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Lismer A, Shao X, Dumargne MC, Lafleur C, Lambrot R, Chan D, Toft G, Bonde JP, MacFarlane AJ, Bornman R, Aneck-Hahn N, Patrick S, Bailey JM, de Jager C, Dumeaux V, Trasler JM, Kimmins S. The Association between Long-Term DDT or DDE Exposures and an Altered Sperm Epigenome-a Cross-Sectional Study of Greenlandic Inuit and South African VhaVenda Men. ENVIRONMENTAL HEALTH PERSPECTIVES 2024; 132:17008. [PMID: 38294233 PMCID: PMC10829569 DOI: 10.1289/ehp12013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/26/2023] [Accepted: 12/20/2023] [Indexed: 02/01/2024]
Abstract
BACKGROUND The organochlorine dichlorodiphenyltrichloroethane (DDT) is banned worldwide owing to its negative health effects. It is exceptionally used as an insecticide for malaria control. Exposure occurs in regions where DDT is applied, as well as in the Arctic, where its endocrine disrupting metabolite, p , p ' -dichlorodiphenyldichloroethylene (p , p ' -DDE) accumulates in marine mammals and fish. DDT and p , p ' -DDE exposures are linked to birth defects, infertility, cancer, and neurodevelopmental delays. Of particular concern is the potential of DDT use to impact the health of generations to come via the heritable sperm epigenome. OBJECTIVES The objective of this study was to assess the sperm epigenome in relation to p , p ' -DDE serum levels between geographically diverse populations. METHODS In the Limpopo Province of South Africa, we recruited 247 VhaVenda South African men and selected 50 paired blood serum and semen samples, and 47 Greenlandic Inuit blood and semen paired samples were selected from a total of 193 samples from the biobank of the INUENDO cohort, an EU Fifth Framework Programme Research and Development project. Sample selection was based on obtaining a range of p , p ' -DDE serum levels (mean = 870.734 ± 134.030 ng / mL ). We assessed the sperm epigenome in relation to serum p , p ' -DDE levels using MethylC-Capture-sequencing (MCC-seq) and chromatin immunoprecipitation followed by sequencing (ChIP-seq). We identified genomic regions with altered DNA methylation (DNAme) and differential enrichment of histone H3 lysine 4 trimethylation (H3K4me3) in sperm. RESULTS Differences in DNAme and H3K4me3 enrichment were identified at transposable elements and regulatory regions involved in fertility, disease, development, and neurofunction. A subset of regions with sperm DNAme and H3K4me3 that differed between exposure groups was predicted to persist in the preimplantation embryo and to be associated with embryonic gene expression. DISCUSSION These findings suggest that DDT and p , p ' -DDE exposure impacts the sperm epigenome in a dose-response-like manner and may negatively impact the health of future generations through epigenetic mechanisms. Confounding factors, such as other environmental exposures, genetic diversity, and selection bias, cannot be ruled out. https://doi.org/10.1289/EHP12013.
