1
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Yang Y, Feng W, Zhou J, Zhang R, Lin X, Sooranna SR, Deng Y, Shi D. Epigenetic modifications of gonadotropin receptors can regulate follicular development. Anim Reprod Sci 2024; 268:107534. [PMID: 39047429 DOI: 10.1016/j.anireprosci.2024.107534] [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: 01/16/2024] [Revised: 05/14/2024] [Accepted: 06/11/2024] [Indexed: 07/27/2024]
Abstract
The spatiotemporal transcription of follicle-stimulating hormone receptor (FSHR) and luteinizing hormone/human chorionic gonadotropin receptor (LHCGR) are crucial events for follicular development. However, their regulatory mechanisms are unclear. DNA methylation and histone acetylation are the main epigenetic modifications, and play important roles in transcriptional expression, which regulate cell responses including cell proliferation, senescence and apoptosis. This review will discuss the dynamic epigenetic modifications of FSHR and LHCGR that occur during the process of follicular development and their response to gonadotropins. In addition, some alteration patterns that occur during these epigenetic modifications, as well as their retrospect retrotransposons, which regulate the gene expression levels of FSHR and LHCGR will be discussed.
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Affiliation(s)
- Yanyan Yang
- Guangxi Key Laboratory of Animal Breeding and Disease Control, College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Wanyou Feng
- School of Environmental and Life Sciences, Nanning Normal University, Nanning 530023, China
| | - Jinhua Zhou
- Guangxi Key Laboratory of Animal Breeding and Disease Control, College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Ruimen Zhang
- Guangxi Key Laboratory of Animal Breeding and Disease Control, College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Xinyue Lin
- Guangxi Key Laboratory of Animal Breeding and Disease Control, College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Suren Rao Sooranna
- Department of Metabolism, Digestion and Reproduction, Imperial College London, Chelsea and Westminster Hospital, London SW10 9NH, United Kingdom
| | - Yanfei Deng
- Guangxi Key Laboratory of Animal Breeding and Disease Control, College of Animal Science and Technology, Guangxi University, Nanning 530004, China.
| | - Deshun Shi
- Guangxi Key Laboratory of Animal Breeding and Disease Control, College of Animal Science and Technology, Guangxi University, Nanning 530004, China.
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2
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Chousal JN, Morey R, Srinivasan S, Lee K, Zhang W, Yeo AL, To C, Cho K, Garzo VG, Parast MM, Laurent LC, Cook-Andersen H. Molecular profiling of human blastocysts reveals primitive endoderm defects among embryos of decreased implantation potential. Cell Rep 2024; 43:113701. [PMID: 38277271 DOI: 10.1016/j.celrep.2024.113701] [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: 03/29/2023] [Revised: 12/12/2023] [Accepted: 01/05/2024] [Indexed: 01/28/2024] Open
Abstract
Human embryo implantation is remarkably inefficient, and implantation failure remains among the greatest obstacles in treating infertility. Gene expression data from human embryos have accumulated rapidly in recent years; however, identification of the subset of genes that determine successful implantation remains a challenge. We leverage clinical morphologic grading-known for decades to correlate with implantation potential-and transcriptome analyses of matched embryonic and abembryonic samples to identify factors and pathways enriched and depleted in human blastocysts of good and poor morphology. Unexpectedly, we discovered that the greatest difference was in the state of extraembryonic primitive endoderm (PrE) development, with relative deficiencies in poor morphology blastocysts. Our results suggest that implantation success is most strongly influenced by the embryonic compartment and that deficient PrE development is common among embryos with decreased implantation potential. Our study provides a valuable resource for those investigating the markers and mechanisms of human embryo implantation.
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Affiliation(s)
- Jennifer N Chousal
- Department of Pathology, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Robert Morey
- Department of Pathology, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Srimeenakshi Srinivasan
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Katherine Lee
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Wei Zhang
- Reproductive Partners Fertility Center - San Diego, La Jolla, CA 92037, USA
| | - Ana Lisa Yeo
- Reproductive Partners Fertility Center - San Diego, La Jolla, CA 92037, USA
| | - Cuong To
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kyucheol Cho
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - V Gabriel Garzo
- Reproductive Partners Fertility Center - San Diego, La Jolla, CA 92037, USA
| | - Mana M Parast
- Department of Pathology, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Louise C Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Heidi Cook-Andersen
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA.
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3
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Gilchrist RB, Ho TM, De Vos M, Sanchez F, Romero S, Ledger WL, Anckaert E, Vuong LN, Smitz J. A fresh start for IVM: capacitating the oocyte for development using pre-IVM. Hum Reprod Update 2024; 30:3-25. [PMID: 37639630 DOI: 10.1093/humupd/dmad023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 06/08/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND While oocyte IVM is practiced sporadically it has not achieved widespread clinical practice globally. However, recently there have been some seminal advances in our understanding of basic aspects of oocyte biology and ovulation from animal studies that have led to novel approaches to IVM. A significant recent advance in IVM technology is the use of biphasic IVM approaches. These involve the collection of immature oocytes from small antral follicles from minimally stimulated patients/animals (without hCG-priming) and an ∼24 h pre-culture of oocytes in an advanced culture system ('pre-IVM') prior to IVM, followed by routine IVF procedures. If safe and efficacious, this novel procedure may stand to make a significant impact on human ART practices. OBJECTIVE AND RATIONALE The objectives of this review are to examine the major scientific advances in ovarian biology with a unique focus on the development of pre-IVM methodologies, to provide an insight into biphasic IVM procedures, and to report on outcomes from animal and clinical human data, including safety data. The potential future impact of biphasic IVM on ART practice is discussed. SEARCH METHODS Peer review original and review articles were selected from PubMed and Web of Science searches for this narrative review. Searches were performed using the following keywords: oocyte IVM, pre-IVM, biphasic IVM, CAPA-IVM, hCG-triggered/primed IVM, natural cycle IVF/M, ex-vivo IVM, OTO-IVM, oocyte maturation, meiotic competence, oocyte developmental competence, oocyte capacitation, follicle size, cumulus cell (CC), granulosa cell, COC, gap-junction communication, trans-zonal process, cAMP and IVM, cGMP and IVM, CNP and IVM, EGF-like peptide and IVM, minimal stimulation ART, PCOS. OUTCOMES Minimizing gonadotrophin use means IVM oocytes will be collected from small antral (pre-dominant) follicles containing oocytes that are still developing. Standard IVM yields suboptimal clinical outcomes using such oocytes, whereas pre-IVM aims to continue the oocyte's development ex vivo, prior to IVM. Pre-IVM achieves this by eliciting profound cellular changes in the oocyte's CCs, which continue to meet the oocyte's developmental needs during the pre-IVM phase. The literature contains 25 years of animal research on various pre-IVM and biphasic IVM procedures, which serves as a large knowledge base for new approaches to human IVM. A pre-IVM procedure based on c-type natriuretic peptide (named 'capacitation-IVM' (CAPA-IVM)) has undergone pre-clinical human safety and efficacy trials and its adoption into clinical practice resulted in healthy live birth rates not different from conventional IVF. WIDER IMPLICATIONS Over many decades, improvements in clinical IVM have been gradual and incremental but there has likely been a turning of the tide in the past few years, with landmark discoveries in animal oocyte biology finally making their way into clinical practice leading to improved outcomes for patients. Demonstration of favorable clinical results with CAPA-IVM, as the first clinically tested biphasic IVM system, has led to renewed interest in IVM as an alternative, low-intervention, low-cost, safe, patient-friendly ART approach, and especially for patients with PCOS. The same new approach is being used as part of fertility preservation in patients with cancer and holds promise for social oocyte freezing.
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Affiliation(s)
- Robert B Gilchrist
- Fertility & Research Centre, Discipline of Women's Health, School of Clinical Medicine, University of New South Wales Sydney, NSW, Australia
| | - Tuong M Ho
- IVFMD, My Duc Hospital, Ho Chi Minh City, Vietnam
| | - Michel De Vos
- Brussels IVF, UZ Brussel, Brussels, Belgium
- Follicle Biology Laboratory, UZ Brussel, Vrije Universiteit Brussel, Brussels, Belgium
| | - Flor Sanchez
- Centro de Estudios e Investigaciones en Biología y Medicina Reproductiva, Lima, Peru
| | - Sergio Romero
- Laboratory of Reproductive Biology and Fertility Preservation, Cayetano Heredia University (UPCH), Lima, Peru
- Centro de Fertilidad y Reproducción Asistida, Lima, Peru
| | - William L Ledger
- Fertility & Research Centre, Discipline of Women's Health, School of Clinical Medicine, University of New South Wales Sydney, NSW, Australia
- City Fertility, Global CHA IVF Partners, Sydney, NSW, Australia
| | - Ellen Anckaert
- Follicle Biology Laboratory, UZ Brussel, Vrije Universiteit Brussel, Brussels, Belgium
| | - Lan N Vuong
- Department of Obstetrics and Gynaecology, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Johan Smitz
- Follicle Biology Laboratory, UZ Brussel, Vrije Universiteit Brussel, Brussels, Belgium
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Liao J, Szabó PE. Role of transcription in imprint establishment in the male and female germ lines. Epigenomics 2024; 16:127-136. [PMID: 38126127 PMCID: PMC10825728 DOI: 10.2217/epi-2023-0344] [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: 10/02/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023] Open
Abstract
The authors highlight an area of research that focuses on the establishment of genomic imprints: how the female and male germlines set up opposite instructions for imprinted genes in the maternally and paternally inherited chromosomes. Mouse genetics studies have solidified the role of transcription across the germline differentially methylated regions in the establishment of maternal genomic imprinting. One work now reveals that such transcription is also important in paternal imprinting establishment. This allows the authors to propose a unifying mechanism, in the form of transcription across germline differentially methylated regions, that specifies DNA methylation imprint establishment. Differences in the timing, genomic location and nature of such transcription events in the male versus female germlines in turn explain the difference between paternal and maternal imprints.
