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Innis S, Alpsoy A, Crodian J, Tseng YC, Dykhuizen E, Cabot B, Cabot R. Identification of SWI/SNF Subcomplex GBAF Presence, Intra-Complex Interactions, and Transcriptional Dynamics during Early Porcine Development. Animals (Basel) 2024; 14:773. [PMID: 38473159 PMCID: PMC10930984 DOI: 10.3390/ani14050773] [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: 02/08/2024] [Revised: 02/26/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024] Open
Abstract
Understanding the complex interplay between genetics and environmental factors is vital for enhancing livestock production efficiency while safeguarding animal health. Despite extensive studies on production-specific genes in livestock, exploring how epigenetic mechanisms and heritable modifications govern animal growth and development remains an under-explored frontier with potential implications across all life stages. This study focuses on the GBAF chromatin remodeling complex and evaluates its presence during embryonic and fetal development in swine. Immunocytochemistry and co-immunoprecipitation techniques were employed to investigate the presence and interactions of GBAF subunits BRD9 and GLTSCR1 in porcine oocytes, preimplantation embryos, and cell lines, and transcriptional dynamics of GBAF subunits across these key developmental stages were analyzed using existing RNA-seq datasets. BRD9 and GLTSCR1 were identified across all represented stages, and an interaction between GLTSCR1 and BAF170 was shown in PTr2 and PFF cells. Our findings highlight the ubiquitous presence of GBAF in porcine early development and the potentially novel association between GLTSCR1 and BAF170 in swine. The transcriptional dynamics findings may suggest GBAF-specific contributions during key developmental events. This study contributes to the growing understanding of epigenetic regulators in both swine and mammalian development, emphasizing the implications of GBAF as a modulator of key developmental events.
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Affiliation(s)
- Sarah Innis
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; (S.I.)
| | - Aktan Alpsoy
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
| | - Jennifer Crodian
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; (S.I.)
| | - Yu-Chun Tseng
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; (S.I.)
| | - Emily Dykhuizen
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
| | - Birgit Cabot
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; (S.I.)
| | - Ryan Cabot
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; (S.I.)
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2
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Braz CU, Passamonti MM, Khatib H. Characterization of genomic regions escaping epigenetic reprogramming in sheep. ENVIRONMENTAL EPIGENETICS 2023; 10:dvad010. [PMID: 38496251 PMCID: PMC10944287 DOI: 10.1093/eep/dvad010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 12/04/2023] [Accepted: 12/15/2023] [Indexed: 03/19/2024]
Abstract
The mammalian genome undergoes two global epigenetic reprogramming events during the establishment of primordial germ cells and in the pre-implantation embryo after fertilization. These events involve the erasure and re-establishment of DNA methylation marks. However, imprinted genes and transposable elements (TEs) maintain their DNA methylation signatures to ensure normal embryonic development and genome stability. Despite extensive research in mice and humans, there is limited knowledge regarding environmentally induced epigenetic marks that escape epigenetic reprogramming in other species. Therefore, the objective of this study was to examine the characteristics and locations of genomic regions that evade epigenetic reprogramming in sheep, as well as to explore the biological functions of the genes within these regions. In a previous study, we identified 107 transgenerationally inherited differentially methylated cytosines (DMCs) in the F1 and F2 generations in response to a paternal methionine-supplemented diet. These DMCs were found in TEs, non-repetitive regions, and imprinted and non-imprinted genes. Our findings suggest that genomic regions, rather than TEs and imprinted genes, have the propensity to escape reprogramming and serve as potential candidates for transgenerational epigenetic inheritance. Notably, 34 transgenerational methylated genes influenced by paternal nutrition escaped reprogramming, impacting growth, development, male fertility, cardiac disorders, and neurodevelopment. Intriguingly, among these genes, 21 have been associated with neural development and brain disorders, such as autism, schizophrenia, bipolar disease, and intellectual disability. This suggests a potential genetic overlap between brain and infertility disorders. Overall, our study supports the concept of transgenerational epigenetic inheritance of environmentally induced marks in mammals.
