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Zhang Y, Zhang C, Chen W, Huo H, Li S, Yu W, Jin L, Wang K, Li S. The landscape of allelic expression and DNA methylation at the bovine SGCE/PEG10 locus. Anim Genet 2024; 55:452-456. [PMID: 38594908 DOI: 10.1111/age.13429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/25/2024] [Accepted: 03/31/2024] [Indexed: 04/11/2024]
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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Affiliation(s)
- Yinjiao Zhang
- College of Life Science, Agricultural University of Hebei, Hebei Baoding, China
| | - Cui Zhang
- College of Life Science, Agricultural University of Hebei, Hebei Baoding, China
| | - Weina Chen
- College of Medical Science, Hebei University, Hebei Baoding, China
| | - Haonan Huo
- College of Life Science, Agricultural University of Hebei, Hebei Baoding, China
| | - Shujing Li
- Shijiazhuang Tianquan Elite Dairy Ltd, Shijiazhuang, Hebei, China
| | - Wenli Yu
- Shijiazhuang Tianquan Elite Dairy Ltd, Shijiazhuang, Hebei, China
| | - Lanjie Jin
- College of Life Science, Agricultural University of Hebei, Hebei Baoding, China
| | - Kun Wang
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
- Key Laboratory of Crop Cultivation Physiology and Green Production in Hebei Province, Shijiazhuang, China
| | - Shijie Li
- College of Life Science, Agricultural University of Hebei, Hebei Baoding, China
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Hossain MN, Gao Y, Hatfield MJ, de Avila JM, McClure MC, Du M. Cold exposure impacts DNA methylation patterns in cattle sperm. Front Genet 2024; 15:1346150. [PMID: 38444759 PMCID: PMC10912962 DOI: 10.3389/fgene.2024.1346150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 01/23/2024] [Indexed: 03/07/2024] Open
Abstract
DNA methylation is influenced by various exogenous factors such as nutrition, temperature, toxicants, and stress. Bulls from the Pacific Northwest region of the United States and other northern areas are exposed to extreme cold temperatures during winter. However, the effects of cold exposure on the methylation patterns of bovine sperm remain unclear. To address, DNA methylation profiles of sperm collected during late spring and winter from the same bulls were analyzed using whole genome bisulfite sequencing (WGBS). Bismark (0.22.3) were used for mapping the WGBS reads and R Bioconductor package DSS was used for differential methylation analysis. Cold exposure induced 3,163 differentially methylated cytosines (DMCs) with methylation difference ≥10% and a q-value < 0.05. We identified 438 differentially methylated regions (DMRs) with q-value < 0.05, which overlapped with 186 unique genes. We also identified eight unique differentially methylated genes (DMGs) (Pax6, Macf1, Mest, Ubqln1, Smg9, Ctnnb1, Lsm4, and Peg10) involved in embryonic development, and nine unique DMGs (Prmt6, Nipal1, C21h15orf40, Slc37a3, Fam210a, Raly, Rgs3, Lmbr1, and Gan) involved in osteogenesis. Peg10 and Mest, two paternally expressed imprinted genes, exhibited >50% higher methylation. The differential methylation patterns of six distinct DMRs: Peg10, Smg9 and Mest related to embryonic development and Lmbr1, C21h15orf40 and Prtm6 related to osteogenesis, were assessed by methylation-specific PCR (MS-PCR), which confirmed the existence of variable methylation patterns in those locations across the two seasons. In summary, cold exposure induces differential DNA methylation patterns in genes that appear to affect embryonic development and osteogenesis in the offspring. Our findings suggest the importance of replicating the results of the current study with a larger sample size and exploring the potential of these changes in affecting offspring development.