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Affiliation(s)
- Ji Liao
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Piroska E Szabó
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
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5
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Fair T, Lonergan P. The oocyte: the key player in the success of assisted reproduction technologies. Reprod Fertil Dev 2023; 36:133-148. [PMID: 38064189 DOI: 10.1071/rd23164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023] Open
Abstract
The ovulation of a mature oocyte at metaphase II of meiosis, with optimal potential to undergo fertilisation by a sperm cell, complete meiosis and sustain the switch to mitotic division, and support early embryo development, involves a protracted and disrupted/delayed series of processes. Many of these are targeted for exploitation in vivo , or recapitulation in vitro , by the livestock industry. Reproductive technologies, including AI, multiple ovulation embryo transfer, ovum pick-up, in vitro embryo production, and oestrus and ovulation synchronisation, offer practitioners and producers the opportunity to produce offspring from genetically valuable dams in much greater numbers than they would normally have in their lifetime, while in vitro oocyte and follicle culture are important platforms for researchers to interrogate the physiological mechanisms driving fertility. The majority of these technologies target the ovarian follicle and the oocyte within; thus, the quality and capability of the recovered oocyte determine the success of the reproductive intervention. Molecular and microscopical technologies have grown exponentially, providing powerful platforms to interrogate the molecular mechanisms which are integral to or affected by ART. The development of the bovine oocyte from its differentiation in the ovary to ovulation is described in the light of its relevance to key aspects of individual interventions, while highlighting the historical timeline.
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Affiliation(s)
- Trudee Fair
- School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, Ireland
| | - Pat Lonergan
- School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, Ireland
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6
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Sainty R, Silver MJ, Prentice AM, Monk D. The influence of early environment and micronutrient availability on developmental epigenetic programming: lessons from the placenta. Front Cell Dev Biol 2023; 11:1212199. [PMID: 37484911 PMCID: PMC10358779 DOI: 10.3389/fcell.2023.1212199] [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: 04/25/2023] [Accepted: 06/27/2023] [Indexed: 07/25/2023] Open
Abstract
DNA methylation is the most commonly studied epigenetic mark in humans, as it is well recognised as a stable, heritable mark that can affect genome function and influence gene expression. Somatic DNA methylation patterns that can persist throughout life are established shortly after fertilisation when the majority of epigenetic marks, including DNA methylation, are erased from the pre-implantation embryo. Therefore, the period around conception is potentially critical for influencing DNA methylation, including methylation at imprinted alleles and metastable epialleles (MEs), loci where methylation varies between individuals but is correlated across tissues. Exposures before and during conception can affect pregnancy outcomes and health throughout life. Retrospective studies of the survivors of famines, such as those exposed to the Dutch Hunger Winter of 1944-45, have linked exposures around conception to later disease outcomes, some of which correlate with DNA methylation changes at certain genes. Animal models have shown more directly that DNA methylation can be affected by dietary supplements that act as cofactors in one-carbon metabolism, and in humans, methylation at birth has been associated with peri-conceptional micronutrient supplementation. However, directly showing a role of micronutrients in shaping the epigenome has proven difficult. Recently, the placenta, a tissue with a unique hypomethylated methylome, has been shown to possess great inter-individual variability, which we highlight as a promising target tissue for studying MEs and mixed environmental exposures. The placenta has a critical role shaping the health of the fetus. Placenta-associated pregnancy complications, such as preeclampsia and intrauterine growth restriction, are all associated with aberrant patterns of DNA methylation and expression which are only now being linked to disease risk later in life.
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Affiliation(s)
- Rebecca Sainty
- Biomedical Research Centre, School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Matt J. Silver
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Andrew M. Prentice
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, Gambia
| | - David Monk
- Biomedical Research Centre, School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
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7
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Wiegel RE, Rubini E, Rousian M, Schoenmakers S, Laven JSE, Willemsen SP, Baart EB, Steegers-Theunissen RPM. Human oocyte area is associated with preimplantation embryo usage and early embryo development: the Rotterdam Periconception Cohort. J Assist Reprod Genet 2023:10.1007/s10815-023-02803-1. [PMID: 37129725 DOI: 10.1007/s10815-023-02803-1] [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: 01/25/2023] [Accepted: 04/05/2023] [Indexed: 05/03/2023] Open
Abstract
PURPOSE To investigate the association between oocyte area and fertilization rate, embryo usage, and preimplantation embryo development in order to establish if oocyte area can be a marker for optimal early embryo development. METHODS From 2017 to 2020, 378 couples with an indication for IVF (n = 124) or ICSI (n = 254) were included preconceptionally in the Rotterdam Periconception Cohort. Resulting oocytes (n = 2810) were fertilized and submitted to time-lapse embryo culture. Oocyte area was measured at the moment of fertilization (t0), pronuclear appearance (tPNa), and fading (tPNf). Fertilization rate, embryo usage and quality, and embryo morphokinetics from 2-cell stage to expanded blastocyst stage (t2-tEB) were used as outcome measures in association with oocyte area. Oocytes were termed "used" if they were fertilized and embryo development resulted in transfer or cryopreservation, and otherwise termed "discarded". Analyses were adjusted for relevant confounders. RESULTS Oocyte area decreased from t0 to tPNf after IVF and ICSI, and oocytes with larger area shrank faster (β - 12.6 µm2/h, 95%CI - 14.6; - 10.5, p < 0.001). Oocytes that resulted in a used embryo were larger at all time-points and reached tPNf faster than oocytes that fertilized but were discarded (oocyte area at tPNf in used 9864 ± 595 µm2 versus discarded 9679 ± 673 µm2, p < 0.001, tPNf in used 23.6 ± 3.2 h versus discarded 25.6 ± 5.9 h, p < 0.001). Larger oocytes had higher odds of being used (oocyte area at tPNf ORused 1.669, 95%CI 1.336; 2.085, p < 0.001), were associated with faster embryo development up to the morula stage (e.g., t9 β - 0.131 min, 95%CI - 0.237; - 0.025, p = 0.016) and higher ICM quality. CONCLUSION Oocyte area is an informative marker for the preimplantation development of the embryo, as a larger oocyte area is associated with higher quality, faster developing embryos, and higher chance of being used. Identifying determinants associated with oocyte and embryo viability and quality could contribute to improved preconception care and subsequently healthy pregnancies.
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Affiliation(s)
- Rosalieke E Wiegel
- Department of Obstetrics and Gynecology, Erasmus MC, University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Eleonora Rubini
- Department of Obstetrics and Gynecology, Erasmus MC, University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Melek Rousian
- Department of Obstetrics and Gynecology, Erasmus MC, University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Sam Schoenmakers
- Department of Obstetrics and Gynecology, Erasmus MC, University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Joop S E Laven
- Department of Obstetrics and Gynecology, Erasmus MC, University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Sten P Willemsen
- Department of Obstetrics and Gynecology, Erasmus MC, University Medical Center, 3015 GD, Rotterdam, The Netherlands
- Department of Biostatistics, Erasmus MC, University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Esther B Baart
- Department of Obstetrics and Gynecology, Erasmus MC, University Medical Center, 3015 GD, Rotterdam, The Netherlands
- Department of Developmental Biology, Erasmus MC, University Medical Center, 3015 GD, Rotterdam, The Netherlands
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8
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Della Rocca Y, Traini EM, Diomede F, Fonticoli L, Trubiani O, Paganelli A, Pizzicannella J, Marconi GD. Current Evidence on Bisphenol A Exposure and the Molecular Mechanism Involved in Related Pathological Conditions. Pharmaceutics 2023; 15:pharmaceutics15030908. [PMID: 36986769 PMCID: PMC10053246 DOI: 10.3390/pharmaceutics15030908] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/07/2023] [Accepted: 03/09/2023] [Indexed: 03/16/2023] Open
Abstract
Bisphenol A (BPA) is one of the so-called endocrine disrupting chemicals (EDCs) and is thought to be involved in the pathogenesis of different morbid conditions: immune-mediated disorders, type-2 diabetes mellitus, cardiovascular diseases, and cancer. The purpose of this review is to analyze the mechanism of action of bisphenol A, with a special focus on mesenchymal stromal/stem cells (MSCs) and adipogenesis. Its uses will be assessed in various fields: dental, orthopedic, and industrial. The different pathological or physiological conditions altered by BPA and the related molecular pathways will be taken into consideration.
