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":1,"journal":{"name":"Accounts of Chemical Research","volume":null,"pages":null},"PeriodicalIF":16.4000,"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\":1,\"journal\":{\"name\":\"Accounts of Chemical Research\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":16.4000,\"publicationDate\":\"2024-04-09\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Accounts of Chemical Research\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://onlinelibrary.wiley.com/doi/10.1111/age.13429\",\"RegionNum\":1,\"RegionCategory\":\"化学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"CHEMISTRY, MULTIDISCIPLINARY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Accounts of Chemical Research","FirstCategoryId":"99","ListUrlMain":"https://onlinelibrary.wiley.com/doi/10.1111/age.13429","RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"CHEMISTRY, MULTIDISCIPLINARY","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.
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Accounts of Chemical Research presents short, concise and critical articles offering easy-to-read overviews of basic research and applications in all areas of chemistry and biochemistry. These short reviews focus on research from the author’s own laboratory and are designed to teach the reader about a research project. In addition, Accounts of Chemical Research publishes commentaries that give an informed opinion on a current research problem. Special Issues online are devoted to a single topic of unusual activity and significance.
Accounts of Chemical Research replaces the traditional article abstract with an article "Conspectus." These entries synopsize the research affording the reader a closer look at the content and significance of an article. Through this provision of a more detailed description of the article contents, the Conspectus enhances the article's discoverability by search engines and the exposure for the research.
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