1
|
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.
Collapse
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
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Capra E, Lazzari B, Milanesi M, Nogueira GP, Garcia JF, Utsunomiya YT, Ajmone-Marsan P, Stella A. Comparison between indicine and taurine cattle DNA methylation reveals epigenetic variation associated to differences in morphological adaptive traits. Epigenetics 2023; 18:2163363. [PMID: 36600398 PMCID: PMC9980582 DOI: 10.1080/15592294.2022.2163363] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Indicine and taurine subspecies present distinct morphological traits as a consequence of environmental adaptation and artificial selection. Although the two subspecies have been characterized and compared at genome-wide level and at specific loci, their epigenetic diversity has not yet been explored. In this work, Reduced Representation Bisulphite Sequencing (RRBS) profiling of the taurine Angus (A) and indicine Nellore (N) cattle breeds was applied to identify methylation differences between the two subspecies. Genotyping by sequencing (GBS) of the same animals was performed to detect single nucleotide polymorphisms (SNPs) at cytosines in CpG dinucleotides and remove them from the differential methylation analysis. A total of 660,845 methylated cytosines were identified within the CpG context (CpGs) across the 10 animals sequenced (5 N and 5 A). A total of 25,765 of these were differentially methylated (DMCs). Most DMCs clustered in CpG stretches nearby genes involved in cellular and anatomical structure morphogenesis. Also, sequences flanking DMC were enriched in SNPs compared to all other CpGs, either methylated or unmethylated in the two subspecies. Our data suggest a contribution of epigenetics to the regulation and divergence of anatomical morphogenesis in the two subspecies relevant for cattle evolution and sub-species differentiation and adaptation.
Collapse
Affiliation(s)
- E Capra
- Institute of Agricultural Biology and Biotechnology, National Research Council IBBA CNR, Lodi, Italy
| | - B Lazzari
- Institute of Agricultural Biology and Biotechnology, National Research Council IBBA CNR, Lodi, Italy
| | - M Milanesi
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (Unesp), Araçatuba, Brazil.,International Atomic Energy Agency, Collaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, Brazil.,Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Viterbo, Italy
| | - G P Nogueira
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (Unesp), Araçatuba, Brazil
| | - J F Garcia
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (Unesp), Araçatuba, Brazil.,International Atomic Energy Agency, Collaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, Brazil
| | - Y T Utsunomiya
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (Unesp), Araçatuba, Brazil
| | - P Ajmone-Marsan
- Department of Animal Science, Food and Nutrition - DIANA, and Nutrigenomics and Proteomics Research Center - PRONUTRIGEN, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - A Stella
- Institute of Agricultural Biology and Biotechnology, National Research Council IBBA CNR, Lodi, Italy
| |
Collapse
|
5
|
Ivanova E, Hue-Beauvais C, Chaulot-Talmon A, Castille J, Laubier J, De Casanove C, Aubert-Frambourg A, Germon P, Jammes H, Le Provost F. DNA methylation and gene expression changes in mouse mammary tissue during successive lactations: part I - the impact of inflammation. Epigenetics 2023; 18:2215633. [PMID: 37302099 PMCID: PMC10732689 DOI: 10.1080/15592294.2023.2215633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 05/10/2023] [Accepted: 05/12/2023] [Indexed: 06/13/2023] Open
Abstract
Mastitis is among the main reasons women cease breastfeeding, which leads to them supplementing breast milk with artificial formula. In farm animals, mastitis results in significant economic losses and the premature culling of some animals. Nevertheless, researchers do not know enough about the effect of inflammation on the mammary gland. This article discusses the changes to DNA methylation in mouse mammary tissue caused by lipopolysaccharide-induced inflammation (4 h post-injection of lipopolysaccharide). We analysed the expression of some genes related to mammary gland function, epigenetic regulation, and the immune response. The analysis focused on three comparisons: inflammation during the first lactation, inflammation during second lactation with no history of inflammation, and inflammation during second lactation with previous inflammation. We identified differentially methylated cytosines (DMCs), differentially methylated regions (DMRs), and some differentially expressed genes (DEGs) for each comparison. The three comparisons shared some DEGs; however, few DMCs and only one DMR were shared. These observations suggest that inflammation is one of several factors affecting epigenetic regulation during successive lactations. Furthermore, the comparison between animals in second lactation with and without inflammation, with no inflammation history during first lactation showed a different pattern compared to the other conditions in this experiment. This indicates that inflammation history plays an important role in determining epigenetic changes. The data presented in this study suggest that lactation rank and previous inflammation history are equally important when explaining mammary tissue gene expression and DNA methylation changes.Abbreviations: RRBS, reduced representation bisulfite sequencing; RT-qPCR, real-time quantitative polymerase chain reaction; MEC, mammary epithelial cells; TSS, transcription start site; TTS, transcription termination site; UTR, untranslated region; SINE, short interspersed nuclear element; LINE, long interspersed nuclear element; CGI, CpG island; DEG, differentially expressed gene; DMC, differentially methylated cytosine; DMR, differentially methylated region; GO term, gene ontology term; MF, molecular function; BP, biological process.