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Affiliation(s)
- Ariane Lismer
- Department of Pharmacology and Therapeutics, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
| | - Xiaojian Shao
- Digital Technologies Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Marie-Charlotte Dumargne
- Department of Animal Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada
| | - Christine Lafleur
- University of Montreal Hospital Research Centre, Montreal, Quebec, Canada
| | - Romain Lambrot
- University of Montreal Hospital Research Centre, Montreal, Quebec, Canada
| | - Donovan Chan
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Gunnar Toft
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
| | - Jens Peter Bonde
- Department of Occupational and Environmental Medicine, Bispebjerg University Hospital, Copenhagen, Denmark
- Institute of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Amanda J. MacFarlane
- Agriculture Food and Nutrition Evidence Center, Texas A&M University, Fort Worth, Texas, USA
| | - Riana Bornman
- Environmental Chemical Pollution and Health Research Unit, School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
- University of Pretoria Institute for Sustainable Malaria Control, School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, South Africa
| | - Natalie Aneck-Hahn
- University of Pretoria Institute for Sustainable Malaria Control, School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, South Africa
| | - Sean Patrick
- University of Pretoria Institute for Sustainable Malaria Control, School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, South Africa
| | - Janice M. Bailey
- Research Centre on Reproduction and Intergenerational Health, Department of Animal Sciences, Université Laval, Quebec, Quebec, Canada
| | - Christiaan de Jager
- Environmental Chemical Pollution and Health Research Unit, School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
- University of Pretoria Institute for Sustainable Malaria Control, School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, South Africa
| | - Vanessa Dumeaux
- Department of Anatomy and Cell Biology, Western University, London, Ontario, Canada
- Department of Oncology, Western University, London, Ontario, Canada
| | - Jacquetta M. Trasler
- Department of Pharmacology and Therapeutics, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
- Department of Pediatrics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Sarah Kimmins
- Department of Pharmacology and Therapeutics, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
- University of Montreal Hospital Research Centre, Montreal, Quebec, Canada
- Department of Pathology and Cell Biology, Faculty of Medicine, University of Montreal, Quebec, Canada
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Han J, Yu G, Zhang X, Dai Y, Zhang H, Zhang B, Wang K. Histone Maps in Gossypium darwinii Reveal Epigenetic Regulation Drives Subgenome Divergence and Cotton Domestication. Int J Mol Sci 2023; 24:10607. [PMID: 37445787 DOI: 10.3390/ijms241310607] [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: 04/21/2023] [Revised: 06/16/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
The functional annotation of genomes, including chromatin modifications, is essential to understand the intricate architecture of chromatin and the consequential gene regulation. However, such an annotation remains limited for cotton genomes. Here, we conducted chromatin profiling in a wild allotetraploid cotton Gossypium darwinii (AD genome) by integrating the data of histone modification, transcriptome, and chromatin accessibility. We revealed that the A subgenome showed a higher level of active histone marks and lower level of repressive histone marks than the D subgenome, which was consistent with the expression bias between the two subgenomes. We show that the bias in transcription and histone modification between the A and D subgenomes may be caused by genes unique to the subgenome but not by homoeologous genes. Moreover, we integrate histone marks and open chromatin to define six chromatin states (S1-S6) across the cotton genome, which index different genomic elements including genes, promoters, and transposons, implying distinct biological functions. In comparison to the domesticated cotton species, we observed that 23.2% of genes in the genome exhibit a transition from one chromatin state to another at their promoter. Strikingly, the S2 (devoid of epigenetic marks) to S3 (enriched for the mark of open chromatin) was the largest transition group. These transitions occurred simultaneously with changes in gene expression, which were significantly associated with several domesticated traits in cotton. Collectively, our study provides a useful epigenetic resource for research on allopolyploid plants. The domestication-induced chromatin dynamics and associated genes identified here will aid epigenetic engineering, improving polyploid crops.