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Affiliation(s)
- Camila U Braz
- Department of Animal Sciences, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
| | - Matilde Maria Passamonti
- Department of Animal Science, Food and Nutrition, Universit’a Cattolica del Sacro Cuore, Piacenza, 29122, Italy
| | - Hasan Khatib
- Department of Animal and Dairy Sciences, University of Wisconsin–Madison, Madison, WI 53706, USA
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Zhang J, Sheng H, Hu C, Li F, Cai B, Ma Y, Wang Y, Ma Y. Effects of DNA Methylation on Gene Expression and Phenotypic Traits in Cattle: A Review. Int J Mol Sci 2023; 24:11882. [PMID: 37569258 PMCID: PMC10419045 DOI: 10.3390/ijms241511882] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/20/2023] [Accepted: 07/22/2023] [Indexed: 08/13/2023] Open
Abstract
Gene expression in cells is determined by the epigenetic state of chromatin. Therefore, the study of epigenetic changes is very important to understand the regulatory mechanism of genes at the molecular, cellular, tissue and organ levels. DNA methylation is one of the most studied epigenetic modifications, which plays an important role in maintaining genome stability and ensuring normal growth and development. Studies have shown that methylation levels in bovine primordial germ cells, the rearrangement of methylation during embryonic development and abnormal methylation during placental development are all closely related to their reproductive processes. In addition, the application of bovine male sterility and assisted reproductive technology is also related to DNA methylation. This review introduces the principle, development of detection methods and application conditions of DNA methylation, with emphasis on the relationship between DNA methylation dynamics and bovine spermatogenesis, embryonic development, disease resistance and muscle and fat development, in order to provide theoretical basis for the application of DNA methylation in cattle breeding in the future.
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Affiliation(s)
- Junxing Zhang
- Key Laboratory of Ruminant Molecular Cell Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China; (J.Z.); (H.S.); (C.H.); (F.L.); (B.C.); (Y.M.)
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Hui Sheng
- Key Laboratory of Ruminant Molecular Cell Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China; (J.Z.); (H.S.); (C.H.); (F.L.); (B.C.); (Y.M.)
| | - Chunli Hu
- Key Laboratory of Ruminant Molecular Cell Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China; (J.Z.); (H.S.); (C.H.); (F.L.); (B.C.); (Y.M.)
| | - Fen Li
- Key Laboratory of Ruminant Molecular Cell Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China; (J.Z.); (H.S.); (C.H.); (F.L.); (B.C.); (Y.M.)
| | - Bei Cai
- Key Laboratory of Ruminant Molecular Cell Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China; (J.Z.); (H.S.); (C.H.); (F.L.); (B.C.); (Y.M.)
| | - Yanfen Ma
- Key Laboratory of Ruminant Molecular Cell Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China; (J.Z.); (H.S.); (C.H.); (F.L.); (B.C.); (Y.M.)
| | - Yachun Wang
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yun Ma
- Key Laboratory of Ruminant Molecular Cell Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China; (J.Z.); (H.S.); (C.H.); (F.L.); (B.C.); (Y.M.)
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4
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Wang X, Li W, Feng X, Li J, Liu GE, Fang L, Yu Y. Harnessing male germline epigenomics for the genetic improvement in cattle. J Anim Sci Biotechnol 2023; 14:76. [PMID: 37277852 PMCID: PMC10242889 DOI: 10.1186/s40104-023-00874-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 04/02/2023] [Indexed: 06/07/2023] Open
Abstract
Sperm is essential for successful artificial insemination in dairy cattle, and its quality can be influenced by both epigenetic modification and epigenetic inheritance. The bovine germline differentiation is characterized by epigenetic reprogramming, while intergenerational and transgenerational epigenetic inheritance can influence the offspring's development through the transmission of epigenetic features to the offspring via the germline. Therefore, the selection of bulls with superior sperm quality for the production and fertility traits requires a better understanding of the epigenetic mechanism and more accurate identifications of epigenetic biomarkers. We have comprehensively reviewed the current progress in the studies of bovine sperm epigenome in terms of both resources and biological discovery in order to provide perspectives on how to harness this valuable information for genetic improvement in the cattle breeding industry.