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Affiliation(s)
- Md Nazmul Hossain
- Nutrigenomics and Growth Biology Laboratory, Department of Animal Sciences, Washington State University, Pullman, WA, United States
- Department of Livestock Production and Management, Faculty of Veterinary, Animal, and Biomedical Sciences, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Yao Gao
- Nutrigenomics and Growth Biology Laboratory, Department of Animal Sciences, Washington State University, Pullman, WA, United States
| | - Michael J. Hatfield
- Nutrigenomics and Growth Biology Laboratory, Department of Animal Sciences, Washington State University, Pullman, WA, United States
| | - Jeanene M. de Avila
- Nutrigenomics and Growth Biology Laboratory, Department of Animal Sciences, Washington State University, Pullman, WA, United States
| | | | - Min Du
- Nutrigenomics and Growth Biology Laboratory, Department of Animal Sciences, Washington State University, Pullman, WA, United States
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Hubert JN, Perret M, Riquet J, Demars J. Livestock species as emerging models for genomic imprinting. Front Cell Dev Biol 2024; 12:1348036. [PMID: 38500688 PMCID: PMC10945557 DOI: 10.3389/fcell.2024.1348036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 01/19/2024] [Indexed: 03/20/2024] Open
Abstract
Genomic imprinting is an epigenetically-regulated process of central importance in mammalian development and evolution. It involves multiple levels of regulation, with spatio-temporal heterogeneity, leading to the context-dependent and parent-of-origin specific expression of a small fraction of the genome. Genomic imprinting studies have therefore been essential to increase basic knowledge in functional genomics, evolution biology and developmental biology, as well as with regard to potential clinical and agrigenomic perspectives. Here we offer an overview on the contribution of livestock research, which features attractive resources in several respects, for better understanding genomic imprinting and its functional impacts. Given the related broad implications and complexity, we promote the use of such resources for studying genomic imprinting in a holistic and integrative view. We hope this mini-review will draw attention to the relevance of livestock genomic imprinting studies and stimulate research in this area.
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Affiliation(s)
| | | | | | - Julie Demars
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France
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Ahn J, Hwang IS, Park MR, Hwang S, Lee K. Imprinting at the KBTBD6 locus involves species-specific maternal methylation and monoallelic expression in livestock animals. J Anim Sci Biotechnol 2023; 14:131. [PMID: 37817239 PMCID: PMC10565993 DOI: 10.1186/s40104-023-00931-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/21/2023] [Indexed: 10/12/2023] Open
Abstract
BACKGROUND The primary differentially methylated regions (DMRs) which are maternally hypermethylated serve as imprinting control regions (ICRs) that drive monoallelic gene expression, and these ICRs have been investigated due to their implications in mammalian development. Although a subset of genes has been identified as imprinted, in-depth comparative approach needs to be developed for identification of species-specific imprinted genes. Here, we examined DNA methylation status and allelic expression at the KBTBD6 locus across species and tissues and explored potential mechanisms of imprinting. RESULTS Using whole-genome bisulfite sequencing and RNA-sequencing on parthenogenetic and normal porcine embryos, we identified a maternally hypermethylated DMR between the embryos at the KBTBD6 promoter CpG island and paternal monoallelic expression of KBTBD6. Also, in analyzed domesticated mammals but not in humans, non-human primates and mice, the KBTBD6 promoter CpG islands were methylated in oocytes and/or allelically methylated in tissues, and monoallelic KBTBD6 expression was observed, indicating livestock-specific imprinting. Further analysis revealed that these CpG islands were embedded within transcripts in porcine and bovine oocytes which coexisted with an active transcription mark and DNA methylation, implying the presence of transcription-dependent imprinting. CONCLUSIONS In this study, our comparative approach revealed an imprinted expression of the KBTBD6 gene in domesticated mammals, but not in humans, non-human primates, and mice which implicates species-specific evolution of genomic imprinting.