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Affiliation(s)
- Ylenia Della Rocca
- Department of Innovative Technologies in Medicine & Dentistry, University “G. d’Annunzio” Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy
| | - Enrico Matteo Traini
- Department of Innovative Technologies in Medicine & Dentistry, University “G. d’Annunzio” Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy
| | - Francesca Diomede
- Department of Innovative Technologies in Medicine & Dentistry, University “G. d’Annunzio” Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy
| | - Luigia Fonticoli
- Department of Innovative Technologies in Medicine & Dentistry, University “G. d’Annunzio” Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy
| | - Oriana Trubiani
- Department of Innovative Technologies in Medicine & Dentistry, University “G. d’Annunzio” Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy
- Correspondence: (O.T.); (A.P.)
| | - Alessia Paganelli
- PhD Course in Clinical and Experimental Medicine, University of Modena and Reggio Emilia, Via del Pozzo 71, 41125 Modena, Italy
- Correspondence: (O.T.); (A.P.)
| | - Jacopo Pizzicannella
- Department of Engineering and Geology, University “G. d’ Annunzio” Chieti-Pescara, Viale Pindaro 42, 65127 Pescara, Italy
| | - Guya Diletta Marconi
- Department of Innovative Technologies in Medicine & Dentistry, University “G. d’Annunzio” Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy
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9
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Demond H, Hanna CW, Castillo-Fernandez J, Santos F, Papachristou EK, Segonds-Pichon A, Kishore K, Andrews S, D'Santos CS, Kelsey G. Multi-omics analyses demonstrate a critical role for EHMT1 methyltransferase in transcriptional repression during oogenesis. Genome Res 2023; 33:18-31. [PMID: 36690445 PMCID: PMC9977154 DOI: 10.1101/gr.277046.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 12/22/2022] [Indexed: 01/25/2023]
Abstract
EHMT1 (also known as GLP) is a multifunctional protein, best known for its role as an H3K9me1 and H3K9me2 methyltransferase through its reportedly obligatory dimerization with EHMT2 (also known as G9A). Here, we investigated the role of EHMT1 in the oocyte in comparison to EHMT2 using oocyte-specific conditional knockout mouse models (Ehmt2 cKO, Ehmt1 cKO, Ehmt1/2 cDKO), with ablation from the early phase of oocyte growth. Loss of EHMT1 in Ehmt1 cKO and Ehmt1/2 cDKO oocytes recapitulated meiotic defects observed in the Ehmt2 cKO; however, there was a significant impairment in oocyte maturation and developmental competence in Ehmt1 cKO and Ehmt1/2 cDKO oocytes beyond that observed in the Ehmt2 cKO. Consequently, loss of EHMT1 in oogenesis results, upon fertilization, in mid-gestation embryonic lethality. To identify H3K9 methylation and other meaningful biological changes in each mutant to explore the molecular functions of EHMT1 and EHMT2, we performed immunofluorescence imaging, multi-omics sequencing, and mass spectrometry (MS)-based proteome analyses in cKO oocytes. Although H3K9me1 was depleted only upon loss of EHMT1, H3K9me2 was decreased, and H3K9me2-enriched domains were eliminated equally upon loss of EHMT1 or EHMT2. Furthermore, there were more significant changes in the transcriptome, DNA methylome, and proteome in Ehmt1/2 cDKO than Ehmt2 cKO oocytes, with transcriptional derepression leading to increased protein abundance and local changes in genic DNA methylation in Ehmt1/2 cDKO oocytes. Together, our findings suggest that EHMT1 contributes to local transcriptional repression in the oocyte, partially independent of EHMT2, and is critical for oogenesis and oocyte developmental competence.
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Affiliation(s)
- Hannah Demond
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom;,Millennium Institute on Immunology and Immunotherapy, Laboratory of Integrative Biology (LIBi), Centro de Excelencia en Medicina Traslacional (CEMT), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, 4810296, Temuco, Chile
| | - Courtney W. Hanna
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom;,Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom;,Department of Physiology, Development, and Neuroscience, University of Cambridge, Cambridge CB2 3EG, United Kingdom
| | | | - Fátima Santos
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom;,Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom
| | - Evangelia K. Papachristou
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Anne Segonds-Pichon
- Bioinformatics Group, Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Kamal Kishore
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Simon Andrews
- Bioinformatics Group, Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Clive S. D'Santos
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Gavin Kelsey
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom;,Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom;,Wellcome-MRC Institute of Metabolic Science–Metabolic Research Laboratories, Cambridge CB2 0QQ, United Kingdom
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10
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Verdikt R, Armstrong AA, Allard P. Transgenerational inheritance and its modulation by environmental cues. Curr Top Dev Biol 2022; 152:31-76. [PMID: 36707214 PMCID: PMC9940302 DOI: 10.1016/bs.ctdb.2022.10.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The epigenome plays an important role in shaping phenotypes. However, whether the environment can alter an organism's phenotype across several generations through epigenetic remodeling in the germline is still a highly debated topic. In this chapter, we briefly review the mechanisms of epigenetic inheritance and their connection with germline development before highlighting specific developmental windows of susceptibility to environmental cues. We further discuss the evidence of transgenerational inheritance to a range of different environmental cues, both epidemiological in humans and experimental in rodent models. Doing so, we pinpoint the current challenges in demonstrating transgenerational inheritance to environmental cues and offer insight in how recent technological advances may help deciphering the epigenetic mechanisms at play. Together, we draw a detailed picture of how our environment can influence our epigenomes, ultimately reshaping our phenotypes, in an extended theory of inheritance.
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Affiliation(s)
- Roxane Verdikt
- Institute for Society and Genetics, University of California, Los Angeles, Los Angeles, CA, United States.
| | - Abigail A Armstrong
- Department of Obstetrics/Gynecology and Division of Reproductive Endocrinology and Infertility, University of California, Los Angeles, CA, United States
| | - Patrick Allard
- Institute for Society and Genetics, University of California, Los Angeles, Los Angeles, CA, United States; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, United States.
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11
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Ishihara T, Griffith OW, Suzuki S, Renfree MB. Placental imprinting of SLC22A3 in the IGF2R imprinted domain is conserved in therian mammals. Epigenetics Chromatin 2022; 15:32. [PMID: 36030241 PMCID: PMC9419357 DOI: 10.1186/s13072-022-00465-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/25/2022] [Indexed: 11/10/2022] Open
Abstract
Background The eutherian IGF2R imprinted domain is regulated by an antisense long non-coding RNA, Airn, which is expressed from a differentially methylated region (DMR) in mice. Airn silences two neighbouring genes, Solute carrier family 22 member 2 (Slc22a2) and Slc22a3, to establish the Igf2r imprinted domain in the mouse placenta. Marsupials also have an antisense non-coding RNA, ALID, expressed from a DMR, although the exact function of ALID is currently unknown. The eutherian IGF2R DMR is located in intron 2, while the marsupial IGF2R DMR is located in intron 12, but it is not yet known whether the adjacent genes SLC22A2 and/or SLC22A3 are also imprinted in the marsupial lineage. In this study, the imprinting status of marsupial SLC22A2 and SLC22A3 in the IGF2R imprinted domain in the chorio-vitelline placenta was examined in a marsupial, the tammar wallaby. Results In the tammar placenta, SLC22A3 but not SLC22A2 was imprinted. Tammar SLC22A3 imprinting was evident in placental tissues but not in the other tissues examined in this study. A putative promoter of SLC22A3 lacked DNA methylation, suggesting that this gene is not directly silenced by a DMR on its promoter as seen in the mouse. Based on immunofluorescence, we confirmed that the tammar SLC22A3 is localised in the endodermal cell layer of the tammar placenta where nutrient trafficking occurs. Conclusions Since SLC22A3 is imprinted in the tammar placenta, we conclude that this placental imprinting of SLC22A3 has been positively selected after the marsupial and eutherian split because of the differences in the DMR location. Since SLC22A3 is known to act as a transporter molecule for nutrient transfer in the eutherian placenta, we suggest it was strongly selected to control the balance between supply and demand of nutrients in marsupial as it does in eutherian placentas. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-022-00465-4.
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Affiliation(s)
- Teruhito Ishihara
- School of BioSciences, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Oliver W Griffith
- School of BioSciences, The University of Melbourne, Melbourne, VIC, 3010, Australia.,Department of Biological Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Shunsuke Suzuki
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, Nagano, 399-4598, Japan
| | - Marilyn B Renfree
- School of BioSciences, The University of Melbourne, Melbourne, VIC, 3010, Australia.
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12
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Lafontaine S, Sirard MA. IGF2R, KCNQ1, PLAGL1, and SNRPN DNA methylation is completed in bovine by the early antral follicle stage. Mol Reprod Dev 2022; 89:290-297. [PMID: 35698757 DOI: 10.1002/mrd.23621] [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: 01/07/2022] [Revised: 05/03/2022] [Accepted: 06/03/2022] [Indexed: 11/06/2022]
Abstract
Imprinted genes are inherited with different DNA methylation patterns depending on the maternal or paternal origin of the allele. In cattle (Bos taurus), abnormal methylation of these genes is linked to the large offspring syndrome, a neonatal overgrowth phenotype analogous to the human Beckwith-Wiedemann syndrome. We hypothesized that in bovine oocytes, some of the methylation patterns on maternally imprinted genes are acquired in the last phase of folliculogenesis. The pyrosequencing analysis of IGF2R, KCNQ1, PLAGL1, and SNRPN imprinted genes showed no clear progression of methylation in oocytes from follicles 1-2 mm (late pre antral/early antral) and up. Instead, these oocytes displayed complete methylation at the imprinted differentially methylated regions (>80%). Other mechanisms related to imprint maintenance should be investigated to explain the hypomethylation at IGF2R, KCNQ1, PLAGL1, and SNRPN maternally imprinted sites observed in some bovine embryos.
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Affiliation(s)
- Simon Lafontaine
- Centre de recherche en reproduction, développement et santé intergénérationnelle, Département des Sciences Animales, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec, Québec, Canada
| | - Marc-André Sirard
- Centre de recherche en reproduction, développement et santé intergénérationnelle, Département des Sciences Animales, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec, Québec, Canada
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13
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Shirane K. The dynamic chromatin landscape and mechanisms of DNA methylation during mouse germ cell development. Gene 2022; 97:3-14. [PMID: 35431282 DOI: 10.1266/ggs.21-00069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Epigenetic marks including DNA methylation (DNAme) play a critical role in the transcriptional regulation of genes and retrotransposons. Defects in DNAme are detected in infertility, imprinting disorders and congenital diseases in humans, highlighting the broad importance of this epigenetic mark in both development and disease. While DNAme in terminally differentiated cells is stably propagated following cell division by the maintenance DNAme machinery, widespread erasure and subsequent de novo establishment of this epigenetic mark occur early in embryonic development as well as in germ cell development. Combined with deep sequencing, low-input methods that have been developed in the past several years have enabled high-resolution and genome-wide mapping of both DNAme and histone post-translational modifications (PTMs) in rare cell populations including developing germ cells. Epigenome studies using these novel methods reveal an unprecedented view of the dynamic chromatin landscape during germ cell development. Furthermore, integrative analysis of chromatin marks in normal germ cells and in those deficient in chromatin-modifying enzymes uncovers a critical interplay between histone PTMs and de novo DNAme in the germline. This review discusses work on mechanisms of the erasure and subsequent de novo DNAme in mouse germ cells as well as the outstanding questions relating to the regulation of the dynamic chromatin landscape in germ cells.
