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Costes V, Sellem E, Marthey S, Hoze C, Bonnet A, Schibler L, Kiefer H, Jaffrezic F. Multi-omics data integration for the identification of biomarkers for bull fertility. PLoS One 2024; 19:e0298623. [PMID: 38394258 PMCID: PMC10890740 DOI: 10.1371/journal.pone.0298623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 01/26/2024] [Indexed: 02/25/2024] Open
Abstract
Bull fertility is an important economic trait, and the use of subfertile semen for artificial insemination decreases the global efficiency of the breeding sector. Although the analysis of semen functional parameters can help to identify infertile bulls, no tools are currently available to enable precise predictions and prevent the commercialization of subfertile semen. Because male fertility is a multifactorial phenotype that is dependent on genetic, epigenetic, physiological and environmental factors, we hypothesized that an integrative analysis might help to refine our knowledge and understanding of bull fertility. We combined -omics data (genotypes, sperm DNA methylation at CpGs and sperm small non-coding RNAs) and semen parameters measured on a large cohort of 98 Montbéliarde bulls with contrasting fertility levels. Multiple Factor Analysis was conducted to study the links between the datasets and fertility. Four methodologies were then considered to identify the features linked to bull fertility variation: Logistic Lasso, Random Forest, Gradient Boosting and Neural Networks. Finally, the features selected by these methods were annotated in terms of genes, to conduct functional enrichment analyses. The less relevant features in -omics data were filtered out, and MFA was run on the remaining 12,006 features, including the 11 semen parameters and a balanced proportion of each type of-omics data. The results showed that unlike the semen parameters studied the-omics datasets were related to fertility. Biomarkers related to bull fertility were selected using the four methodologies mentioned above. The most contributory CpGs, SNPs and miRNAs targeted genes were all found to be involved in development. Interestingly, fragments derived from ribosomal RNAs were overrepresented among the selected features, suggesting roles in male fertility. These markers could be used in the future to identify subfertile bulls in order to increase the global efficiency of the breeding sector.
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Affiliation(s)
- Valentin Costes
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d’Alfort, BREED, Maisons-Alfort, France
- R&D Department, ELIANCE, 149 rue de Bercy, Paris, France
- Université Paris-Saclay, AgroParisTech, INRAE, GABI, Jouy-en-Josas, France
| | - Eli Sellem
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d’Alfort, BREED, Maisons-Alfort, France
- R&D Department, ELIANCE, 149 rue de Bercy, Paris, France
| | - Sylvain Marthey
- Université Paris-Saclay, AgroParisTech, INRAE, GABI, Jouy-en-Josas, France
- INRAE, MaIAGE, Université Paris-Saclay, Jouy-en-Josas, France
| | - Chris Hoze
- R&D Department, ELIANCE, 149 rue de Bercy, Paris, France
- Université Paris-Saclay, AgroParisTech, INRAE, GABI, Jouy-en-Josas, France
| | - Aurélie Bonnet
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d’Alfort, BREED, Maisons-Alfort, France
- R&D Department, ELIANCE, 149 rue de Bercy, Paris, France
| | | | - Hélène Kiefer
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d’Alfort, BREED, Maisons-Alfort, France
| | - Florence Jaffrezic
- Université Paris-Saclay, AgroParisTech, INRAE, GABI, Jouy-en-Josas, France
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2
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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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Tennenbaum SR, Bortner R, Lynch C, Santymire R, Crosier A, Santiestevan J, Marinari P, Pukazhenthi BS, Comizzoli P, Hawkins MTR, Maldonado JE, Koepfli K, vonHoldt BM, DeCandia AL. Epigenetic changes to gene pathways linked to male fertility in ex situ black-footed ferrets. Evol Appl 2024; 17:e13634. [PMID: 38283602 PMCID: PMC10818088 DOI: 10.1111/eva.13634] [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: 02/22/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 01/30/2024] Open
Abstract
Environmental variation can influence the reproductive success of species managed under human care and in the wild, yet the mechanisms underlying this phenomenon remain largely mysterious. Molecular mechanisms such as epigenetic modifiers are important in mediating the timing and progression of reproduction in humans and model organisms, but few studies have linked epigenetic variation to reproductive fitness in wildlife. Here, we investigated epigenetic variation in black-footed ferrets (Mustela nigripes), an endangered North American mammal reliant on ex situ management for survival and persistence in the wild. Despite similar levels of genetic diversity in human-managed and wild-born populations, individuals in ex situ facilities exhibit reproductive problems, such as poor sperm quality. Differences across these settings suggest that an environmentally driven decline in reproductive capacity may be occurring in this species. We examined the role of DNA methylation, one well-studied epigenetic modifier, in this emergent condition. We leveraged blood, testes, and semen samples from male black-footed ferrets bred in ex situ facilities and found tissue-type specificity in DNA methylation across the genome, although 1360 Gene Ontology terms associated with male average litter size shared functions across tissues. We then constructed gene networks of differentially methylated genomic sites associated with three different reproductive phenotypes to explore the putative biological impact of variation in DNA methylation. Sperm gene networks associated with average litter size and sperm count were functionally enriched for candidate genes involved in reproduction, development, and its regulation through transcriptional repression. We propose that DNA methylation plays an important role in regulating these reproductive phenotypes, thereby impacting the fertility of male ex situ individuals. Our results provide information into how DNA methylation may function in the alteration of reproductive pathways and phenotypes in artificial environments. These findings provide early insights to conservation hurdles faced in the protection of this rare species.