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Affiliation(s)
- Jinlei Han
- School of Life Sciences, Nantong University, Nantong 226019, China
| | - Guangrun Yu
- School of Life Sciences, Nantong University, Nantong 226019, China
| | - Xin Zhang
- School of Life Sciences, Nantong University, Nantong 226019, China
| | - Yan Dai
- School of Life Sciences, Nantong University, Nantong 226019, China
| | - Hui Zhang
- School of Life Sciences, Nantong University, Nantong 226019, China
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - Kai Wang
- School of Life Sciences, Nantong University, Nantong 226019, China
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Lismer A, Kimmins S. Emerging evidence that the mammalian sperm epigenome serves as a template for embryo development. Nat Commun 2023; 14:2142. [PMID: 37059740 PMCID: PMC10104880 DOI: 10.1038/s41467-023-37820-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 03/31/2023] [Indexed: 04/16/2023] Open
Abstract
Although more studies are demonstrating that a father's environment can influence child health and disease, the molecular mechanisms underlying non-genetic inheritance remain unclear. It was previously thought that sperm exclusively contributed its genome to the egg. More recently, association studies have shown that various environmental exposures including poor diet, toxicants, and stress, perturbed epigenetic marks in sperm at important reproductive and developmental loci that were associated with offspring phenotypes. The molecular and cellular routes that underlie how epigenetic marks are transmitted at fertilization, to resist epigenetic reprogramming in the embryo, and drive phenotypic changes are only now beginning to be unraveled. Here, we provide an overview of the state of the field of intergenerational paternal epigenetic inheritance in mammals and present new insights into the relationship between embryo development and the three pillars of epigenetic inheritance: chromatin, DNA methylation, and non-coding RNAs. We evaluate compelling evidence of sperm-mediated transmission and retention of paternal epigenetic marks in the embryo. Using landmark examples, we discuss how sperm-inherited regions may escape reprogramming to impact development via mechanisms that implicate transcription factors, chromatin organization, and transposable elements. Finally, we link paternally transmitted epigenetic marks to functional changes in the pre- and post-implantation embryo. Understanding how sperm-inherited epigenetic factors influence embryo development will permit a greater understanding related to the developmental origins of health and disease.
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Affiliation(s)
- Ariane Lismer
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, QC, H3G 1Y6, Canada
| | - Sarah Kimmins
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, QC, H3G 1Y6, Canada.
- Department of Pathology and Cell Biology, Faculty of Medicine, University of Montreal Hospital Research Centre, Montreal, QC, H2X 0A9, Canada.
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Huang L, Li F, Ye L, Yu F, Wang C. Epigenetic regulation of embryonic ectoderm development in stem cell differentiation and transformation during ontogenesis. Cell Prolif 2023; 56:e13413. [PMID: 36727213 PMCID: PMC10068960 DOI: 10.1111/cpr.13413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 01/09/2023] [Accepted: 01/18/2023] [Indexed: 02/03/2023] Open
Abstract
Dynamic chromatin accessibility regulates stem cell fate determination and tissue homeostasis via controlling gene expression. As a histone-modifying enzyme that predominantly mediates methylation of lysine 27 in histone H3 (H3K27me1/2/3), Polycomb repressive complex 2 (PRC2) plays the canonical role in targeting developmental regulators during stem cell differentiation and transformation. Embryonic ectoderm development (EED), the core scaffold subunit of PRC2 and as an H3K27me3-recognizing protein, has been broadly implicated with PRC2 stabilization and allosterically stimulated PRC2. Accumulating evidences from experimental data indicate that EED-associating epigenetic modifications are indispensable for stem cell maintenance and differentiation into specific cell lineages. In this review, we discuss the most updated advances to summarize the structural architecture of EED and its contributions and underlying mechanisms to mediating lineage differentiation of different stem cells during epigenetic modification to expand our understanding of PRC2.
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Affiliation(s)
- Liuyan Huang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.,Department of Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Feifei Li
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Ling Ye
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.,Department of Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Fanyuan Yu
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.,Department of Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Chenglin Wang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.,Department of Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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Regulation, functions and transmission of bivalent chromatin during mammalian development. Nat Rev Mol Cell Biol 2023; 24:6-26. [PMID: 36028557 DOI: 10.1038/s41580-022-00518-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/05/2022] [Indexed: 12/25/2022]
Abstract
Cells differentiate and progress through development guided by a dynamic chromatin landscape that mediates gene expression programmes. During development, mammalian cells display a paradoxical chromatin state: histone modifications associated with gene activation (trimethylated histone H3 Lys4 (H3K4me3)) and with gene repression (trimethylated H3 Lys27 (H3K27me3)) co-occur at promoters of developmental genes. This bivalent chromatin modification state is thought to poise important regulatory genes for expression or repression during cell-lineage specification. In this Review, we discuss recent work that has expanded our understanding of the molecular basis of bivalent chromatin and its contributions to mammalian development. We describe the factors that establish bivalency, especially histone-lysine N-methyltransferase 2B (KMT2B) and Polycomb repressive complex 2 (PRC2), and consider evidence indicating that PRC1 shapes bivalency and may contribute to its transmission between generations. We posit that bivalency is a key feature of germline and embryonic stem cells, as well as other types of stem and progenitor cells. Finally, we discuss the relevance of bivalent chromtin to human development and cancer, and outline avenues of future research.