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Affiliation(s)
- Kenjiro Shirane
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University
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14
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Ishihara T, Griffith OW, Suzuki S, Renfree MB. Presence of H3K4me3 on Paternally Expressed Genes of the Paternal Genome From Sperm to Implantation. Front Cell Dev Biol 2022; 10:838684. [PMID: 35359448 PMCID: PMC8960379 DOI: 10.3389/fcell.2022.838684] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 01/27/2022] [Indexed: 12/13/2022] Open
Abstract
Genomic imprinting, parent-of-origin-specific gene expression, is controlled by differential epigenetic status of the parental chromosomes. While DNA methylation and suppressive histone modifications established during gametogenesis suppress imprinted genes on the inactive allele, how and when the expressed allele gains its active status is not clear. In this study, we asked whether the active histone-3 lysine-4 trimethylation (H3K4me3) marks remain at paternally expressed genes (PEGs) in sperm and embryos before and after fertilization using published data. Here we show that mouse sperm had the active H3K4me3 at more than half of known PEGs, and these genes were present even after fertilization. Using reciprocal cross data, we identified 13 new transient PEGs during zygotic genome activation. Next, we confirmed that the 12 out of the 13 new transient PEGs were associated with the paternal H3K4me3 in sperm. Nine out of the 12 genes were associated with the paternal H3K4me3 in zygotes. Our results show that paternal H3K4me3 marks escape inactivation during the histone-to-protamine transition that occurs during sperm maturation and are present in embryos from early zygotic stages up to implantation.
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Affiliation(s)
- Teruhito Ishihara
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Oliver W. Griffith
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| | - Shunsuke Suzuki
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, Nagano, Japan
| | - Marilyn B. Renfree
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
- *Correspondence: Marilyn B. Renfree,
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15
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Li Q, Zhao T, He H, Robert N, Ding T, Hu X, Zhang T, Pan Y, Cui Y, Yu S. Ascorbic acid protects the toxic effects of aflatoxin B 1 on yak oocyte maturation. Anim Sci J 2022; 93:e13702. [PMID: 35257449 DOI: 10.1111/asj.13702] [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: 09/26/2021] [Revised: 01/26/2022] [Accepted: 02/03/2022] [Indexed: 11/29/2022]
Abstract
High-quality oocytes are a prerequisite for successful fertilization. Mammals feeding on aflatoxin-contaminated feed can cause reproductive toxicity, including follicular atresia, poor oocyte development and maturation, and aberrant epigenetic modifications of oocytes. In addition, the important role of ascorbic acid (AA) in reproductive biology has been confirmed, and AA is widely used as an antioxidant in cell culture. However, the toxic effects of aflatoxin B1 (AFB1 ) on yak oocytes and whether AA has protective effects remain unknown. In this study, we found that exposure to AFB1 impedes meiotic maturation of oocytes, promotes apoptosis by triggering high levels of reactive oxygen species (ROS), and disrupts mitochondrial distribution and actin integrity, resulting in a decrease in the fertilization ability and parthenogenetic development ability of oocytes. In addition, these injuries changed the DNA methylation transferase transcription level of mature oocytes. After adding 50 μg/ml AA, the indices recovered to levels close to those of the control group. The results showed that AA could protect yak oocytes from the toxic effects of AFB1 and improve the quality of oocytes.
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Affiliation(s)
- Qin Li
- Gansu Province Livestock Embryo Engineering Research Center, College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China
| | - Tian Zhao
- Gansu Province Livestock Embryo Engineering Research Center, College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China
| | - Honghong He
- Gansu Province Livestock Embryo Engineering Research Center, College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China
| | - Niayale Robert
- Laboratory of Animal Anatomy & Tissue Embryology, College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China
| | - Tianyi Ding
- Gansu Province Livestock Embryo Engineering Research Center, College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China
| | - Xuequan Hu
- Gansu Province Livestock Embryo Engineering Research Center, College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China
| | - Tongxiang Zhang
- Gansu Province Livestock Embryo Engineering Research Center, College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China
| | - Yangyang Pan
- Gansu Province Livestock Embryo Engineering Research Center, College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China
| | - Yan Cui
- Laboratory of Animal Anatomy & Tissue Embryology, College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China
| | - Sijiu Yu
- Gansu Province Livestock Embryo Engineering Research Center, College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China
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16
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Kaneko-Ishino T, Ishino F. The Evolutionary Advantage in Mammals of the Complementary Monoallelic Expression Mechanism of Genomic Imprinting and Its Emergence From a Defense Against the Insertion Into the Host Genome. Front Genet 2022; 13:832983. [PMID: 35309133 PMCID: PMC8928582 DOI: 10.3389/fgene.2022.832983] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 02/11/2022] [Indexed: 12/30/2022] Open
Abstract
In viviparous mammals, genomic imprinting regulates parent-of-origin-specific monoallelic expression of paternally and maternally expressed imprinted genes (PEGs and MEGs) in a region-specific manner. It plays an essential role in mammalian development: aberrant imprinting regulation causes a variety of developmental defects, including fetal, neonatal, and postnatal lethality as well as growth abnormalities. Mechanistically, PEGs and MEGs are reciprocally regulated by DNA methylation of germ-line differentially methylated regions (gDMRs), thereby exhibiting eliciting complementary expression from parental genomes. The fact that most gDMR sequences are derived from insertion events provides strong support for the claim that genomic imprinting emerged as a host defense mechanism against the insertion in the genome. Recent studies on the molecular mechanisms concerning how the DNA methylation marks on the gDMRs are established in gametes and maintained in the pre- and postimplantation periods have further revealed the close relationship between genomic imprinting and invading DNA, such as retroviruses and LTR retrotransposons. In the presence of gDMRs, the monoallelic expression of PEGs and MEGs confers an apparent advantage by the functional compensation that takes place between the two parental genomes. Thus, it is likely that genomic imprinting is a consequence of an evolutionary trade-off for improved survival. In addition, novel genes were introduced into the mammalian genome via this same surprising and complex process as imprinted genes, such as the genes acquired from retroviruses as well as those that were duplicated by retropositioning. Importantly, these genes play essential/important roles in the current eutherian developmental system, such as that in the placenta and/or brain. Thus, genomic imprinting has played a critically important role in the evolutionary emergence of mammals, not only by providing a means to escape from the adverse effects of invading DNA with sequences corresponding to the gDMRs, but also by the acquisition of novel functions in development, growth and behavior via the mechanism of complementary monoallelic expression.
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Affiliation(s)
- Tomoko Kaneko-Ishino
- School of Medicine, Tokai University, Isehara, Japan
- *Correspondence: Tomoko Kaneko-Ishino, ; Fumitoshi Ishino,
| | - Fumitoshi Ishino
- Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
- *Correspondence: Tomoko Kaneko-Ishino, ; Fumitoshi Ishino,
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17
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Yamazaki W, Tan SL, Taketo T. Role of the X and Y Chromosomes in the Female Germ Cell Line Development in the Mouse (Mus musculus). Sex Dev 2022:1-10. [PMID: 35235936 DOI: 10.1159/000521151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 11/18/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND In eutherian mammals, the sex chromosome complement, XX and XY, determines sexual differentiation of gonadal primordia into testes and ovaries, which in turn direct differentiation of germ cells into haploid sperm and oocytes, respectively. When gonadal sex is reversed, however, the germ cell sex becomes discordant with the chromosomal sex. XY females in humans are infertile, while XY females in the mouse (Mus musculus) are subfertile or infertile dependent on the cause of sex reversal and the genetic background. This article reviews publications to understand how the sex chromosome complement affects the fertility of XY oocytes by comparing with XX and monosomy X (XO) oocytes. SUMMARY The results highlight 2 folds disadvantage of XY oocytes over XX oocytes: (1) the X and Y chromosomes fail to pair during the meiotic prophase I, resulting in sex chromosome aneuploidy at the first meiotic division and (2) expression of the Y-linked genes during oocyte growth affects the transcriptome landscape and renders the ooplasmic component incompetent for embryonic development. Key Message: The XX chromosome complement gives the oocyte the highest competence for embryonic development.
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Affiliation(s)
- Wataru Yamazaki
- Department of Surgery, McGill University, Montreal, Québec, Canada.,Research Institute of McGill University Health Centre, Montreal, Québec, Canada
| | - Seang Lin Tan
- Department of Obstetrics and Gynecology, McGill University, Montreal, Québec, Canada.,Research Institute of McGill University Health Centre, Montreal, Québec, Canada.,OriginElle Fertility Clinic and Women's Health Centre, Montreal, Québec, Canada
| | - Teruko Taketo
- Department of Surgery, McGill University, Montreal, Québec, Canada.,Department of Obstetrics and Gynecology, McGill University, Montreal, Québec, Canada.,Department of Biology, McGill University, Montreal, Québec, Canada.,Research Institute of McGill University Health Centre, Montreal, Québec, Canada
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18
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Kobayashi H. Canonical and Non-canonical Genomic Imprinting in Rodents. Front Cell Dev Biol 2021; 9:713878. [PMID: 34422832 PMCID: PMC8375499 DOI: 10.3389/fcell.2021.713878] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 07/16/2021] [Indexed: 11/13/2022] Open
Abstract
Genomic imprinting is an epigenetic phenomenon that results in unequal expression of homologous maternal and paternal alleles. This process is initiated in the germline, and the parental epigenetic memories can be maintained following fertilization and induce further allele-specific transcription and chromatin modifications of single or multiple neighboring genes, known as imprinted genes. To date, more than 260 imprinted genes have been identified in the mouse genome, most of which are controlled by imprinted germline differentially methylated regions (gDMRs) that exhibit parent-of-origin specific DNA methylation, which is considered primary imprint. Recent studies provide evidence that a subset of gDMR-less, placenta-specific imprinted genes is controlled by maternal-derived histone modifications. To further understand DNA methylation-dependent (canonical) and -independent (non-canonical) imprints, this review summarizes the loci under the control of each type of imprinting in the mouse and compares them with the respective homologs in other rodents. Understanding epigenetic systems that differ among loci or species may provide new models for exploring genetic regulation and evolutionary divergence.