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Affiliation(s)
| | - Robyn Bortner
- U.S. Fish & Wildlife Service National Black‐Footed Ferret Conservation CenterCarrColoradoUSA
| | | | - Rachel Santymire
- Biology DepartmentGeorgia State UniversityAtlantaGeorgiaUSA
- Center for Species SurvivalSmithsonian's National Zoo and Conservation Biology InstituteFront RoyalVirginiaUSA
| | - Adrienne Crosier
- Center for Animal Care SciencesSmithsonian's National Zoo & Conservation Biology InstituteFront RoyalVirginiaUSA
| | - Jenny Santiestevan
- Center for Species SurvivalSmithsonian's National Zoo and Conservation Biology InstituteFront RoyalVirginiaUSA
| | - Paul Marinari
- Center for Animal Care SciencesSmithsonian's National Zoo & Conservation Biology InstituteFront RoyalVirginiaUSA
| | - Budhan S. Pukazhenthi
- Center for Species SurvivalSmithsonian's National Zoo and Conservation Biology InstituteFront RoyalVirginiaUSA
| | - Pierre Comizzoli
- Center for Species SurvivalSmithsonian's National Zoo and Conservation Biology InstituteFront RoyalVirginiaUSA
| | - Melissa T. R. Hawkins
- Division of Mammals, Department of Vertebrate ZoologyNational Museum of Natural HistoryWashingtonDCUSA
| | - Jesús E. Maldonado
- Center for Conservation GenomicsSmithsonian's National Zoo and Conservation Biology InstituteWashingtonDCUSA
| | - Klaus‐Peter Koepfli
- Center for Species SurvivalSmithsonian's National Zoo and Conservation Biology InstituteFront RoyalVirginiaUSA
- Smithsonian‐Mason School of ConservationGeorge Mason UniversityFront RoyalVirginiaUSA
| | | | - Alexandra L. DeCandia
- Center for Conservation GenomicsSmithsonian's National Zoo and Conservation Biology InstituteWashingtonDCUSA
- BiologyGeorgetown UniversityWashingtonDCUSA
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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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5
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Li W, Mi S, Zhang J, Liu X, Chen S, Liu S, Feng X, Tang Y, Li Y, Liu L, Fang L, Zhang S, Yu Y. Integrating sperm cell transcriptome and seminal plasma metabolome to analyze the molecular regulatory mechanism of sperm motility in Holstein stud bulls. J Anim Sci 2023; 101:skad214. [PMID: 37366074 PMCID: PMC10355371 DOI: 10.1093/jas/skad214] [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: 09/12/2022] [Accepted: 06/26/2023] [Indexed: 06/28/2023] Open
Abstract
Considering that artificial insemination is the most widely used assisted reproductive technique in the dairy industry, the semen quality of bulls is very important for selecting excellent stud bulls. Sperm motility is one of the important traits of semen quality, and related genes may be regulated by environmental factors. Seminal plasma can affect sperm cell transcriptome and further affect sperm motility through exosome or other processes. However, the molecular regulation mechanism of bull sperm motility has not been studied by combining the sperm cell transcriptome with seminal plasma metabolome. The number of motile sperm per ejaculate (NMSPE) is an integrated indicator for assessing sperm motility in stud bulls. In the present study, we selected 7 bulls with higher NMSPE (5,698.55 million +/- 945.40 million) as group H and 7 bulls with lower NMSPE (2,279.76 million +/- 1,305.69 million) as group L from 53 Holstein stud bulls. The differentially expressed genes (DEGs) in sperm cells were evaluated between the two groups (H vs. L). We conducted gene co-expression network analysis (WGCNA) on H and L groups of bulls, as well as two monozygotic twin Holstein bulls with different NMSPE values, to screen candidate genes for NMSPE. The regulatory effect of seminal plasma metabolome on the candidate genes of NMSPE was also investigated. A total of 1,099 DEGs were identified in the sperm cells of H and L groups. These DEGs were primarily concentrated in energy metabolism and sperm cell transcription. The significantly enriched Kyoto encyclopedia of genes and genomes (KEGG) pathways of the 57 differential metabolites were the aminoacyl-tRNA biosynthesis pathway and vitamin B6 metabolism pathway. Our study discovered 14 genes as the potential candidate markers for sperm motility, including FBXO39. We observed a broad correlation between transcriptome of sperm cells and seminal plasma metabolome, such as three metabolites, namely, mesaconic acid, 2-coumaric acid, and 4-formylaminoantipyrine, might regulate FBXO39 expression through potential pathways. The genes related to seminal plasma metabolites expressed in sperm cells are not only located near the quantitative trait loci of reproductive traits, but also enriched in the genome-wide association study signal of sire conception rate. Collectively, this study was the first to investigate the interplays among transcriptome of sperm cells and seminal plasma metabolome from Holstein stud bulls with different sperm motility.
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Affiliation(s)