Collapse
Affiliation(s)
- E. Ivanova
- Université Paris-Saclay, INRAE, AgroParistech, GABI, France
| | | | - A. Chaulot-Talmon
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-En-Josas, France
- Ecole Nationale Vétérinaire d’Alfort, BREED, Maisons-Alfort, France
| | - J. Castille
- Université Paris-Saclay, INRAE, AgroParistech, GABI, France
| | - J Laubier
- Université Paris-Saclay, INRAE, AgroParistech, GABI, France
| | - C De Casanove
- Université Paris-Saclay, INRAE, AgroParistech, GABI, France
| | - A. Aubert-Frambourg
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-En-Josas, France
- Ecole Nationale Vétérinaire d’Alfort, BREED, Maisons-Alfort, France
| | - P. Germon
- INRAE, Université de Tours, ISP, Nouzilly, France
| | - H. Jammes
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-En-Josas, France
- Ecole Nationale Vétérinaire d’Alfort, BREED, Maisons-Alfort, France
| | - F. Le Provost
- Université Paris-Saclay, INRAE, AgroParistech, GABI, France
| |
Collapse
|
6
|
Klutstein M, Gonen N. Epigenetic aging of mammalian gametes. Mol Reprod Dev 2023; 90:785-803. [PMID: 37997675 DOI: 10.1002/mrd.23717] [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: 12/18/2022] [Revised: 11/09/2023] [Accepted: 11/12/2023] [Indexed: 11/25/2023]
Abstract
The process of aging refers to physiological changes that occur to an organism as time progresses and involves changes to DNA, proteins, metabolism, cells, and organs. Like the rest of the cells in the body, gametes age, and it is well established that there is a decline in reproductive capabilities in females and males with aging. One of the major pathways known to be involved in aging is epigenetic changes. The epigenome is the multitude of chemical modifications performed on DNA and chromatin that affect the ability of chromatin to be transcribed. In this review, we explore the effects of aging on female and male gametes with a focus on the epigenetic changes that occur in gametes throughout aging. Quality decline in oocytes occurs at a relatively early age. Epigenetic changes constitute an important part of oocyte aging. DNA methylation is reduced with age, along with reduced expression of DNA methyltransferases (DNMTs). Histone deacetylases (HDAC) expression is also reduced, and a loss of heterochromatin marks occurs with age. As a consequence of heterochromatin loss, retrotransposon expression is elevated, and aged oocytes suffer from DNA damage. In sperm, aging affects sperm number, motility and fecundity, and epigenetic changes may constitute a part of this process. 5 methyl-cytosine (5mC) methylation is elevated in sperm from aged men, but methylation on Long interspersed nuclear elements (LINE) elements is reduced. Di and trimethylation of histone 3 lysine 9 (H3K9me2/3) is reduced in sperm from aged men and trimethylation of histone 3 lysine 27 (H3K27me3) is elevated. The protamine makeup of sperm from aged men is also changed, with reduced protamine expression and a misbalanced ratio between protamine proteins protamine P1 and protamine P2. The study of epigenetic reproductive aging is recently gaining interest. The current status of the field suggests that many aspects of gamete epigenetic aging are still open for investigation. The clinical applications of these investigations have far-reaching consequences for fertility and sociological human behavior.