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Affiliation(s)
- Hisato Kobayashi
- Department of Embryology, Nara Medical University, Kashihara, Japan
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19
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Naillat F, Saadeh H, Nowacka-Woszuk J, Gahurova L, Santos F, Tomizawa SI, Kelsey G. Oxygen concentration affects de novo DNA methylation and transcription in in vitro cultured oocytes. Clin Epigenetics 2021; 13:132. [PMID: 34183052 PMCID: PMC8240245 DOI: 10.1186/s13148-021-01116-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 06/15/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Reproductive biology methods rely on in vitro follicle cultures from mature follicles obtained by hormonal stimulation for generating metaphase II oocytes to be fertilised and developed into a healthy embryo. Such techniques are used routinely in both rodent and human species. DNA methylation is a dynamic process that plays a role in epigenetic regulation of gametogenesis and development. In mammalian oocytes, DNA methylation establishment regulates gene expression in the embryos. This regulation is particularly important for a class of genes, imprinted genes, whose expression patterns are crucial for the next generation. The aim of this work was to establish an in vitro culture system for immature mouse oocytes that will allow manipulation of specific factors for a deeper analysis of regulatory mechanisms for establishing transcription regulation-associated methylation patterns. RESULTS An in vitro culture system was developed from immature mouse oocytes that were grown to germinal vesicles (GV) under two different conditions: normoxia (20% oxygen, 20% O2) and hypoxia (5% oxygen, 5% O2). The cultured oocytes were sorted based on their sizes. Reduced representative bisulphite sequencing (RRBS) and RNA-seq libraries were generated from cultured and compared to in vivo-grown oocytes. In the in vitro cultured oocytes, global and CpG-island (CGI) methylation increased gradually along with oocyte growth, and methylation of the imprinted genes was similar to in vivo-grown oocytes. Transcriptomes of the oocytes grown in normoxia revealed chromatin reorganisation and enriched expression of female reproductive genes, whereas in the 5% O2 condition, transcripts were biased towards cellular stress responses. To further confirm the results, we developed a functional assay based on our model for characterising oocyte methylation using drugs that reduce methylation and transcription. When histone methylation and transcription processes were reduced, DNA methylation at CGIs from gene bodies of grown oocytes presented a lower methylation profile. CONCLUSIONS Our observations reveal changes in DNA methylation and transcripts between oocytes cultured in vitro with different oxygen concentrations and in vivo-grown murine oocytes. Oocytes grown under 20% O2 had a higher correlation with in vivo oocytes for DNA methylation and transcription demonstrating that higher oxygen concentration is beneficial for the oocyte maturation in ex vivo culture condition. Our results shed light on epigenetic mechanisms for the development of oocytes from an immature to GV oocyte in an in vitro culture model.
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Affiliation(s)
- Florence Naillat
- Epigenetics Program, Babraham Institute, Cambridge, CB22 3AT, UK. .,Diseases Network Research Unit, Faculty of Biochemistry and Molecular Medicine, Oulu University, Oulu, Finland.
| | - Heba Saadeh
- Epigenetics Program, Babraham Institute, Cambridge, CB22 3AT, UK.,Department of Computer Science, King Abdullah II School of Information Technology, The University of Jordan, Amman, Jordan
| | - Joanna Nowacka-Woszuk
- Epigenetics Program, Babraham Institute, Cambridge, CB22 3AT, UK.,Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Poznan, Poland
| | - Lenka Gahurova
- Epigenetics Program, Babraham Institute, Cambridge, CB22 3AT, UK.,Laboratory of Early Mammalian Development, Department of Molecular Biology and Genetics, University of South Bohemia, 37005, České Budějovice, Czech Republic
| | - Fatima Santos
- Epigenetics Program, Babraham Institute, Cambridge, CB22 3AT, UK
| | - Shin-Ichi Tomizawa
- Epigenetics Program, Babraham Institute, Cambridge, CB22 3AT, UK.,School of Medicine, Yokohama City University, Yokohama, Japan
| | - Gavin Kelsey
- Epigenetics Program, Babraham Institute, Cambridge, CB22 3AT, UK. .,Centre for Trophoblast Research, University of Cambridge, Cambridge, CB2 3EG, UK.
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20
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The Improvement and Clinical Application of Human Oocyte In Vitro Maturation (IVM). Reprod Sci 2021; 29:2127-2135. [PMID: 34076873 DOI: 10.1007/s43032-021-00613-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 05/10/2021] [Indexed: 12/15/2022]
Abstract
Oocyte in vitro maturation (IVM) is a technology with a long history that was established before IVF. Although it has been studied extensively, the efficiency of IVM has been poor for almost 30 years. In terms of the benefits of IVM, the efficiency and adoption of IVM are being improved by some notable improvements that have occurred in recent years. The establishment of biphasic IVM is the most important advancement in recent years. Biphasic IVM includes the pre-IVM culturing phase and IVM phase. The CNP-mediated pre-IVM culturing system is specifically tailored for non/minimally stimulated immature oocytes, and its efficiency has been shown. This is the most significant improvement made in recent decades in this area. In the clinic, IVM can be used for PCOS patients to avoid the occurrence of ovarian hyperstimulation syndrome (OHSS). Additionally, this method can solve the reproductive problems of some patients with special diseases (resistant ovary syndrome) that cannot be solved by IVF. In most fertility preservation procedures, oocytes in small antral follicles are lost. However, IVM has the ability to capture this kind of oocyte and save reproductive potential. IVM can be easily combined with fertility preservation strategies that have been applied in the clinic and improve the efficiency of fertility preservation. IVM is a useful and attractive technology and may be used widely worldwide in the near future.
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21
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Castillo‐Fernandez J, Herrera‐Puerta E, Demond H, Clark SJ, Hanna CW, Hemberger M, Kelsey G. Increased transcriptome variation and localised DNA methylation changes in oocytes from aged mice revealed by parallel single-cell analysis. Aging Cell 2020; 19:e13278. [PMID: 33201571 PMCID: PMC7744954 DOI: 10.1111/acel.13278] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/27/2020] [Accepted: 10/18/2020] [Indexed: 01/08/2023] Open
Abstract
Advancing maternal age causes a progressive reduction in fertility. The decline in developmental competence of the oocyte with age is likely to be a consequence of multiple contributory factors. Loss of epigenetic quality of the oocyte could impair early developmental events or programme adverse outcomes in offspring that manifest only later in life. Here, we undertake joint profiling of the transcriptome and DNA methylome of individual oocytes from reproductively young and old mice undergoing natural ovulation. We find reduced complexity as well as increased variance in the transcriptome of oocytes from aged females. This transcriptome heterogeneity is reflected in the identification of discrete sub‐populations. Oocytes with a transcriptome characteristic of immature chromatin configuration (NSN) clustered into two groups: one with reduced developmental competence, as indicated by lower expression of maternal effect genes, and one with a young‐like transcriptome. Oocytes from older females had on average reduced CpG methylation, but the characteristic bimodal methylation landscape of the oocyte was preserved. Germline differentially methylated regions of imprinted genes were appropriately methylated irrespective of age. For the majority of differentially expressed transcripts, the absence of correlated methylation changes suggests a post‐transcriptional basis for most age‐related effects on the transcriptome. However, we did find differences in gene body methylation at which there were corresponding changes in gene expression, indicating age‐related effects on transcription that translate into methylation differences. Interestingly, oocytes varied in expression and methylation of these genes, which could contribute to variable competence of oocytes or penetrance of maternal age‐related phenotypes in offspring.
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Affiliation(s)
| | - Erika Herrera‐Puerta
- Epigenetics Programme Babraham Institute Cambridge UK
- Science and Biotechnology Faculty, Biology Program CES University Medellin Colombia
| | - Hannah Demond
- Epigenetics Programme Babraham Institute Cambridge UK
| | | | - Courtney W. Hanna
- Epigenetics Programme Babraham Institute Cambridge UK
- Centre for Trophoblast Research University of Cambridge Cambridge UK
| | - Myriam Hemberger
- Epigenetics Programme Babraham Institute Cambridge UK
- Centre for Trophoblast Research University of Cambridge Cambridge UK
- Departments of Biochemistry & Molecular Biology and Medical Genetics Cumming School of Medicine University of Calgary Calgary AL Canada
- Alberta Children’s Hospital Research InstituteUniversity of Calgary Calgary AL Canada
| | - Gavin Kelsey
- Epigenetics Programme Babraham Institute Cambridge UK
- Centre for Trophoblast Research University of Cambridge Cambridge UK
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22
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Wanigasuriya I, Gouil Q, Kinkel SA, Tapia Del Fierro A, Beck T, Roper EA, Breslin K, Stringer J, Hutt K, Lee HJ, Keniry A, Ritchie ME, Blewitt ME. Smchd1 is a maternal effect gene required for genomic imprinting. eLife 2020; 9:55529. [PMID: 33186096 PMCID: PMC7665889 DOI: 10.7554/elife.55529] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 10/26/2020] [Indexed: 12/17/2022] Open
Abstract
Genomic imprinting establishes parental allele-biased expression of a suite of mammalian genes based on parent-of-origin specific epigenetic marks. These marks are under the control of maternal effect proteins supplied in the oocyte. Here we report epigenetic repressor Smchd1 as a novel maternal effect gene that regulates the imprinted expression of ten genes in mice. We also found zygotic SMCHD1 had a dose-dependent effect on the imprinted expression of seven genes. Together, zygotic and maternal SMCHD1 regulate three classic imprinted clusters and eight other genes, including non-canonical imprinted genes. Interestingly, the loss of maternal SMCHD1 does not alter germline DNA methylation imprints pre-implantation or later in gestation. Instead, what appears to unite most imprinted genes sensitive to SMCHD1 is their reliance on polycomb-mediated methylation as germline or secondary imprints, therefore we propose that SMCHD1 acts downstream of polycomb imprints to mediate its function.