- Wenlong Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs & National Engineering Laboratory for Animal Breeding, Department of Animal Breeding and Genetics, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Siyuan Mi
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs & National Engineering Laboratory for Animal Breeding, Department of Animal Breeding and Genetics, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Jinning Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs & National Engineering Laboratory for Animal Breeding, Department of Animal Breeding and Genetics, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xueqin Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs & National Engineering Laboratory for Animal Breeding, Department of Animal Breeding and Genetics, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Siqian Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs & National Engineering Laboratory for Animal Breeding, Department of Animal Breeding and Genetics, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Shuli Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs & National Engineering Laboratory for Animal Breeding, Department of Animal Breeding and Genetics, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
| | - Xia Feng
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs & National Engineering Laboratory for Animal Breeding, Department of Animal Breeding and Genetics, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yongjie Tang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs & National Engineering Laboratory for Animal Breeding, Department of Animal Breeding and Genetics, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yanhua Li
- Beijing Dairy Cattle Center, Qinghe’nanzhen Deshengmenwai Road, Beijing 100192, China
| | - Lin Liu
- Beijing Dairy Cattle Center, Qinghe’nanzhen Deshengmenwai Road, Beijing 100192, China
| | - Lingzhao Fang
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
- Center for Quantitative Genetics and Genomics (QGG), Aarhus University, Aarhus, Denmark
| | - Shengli Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs & National Engineering Laboratory for Animal Breeding, Department of Animal Breeding and Genetics, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Ying Yu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs & National Engineering Laboratory for Animal Breeding, Department of Animal Breeding and Genetics, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
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Štiavnická M, Chaulot-Talmon A, Perrier JP, Hošek P, Kenny DA, Lonergan P, Kiefer H, Fair S. Sperm DNA methylation patterns at discrete CpGs and genes involved in embryonic development are related to bull fertility. BMC Genomics 2022; 23:379. [PMID: 35585482 PMCID: PMC9118845 DOI: 10.1186/s12864-022-08614-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 05/05/2022] [Indexed: 02/11/2023] Open
Abstract
Background Despite a multifactorial approach being taken for the evaluation of bull semen quality in many animal breeding centres worldwide, reliable prediction of bull fertility is still a challenge. Recently, attention has turned to molecular mechanisms, which could uncover potential biomarkers of fertility. One of these mechanisms is DNA methylation, which together with other epigenetic mechanisms is essential for the fertilising sperm to drive normal embryo development and establish a viable pregnancy. In this study, we hypothesised that bull sperm DNA methylation patterns are related to bull fertility. We therefore investigated DNA methylation patterns from bulls used in artificial insemination with contrasting fertility scores. Results The DNA methylation patterns were obtained by reduced representative bisulphite sequencing from 10 high-fertility bulls and 10 low-fertility bulls, having average fertility scores of − 6.6 and + 6.5%, respectively (mean of the population was zero). Hierarchical clustering analysis did not distinguish bulls based on fertility but did highlight individual differences. Despite this, using stringent criteria (DNA methylation difference ≥ 35% and a q-value < 0.001), we identified 661 differently methylated cytosines (DMCs). DMCs were preferentially located in intergenic regions, introns, gene downstream regions, repetitive elements, open sea, shores and shelves of CpG islands. We also identified 10 differently methylated regions, covered by 7 unique genes (SFRP1, STXBP4, BCR, PSMG4, ARSG, ATP11A, RXRA), which are involved in spermatogenesis and early embryonic development. Conclusion This study demonstrated that at specific CpG sites, sperm DNA methylation status is related to bull fertility, and identified seven differently methylated genes in sperm of subfertile bulls that may lead to altered gene expression and potentially influence embryo development. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08614-5.