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Jarred EG, Qu Z, Tsai T, Oberin R, Petautschnig S, Bildsoe H, Pederson S, Zhang QH, Stringer JM, Carroll J, Gardner DK, Van den Buuse M, Sims NA, Gibson WT, Adelson DL, Western PS. Transient Polycomb activity represses developmental genes in growing oocytes. Clin Epigenetics 2022; 14:183. [PMID: 36544159 PMCID: PMC9769065 DOI: 10.1186/s13148-022-01400-w] [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: 06/21/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Non-genetic disease inheritance and offspring phenotype are substantially influenced by germline epigenetic programming, including genomic imprinting. Loss of Polycomb Repressive Complex 2 (PRC2) function in oocytes causes non-genetically inherited effects on offspring, including embryonic growth restriction followed by post-natal offspring overgrowth. While PRC2-dependent non-canonical imprinting is likely to contribute, less is known about germline epigenetic programming of non-imprinted genes during oocyte growth. In addition, de novo germline mutations in genes encoding PRC2 lead to overgrowth syndromes in human patients, but the extent to which PRC2 activity is conserved in human oocytes is poorly understood. RESULTS In this study, we identify a discrete period of early oocyte growth during which PRC2 is expressed in mouse growing oocytes. Deletion of Eed during this window led to the de-repression of 343 genes. A high proportion of these were developmental regulators, and the vast majority were not imprinted genes. Many of the de-repressed genes were also marked by the PRC2-dependent epigenetic modification histone 3 lysine 27 trimethylation (H3K27me3) in primary-secondary mouse oocytes, at a time concurrent with PRC2 expression. In addition, we found H3K27me3 was also enriched on many of these genes by the germinal vesicle (GV) stage in human oocytes, strongly indicating that this PRC2 function is conserved in the human germline. However, while the 343 genes were de-repressed in mouse oocytes lacking EED, they were not de-repressed in pre-implantation embryos and lost H3K27me3 during pre-implantation development. This implies that H3K27me3 is a transient feature that represses a wide range of genes in oocytes. CONCLUSIONS Together, these data indicate that EED has spatially and temporally distinct functions in the female germline to repress a wide range of developmentally important genes and that this activity is conserved in the mouse and human germlines.
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Affiliation(s)
- Ellen G. Jarred
- grid.452824.dCentre for Reproductive Health, Hudson Institute of Medical Research, Clayton, VIC Australia ,grid.1002.30000 0004 1936 7857Department of Molecular and Translational Science, Monash University, Clayton, VIC Australia
| | - Zhipeng Qu
- grid.1010.00000 0004 1936 7304Department of Molecular and Biomedical Science, School of Biological Sciences, University of Adelaide, Adelaide, SA Australia
| | - Tesha Tsai
- grid.452824.dCentre for Reproductive Health, Hudson Institute of Medical Research, Clayton, VIC Australia ,grid.1002.30000 0004 1936 7857Department of Molecular and Translational Science, Monash University, Clayton, VIC Australia
| | - Ruby Oberin
- grid.452824.dCentre for Reproductive Health, Hudson Institute of Medical Research, Clayton, VIC Australia ,grid.1002.30000 0004 1936 7857Department of Molecular and Translational Science, Monash University, Clayton, VIC Australia
| | - Sigrid Petautschnig
- grid.452824.dCentre for Reproductive Health, Hudson Institute of Medical Research, Clayton, VIC Australia ,grid.1002.30000 0004 1936 7857Department of Molecular and Translational Science, Monash University, Clayton, VIC Australia