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Affiliation(s)
- Xiao Wang
- Laboratory of Animal Genetics and Breeding, Ministry of Agriculture and Rural Affairs of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
- Konge Larsen ApS, Kongens Lyngby, 2800, Denmark
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Wenlong Li
- Laboratory of Animal Genetics and Breeding, Ministry of Agriculture and Rural Affairs of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xia Feng
- Laboratory of Animal Genetics and Breeding, Ministry of Agriculture and Rural Affairs of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jianbing Li
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, Henry A. Wallace Beltsville Agricultural Research Center, USDA, Beltsville, MD, 20705, USA
| | - Lingzhao Fang
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, 8000, Denmark.
| | - Ying Yu
- Laboratory of Animal Genetics and Breeding, Ministry of Agriculture and Rural Affairs of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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Corbett RJ, Luttman AM, Herrera-Uribe J, Liu H, Raney NE, Grabowski JM, Loving CL, Tuggle CK, Ernst CW. Assessment of DNA methylation in porcine immune cells reveals novel regulatory elements associated with cell-specific gene expression and immune capacity traits. BMC Genomics 2022; 23:575. [PMID: 35953767 PMCID: PMC9367135 DOI: 10.1186/s12864-022-08773-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 07/18/2022] [Indexed: 11/15/2022] Open
Abstract
Background Genetics studies in the porcine immune system have enhanced selection practices for disease resistance phenotypes and increased the efficacy of porcine models in biomedical research; however limited functional annotation of the porcine immunome has hindered progress on both fronts. Among epigenetic mechanisms that regulate gene expression, DNA methylation is the most ubiquitous modification made to the DNA molecule and influences transcription factor binding as well as gene and phenotype expression. Human and mouse DNA methylation studies have improved mapping of regulatory elements in these species, but comparable studies in the pig have been limited in scope. Results We performed whole-genome bisulfite sequencing to assess DNA methylation patterns in nine pig immune cell populations: CD21+ and CD21− B cells, four T cell fractions (CD4+, CD8+, CD8+CD4+, and SWC6γδ+), natural killer and myeloid cells, and neutrophils. We identified 54,391 cell differentially methylated regions (cDMRs), and clustering by cDMR methylation rate grouped samples by cell lineage. 32,737 cDMRs were classified as cell lowly methylated regions (cLMRs) in at least one cell type, and cLMRs were broadly enriched in genes and regions of intermediate CpG density. We observed strong correlations between differential methylation and expression across immune cell populations, with cell-specific low methylation disproportionately impacting genes exhibiting enriched gene expression in the same cell type. Motif analysis of cLMRs revealed cell type-specific enrichment of transcription factor binding motifs, indicating that cell-specific methylation patterns may influence accessibility by trans-acting factors. Lastly, cDMRs were enriched for immune capacity GWAS SNPs, and many such overlaps occurred within genes known to influence immune cell development and function (CD8B, NDRG1). Conclusion Our DNA methylation data improve functional annotation of the porcine genome through characterization of epigenomic regulatory patterns that contribute to immune cell identity and function, and increase the potential for identifying mechanistic links between genotype and phenotype. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08773-5.
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Affiliation(s)
- Ryan J Corbett
- Genetics & Genome Sciences Graduate Program, Michigan State University, East Lansing, MI, USA
| | - Andrea M Luttman
- Genetics & Genome Sciences Graduate Program, Michigan State University, East Lansing, MI, USA
| | | | - Haibo Liu
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | - Nancy E Raney
- Department of Animal Science, Michigan State University, East Lansing, MI, USA
| | - Jenna M Grabowski
- Department of Animal Science, Michigan State University, East Lansing, MI, USA
| | | | | | - Catherine W Ernst
- Department of Animal Science, Michigan State University, East Lansing, MI, USA.