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Affiliation(s)
- Jinsoo Ahn
- Department of Animal Sciences, The Ohio State University, Columbus, OH 43210 USA
| | - In-Sul Hwang
- Animal Biotechnology Division, Rural Development Administration, National Institute of Animal Science, Jeonbuk, 55365 Republic of Korea
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, Columbia University, New York, NY 10032 USA
| | - Mi-Ryung Park
- Animal Biotechnology Division, Rural Development Administration, National Institute of Animal Science, Jeonbuk, 55365 Republic of Korea
| | - Seongsoo Hwang
- Animal Welfare Research Team, National Institute of Animal Science, RDA, 1500, Kongjwipatjwi-ro, Jeollabuk-do, 55365 Republic of Korea
| | - Kichoon Lee
- Department of Animal Sciences, The Ohio State University, Columbus, OH 43210 USA
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Chen F, Ma B, Lin Y, Luo X, Xu T, Zhang Y, Chen F, Li Y, Zhang Y, Luo B, Zhang Q, Xie X. Comparative maternal protein profiling of mouse biparental and uniparental embryos. Gigascience 2022; 11:6691138. [PMID: 36056732 PMCID: PMC9440387 DOI: 10.1093/gigascience/giac084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 06/29/2022] [Accepted: 08/01/2022] [Indexed: 12/25/2022] Open
Abstract
Background Maternal proteins have important roles during early embryonic development. However, our understanding of maternal proteins is still very limited. The integrated analysis of mouse uniparental (parthenogenetic) and biparental (fertilized) embryos at the protein level creates a protein expression landscape that can be used to explore preimplantation mouse development. Results Using label-free quantitative mass spectrometry (MS) analysis, we report on the maternal proteome of mouse parthenogenetic embryos at pronucleus, 2-cell, 4-cell, 8-cell, morula, and blastocyst stages and highlight dynamic changes in protein expression. In addition, comparison of proteomic profiles of parthenogenotes and fertilized embryos highlights the different fates of maternal proteins. Enrichment analysis uncovered a set of maternal proteins that are strongly correlated with the subcortical maternal complex, and we report that in parthenogenotes, some of these maternal proteins escape the fate of protein degradation. Moreover, we identified a new maternal factor-Fbxw24, and highlight its importance in early embryonic development. We report that Fbxw24 interacts with Ddb1-Cul4b and may regulate maternal protein degradation in mouse. Conclusions Our study provides an invaluable resource for mechanistic analysis of maternal proteins and highlights the role of the novel maternal factor Fbw24 in regulating maternal protein degradation during preimplantation embryo development.
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Affiliation(s)
- Fumei Chen
- Department of Histology and Embryology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China
| | - Buguo Ma
- Department of Histology and Embryology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China.,Central Laboratory, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China
| | - Yongda Lin
- Department of Histology and Embryology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China.,Central Laboratory, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China
| | - Xin Luo
- Department of Histology and Embryology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China
| | - Tao Xu
- Department of Histology and Embryology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China
| | - Yuan Zhang
- Department of Histology and Embryology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China
| | - Fang Chen
- Department of Histology and Embryology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China.,Central Laboratory, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China
| | - Yanfei Li
- Department of Histology and Embryology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China.,Central Laboratory, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China
| | - Yaoyao Zhang
- Department of Histology and Embryology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China.,Central Laboratory, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China
| | - Bin Luo
- Department of Histology and Embryology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China.,Central Laboratory, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China
| | - Qingmei Zhang
- Department of Histology and Embryology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China.,Central Laboratory, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China
| | - Xiaoxun Xie
- Department of Histology and Embryology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China.,Central Laboratory, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China
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Ahn J, Hwang IS, Park MR, Hwang S, Lee K. Genomic Imprinting at the Porcine DIRAS3 Locus. Animals (Basel) 2021; 11:ani11051315. [PMID: 34063661 PMCID: PMC8147596 DOI: 10.3390/ani11051315] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 04/30/2021] [Accepted: 05/01/2021] [Indexed: 12/17/2022] Open