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Affiliation(s)
- Miriama Štiavnická
- Department of Biological Sciences, Laboratory of Animal Reproduction, Biomaterials Research Cluster, Bernal Institute, Faculty of Science and Engineering, University of Limerick, Limerick, Ireland.
| | - Aurélie Chaulot-Talmon
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, France.,Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort, France
| | - Jean-Philippe Perrier
- Department of Biological Sciences, Laboratory of Animal Reproduction, Biomaterials Research Cluster, Bernal Institute, Faculty of Science and Engineering, University of Limerick, Limerick, Ireland
| | - Petr Hošek
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - David A Kenny
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Meath, Ireland
| | - Patrick Lonergan
- School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Hélène Kiefer
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, France.,Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort, France
| | - Sean Fair
- Department of Biological Sciences, Laboratory of Animal Reproduction, Biomaterials Research Cluster, Bernal Institute, Faculty of Science and Engineering, University of Limerick, Limerick, Ireland
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7
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Costes V, Chaulot-Talmon A, Sellem E, Perrier JP, Aubert-Frambourg A, Jouneau L, Pontlevoy C, Hozé C, Fritz S, Boussaha M, Le Danvic C, Sanchez MP, Boichard D, Schibler L, Jammes H, Jaffrézic F, Kiefer H. Predicting male fertility from the sperm methylome: application to 120 bulls with hundreds of artificial insemination records. Clin Epigenetics 2022; 14:54. [PMID: 35477426 PMCID: PMC9047354 DOI: 10.1186/s13148-022-01275-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 04/08/2022] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Conflicting results regarding alterations to sperm DNA methylation in cases of spermatogenesis defects, male infertility and poor developmental outcomes have been reported in humans. Bulls used for artificial insemination represent a relevant model in this field, as the broad dissemination of bull semen considerably alleviates confounding factors and enables the precise assessment of male fertility. This study was therefore designed to assess the potential for sperm DNA methylation to predict bull fertility. RESULTS A unique collection of 100 sperm samples was constituted by pooling 2-5 ejaculates per bull from 100 Montbéliarde bulls of comparable ages, assessed as fertile (n = 57) or subfertile (n = 43) based on non-return rates 56 days after insemination. The DNA methylation profiles of these samples were obtained using reduced representation bisulfite sequencing. After excluding putative sequence polymorphisms, 490 fertility-related differentially methylated cytosines (DMCs) were identified, most of which were hypermethylated in subfertile bulls. Interestingly, 46 genes targeted by DMCs are involved in embryonic and fetal development, sperm function and maturation, or have been related to fertility in genome-wide association studies; five of these were further analyzed by pyrosequencing. In order to evaluate the prognostic value of fertility-related DMCs, the sperm samples were split between training (n = 67) and testing (n = 33) sets. Using a Random Forest approach, a predictive model was built from the methylation values obtained on the training set. The predictive accuracy of this model was 72% on the testing set and 72% on individual ejaculates collected from an independent cohort of 20 bulls. CONCLUSION This study, conducted on the largest set of bull sperm samples so far examined in epigenetic analyses, demonstrated that the sperm methylome is a valuable source of male fertility biomarkers. The next challenge is to combine these results with other data on the same sperm samples in order to improve the quality of the model and better understand the interplay between DNA methylation and other molecular features in the regulation of fertility. This research may have potential applications in human medicine, where infertility affects the interaction between a male and a female, thus making it difficult to isolate the male factor.