| | - Heidi Bildsoe
- grid.452824.dCentre for Reproductive Health, Hudson Institute of Medical Research, Clayton, VIC Australia ,grid.1002.30000 0004 1936 7857Department of Molecular and Translational Science, Monash University, Clayton, VIC Australia
| | - Stephen Pederson
- grid.1010.00000 0004 1936 7304Department of Molecular and Biomedical Science, School of Biological Sciences, University of Adelaide, Adelaide, SA Australia
| | - Qing-hua Zhang
- grid.1002.30000 0004 1936 7857Biomedicine Discovery Institute, Monash University, Clayton, VIC Australia
| | - Jessica M. Stringer
- grid.1002.30000 0004 1936 7857Biomedicine Discovery Institute, Monash University, Clayton, VIC Australia
| | - John Carroll
- grid.1002.30000 0004 1936 7857Biomedicine Discovery Institute, Monash University, Clayton, VIC Australia
| | - David K. Gardner
- grid.1008.90000 0001 2179 088XSchool of BioSciences, University of Melbourne, Parkville, VIC Australia
| | - Maarten Van den Buuse
- grid.1018.80000 0001 2342 0938School of Psychology and Public Health, La Trobe University, Melbourne, VIC Australia
| | - Natalie A. Sims
- grid.1073.50000 0004 0626 201XBone Cell Biology and Disease Unit, St. Vincent’s Institute of Medical Research, Fitzroy, VIC Australia ,grid.413105.20000 0000 8606 2560Department of Medicine at St, Vincent’s Hospital, Fitzroy, VIC Australia
| | - William T. Gibson
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, University of British Columbia and British Columbia Children’s Hospital Research Institute, Vancouver, BC Canada
| | - David L. Adelson
- grid.1010.00000 0004 1936 7304Department of Molecular and Biomedical Science, School of Biological Sciences, University of Adelaide, Adelaide, SA Australia ,grid.437963.c0000 0001 1349 5098South Australian Museum, SA Adelaide, Australia
| | - Patrick S. Western
- grid.452824.dCentre for Reproductive Health, Hudson Institute of Medical Research, Clayton, VIC Australia ,grid.1002.30000 0004 1936 7857Department of Molecular and Translational Science, Monash University, Clayton, VIC Australia
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Lowe MG, Yen MR, Hsu FM, Hosohama L, Hu Z, Chitiashvili T, Hunt TJ, Gorgy I, Bernard M, Wamaitha SE, Chen PY, Clark AT. EED is required for mouse primordial germ cell differentiation in the embryonic gonad. Dev Cell 2022; 57:1482-1495.e5. [PMID: 35679863 DOI: 10.1016/j.devcel.2022.05.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 12/14/2021] [Accepted: 05/16/2022] [Indexed: 11/18/2022]
Abstract
Development of primordial germ cells (PGCs) is required for reproduction. During PGC development in mammals, major epigenetic remodeling occurs, which is hypothesized to establish an epigenetic landscape for sex-specific germ cell differentiation and gametogenesis. In order to address the role of embryonic ectoderm development (EED) and histone 3 lysine 27 trimethylation (H3K27me3) in this process, we created an EED conditional knockout mouse and show that EED is essential for regulating the timing of sex-specific PGC differentiation in both ovaries and testes, as well as X chromosome dosage decompensation in testes. Integrating chromatin and whole genome bisulfite sequencing of epiblast and PGCs, we identified a poised repressive signature of H3K27me3/DNA methylation that we propose is established in the epiblast where EED and DNMT1 interact. Thus, EED joins DNMT1 in regulating the timing of sex-specific PGC differentiation during the critical window when the gonadal niche cells specialize into an ovary or testis.