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Affiliation(s)
- Iromi Wanigasuriya
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,The Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Quentin Gouil
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,The Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Sarah A Kinkel
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,The Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Andrés Tapia Del Fierro
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,The Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Tamara Beck
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Ellise A Roper
- Faculty of Health and Medicine, The University of Newcastle, Newcastle, Australia
| | - Kelsey Breslin
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Jessica Stringer
- Monash Biomedicine Discovery institute, Monash University, Clayton, Australia
| | - Karla Hutt
- Monash Biomedicine Discovery institute, Monash University, Clayton, Australia
| | - Heather J Lee
- Faculty of Health and Medicine, The University of Newcastle, Newcastle, Australia
| | - Andrew Keniry
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,The Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Matthew E Ritchie
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,The Department of Medical Biology, The University of Melbourne, Parkville, Australia.,The Department of Mathematics and Statistics, The University of Melbourne, Parkville, Australia
| | - Marnie E Blewitt
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,The Department of Medical Biology, The University of Melbourne, Parkville, Australia
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Lafontaine S, Labrecque R, Palomino JM, Blondin P, Sirard MA. Specific imprinted genes demethylation in association with oocyte donor's age and culture conditions in bovine embryos assessed at day 7 and 12 post insemination. Theriogenology 2020; 158:321-330. [PMID: 33010654 DOI: 10.1016/j.theriogenology.2020.09.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 08/24/2020] [Accepted: 09/23/2020] [Indexed: 12/30/2022]
Abstract
The production of bovine embryos through in vitro maturation and fertilization is an important tool of the genomic revolution in dairy cattle. Gene expression analysis of these embryos revealed differences according to the culture conditions or oocyte donor's pubertal status compared to in vivo derived embryos. We hypothesized that some of the methylation patterns in oocytes are acquired in the last step of folliculogenesis and could be influenced by the environment created in the follicles containing these oocytes. These altered patterns may not be erased during the first week of embryonic development in culture or may be sensitive to the conditions during that time. To quantify the changes related to culture conditions, an in vivo control group consisting of embryos (Day 12 post fertilization for all groups) obtained from superovulated and artificially inseminated cows was compared to in vitro produced (IVP) embryos cultured with or without Fetal Bovine Serum (FBS). To measure the effect of the oocytes donor's age, we also compared a fourth group consisting of IVP embryos produced with oocytes collected following ovarian stimulation of pre-pubertal animals. Embryonic disk and trophoblast cells were processed separately and the methylation status of ten imprinted genes (H19, MEST, KCNQ1, SNRPN, PEG3, NNAT, GNASXL, IGF2R, PEG10, and PLAGL1) was assessed by pyrosequencing. Next, ten Day 7 blastocysts were produced following the same methodology as for the D12 embryos (four groups) to observe the most interesting genes (KCNQ1, SNRPN, IGF2R and PLAGL1) at an earlier developmental stage. For all samples, we observed overall lower methylation levels and greater variability in the three in vitro groups compared to the in vivo group. The individual embryo analysis indicated that some embryos were deviant from the others and some were not affected. We concluded that IGF2R, SNRPN, and PEG10 were particularly sensitive to culture conditions and the presence of FBS, while KCNQ1 and PLAGL1 were more affected in embryos derived from pre-pubertal donors. This work provides markers at the single imprinted control region (ICR) resolution to assess the culture environment required to minimize epigenetic perturbations in bovine embryos generated by assisted reproduction techniques, thus laying the groundwork for a better comprehension of the complex interplay between in vitro conditions and imprinted genes.
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Affiliation(s)
- Simon Lafontaine
- Centre de Recherche en Reproduction, Développement et Santé Intergénérationnelle (CRDSI), Département des Sciences Animals, Faculté des Sciences de l'agriculture et de l'alimentation, Université Laval, Québec, Canada
| | - Rémi Labrecque
- SEMEX Boviteq, 3450 Rue Sicotte, Saint-Hyacinthe, QC J2S, Canada
| | | | - Patrick Blondin
- SEMEX Boviteq, 3450 Rue Sicotte, Saint-Hyacinthe, QC J2S, Canada
| | - Marc-André Sirard
- Centre de Recherche en Reproduction, Développement et Santé Intergénérationnelle (CRDSI), Département des Sciences Animals, Faculté des Sciences de l'agriculture et de l'alimentation, Université Laval, Québec, Canada.
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24
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The role and mechanisms of DNA methylation in the oocyte. Essays Biochem 2020; 63:691-705. [PMID: 31782490 PMCID: PMC6923320 DOI: 10.1042/ebc20190043] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/29/2019] [Accepted: 10/29/2019] [Indexed: 12/27/2022]
Abstract
Epigenetic information in the mammalian oocyte has the potential to be transmitted to the next generation and influence gene expression; this occurs naturally in the case of imprinted genes. Therefore, it is important to understand how epigenetic information is patterned during oocyte development and growth. Here, we review the current state of knowledge of de novo DNA methylation mechanisms in the oocyte: how a distinctive gene-body methylation pattern is created, and the extent to which the DNA methylation machinery reads chromatin states. Recent epigenomic studies building on advances in ultra-low input chromatin profiling methods, coupled with genetic studies, have started to allow a detailed interrogation of the interplay between DNA methylation establishment and chromatin states; however, a full mechanistic description awaits.
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25
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Zhou Q, Meng QR, Meng TG, He QL, Zhao ZH, Li QN, Lei WL, Liu SZ, Schatten H, Wang ZB, Sun QY. Deletion of BAF250a affects oocyte epigenetic modifications and embryonic development. Mol Reprod Dev 2020; 87:550-564. [PMID: 32215983 DOI: 10.1002/mrd.23339] [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: 02/04/2020] [Accepted: 03/11/2020] [Indexed: 11/10/2022]
Abstract
BRG1-associated factor 250a (BAF250a) is a component of the SWI/SNF adenosine triphosphate-dependent chromatin remodeling complex, which has been shown to control chromatin structure and transcription. BAF250a was reported to be a key component of the gene regulatory machinery in embryonic stem cells controlling self-renewal, differentiation, and cell lineage decisions. Here we constructed Baf250aF/F ;Gdf9-cre (Baf250aCKO ) mice to specifically delete BAF250a in oocytes to investigate the role of maternal BAF250a in female germ cells and embryo development. Our results showed that BAF250a deletion did not affect folliculogenesis, ovulation, and fertilization, but it caused late embryonic death. RNA sequencing analysis showed that the expression of genes involved in cell proliferation and differentiation, tissue morphogenesis, histone modification, and nucleosome remodeling were perturbed in Baf250aCKO MII oocytes. We showed that covalent histone modifications such as H3K27me3 and H3K27ac were also significantly affected in oocytes, which may reduce oocyte quality and lead to birth defects. In addition, the DNA methylation level of Igf2r, Snrpn, and Peg3 differentially methylated regions was decreased in Baf250aCKO oocytes. Quantitative real-time polymerase chain reaction analysis showed that the relative messenger RNA (mRNA) expression levels of Igf2r and Snrpn were significantly increased. The mRNA expression level of Dnmt1, Dnmt3a, Dnmt3l, and Uhrf1 was decreased, and the protein expression in these genes was also reduced, which might be the cause for impaired imprinting establishment. In conclusion, our results demonstrate that BAF250a plays an important role in oocyte transcription regulation, epigenetic modifications, and embryo development.
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Affiliation(s)
- Qian Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qing-Ren Meng
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Tie-Gang Meng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Qi-Long He
- Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Zheng-Hui Zhao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qian-Nan Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Wen-Long Lei
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Shu-Zhen Liu
- Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Heide Schatten
- Department of Veterinary Pathobiology, University of Missouri, Columbia, Missouri
| | - Zhen-Bo Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qing-Yuan Sun
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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26
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Ly L, Chan D, Landry M, Angle C, Martel J, Trasler J. Impact of mothers' early life exposure to low or high folate on progeny outcome and DNA methylation patterns. ENVIRONMENTAL EPIGENETICS 2020; 6:dvaa018. [PMID: 33240529 PMCID: PMC7673481 DOI: 10.1093/eep/dvaa018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 09/03/2020] [Accepted: 09/19/2020] [Indexed: 05/14/2023]
Abstract
The dynamic patterning of DNA and histone methylation during oocyte development presents a potentially susceptible time for epigenetic disruption due to early life environmental exposure of future mothers. We investigated whether maternal exposure to folic acid deficient and supplemented diets starting in utero could affect oocytes and cause adverse developmental and epigenetic effects in next generation progeny. Female BALB/c mice (F0) were placed on one of four amino acid defined diets for 4 weeks before pregnancy and throughout gestation and lactation: folic acid control (rodent recommended daily intake; Ctrl), 7-fold folic acid deficient, 10-fold folic acid supplemented or 20-fold folic acid supplemented diets. F1 female pups were weaned onto Ctrl diets, mated to produce the F2 generation and the F2 offspring were examined at E18.5 for developmental and epigenetic abnormalities. Resorption rates were increased and litter sizes decreased amongst F2 E18.5-day litters in the 20-fold folic acid supplemented group. Increases in abnormal embryo outcomes were observed in all three folic acid deficient and supplemented groups. Subtle genome-wide DNA methylation alterations were found in the placentas and brains of F2 offspring in the 7-fold folic acid deficient , 10-fold folic acid supplemented and 20-fold folic acid supplemented groups; in contrast, global and imprinted gene methylation were not affected. The findings show that early life female environmental exposures to both low and high folate prior to oocyte maturation can compromise oocyte quality, adversely affecting offspring of the next generation, in part by altering DNA methylation patterns.