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6
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Mi S, Chen S, Li W, Fang L, Yu Y. Effects of sperm DNA methylation on domesticated animal performance and perspectives on cross-species epigenetics in animal breeding. Anim Front 2021; 11:39-47. [PMID: 34934528 PMCID: PMC8683132 DOI: 10.1093/af/vfab053] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Siyuan Mi
- Laboratory of Animal Genetics and Breeding, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Siqian Chen
- Laboratory of Animal Genetics and Breeding, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Wenlong Li
- Laboratory of Animal Genetics and Breeding, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lingzhao Fang
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Ying Yu
- Laboratory of Animal Genetics and Breeding, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
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7
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Misztal I, Aguilar I, Lourenco D, Ma L, Steibel JP, Toro M. Emerging issues in genomic selection. J Anim Sci 2021; 99:skab092. [PMID: 33773494 PMCID: PMC8186541 DOI: 10.1093/jas/skab092] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 03/26/2021] [Indexed: 12/22/2022] Open
Abstract
Genomic selection (GS) is now practiced successfully across many species. However, many questions remain, such as long-term effects, estimations of genomic parameters, robustness of genome-wide association study (GWAS) with small and large datasets, and stability of genomic predictions. This study summarizes presentations from the authors at the 2020 American Society of Animal Science (ASAS) symposium. The focus of many studies until now is on linkage disequilibrium between two loci. Ignoring higher-level equilibrium may lead to phantom dominance and epistasis. The Bulmer effect leads to a reduction of the additive variance; however, the selection for increased recombination rate can release anew genetic variance. With genomic information, estimates of genetic parameters may be biased by genomic preselection, but costs of estimation can increase drastically due to the dense form of the genomic information. To make the computation of estimates feasible, genotypes could be retained only for the most important animals, and methods of estimation should use algorithms that can recognize dense blocks in sparse matrices. GWASs using small genomic datasets frequently find many marker-trait associations, whereas studies using much bigger datasets find only a few. Most of the current tools use very simple models for GWAS, possibly causing artifacts. These models are adequate for large datasets where pseudo-phenotypes such as deregressed proofs indirectly account for important effects for traits of interest. Artifacts arising in GWAS with small datasets can be minimized by using data from all animals (whether genotyped or not), realistic models, and methods that account for population structure. Recent developments permit the computation of P-values from genomic best linear unbiased prediction (GBLUP), where models can be arbitrarily complex but restricted to genotyped animals only, and single-step GBLUP that also uses phenotypes from ungenotyped animals. Stability was an important part of nongenomic evaluations, where genetic predictions were stable in the absence of new data even with low prediction accuracies. Unfortunately, genomic evaluations for such animals change because all animals with genotypes are connected. A top-ranked animal can easily drop in the next evaluation, causing a crisis of confidence in genomic evaluations. While correlations between consecutive genomic evaluations are high, outliers can have differences as high as 1 SD. A solution to fluctuating genomic evaluations is to base selection decisions on groups of animals. Although many issues in GS have been solved, many new issues that require additional research continue to surface.
