> genes, respectively. The <i>SGCE/PEG10</i> DMR is a maternally hypermethylated germline DMR, but <i>TFPI2</i>, <i>COL1A2</i>, <i>PON3</i>, and <i>ASB4</i> DMRs are secondary DMRs. In summary, we identified five novel bovine imprinted genes (<i>GNG11</i>, <i>BET1</i>, <i>COL1A2</i>, <i>CASD1</i>, and <i>PON1</i>) and four secondary DMRs at the <i>SGCE/PEG10</i> locus.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":1.8000,"publicationDate":"2024-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"The landscape of allelic expression and DNA methylation at the bovine SGCE/PEG10 locus\",\"authors\":\"Yinjiao Zhang, Cui Zhang, Weina Chen, Haonan Huo, Shujing Li, Wenli Yu, Lanjie Jin, Kun Wang, Shijie Li\",\"doi\":\"10.1111/age.13429\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p>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, <i>SGCE/PEG10</i> locus, is located on human chromosome 7q21s and mouse proximal chromosome 6. However, genomic imprinting of bovine <i>SGCE/PEG10</i> cluster has not been systematically studied. In this study, we investigated allele expression of 14 genes of the <i>SGCE/PEG10</i> locus in bovine somatic tissues and term placenta using a single nucleotide polymorphism (SNP)-based sequencing method. In addition to <i>SGCE</i> and <i>PEG10</i>, two conserved paternally expressed genes in human and mice, five other genes (<i>TFPI2</i>, <i>GNG11</i>, <i>ASB4</i>, <i>PON1</i>, and <i>PON3</i>) were paternally expressed. Three genes, <i>BET1</i>, <i>COL1A2</i>, and <i>CASD1</i>, exhibited tissue-specific monoallelic expression. <i>CALCR</i> showed monoallelic expression in tissues but biallelic expression in the placenta. Three genes, <i>GNGT1</i>, <i>PPP1R9A</i>, and <i>PON2</i>, showed biallelic expression in cattle. Five differentially methylated regions (DMRs) were found to be associated with the allelic expression of <i>TFPI2</i>, <i>COL1A2</i>, <i>SGCE/PEG10</i>, <i>PON3</i>, and <i>ASB4</i> genes, respectively. The <i>SGCE/PEG10</i> DMR is a maternally hypermethylated germline DMR, but <i>TFPI2</i>, <i>COL1A2</i>, <i>PON3</i>, and <i>ASB4</i> DMRs are secondary DMRs. In summary, we identified five novel bovine imprinted genes (<i>GNG11</i>, <i>BET1</i>, <i>COL1A2</i>, <i>CASD1</i>, and <i>PON1</i>) and four secondary DMRs at the <i>SGCE/PEG10</i> locus.</p>\",\"PeriodicalId\":7905,\"journal\":{\"name\":\"Animal genetics\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":1.8000,\"publicationDate\":\"2024-04-09\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Animal genetics\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://onlinelibrary.wiley.com/doi/10.1111/age.13429\",\"RegionNum\":3,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"AGRICULTURE, DAIRY & ANIMAL SCIENCE\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Animal genetics","FirstCategoryId":"99","ListUrlMain":"https://onlinelibrary.wiley.com/doi/10.1111/age.13429","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"AGRICULTURE, DAIRY & ANIMAL SCIENCE","Score":null,"Total":0}
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.
期刊介绍：
Animal Genetics reports frontline research on immunogenetics, molecular genetics and functional genomics of economically important and domesticated animals. Publications include the study of variability at gene and protein levels, mapping of genes, traits and QTLs, associations between genes and traits, genetic diversity, and characterization of gene or protein expression and control related to phenotypic or genetic variation.
The journal publishes full-length articles, short communications and brief notes, as well as commissioned and submitted mini-reviews on issues of interest to Animal Genetics readers.
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