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

IF 1.8 3区生物学 Q2 AGRICULTURE, DAIRY & ANIMAL SCIENCE Animal genetics Pub Date : 2024-04-09 DOI:10.1111/age.13429

Yinjiao Zhang, Cui Zhang, Weina Chen, Haonan Huo, Shujing Li, Wenli Yu, Lanjie Jin, Kun Wang, Shijie Li

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Abstract

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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牛 SGCE/PEG10 基因座的等位基因表达和 DNA 甲基化状况

基因组印记是哺乳动物的一种表观遗传调控，其中一小部分基因的单平行表达取决于其亲本来源。人类染色体 7q21s 和小鼠近端 6 号染色体上有一个大的印记域，即 SGCE/PEG10 基因座。然而，牛 SGCE/PEG10 簇的基因组印迹尚未得到系统研究。本研究采用基于单核苷酸多态性（SNP）的测序方法，研究了牛体细胞组织和足月胎盘中 SGCE/PEG10 基因座 14 个基因的等位基因表达。除了 SGCE 和 PEG10 这两个在人类和小鼠中保守的父系表达基因外，还有五个基因（TFPI2、GNG11、ASB4、PON1 和 PON3）是父系表达的。三个基因（BET1、COL1A2 和 CASD1）表现出组织特异性单倍表达。CALCR 在组织中呈单倍表达，但在胎盘中呈双倍表达。三个基因，即 GNGT1、PPP1R9A 和 PON2，在牛体内呈双复制表达。发现五个差异甲基化区域（DMR）分别与 TFPI2、COL1A2、SGCE/PEG10、PON3 和 ASB4 基因的等位基因表达相关。SGCE/PEG10 DMR是母系高甲基化的种系DMR，而TFPI2、COL1A2、PON3和ASB4 DMR则是次级DMR。总之，我们在 SGCE/PEG10 基因座上发现了五个新的牛印迹基因（GNG11、BET1、COL1A2、CASD1 和 PON1）和四个次级 DMR。

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来源期刊

Animal genetics 生物-奶制品与动物科学

CiteScore

4.60

自引率

4.20%

发文量

115

审稿时长

5 months

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.