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Affiliation(s)
- Ignacy Misztal
- Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602, USA
| | - Ignacio Aguilar
- Instituto Nacional de Investigación Agropecuaria (INIA), 90200 Canelones, Uruguay
| | - Daniela Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602, USA
| | - Li Ma
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA
| | - Juan Pedro Steibel
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
| | - Miguel Toro
- Departamento de Producción Agraria, Universidad Politécnica de Madrid, Madrid, Spain
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8
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Khambata K, Raut S, Deshpande S, Mohan S, Sonawane S, Gaonkar R, Ansari Z, Datar M, Bansal V, Patil A, Warke H, Balasinor NH. DNA methylation defects in spermatozoa of male partners from couples experiencing recurrent pregnancy loss. Hum Reprod 2021; 36:48-60. [PMID: 33319906 DOI: 10.1093/humrep/deaa278] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 09/16/2020] [Indexed: 12/13/2022] Open
Abstract
STUDY QUESTION What is the sperm DNA methylation status of imprinted genes in male partners from couples experiencing recurrent pregnancy loss (RPL)? SUMMARY ANSWER Aberrations in sperm DNA methylation status of several imprinted genes, such as insulin like growth factor-2-H19 differentially methylated region (IGF2-H19 DMR), intergenic differentially methylated region (IG-DMR), mesoderm specific transcript (MEST), zinc finger protein which regulates apoptosis and cell cycle arrest (ZAC), DMR in intron 10 of KCNQ1 gene (KvDMR), paternally expressed gene 3 (PEG3) and paternally expressed gene 10 (PEG10), as well as decreased sperm global 5-methylcytosine (5mC) levels, are associated with RPL. WHAT IS KNOWN ALREADY RPL is defined as loss of two or more pregnancies, affecting 1-2% of couples of reproductive age. Although there are several maternal and paternal aetiological factors contributing to RPL, nearly 50% of the cases remain idiopathic. Thus, there is a need to identify putative paternal factors that could be contributing towards pregnancy loss in cases of idiopathic RPL. STUDY DESIGN, SIZE, DURATION In this case-control study, 112 couples undergoing RPL with no identifiable cause were recruited from September 2015 to May 2018. The control group comprised of 106 healthy proven fertile couples with no history of infertility or miscarriage. PARTICIPANTS/MATERIALS, SETTING, METHODS In this study, we investigated the paternal genetic and epigenetic factors that could be associated with RPL. We studied DNA methylation, by pyrosequencing, of selected imprinted genes implicated in embryo development, such as IGF2-H19 DMR, IG-DMR, MEST, ZAC, KvDMR, PEG3, PEG10 and small nuclear ribonucleoprotein polypeptide N (SNRPN) in sperm of men whose partners present RPL. Global DNA methylation in sperm was evaluated by studying 5mC content and long interspersed nuclear element 1 (LINE1) promoter methylation. We also studied polymorphisms by pyrosequencing in the IGF2-H19 DMR as well in the IGF2 promoter in both groups. MAIN RESULTS AND THE ROLE OF CHANCE In the RPL group, we found a significant decrease in the global sperm 5mC levels and significant decrease in DNA methylation at three CpG sites in LINE1 promoter. For IGF2-H19 DMR and IG-DMR, a significant decrease in sperm DNA methylation at specific CpG sites was observed in RPL group. For maternally imprinted genes like MEST, ZAC, KvDMR, PEG3 and PEG10 hypermethylation was noted. Polymorphism studies for IGF2-H19 DMR and IGF2 revealed significant differences in the genotypic frequencies in males. LIMITATIONS, REASONS FOR CAUTION In this study, we analysed the methylation levels of selected candidate imprinted genes implicated in embryo development. Detection of methylation changes occurring at the genome-wide level may reveal further candidate genes having a better distinction between the control and study groups. WIDER IMPLICATIONS OF THE FINDINGS Our study demonstrates that certain polymorphisms and aberrant sperm methylation status in imprinted genes are associated with RPL and could contribute to the aetiology of RPL. This study suggests that investigation of paternal genetic and epigenetic factors could be useful in identification of possible causes of idiopathic RPL. STUDY FUNDING/COMPETING INTEREST(S) This study was funded by Department of Science and Technology-Science and Engineering Research Board (EMR/2014/000145) and National Institute for Research in Reproductive Health intramural funds (RA/872/01-2020). All authors declare no conflict of interest. TRIAL REGISTRATION NUMBER N/A.