Collapse
Affiliation(s)
- Michael Klutstein
- Institute of Biomedical and Oral Research, Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Nitzan Gonen
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
- Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| |
Collapse
|
7
|
Ivanova E, Hue-Beauvais C, Chaulot-Talmon A, Castille J, Laubier J, De Casanove C, Aubert-Frambourg A, Germon P, Jammes H, Le Provost F. DNA methylation and gene expression changes in mouse mammary tissue during successive lactations: part II - the impact of lactation rank. Epigenetics 2023; 18:2215620. [PMID: 37219968 DOI: 10.1080/15592294.2023.2215620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 05/09/2023] [Accepted: 05/12/2023] [Indexed: 05/25/2023] Open
Abstract
Mastitis is among the main reasons women cease breastfeeding. In farm animals, mastitis results in significant economic losses and the premature culling of some animals. Nevertheless, the effect of inflammation on the mammary gland is not completely understood. This article discusses the changes to DNA methylation in mouse mammary tissue caused by lipopolysaccharide-induced inflammation after in vivo intramammary challenges and the differences in DNA methylation between 1st and 2nd lactations. Lactation rank induces 981 differential methylations of cytosines (DMCs) in mammary tissue. Inflammation in 1st lactation compared to inflammation in 2nd lactation results in the identification of 964 DMCs. When comparing inflammation in 1st vs. 2nd lactations with previous inflammation history, 2590 DMCs were identified. Moreover, Fluidigm PCR data show changes in the expression of several genes related to mammary function, epigenetic regulation, and the immune response. We show that the epigenetic regulation of two successive physiological lactations is not the same in terms of DNA methylation and that the effect of lactation rank on DNA methylation is stronger than that of the onset of inflammation. The conditions presented here show that few DMCs are shared between comparisons, suggesting a specific epigenetic response depending on lactation rank, the presence of inflammation, and even whether the cells had previously suffered inflammation. In the long term, this information could lead to a better understanding of the epigenetic regulation of lactation in both physiological and pathological conditions.Abbreviations: RRBS, reduced representation bisulphite sequencing; RT-qPCR, real-time quantitative polymerase chain reaction; MEC, mammary epithelial cells; MaSC, mammary stem cell; TSS, transcription start site; TTS, transcription termination site; UTR, untranslated region; SINE, short interspersed nuclear element; LINE, long interspersed nuclear element; CGI, CpG island; DEG, differentially expressed gene; DMC, differentially methylated cytosine; DMR, differentially methylated region; GO term, gene ontology term; MF, molecular function; BP, biological process.
Collapse
Affiliation(s)
- E Ivanova
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, France
| | - C Hue-Beauvais
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, France
| | - A Chaulot-Talmon
- UVSQ, INRAE, BREED, Université Paris-Saclay, Jouy-en-Josas, France
- BREED, Ecole Nationale Vétérinaire d'Alfort, Maisons-Alfort, France
| | - J Castille
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, France
| | - J Laubier
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, France
| | - C De Casanove
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, France
| | - A Aubert-Frambourg
- UVSQ, INRAE, BREED, Université Paris-Saclay, Jouy-en-Josas, France
- BREED, Ecole Nationale Vétérinaire d'Alfort, Maisons-Alfort, France
| | - P Germon
- INRAE, Université de Tours, Nouzilly, France
| | - H Jammes
- UVSQ, INRAE, BREED, Université Paris-Saclay, Jouy-en-Josas, France
- BREED, Ecole Nationale Vétérinaire d'Alfort, Maisons-Alfort, France
| | - F Le Provost
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, France
| |
Collapse
|
8
|
Dahlen CR, Amat S, Caton JS, Crouse MS, Diniz WJDS, Reynolds LP. Paternal effects on fetal programming. Anim Reprod 2023; 20:e20230076. [PMID: 37700908 PMCID: PMC10494885 DOI: 10.1590/1984-3143-ar2023-0076] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 07/18/2023] [Indexed: 09/13/2023] Open
Abstract
Paternal programming is the concept that the environmental signals from the sire's experiences leading up to mating can alter semen and ultimately affect the phenotype of resulting offspring. Potential mechanisms carrying the paternal effects to offspring can be associated with epigenetic signatures (DNA methylation, histone modification and non-coding RNAs), oxidative stress, cytokines, and the seminal microbiome. Several opportunities exist for sperm/semen to be influenced during development; these opportunities are within the testicle, the epididymis, or accessory sex glands. Epigenetic signatures of sperm can be impacted during the pre-natal and pre-pubertal periods, during sexual maturity and with advancing sire age. Sperm are susceptible to alterations as dictated by their developmental stage at the time of the perturbation, and sperm and seminal plasma likely have both dependent and independent effects on offspring. Research using rodent models has revealed that many factors including over/under nutrition, dietary fat, protein, and ingredient composition (e.g., macro- or micronutrients), stress, exercise, and exposure to drugs, alcohol, and endocrine disruptors all elicit paternal programming responses that are evident in offspring phenotype. Research using livestock species has also revealed that sire age, fertility level, plane of nutrition, and heat stress can induce alterations in the epigenetic, oxidative stress, cytokine, and microbiome profiles of sperm and/or seminal plasma. In addition, recent findings in pigs, sheep, and cattle have indicated programming effects in blastocysts post-fertilization with some continuing into post-natal life of the offspring. Our research group is focused on understanding the effects of common management scenarios of plane of nutrition and growth rates in bulls and rams on mechanisms resulting in paternal programming and subsequent offspring outcomes. Understanding the implication of paternal programming is imperative as short-term feeding and management decisions have the potential to impact productivity and profitability of our herds for generations to come.