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Affiliation(s)
- Matthew G Lowe
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA 90095, USA
| | - Ming-Ren Yen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Fei-Man Hsu
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA 90095, USA
| | - Linzi Hosohama
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA
| | - Zhongxun Hu
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA
| | - Tsotne Chitiashvili
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA; Department of Biological Chemistry, University of California, Los Angeles, CA 90095, USA
| | - Timothy J Hunt
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA
| | - Isaac Gorgy
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA
| | - Matthew Bernard
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
| | - Sissy E Wamaitha
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA
| | - Pao-Yang Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Amander T Clark
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA 90095, USA.
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Sperm Histone H3 Lysine 4 tri-methylation serves as a metabolic sensor of paternal obesity and is associated with the inheritance of metabolic dysfunction. Mol Metab 2022; 59:101463. [PMID: 35183795 PMCID: PMC8931445 DOI: 10.1016/j.molmet.2022.101463] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/12/2022] [Accepted: 02/14/2022] [Indexed: 11/28/2022] Open
Abstract
Objective Parental environmental exposures can strongly influence descendant risks for adult disease. How paternal obesity changes the sperm chromatin leading to the acquisition of metabolic disease in offspring remains controversial and ill-defined. The objective of this study was to assess (1) whether obesity induced by a high-fat diet alters sperm histone methylation; (2) whether paternal obesity can induce metabolic disturbances across generations; (3) whether there could be cumulative damage to the sperm epigenome leading to enhanced metabolic dysfunction in descendants; and (4) whether obesity-sensitive regions associate with embryonic epigenetic and transcriptomic profiles. Using a genetic mouse model of epigenetic inheritance, we investigated the role of histone H3 lysine 4 methylation (H3K4me3) in the paternal transmission of metabolic dysfunction. This transgenic mouse overexpresses the histone demethylase enzyme KDM1A in the developing germline and has an altered sperm epigenome at the level of histone H3K4 methylation. We hypothesized that challenging transgenic sires with a high-fat diet would further erode the sperm epigenome and lead to enhanced metabolic disturbances in the next generations. Methods To assess whether paternal obesity can have inter- or transgenerational impacts, and if so to identify potential mechanisms of this non-genetic inheritance, we used wild-type C57BL/6NCrl and transgenic males with a pre-existing altered sperm epigenome. To induce obesity, sires were fed either a control or high-fat diet (10% or 60% kcal fat, respectively) for 10–12 weeks, then bred to wild-type C57BL/6NCrl females fed a regular diet. F1 and F2 descendants were characterized for metabolic phenotypes by examining the effects of paternal obesity by sex, on body weight, fat mass distribution, the liver transcriptome, intraperitoneal glucose, and insulin tolerance tests. To determine whether obesity altered the F0 sperm chromatin, native chromatin immunoprecipitation-sequencing targeting H3K4me3 was performed. To gain insight into mechanisms of paternal transmission, we compared our sperm H3K4me3 profiles with embryonic and placental chromatin states, histone modification, and gene expression profiles. Results Obesity-induced alterations in H3K4me3 occurred in genes implicated in metabolic, inflammatory, and developmental processes. These processes were associated with offspring metabolic dysfunction and corresponded to genes enriched for H3K4me3 in embryos and overlapped embryonic and placenta gene expression profiles. Transgenerational susceptibility to metabolic disease was only observed when obese F0 had a pre-existing modified sperm epigenome. This coincided with increased H3K4me3 alterations in sperm and more severe phenotypes affecting their offspring. Conclusions Our data suggest sperm H3K4me3 might serve as a metabolic sensor that connects paternal diet with offspring phenotypes via the placenta. This non-DNA-based knowledge of inheritance has the potential to improve our understanding of how environment shapes heritability and may lead to novel routes for the prevention of disease. This study highlights the need to further study the connection between the sperm epigenome, placental development, and children's health. Summary sentence Paternal obesity impacts sperm H3K4me3 and is associated with placenta, embryonic and metabolic outcomes in descendants. Sperm H3K4me3 serves as a metabolic sensor of HFD-induced obesity. Obesity-altered sperm H3K4me3 corresponds to embryonic transcription and chromatin profiles. HFD- and KDM1A-induced cumulative sperm epimutations enhanced F1 metabolic dysfunction. Sperm epimutations may influence placenta function inducing F1 metabolic phenotypes.