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Affiliation(s)
- Kushaan Khambata
- Neuroendocrinology Department, Indian Council of Medical Research-National Institute for Research in Reproductive Health, Mumbai, India
| | - Sanketa Raut
- Neuroendocrinology Department, Indian Council of Medical Research-National Institute for Research in Reproductive Health, Mumbai, India
| | - Sharvari Deshpande
- Neuroendocrinology Department, Indian Council of Medical Research-National Institute for Research in Reproductive Health, Mumbai, India
| | - Sweta Mohan
- Neuroendocrinology Department, Indian Council of Medical Research-National Institute for Research in Reproductive Health, Mumbai, India
| | - Shobha Sonawane
- Neuroendocrinology Department, Indian Council of Medical Research-National Institute for Research in Reproductive Health, Mumbai, India
| | - Reshma Gaonkar
- Neuroendocrinology Department, Indian Council of Medical Research-National Institute for Research in Reproductive Health, Mumbai, India
| | - Zakiya Ansari
- Neuroendocrinology Department, Indian Council of Medical Research-National Institute for Research in Reproductive Health, Mumbai, India
| | - Mamata Datar
- Neuroendocrinology Department, Indian Council of Medical Research-National Institute for Research in Reproductive Health, Mumbai, India
| | - Vandana Bansal
- Department of Obstetrics and Gynecology, Nowrosjee Wadia Maternity Hospital, Mumbai, India
| | - Anushree Patil
- Department of Reproductive Endocrinology & Infertility, Indian Council of Medical Research-National Institute for Research in Reproductive Health (ICMR-NIRRH), Mumbai, India
| | - Himangi Warke
- Department of Obstetrics and Gynecology, Seth G. S. Medical College & King Edward Memorial Hospital (KEM), Mumbai, India
| | - Nafisa H Balasinor
- Neuroendocrinology Department, Indian Council of Medical Research-National Institute for Research in Reproductive Health, Mumbai, India
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Wang M, Ibeagha-Awemu EM. Impacts of Epigenetic Processes on the Health and Productivity of Livestock. Front Genet 2021; 11:613636. [PMID: 33708235 PMCID: PMC7942785 DOI: 10.3389/fgene.2020.613636] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 12/21/2020] [Indexed: 12/23/2022] Open
Abstract
The dynamic changes in the epigenome resulting from the intricate interactions of genetic and environmental factors play crucial roles in individual growth and development. Numerous studies in plants, rodents, and humans have provided evidence of the regulatory roles of epigenetic processes in health and disease. There is increasing pressure to increase livestock production in light of increasing food needs of an expanding human population and environment challenges, but there is limited related epigenetic data on livestock to complement genomic information and support advances in improvement breeding and health management. This review examines the recent discoveries on epigenetic processes due to DNA methylation, histone modification, and chromatin remodeling and their impacts on health and production traits in farm animals, including bovine, swine, sheep, goat, and poultry species. Most of the reports focused on epigenome profiling at the genome-wide or specific genic regions in response to developmental processes, environmental stressors, nutrition, and disease pathogens. The bulk of available data mainly characterized the epigenetic markers in tissues/organs or in relation to traits and detection of epigenetic regulatory mechanisms underlying livestock phenotype diversity. However, available data is inadequate to support gainful exploitation of epigenetic processes for improved animal health and productivity management. Increased research effort, which is vital to elucidate how epigenetic mechanisms affect the health and productivity of livestock, is currently limited due to several factors including lack of adequate analytical tools. In this review, we (1) summarize available evidence of the impacts of epigenetic processes on livestock production and health traits, (2) discuss the application of epigenetics data in livestock production, and (3) present gaps in livestock epigenetics research. Knowledge of the epigenetic factors influencing livestock health and productivity is vital for the management and improvement of livestock productivity.
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Affiliation(s)
- Mengqi Wang
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada
- Department of Animal Science, Laval University, Quebec, QC, Canada
| | - Eveline M. Ibeagha-Awemu
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada
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10
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Marker-assisted selection vis-à-vis bull fertility: coming full circle-a review. Mol Biol Rep 2020; 47:9123-9133. [PMID: 33099757 DOI: 10.1007/s11033-020-05919-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 10/13/2020] [Indexed: 10/23/2022]
Abstract
Bull fertility is considered an indispensable trait, as far as farm economics is concerned since it is the successful conception in a cow that provides calf crop, along with the ensuing lactation. This ensures sustainability of a dairy farm. Traditionally, bull fertility did not receive much attention by the farm managers and breeding animals were solely evaluated based on phenotypic predictors, namely, sire conception rate and seminal parameters in bull. With the advent of the molecular era in animal breeding, attempts were made to unravel the genetic complexity of bull fertility by the identification of genetic markers related to the trait. Marker-Assisted Selection (MAS) is a methodology that aims at utilizing the genetic information at markers and selecting improved populations for important traits. Traditionally, MAS was pursued using a candidate gene approach for identifying markers related to genes that are already known to have a physiological function related to the trait but this approach had certain shortcomings like stringent criteria for significance testing. Now, with the availability of genome-wide data, the number of markers identified and variance explained in relation to bull fertility has gone up. So, this presents a unique opportunity to revisit MAS by selection based on the information of a large number of genome-wide markers and thus, improving the accuracy of selection.