Collapse
Affiliation(s)
- Carl Robertson Dahlen
- Center for Nutrition and Pregnancy and Department of Animal Sciences, North Dakota State University, Fargo, ND, United States
| | - Samat Amat
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, United States
| | - Joel S. Caton
- Center for Nutrition and Pregnancy and Department of Animal Sciences, North Dakota State University, Fargo, ND, United States
| | - Matthew S. Crouse
- U.S. Meat Animal Research Center, Agricultural Research Service, U.S. Department of Agriculture, Clay Center, NE, United States
| | | | - Lawrence P. Reynolds
- Center for Nutrition and Pregnancy and Department of Animal Sciences, North Dakota State University, Fargo, ND, United States
| |
Collapse
|
9
|
Lahimer M, Montjean D, Cabry R, Capelle S, Lefranc E, Bach V, Ajina M, Ben Ali H, Khorsi-Cauet H, Benkhalifa M. Paternal Age Matters: Association with Sperm Criteria's- Spermatozoa DNA Integrity and Methylation Profile. J Clin Med 2023; 12:4928. [PMID: 37568329 PMCID: PMC10420110 DOI: 10.3390/jcm12154928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/24/2023] [Accepted: 07/24/2023] [Indexed: 08/13/2023] Open
Abstract
Advanced age has been reported to negatively affect sperm parameters and spermatozoa DNA integrity. A decline in sperm criteria was also associated with altered epigenetic marks such as DNA methylation with a potential downstream impact on in vitro fertilization success and clinical outcomes. The aim of the present retrospective study was to clarify the association between advanced paternal age (APA) and sperm parameters, DNA integrity and DNA methylation profile. A total of 671 patients consulting for infertility underwent sperm analysis, sperm DNA integrity assessment and methylation level measurement. The principal finding was that individuals over 40 years of age exhibit a significant increase in DNA fragmentation levels compared to the younger group (15% versus 9%, respectively, p = 0.04). However, there was no significant difference in DNA decondensation and sperm parameters in association with APA. In addition, a drop in the global methylation level was also found in men over 40 years (6% in the young group versus 2% in the old group, p = 0.03). As a conclusion, men over 40 years are at higher risk of elevated sperm DNA fragmentation and lower methylation level. Based on these observations, it is recommended that the assessment of sperm DNA fragmentation should be taken into consideration particularly after the age of 40. Our findings support the idea that paternal age is a crucial factor that should not be neglected during fertility evaluation and treatment since it is associated with epigenetics changes in sperm. Although the underlying mechanism remains to be clarified, we believe that environmental and professional exposure factors are likely involved in the process.
Collapse
Affiliation(s)
- Marwa Lahimer
- Reproductive Medicine, Reproductive Biology & Genetics, University Hospital and School of Medicine, Picardie University Jules Verne, CHU Sud, 80054 Amiens, France; (M.L.); (R.C.); (S.C.); (E.L.); (M.B.)
- PERITOX—Périnatalité et Risques Toxiques—UMR-I1, Picardie University Jules Verne, CHU Sud, 80025 Amiens, France;
- Exercise Physiology and Physiopathology: From Integrated to Molecular “Biology, Medicine and Health” (Code: LR19ES09), Sousse 4002, Tunisia
| | - Debbie Montjean
- Fertilys, Centres de Fertilité, Laval and Brossard, Québec, QC H7S 1Z5, Canada;
| | - Rosalie Cabry
- Reproductive Medicine, Reproductive Biology & Genetics, University Hospital and School of Medicine, Picardie University Jules Verne, CHU Sud, 80054 Amiens, France; (M.L.); (R.C.); (S.C.); (E.L.); (M.B.)