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Affiliation(s)
- Lundi Ly
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Donovan Chan
- Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Mylène Landry
- Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Camille Angle
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada
| | - Josée Martel
- Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Jacquetta Trasler
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada
- Department of Pediatrics, McGill University, Montreal, QC, Canada
- Correspondence address. Research Institute of the McGill University Health Centre, 1001 Boulevard Décarie, Block E.M.0.3211, Montreal, QC, Canada H4A 3J1. Tel: +1-514-934-1934 (ext. 25235); Fax: +1-514-933-9673; E-mail:
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27
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Demond H, Anvar Z, Jahromi BN, Sparago A, Verma A, Davari M, Calzari L, Russo S, Jahromi MA, Monk D, Andrews S, Riccio A, Kelsey G. A KHDC3L mutation resulting in recurrent hydatidiform mole causes genome-wide DNA methylation loss in oocytes and persistent imprinting defects post-fertilisation. Genome Med 2019; 11:84. [PMID: 31847873 PMCID: PMC6918611 DOI: 10.1186/s13073-019-0694-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 11/15/2019] [Indexed: 12/15/2022] Open
Abstract
Background Maternal effect mutations in the components of the subcortical maternal complex (SCMC) of the human oocyte can cause early embryonic failure, gestational abnormalities and recurrent pregnancy loss. Enigmatically, they are also associated with DNA methylation abnormalities at imprinted genes in conceptuses: in the devastating gestational abnormality biparental complete hydatidiform mole (BiCHM) or in multi-locus imprinting disease (MLID). However, the developmental timing, genomic extent and mechanistic basis of these imprinting defects are unknown. The rarity of these disorders and the possibility that methylation defects originate in oocytes have made these questions very challenging to address. Methods Single-cell bisulphite sequencing (scBS-seq) was used to assess methylation in oocytes from a patient with BiCHM identified to be homozygous for an inactivating mutation in the human SCMC component KHDC3L. Genome-wide methylation analysis of a preimplantation embryo and molar tissue from the same patient was also performed. Results High-coverage scBS-seq libraries were obtained from five KHDC3Lc.1A>G oocytes, which revealed a genome-wide deficit of DNA methylation compared with normal human oocytes. Importantly, germline differentially methylated regions (gDMRs) of imprinted genes were affected similarly to other sequence features that normally become methylated in oocytes, indicating no selectivity towards imprinted genes. A range of methylation losses was observed across genomic features, including gDMRs, indicating variable sensitivity to defects in the SCMC. Genome-wide analysis of a pre-implantation embryo and molar tissue from the same patient showed that following fertilisation methylation defects at imprinted genes persist, while most non-imprinted regions of the genome recover near-normal methylation post-implantation. Conclusions We show for the first time that the integrity of the SCMC is essential for de novo methylation in the female germline. These findings have important implications for understanding the role of the SCMC in DNA methylation and for the origin of imprinting defects, for counselling affected families, and will help inform future therapeutic approaches.
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Affiliation(s)
- Hannah Demond
- Epigenetics Programme, Babraham Institute, Cambridge, UK
| | - Zahra Anvar
- Infertility Research Center, Shiraz University of Medical Sciences, Shiraz, Iran. .,Department of Obstetrics and Gynecology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran. .,Institute of Genetics and Biophysics 'Adriano Buzzati-Traverso', Consiglio Nazionale delle Ricerche (CNR), Naples, Italy.
| | - Bahia Namavar Jahromi
- Infertility Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.,Department of Obstetrics and Gynecology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Angela Sparago
- Dipartimento di Scienze e Tecnologie Ambientali Biologiche e Farmaceutiche, Università degli Studi della Campania 'Luigi Vanvitelli', Caserta, Italy
| | - Ankit Verma
- Institute of Genetics and Biophysics 'Adriano Buzzati-Traverso', Consiglio Nazionale delle Ricerche (CNR), Naples, Italy.,Dipartimento di Scienze e Tecnologie Ambientali Biologiche e Farmaceutiche, Università degli Studi della Campania 'Luigi Vanvitelli', Caserta, Italy
| | - Maryam Davari
- Department of Obstetrics and Gynecology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.,IVF Section, Ghadir-Mother and Child Hospital of Shiraz, Shiraz, Iran
| | - Luciano Calzari
- Medical Cytogenetics and Molecular Genetics Laboratory, Centro di Ricerche e Tecnologie Biomediche IRCCS, Istituto Auxologico Italiano, Milan, Italy
| | - Silvia Russo
- Medical Cytogenetics and Molecular Genetics Laboratory, Centro di Ricerche e Tecnologie Biomediche IRCCS, Istituto Auxologico Italiano, Milan, Italy
| | | | - David Monk
- Imprinting and Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Simon Andrews
- Bioinformatics Group, Babraham Institute, Cambridge, UK
| | - Andrea Riccio
- Institute of Genetics and Biophysics 'Adriano Buzzati-Traverso', Consiglio Nazionale delle Ricerche (CNR), Naples, Italy. .,Dipartimento di Scienze e Tecnologie Ambientali Biologiche e Farmaceutiche, Università degli Studi della Campania 'Luigi Vanvitelli', Caserta, Italy.
| | - Gavin Kelsey
- Epigenetics Programme, Babraham Institute, Cambridge, UK. .,Centre for Trophoblast Research, University of Cambridge, Cambridge, UK.
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28
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Bogutz AB, Brind'Amour J, Kobayashi H, Jensen KN, Nakabayashi K, Imai H, Lorincz MC, Lefebvre L. Evolution of imprinting via lineage-specific insertion of retroviral promoters. Nat Commun 2019; 10:5674. [PMID: 31831741 PMCID: PMC6908575 DOI: 10.1038/s41467-019-13662-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 11/14/2019] [Indexed: 01/09/2023] Open
Abstract
Imprinted genes are expressed from a single parental allele, with the other allele often silenced by DNA methylation (DNAme) established in the germline. While species-specific imprinted orthologues have been documented, the molecular mechanisms underlying the evolutionary switch from biallelic to imprinted expression are unknown. During mouse oogenesis, gametic differentially methylated regions (gDMRs) acquire DNAme in a transcription-guided manner. Here we show that oocyte transcription initiating in lineage-specific endogenous retroviruses (ERVs) is likely responsible for DNAme establishment at 4/6 mouse-specific and 17/110 human-specific imprinted gDMRs. The latter are divided into Catarrhini- or Hominoidea-specific gDMRs embedded within transcripts initiating in ERVs specific to these primate lineages. Strikingly, imprinting of the maternally methylated genes Impact and Slc38a4 was lost in the offspring of female mice harboring deletions of the relevant murine-specific ERVs upstream of these genes. Our work reveals an evolutionary mechanism whereby maternally silenced genes arise from biallelically expressed progenitors. Although many species-specific imprinted genes have been identified, how the evolutionary switch from biallelic to imprinted expression occurs is still unknown. Here authors find that lineage-specific ERVs active as oocyte promoters can induce de novo DNA methylation at gDMRs and imprinting.
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Affiliation(s)
- Aaron B Bogutz
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Julie Brind'Amour
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Hisato Kobayashi
- Department of Embryology, Nara Medical University, Kashihara, Nara, 634-8521, Japan
| | - Kristoffer N Jensen
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Kazuhiko Nakabayashi
- Division of Developmental Genomics, Research Institute, National Center for Child Health and Development, Setagaya, Tokyo, 157-8535, Japan
| | - Hiroo Imai
- Molecular Biology Section, Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, Inuyama, Aichi, 484-8506, Japan
| | - Matthew C Lorincz
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
| | - Louis Lefebvre
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
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29
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Kindsfather AJ, Czekalski MA, Pressimone CA, Erisman MP, Mann MRW. Perturbations in imprinted methylation from assisted reproductive technologies but not advanced maternal age in mouse preimplantation embryos. Clin Epigenetics 2019; 11:162. [PMID: 31767035 PMCID: PMC6878706 DOI: 10.1186/s13148-019-0751-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 09/23/2019] [Indexed: 12/19/2022] Open
Abstract
Background Over the last several decades, the average age of first-time mothers has risen steadily. With increasing maternal age comes a decrease in fertility, which in turn has led to an increase in the use of assisted reproductive technologies by these women. Assisted reproductive technologies (ARTs), including superovulation and embryo culture, have been shown separately to alter imprinted DNA methylation maintenance in blastocysts. However, there has been little investigation on the effects of advanced maternal age, with or without ARTs, on genomic imprinting. We hypothesized that ARTs and advanced maternal age, separately and together, alter imprinted methylation in mouse preimplantation embryos. For this study, we examined imprinted methylation at three genes, Snrpn, Kcnq1ot1, and H19, which in humans are linked to ART-associated methylation errors that lead to imprinting disorders. Results Our data showed that imprinted methylation acquisition in oocytes was unaffected by increasing maternal age. Furthermore, imprinted methylation was normally acquired when advanced maternal age was combined with superovulation. Analysis of blastocyst-stage embryos revealed that imprinted methylation maintenance was also not affected by increasing maternal age. In a comparison of ARTs, we observed that the frequency of blastocysts with imprinted methylation loss was similar between the superovulation only and the embryo culture only groups, while the combination of superovulation and embryo culture resulted in a higher frequency of mouse blastocysts with maternal imprinted methylation perturbations than superovulation alone. Finally, the combination of increasing maternal age with ARTs had no additional effect on the frequency of imprinted methylation errors. Conclusion Collectively, increasing maternal age with or without superovulation had no effect of imprinted methylation acquisition at Snrpn, Kcnq1ot1, and H19 in oocytes. Furthermore, during preimplantation development, while ARTs generated perturbations in imprinted methylation maintenance in blastocysts, advanced maternal age did not increase the burden of imprinted methylation errors at Snrpn, Kcnq1ot1, and H19 when combined with ARTs. These results provide cautious optimism that advanced maternal age is not a contributing factor to imprinted methylation errors in embryos produced in the clinic. Furthermore, our data on the effects of ARTs strengthen the need to advance clinical methods to reduce imprinted methylation errors in in vitro-produced embryos.