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11
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Long JA. The ‘omics’ revolution: Use of genomic, transcriptomic, proteomic and metabolomic tools to predict male reproductive traits that impact fertility in livestock and poultry. Anim Reprod Sci 2020; 220:106354. [DOI: 10.1016/j.anireprosci.2020.106354] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/20/2020] [Accepted: 03/21/2020] [Indexed: 12/17/2022]
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12
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Gross N, Peñagaricano F, Khatib H. Integration of whole-genome DNA methylation data with RNA sequencing data to identify markers for bull fertility. Anim Genet 2020; 51:502-510. [PMID: 32323873 DOI: 10.1111/age.12941] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/25/2020] [Indexed: 02/06/2023]
Abstract
Predicting bull fertility prior to breeding is a current challenge for the dairy industry. The use of molecular biomarkers has been previously assessed. However, the integration of this information has not been performed to extract biologically relevant markers. The goal of this study was to integrate DNA methylation data with previously published RNA-sequencing results in order to identify candidate markers for sire fertility. A total of 1765 differentially methylated cytosines were found between high- and low-fertility sires. Ten genes associated with 11 differentially methylated cytosines were found in a previous study of gene expression between high- and low-fertility sires. Additionally, two of these genes code for proteins found exclusively in bull seminal plasma. Collectively, our results reveal 10 genes that could be used in the future as a panel for predicting bull fertility.
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Affiliation(s)
- Nicole Gross
- Department of Animal Sciences, University of Wisconsin, Madison, WI, 53706, USA
| | | | - Hasan Khatib
- Department of Animal Sciences, University of Wisconsin, Madison, WI, 53706, USA
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13
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Gross N, Strillacci MG, Peñagaricano F, Khatib H. Characterization and functional roles of paternal RNAs in 2-4 cell bovine embryos. Sci Rep 2019; 9:20347. [PMID: 31889064 PMCID: PMC6937301 DOI: 10.1038/s41598-019-55868-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 12/03/2019] [Indexed: 12/26/2022] Open
Abstract
Embryos utilize oocyte-donated RNAs until they become capable of producing RNAs through embryonic genome activation (EGA). The sperm's influence over pre-EGA RNA content of embryos remains unknown. Recent studies have revealed that sperm donate non-genomic components upon fertilization. Thus, sperm may also contribute to RNA presence in pre-EGA embryos. The first objective of this study was to investigate whether male fertility status is associated with the RNAs present in the bovine embryo prior to EGA. A total of 65 RNAs were found to be differentially expressed between 2-4 cell bovine embryos derived from high and low fertility sires. Expression patterns were confirmed for protein phosphatase 1 regulatory subunit 36 (PPP1R36) and ataxin 2 like (ATXN2L) in three new biological replicates. The knockdown of ATXN2L led to a 22.9% increase in blastocyst development. The second objective of this study was to characterize the parental origin of RNAs present in pre-EGA embryos. Results revealed 472 sperm-derived RNAs, 2575 oocyte-derived RNAs, 2675 RNAs derived from both sperm and oocytes, and 663 embryo-exclusive RNAs. This study uncovers an association of male fertility with developmentally impactful RNAs in 2-4 cell embryos. This study also provides an initial characterization of paternally-contributed RNAs to pre-EGA embryos. Furthermore, a subset of 2-4 cell embryo-specific RNAs was identified.