- PERITOX—Périnatalité et Risques Toxiques—UMR-I1, Picardie University Jules Verne, CHU Sud, 80025 Amiens, France;
| | - Severine Capelle
- Reproductive Medicine, Reproductive Biology & Genetics, University Hospital and School of Medicine, Picardie University Jules Verne, CHU Sud, 80054 Amiens, France; (M.L.); (R.C.); (S.C.); (E.L.); (M.B.)
| | - Elodie Lefranc
- Reproductive Medicine, Reproductive Biology & Genetics, University Hospital and School of Medicine, Picardie University Jules Verne, CHU Sud, 80054 Amiens, France; (M.L.); (R.C.); (S.C.); (E.L.); (M.B.)
| | - Véronique Bach
- PERITOX—Périnatalité et Risques Toxiques—UMR-I1, Picardie University Jules Verne, CHU Sud, 80025 Amiens, France;
| | - Mounir Ajina
- Unit of Reproductive Medicine, University Hospital Farhat Hached, Sousse 4000, Tunisia;
| | - Habib Ben Ali
- Faculty of Medicine of Sousse, University of Sousse, Sousse 4000, Tunisia;
| | - Hafida Khorsi-Cauet
- Reproductive Medicine, Reproductive Biology & Genetics, University Hospital and School of Medicine, Picardie University Jules Verne, CHU Sud, 80054 Amiens, France; (M.L.); (R.C.); (S.C.); (E.L.); (M.B.)
- PERITOX—Périnatalité et Risques Toxiques—UMR-I1, Picardie University Jules Verne, CHU Sud, 80025 Amiens, France;
| | - Moncef Benkhalifa
- Reproductive Medicine, Reproductive Biology & Genetics, University Hospital and School of Medicine, Picardie University Jules Verne, CHU Sud, 80054 Amiens, France; (M.L.); (R.C.); (S.C.); (E.L.); (M.B.)
- PERITOX—Périnatalité et Risques Toxiques—UMR-I1, Picardie University Jules Verne, CHU Sud, 80025 Amiens, France;
| |
Collapse
|
10
|
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.
Collapse
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.)
| |
Collapse
|
11
|
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.
Collapse
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.
| |
Collapse
|
12
|
Capra E, Turri F, Lazzari B, Biffani S, Lange Consiglio A, Ajmone Marsan P, Stella A, Pizzi F. CpG DNA methylation changes during epididymal sperm maturation in bulls. Epigenetics Chromatin 2023; 16:20. [PMID: 37254160 DOI: 10.1186/s13072-023-00495-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 05/19/2023] [Indexed: 06/01/2023] Open
Abstract
BACKGROUND During epididymal transit spermatozoa acquire specific morphological features which enhance their ability to swim in a progressive manner and interact with the oocytes. At the same time, sperm cells undergo specific molecular rearrangements essential for the fertilizing sperm to drive a correct embryo development. To assess epigenetic sperm changes during epididymal maturation, the caput, corpus and cauda epididymis sperm tracts were isolated from eight bulls and characterized for different sperm quality parameters and for CpG DNA methylation using Reduced Representation Bisulfite Sequencing (RRBS) able to identify differentially methylated regions (DMRs) in higher CpG density regions. RESULTS Caput sperm showed significant variation in motility and sperm kinetics variables, whereas spermatozoa collected from the corpus presented morphology variation and significant alterations in variables related to acrosome integrity. A total of 57,583 methylated regions were identified across the eight bulls, showing a significantly diverse distribution for sperm collected in the three epididymal regions. Differential methylation was observed between caput vs corpus (n = 11,434), corpus vs cauda (n = 12,372) and caput vs cauda (n = 2790). During epididymal transit a high proportion of the epigenome was remodeled, showing several regions in which methylation decreases from caput to corpus and increases from corpus to cauda. CONCLUSIONS Specific CpG DNA methylation changes in sperm isolated from the caput, corpus, and cauda epididymis tracts are likely to refine the sperm epigenome during sperm maturation, potentially impacting sperm fertilization ability and spatial organization of the genome during early embryo development.