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Fesser EA, Gianatiempo O, Berardino BG, Ferroni NM, Cambiasso M, Fontana VA, Calvo JC, Sonzogni SV, Cánepa ET. Limited contextual memory and transcriptional dysregulation in the medial prefrontal cortex of mice exposed to early protein malnutrition are intergenerationally transmitted. J Psychiatr Res 2021; 139:139-149. [PMID: 34058653 DOI: 10.1016/j.jpsychires.2021.05.041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/15/2021] [Accepted: 05/20/2021] [Indexed: 12/21/2022]
Abstract
Memory contextualization is vital for the subsequent retrieval of relevant memories in specific situations and is a critical dimension of social cognition. The inability to properly contextualize information has been described as characteristic of psychiatric disorders like autism spectrum disorders, schizophrenia, and post-traumatic stress disorder. The exposure to early-life adversities, such as nutritional deficiency, increases the risk to trigger alterations in different domains of cognition related to those observed in mental diseases. In this work, we explored the consequences of exposure to perinatal protein malnutrition on contextual memory in a mouse model and assessed whether these consequences are transmitted to the next generation. Female mice were fed with a normal or hypoproteic diet during pregnancy and lactation. To evaluate contextual memory, the object-context mismatch test was performed in both sexes of F1 offspring and in the subsequent F2 generation. We observed that contextual memory was altered in mice of both sexes that had been subjected to maternal protein malnutrition and that the deficit in contextual memory was transmitted to the next generation. The basis of this alteration seems to be a transcriptional dysregulation of genes involved in the excitatory and inhibitory balance and immediate-early genes within the medial prefrontal cortex (mPFC) of both generations. The expression of genes encoding enzymes that regulate H3K27me3 levels was altered in the mPFC and partially in sperm of F1 malnourished mice. These results support the hypothesis that early nutritional deficiency represents a risk factor for the emergence of symptoms associated with mental disorders.
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Affiliation(s)
- Estefanía A Fesser
- Laboratorio de Neuroepigenética y Adversidades Tempranas, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Ciudad de Buenos Aires, Argentina
| | - Octavio Gianatiempo
- Laboratorio de Neuroepigenética y Adversidades Tempranas, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Ciudad de Buenos Aires, Argentina
| | - Bruno G Berardino
- Laboratorio de Neuroepigenética y Adversidades Tempranas, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Ciudad de Buenos Aires, Argentina
| | - Nadina M Ferroni
- Laboratorio de Neuroepigenética y Adversidades Tempranas, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Ciudad de Buenos Aires, Argentina
| | - Maite Cambiasso
- Laboratorio de Matriz Extracelular, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina; Instituto de Biología y Medicina Experimental (IBYME), CONICET, Ciudad de Buenos Aires, Argentina
| | - Vanina A Fontana
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Ciudad de Buenos Aires, Argentina; Laboratorio de Matriz Extracelular, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
| | - Juan C Calvo
- Laboratorio de Matriz Extracelular, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina; Instituto de Biología y Medicina Experimental (IBYME), CONICET, Ciudad de Buenos Aires, Argentina
| | - Silvina V Sonzogni
- Laboratorio de Neuroepigenética y Adversidades Tempranas, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Ciudad de Buenos Aires, Argentina
| | - Eduardo T Cánepa
- Laboratorio de Neuroepigenética y Adversidades Tempranas, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Ciudad de Buenos Aires, Argentina.