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Affiliation(s)
- Nicole Gross
- University of Wisconsin, Department of Animal Sciences, Madison, WI, 53706, USA
| | | | | | - Hasan Khatib
- University of Wisconsin, Department of Animal Sciences, Madison, WI, 53706, USA.
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Liu S, Chen S, Cai W, Yin H, Liu A, Li Y, Liu GE, Wang Y, Yu Y, Zhang S. Divergence Analyses of Sperm DNA Methylomes between Monozygotic Twin AI Bulls. EPIGENOMES 2019; 3:21. [PMID: 34968253 PMCID: PMC8594723 DOI: 10.3390/epigenomes3040021] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 09/01/2019] [Accepted: 09/17/2019] [Indexed: 02/07/2023] Open
Abstract
Semen quality is critical for fertility. However, it is easily influenced by environmental factors and can induce subfertility in the next generations. Here, we aimed to assess the impacts of differentially methylated regions and genes on semen quality and offspring fertility. A specific pair of monozygotic (MZ) twin artificial insemination (AI) Holstein bulls with moderately different sperm qualities (Bull1 > Bull2) was used in the study, and each twin bull had produced ~6000 recorded daughters nationwide in China. Using whole genome bisulfite sequencing, we profiled the landscape of the twin bulls' sperm methylomes, and we observed markedly higher sperm methylation levels in Bull1 than in Bull2. Furthermore, we found 528 differentially methylated regions (DMR) between the MZ twin bulls, which spanned or overlapped with 309 differentially methylated genes (DMG). These DMG were particularly associated with embryo development, organ development, reproduction, and the nervous system. Several DMG were also shown to be differentially expressed in the sperm cells. Moreover, the significant differences in DNA methylation on gene INSL3 between the MZ twin bulls were confirmed at three different age points. Our results provided new insights into the impacts of AI bull sperm methylomes on offspring fertility.
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Affiliation(s)
- Shuli Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, 2rd, Yuanmingyuan West Road, Beijing 100193, China; (S.L.); (S.C.); (W.C.); (H.Y.); (A.L.); (Y.L.); (Y.W.)
| | - Siqian Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, 2rd, Yuanmingyuan West Road, Beijing 100193, China; (S.L.); (S.C.); (W.C.); (H.Y.); (A.L.); (Y.L.); (Y.W.)
| | - Wentao Cai
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, 2rd, Yuanmingyuan West Road, Beijing 100193, China; (S.L.); (S.C.); (W.C.); (H.Y.); (A.L.); (Y.L.); (Y.W.)
| | - Hongwei Yin
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, 2rd, Yuanmingyuan West Road, Beijing 100193, China; (S.L.); (S.C.); (W.C.); (H.Y.); (A.L.); (Y.L.); (Y.W.)
| | - Aoxing Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, 2rd, Yuanmingyuan West Road, Beijing 100193, China; (S.L.); (S.C.); (W.C.); (H.Y.); (A.L.); (Y.L.); (Y.W.)
| | - Yanhua Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, 2rd, Yuanmingyuan West Road, Beijing 100193, China; (S.L.); (S.C.); (W.C.); (H.Y.); (A.L.); (Y.L.); (Y.W.)
- Beijing Dairy Cattle Center, Qinghe South Town, Beijing 100085, China
| | - George E. Liu
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, BARC-East, Beltsville, MD 20705, USA;
| | - Yachun Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, 2rd, Yuanmingyuan West Road, Beijing 100193, China; (S.L.); (S.C.); (W.C.); (H.Y.); (A.L.); (Y.L.); (Y.W.)
| | - Ying Yu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, 2rd, Yuanmingyuan West Road, Beijing 100193, China; (S.L.); (S.C.); (W.C.); (H.Y.); (A.L.); (Y.L.); (Y.W.)
| | - Shengli Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, 2rd, Yuanmingyuan West Road, Beijing 100193, China; (S.L.); (S.C.); (W.C.); (H.Y.); (A.L.); (Y.L.); (Y.W.)
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