Collapse
Affiliation(s)
- Emanuele Capra
- Institute of Agricultural Biology and Biotechnology, National Research Council IBBA CNR, 26900, Lodi, Italy.
| | - F Turri
- Institute of Agricultural Biology and Biotechnology, National Research Council IBBA CNR, 26900, Lodi, Italy
| | - B Lazzari
- Institute of Agricultural Biology and Biotechnology, National Research Council IBBA CNR, 26900, Lodi, Italy
- Institute of Agricultural Biology and Biotechnology, National Research Council IBBA CNR, 20133, Milano, Italy
| | - S Biffani
- Institute of Agricultural Biology and Biotechnology, National Research Council IBBA CNR, 20133, Milano, Italy
| | - A Lange Consiglio
- Department of Veterinary Medicine and Animal Sciences (DIVAS), Università degli Studi di Milano, 26900, Lodi, Italy
| | - P Ajmone Marsan
- Department of Animal Science, Food and Technology-DIANA, and Romeo and Enrica Invernizzi Research Center on Sustainable Dairy Production-CREI, Università Cattolica del Sacro Cuore, 29122, Piacenza, Italy
| | - A Stella
- Institute of Agricultural Biology and Biotechnology, National Research Council IBBA CNR, 20133, Milano, Italy
| | - F Pizzi
- Institute of Agricultural Biology and Biotechnology, National Research Council IBBA CNR, 26900, Lodi, Italy
| |
Collapse
|
13
|
Shi L, Shi J, Feng J, Zhang P, Ren Y. Proteomic analysis reveals the potential positive effects of Mito-TEMPO on ram sperm motility and fertility during cryopreservation. Theriogenology 2023; 205:27-39. [PMID: 37084501 DOI: 10.1016/j.theriogenology.2023.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/04/2023] [Accepted: 04/15/2023] [Indexed: 04/23/2023]
Abstract
The aim of this study was to investigate the effects of mitochondria-targeted antioxidant Mito-TEMPO on the protein profile of ram sperm during cryopreservation and evaluate the cryoprotective roles of Mito-TEMPO on ram sperm quality and fertilization capacity. Semen collected from 8 Dorper rams was cryopreserved in TCG-egg yolk extender supplemented with various concentrations of Mito-TEMPO (0, 20, 40 and 60 μM). After thawing, sperm characteristics, antioxidant status and the abundance of hexose transporters (GLUT 3 and 8) were analyzed. The cervical artificial insemination (AI) was performed to evaluate the fertilization ability of cryopreserved ram sperm. The alterations of sperm proteomic profile between the control and MT40 groups were determined using iTRAQ-coupled LC-MS. Supplementation with 40 μM of Mito-TEMPO resulted in the highest post-thaw sperm motility and kinematics. Sperm quality, antioxidant capacity and glucose transporter abundance of frozen-thawed ram sperm were elevated in the MT40 group. The inclusion of 40 μM Mito-TEMPO in freezing extender also resulted in the higher pregnancy rate of ewes. A total of 457 proteins including 179 upregulated proteins and 278 downregulated proteins were defied as differentially expressed proteins (DEPs) using fold change (FC) > 1.2 with P < 0.05. Sixty-one DEPs with (FC > 1.5) were dramatically regulated by Mito-TEMPO. These DEPs are mainly involved in sperm motility, energy metabolism and capacitation. Our data suggest that the beneficial effects of Mito-TEMPO on sperm motility and fertility potential of cryopreserved ram semen are achieved by regulating sperm antioxidant capacity and sperm proteins related to energy metabolism and fertility.
Collapse
Affiliation(s)
- Lei Shi
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, PR China; Lab of Animal Reproductive Biotechnology, Shanxi Agricultural University, Taigu, 030801, PR China
| | - Juanjuan Shi
- Lab of Animal Reproductive Biotechnology, Shanxi Agricultural University, Taigu, 030801, PR China
| | - Jingjuan Feng
- Lab of Animal Reproductive Biotechnology, Shanxi Agricultural University, Taigu, 030801, PR China
| | - Pengcheng Zhang
- Lab of Animal Reproductive Biotechnology, Shanxi Agricultural University, Taigu, 030801, PR China
| | - Youshe Ren
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, PR China; Lab of Animal Reproductive Biotechnology, Shanxi Agricultural University, Taigu, 030801, PR China.
| |
Collapse
|
14
|
Laporta J, Lemley C, Chavatte-Palmer P. Editorial: The Influences of Early Life Experiences on Future Health and Productivity. FRONTIERS IN ANIMAL SCIENCE 2022. [DOI: 10.3389/fanim.2022.962580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|