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Nilsson E, Ben Maamar M, Skinner MK. Environmental impacts on sperm and oocyte epigenetics affect embryo cell epigenetics and transcription to promote the epigenetic inheritance of pathology and phenotypic variation. Reprod Fertil Dev 2021; 33:102-107. [PMID: 38769672 DOI: 10.1071/rd20255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024] Open
Abstract
Previous studies have demonstrated that exposure to environmental factors can cause epigenetic modifications to germ cells, particularly sperm, to promote epigenetic and transcriptome changes in the embryo. These germ cell and embryo cell epigenetic alterations are associated with phenotypic changes in offspring. Epigenetic inheritance requires epigenetic changes (i.e. epimutations) in germ cells that promote epigenetic and gene expression changes in embryos. The objective of this perspective is to examine the evidence that germ cell epigenome modifications are associated with embryo cell epigenetic and transcriptome changes that affect the subsequent development of all developing somatic cells to promote phenotype change. Various epigenetic changes in sperm, including changes to histone methylation, histone retention, non-coding RNA expression and DNA methylation, have been associated with alterations in embryo cell epigenetics and gene expression. Few studies have investigated this link for oocytes. The studies reviewed herein support the idea that environmentally induced epigenetic changes in germ cells affect alterations in embryo cell epigenetics and transcriptomes that have an important role in the epigenetic inheritance of pathology and phenotypic change.
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Affiliation(s)
- Eric Nilsson
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - Millissia Ben Maamar
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - Michael K Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA; and Corresponding author
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Genetic control of non-genetic inheritance in mammals: state-of-the-art and perspectives. Mamm Genome 2020; 31:146-156. [PMID: 32529318 PMCID: PMC7369129 DOI: 10.1007/s00335-020-09841-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 06/03/2020] [Indexed: 12/12/2022]
Abstract
Thought to be directly and uniquely dependent from genotypes, the ontogeny of individual phenotypes is much more complicated. Individual genetics, environmental exposures, and their interaction are the three main determinants of individual's phenotype. This picture has been further complicated a decade ago when the Lamarckian theory of acquired inheritance has been rekindled with the discovery of epigenetic inheritance, according to which acquired phenotypes can be transmitted through fertilization and affect phenotypes across generations. The results of Genome-Wide Association Studies have also highlighted a big degree of missing heritability in genetics and have provided hints that not only acquired phenotypes, but also individual's genotypes affect phenotypes intergenerationally through indirect genetic effects. Here, we review available examples of indirect genetic effects in mammals, what is known of the underlying molecular mechanisms and their potential impact for our understanding of missing heritability, phenotypic variation. and individual disease risk.
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Jarred EG, Bildsoe H, Western PS. Out of sight, out of mind? Germ cells and the potential impacts of epigenomic drugs. F1000Res 2018; 7. [PMID: 30613387 PMCID: PMC6305226 DOI: 10.12688/f1000research.15935.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/12/2018] [Indexed: 12/12/2022] Open
Abstract
Epigenetic modifications, including DNA methylation and histone modifications, determine the way DNA is packaged within the nucleus and regulate cell-specific gene expression. The heritability of these modifications provides a memory of cell identity and function. Common dysregulation of epigenetic modifications in cancer has driven substantial interest in the development of epigenetic modifying drugs. Although these drugs have the potential to be highly beneficial for patients, they act systemically and may have “off-target” effects in other cells such as the patients’ sperm or eggs. This review discusses the potential for epigenomic drugs to impact on the germline epigenome and subsequent offspring and aims to foster further examination into the possible effects of these drugs on gametes. Ultimately, the information gained by further research may improve the clinical guidelines for the use of such drugs in patients of reproductive age.
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Affiliation(s)
- Ellen G Jarred
- Centre for Reproductive Health, Hudson Institute of Medical Research, Clayton, Victoria, 3168, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria, 3168, Australia
| | - Heidi Bildsoe
- Centre for Reproductive Health, Hudson Institute of Medical Research, Clayton, Victoria, 3168, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria, 3168, Australia
| | - Patrick S Western
- Centre for Reproductive Health, Hudson Institute of Medical Research, Clayton, Victoria, 3168, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria, 3168, Australia
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