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Affiliation(s)
- Valentin Costes
- INRAE, BREED, Université Paris-Saclay, UVSQ, 78350, Jouy-en-Josas, France.,Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France.,R&D Department, ALLICE, 149 rue de Bercy, 75012, Paris, France.,Université Paris-Saclay, AgroParisTech, INRAE, GABI, 78350, Jouy-en-Josas, France
| | - Aurélie Chaulot-Talmon
- INRAE, BREED, Université Paris-Saclay, UVSQ, 78350, Jouy-en-Josas, France.,Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Eli Sellem
- INRAE, BREED, Université Paris-Saclay, UVSQ, 78350, Jouy-en-Josas, France.,Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France.,R&D Department, ALLICE, 149 rue de Bercy, 75012, Paris, France
| | - Jean-Philippe Perrier
- INRAE, BREED, Université Paris-Saclay, UVSQ, 78350, Jouy-en-Josas, France.,Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Anne Aubert-Frambourg
- INRAE, BREED, Université Paris-Saclay, UVSQ, 78350, Jouy-en-Josas, France.,Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Luc Jouneau
- INRAE, BREED, Université Paris-Saclay, UVSQ, 78350, Jouy-en-Josas, France.,Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Charline Pontlevoy
- INRAE, BREED, Université Paris-Saclay, UVSQ, 78350, Jouy-en-Josas, France.,Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Chris Hozé
- R&D Department, ALLICE, 149 rue de Bercy, 75012, Paris, France.,Université Paris-Saclay, AgroParisTech, INRAE, GABI, 78350, Jouy-en-Josas, France
| | - Sébastien Fritz
- R&D Department, ALLICE, 149 rue de Bercy, 75012, Paris, France.,Université Paris-Saclay, AgroParisTech, INRAE, GABI, 78350, Jouy-en-Josas, France
| | - Mekki Boussaha
- Université Paris-Saclay, AgroParisTech, INRAE, GABI, 78350, Jouy-en-Josas, France
| | | | - Marie-Pierre Sanchez
- Université Paris-Saclay, AgroParisTech, INRAE, GABI, 78350, Jouy-en-Josas, France
| | - Didier Boichard
- Université Paris-Saclay, AgroParisTech, INRAE, GABI, 78350, Jouy-en-Josas, France
| | | | - Hélène Jammes
- INRAE, BREED, Université Paris-Saclay, UVSQ, 78350, Jouy-en-Josas, France.,Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Florence Jaffrézic
- Université Paris-Saclay, AgroParisTech, INRAE, GABI, 78350, Jouy-en-Josas, France
| | - Hélène Kiefer
- INRAE, BREED, Université Paris-Saclay, UVSQ, 78350, Jouy-en-Josas, France. .,Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France.
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8
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Kiefer H, Sellem E, Bonnet-Garnier A, Pannetier M, Costes V, Schibler L, Jammes H. The epigenome of male germ cells and the programming of phenotypes in cattle. Anim Front 2021; 11:28-38. [PMID: 34934527 PMCID: PMC8683155 DOI: 10.1093/af/vfab062] [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: 12/22/2022] Open
Affiliation(s)
- Hélène Kiefer
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France.,Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Eli Sellem
- R&D Department, ALLICE, 149 rue de Bercy, 75012, Paris, France
| | - Amélie Bonnet-Garnier
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France.,Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Maëlle Pannetier
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France.,Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Valentin Costes
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France.,Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France.,R&D Department, ALLICE, 149 rue de Bercy, 75012, Paris, France
| | | | - Hélène Jammes
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France.,Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
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9
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Sirard MA. How the environment affects early embryonic development. Reprod Fertil Dev 2021; 34:203-213. [PMID: 35231267 DOI: 10.1071/rd21266] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
In the field of animal reproduction, the environment associated with gametes and embryos refers to the parents' condition as well as conditions surrounding gametes and embryos in vivo or in vitro . This environment is now known to influence not only the functionality of the early embryo but potentially the future phenotype of the offspring. Using transcriptomic and epigenetic molecular analysis, and the bovine model, recent research has shown that both the female and the male metabolic status, for example age, can affect gene expression and gene programming in the embryo. Evidence demonstrates that milking cows, which are losing weight at the time of conception, generates compromised embryos and offspring with a unique metabolic signature. A similar phenomenon has been associated with different culture conditions and the IVF procedure. The general common consequence of these situations is an embryo behaving on 'economy' mode where translation, cell division and ATP production is reduced, potentially to adapt to the perceived future environment. Few epidemiological studies have been done in bovines to assess if these changes result in a different phenotype and more studies are required to associate specific molecular changes in embryos with visible consequences later in life.
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Affiliation(s)
- Marc-André Sirard
- Faculté des Sciences de l'Agriculture et de l'Alimentation, Département des Sciences Animales, Centre de Recherche en Reproduction, Développement et Santé Intergénérationnelle (CRDSI), Université Laval, Québec, QC G1V 0A6, Canada
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10
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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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