Abstract
Simple Summary DNA methylation associated with one of the two alleles from parents is an important mechanism that causes a silencing of that allele, leading to expression of another allele only. There has been a lack of detailed studies on DNA methylation and expression patterns that are related to the DIRAS3 gene in pigs. The objective of this study was to provide a comprehensive overview of DNA methylation and expression associated with the DIRAS3 gene in pigs by generating an embryonic pig model and analyzing next-generation sequencing using pig embryos and adult pigs. Our results clearly showed the presence of DNA methylation near the DIRAS3 gene in pigs and high expression of DIRAS3 in the hypothalamus from adult pigs and expression of only one allele in all the tested tissues including the hypothalamus. In summary, our findings suggested DNA methylation might be related to those unique gene expression patterns during the development of pigs. Abstract The epigenetic mechanisms underlying genomic imprinting include DNA methylation and monoallelic expression of genes in close proximity. Although genes imprinted in humans and mice have been widely characterized, there is a lack of detailed and comprehensive studies in livestock species including pigs. The purpose of this study was to investigate a detailed methylation status and parent-of-origin-specific gene expression within the genomic region containing an underexamined porcine DIRAS3 locus. Through whole-genome bisulfite sequencing (WGBS) and RNA sequencing (RNA-seq) of porcine parthenogenetic embryos and analyses of public RNA-seq data from adult pigs, DNA methylation and monoallelic expression pattern were investigated. As a result, maternal hypermethylation at the DIRAS3 locus and hypothalamus-specific and monoallelic expression of the DIRAS3 gene were found in pigs. In conclusion, the findings from this study suggest that the presence of maternal hypermethylation, or imprints, might be maintained and related to monoallelic expression of DIRAS3 during pig development.
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Affiliation(s)
- Jinsoo Ahn
- Functional Genomics Laboratory, Department of Animal Sciences, The Ohio State University, Columbus, OH 43210, USA;
| | - In-Sul Hwang
- Animal Biotechnology Division, National Institute of Animal Science, Rural Development Administration, Wanju 55365, Korea; (I.-S.H.); (M.-R.P.); (S.H.)
| | - Mi-Ryung Park
- Animal Biotechnology Division, National Institute of Animal Science, Rural Development Administration, Wanju 55365, Korea; (I.-S.H.); (M.-R.P.); (S.H.)
| | - Seongsoo Hwang
- Animal Biotechnology Division, National Institute of Animal Science, Rural Development Administration, Wanju 55365, Korea; (I.-S.H.); (M.-R.P.); (S.H.)
| | - Kichoon Lee
- Functional Genomics Laboratory, Department of Animal Sciences, The Ohio State University, Columbus, OH 43210, USA;
- Correspondence: ; Tel.: +1-614-688-7963
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Genomic Imprinting at the Porcine PLAGL1 Locus and the Orthologous Locus in the Human. Genes (Basel) 2021; 12:genes12040541. [PMID: 33918057 PMCID: PMC8069715 DOI: 10.3390/genes12040541] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 04/06/2021] [Indexed: 12/27/2022] Open
Abstract
Implementation of genomic imprinting in mammals often results in cis-acting silencing of a gene cluster and monoallelic expression, which are important for mammalian growth and function. Compared with widely documented imprinting status in humans and mice, current understanding of genomic imprinting in pigs is relatively limited. The objectives of this study were to identify DNA methylation status and allelic expression of alternative spliced isoforms at the porcine PLAGL1 locus and assess the conservation of the locus compared to the orthologous human locus. DNA methylome and transcriptome were constructed using porcine parthenogenetic or biparental control embryos. Using methylome, differentially methylated regions between those embryos were identified. Alternative splicing was identified by differential splicing analysis, and monoallelic expression was examined using single nucleotide polymorphism sites. Moreover, topological boundary regions were identified by analyzing CTCF binding sites and compared with the boundary of human orthologous locus. As a result, it was revealed that the monoallelic expression of the PLAGL1 gene in porcine embryos via genomic imprinting was maintained in the adult stage. The porcine PLAGL1 locus was largely conserved in regard to maternal hypermethylation, tissue distribution of mRNA expression, monoallelic expression, and biallelic CTCF-binding, with exceptions on transcript isoforms produced by alternative splicing instead of alternative promoter usage. These findings laid the groundwork for comparative studies on the imprinted PLAGL1 gene and related regulatory mechanisms across species.
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