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Affiliation(s)
- Audrey J Kindsfather
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, 204 Craft Ave, Pittsburgh, PA, 15213, USA.,Magee-Womens Research Institute, 204 Craft Ave, Pittsburgh, PA, 15213, USA
| | - Megan A Czekalski
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, 204 Craft Ave, Pittsburgh, PA, 15213, USA.,Magee-Womens Research Institute, 204 Craft Ave, Pittsburgh, PA, 15213, USA
| | - Catherine A Pressimone
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, 204 Craft Ave, Pittsburgh, PA, 15213, USA.,Magee-Womens Research Institute, 204 Craft Ave, Pittsburgh, PA, 15213, USA
| | - Margaret P Erisman
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, 204 Craft Ave, Pittsburgh, PA, 15213, USA.,Magee-Womens Research Institute, 204 Craft Ave, Pittsburgh, PA, 15213, USA
| | - Mellissa R W Mann
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, 204 Craft Ave, Pittsburgh, PA, 15213, USA. .,Magee-Womens Research Institute, 204 Craft Ave, Pittsburgh, PA, 15213, USA.
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30
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Saenz-de-Juano MD, Ivanova E, Romero S, Lolicato F, Sánchez F, Van Ranst H, Krueger F, Segonds-Pichon A, De Vos M, Andrews S, Smitz J, Kelsey G, Anckaert E. DNA methylation and mRNA expression of imprinted genes in blastocysts derived from an improved in vitro maturation method for oocytes from small antral follicles in polycystic ovary syndrome patients. Hum Reprod 2019; 34:1640-1649. [PMID: 31398248 DOI: 10.1093/humrep/dez121] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 06/04/2019] [Accepted: 06/17/2019] [Indexed: 11/08/2023] Open
Abstract
STUDY QUESTION Does imprinted DNA methylation or imprinted gene expression differ between human blastocysts from conventional ovarian stimulation (COS) and an optimized two-step IVM method (CAPA-IVM) in age-matched polycystic ovary syndrome (PCOS) patients? SUMMARY ANSWER No significant differences in imprinted DNA methylation and gene expression were detected between COS and CAPA-IVM blastocysts. WHAT IS KNOWN ALREADY Animal models have revealed alterations in DNA methylation maintenance at imprinted germline differentially methylated regions (gDMRs) after use of ARTs. This effect increases as more ART interventions are applied to oocytes or embryos. IVM is a minimal-stimulation ART with reduced hormone-related side effects and risks for patients. CAPA-IVM is an improved IVM system that includes a pre-maturation step (CAPA), followed by an IVM step, both in the presence of physiological compounds that promote oocyte developmental capacity. STUDY DESIGN, SIZE, DURATION For DNA methylation analysis 20 CAPA-IVM blastocysts were compared to 12 COS blastocysts. For RNA-Seq analysis a separate set of 15 CAPA-IVM blastocysts were compared to 5 COS blastocysts. PARTICIPANTS/MATERIALS, SETTING, METHODS COS embryos originated from 12 patients with PCOS (according to Rotterdam criteria) who underwent conventional ovarian stimulation. For CAPA-IVM 23 women were treated for 3-5 days with highly purified hMG (HP-hMG) and no hCG trigger was given before oocyte retrieval. Oocytes were first cultured in pre-maturation medium (CAPA for 24 h containing C-type natriuretic peptide), followed by an IVM step (30 h) in medium containing FSH and Amphiregulin. After ICSI, Day 5 or 6 embryos in both groups were vitrified and used for post-bisulphite adaptor tagging (PBAT) DNA methylation analysis or RNA-seq gene expression analysis of individual embryos. Data from specific genes and gDMRs were extracted from the PABT and RNA-seq datasets. MAIN RESULTS AND THE ROLE OF CHANCE CAPA-IVM blastocysts showed similar rates of methylation and gene expression at gDMRs compared to COS embryos. In addition, expression of major epigenetic regulators was similar between the groups. LIMITATIONS, REASONS FOR CAUTION The embryos from the COS group were generated in a range of culture media. The CAPA-IVM embryos were all generated using the same sperm donor. The DNA methylation level of gDMRs in purely in vivo-derived human blastocysts is not known. WIDER IMPLICATIONS OF THE FINDINGS A follow-up of children born after CAPA-IVM is important as it is for other new ARTs, which are generally introduced into clinical practice without prior epigenetic safety studies on human blastocysts. CAPA-IVM opens new perspectives for patient-friendly ART in PCOS. STUDY FUNDING/COMPETING INTEREST(S) IVM research at the Vrije Universiteit Brussel has been supported by grants from the Institute for the Promotion of Innovation by Science and Technology in Flanders (Agentschap voor Innovatie door Wetenschap en Technologie-IWT, project 110680), the Fund for Research Flanders (Fonds voor Wetenschappelijk Onderzoek-Vlaanderen-FWO-AL 679 project, project G.0343.13), the Belgian Foundation Against Cancer (HOPE project, Dossier C69Ref Nr 2016-119) and the Vrije Universiteit Brussel (IOF Project 4R-ART Nr 2042). Work in G.K.'s laboratory is supported by the UK Biotechnology and Biological Sciences Research Council and Medical Research Council. The authors have no conflicts of interest.
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Affiliation(s)
- M D Saenz-de-Juano
- Follicle Biology Laboratory (FOBI), UZ Brussel, Vrije Universiteit Brussel, Brussels, Belgium
- Animal Physiology, Institute of Agricultural Sciences, ETH Zurich, Switzerland
| | - E Ivanova
- Epigenetics Programme, The Babraham Institute, Cambridge, UK
| | - S Romero
- Follicle Biology Laboratory (FOBI), UZ Brussel, Vrije Universiteit Brussel, Brussels, Belgium
- Laboratory of Reproductive Biology and Fertility Preservation, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - F Lolicato
- Follicle Biology Laboratory (FOBI), UZ Brussel, Vrije Universiteit Brussel, Brussels, Belgium
- Fertilab Barcelona, Via Augusta, 237-239, Barcelona 08021, Spain
| | - F Sánchez
- Follicle Biology Laboratory (FOBI), UZ Brussel, Vrije Universiteit Brussel, Brussels, Belgium
- Laboratory of Reproductive Biology and Fertility Preservation, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - H Van Ranst
- Follicle Biology Laboratory (FOBI), UZ Brussel, Vrije Universiteit Brussel, Brussels, Belgium
| | - F Krueger
- Bioinformatics Unit, The Babraham Institute, Cambridge, UK
| | | | - M De Vos
- Follicle Biology Laboratory (FOBI), UZ Brussel, Vrije Universiteit Brussel, Brussels, Belgium
- Centre for Reproductive Medicine, UZ Brussel, Brussels 1090, Belgium
| | - S Andrews
- Bioinformatics Unit, The Babraham Institute, Cambridge, UK
| | - J Smitz
- Follicle Biology Laboratory (FOBI), UZ Brussel, Vrije Universiteit Brussel, Brussels, Belgium
| | - G Kelsey
- Epigenetics Programme, The Babraham Institute, Cambridge, UK
| | - E Anckaert
- Follicle Biology Laboratory (FOBI), UZ Brussel, Vrije Universiteit Brussel, Brussels, Belgium
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31
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Genomic imprinting disorders: lessons on how genome, epigenome and environment interact. Nat Rev Genet 2019; 20:235-248. [PMID: 30647469 DOI: 10.1038/s41576-018-0092-0] [Citation(s) in RCA: 214] [Impact Index Per Article: 42.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Genomic imprinting, the monoallelic and parent-of-origin-dependent expression of a subset of genes, is required for normal development, and its disruption leads to human disease. Imprinting defects can involve isolated or multilocus epigenetic changes that may have no evident genetic cause, or imprinting disruption can be traced back to alterations of cis-acting elements or trans-acting factors that control the establishment, maintenance and erasure of germline epigenetic imprints. Recent insights into the dynamics of the epigenome, including the effect of environmental factors, suggest that the developmental outcomes and heritability of imprinting disorders are influenced by interactions between the genome, the epigenome and the environment in germ cells and early embryos.
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32
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Lewis MW, Vargas-Franco D, Morse DA, Resnick JL. A mouse model of Angelman syndrome imprinting defects. Hum Mol Genet 2019; 28:220-229. [PMID: 30260400 DOI: 10.1093/hmg/ddy345] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 09/21/2018] [Indexed: 02/07/2023] Open
Abstract
Angelman syndrome, Prader-Will syndrome and Dup15q syndrome map to a cluster of imprinted genes located at 15q11-q13. Imprinting at this domain is regulated by an imprinting control region consisting of two distinct elements, the Angelman syndrome imprinting center (AS-IC) and the Prader-Willi syndrome imprinting center (PWS-IC). Individuals inheriting deletions of the AS-IC exhibit reduced expression of the maternally expressed UBE3A gene and biallelic expression of paternal-only genes. We have previously demonstrated that AS-IC activity partly consists of providing transcription across the PWS-IC in oocytes, and that these transcripts are necessary for maternal imprinting of Snrpn. Here we report a novel mouse mutation that truncates transcripts prior to transiting the PWS-IC and results in a domain-wide imprinting defect. These results confirm a transcription-based model for imprint setting at this domain. The imprinting defect can be preempted by removal of the transcriptional block in oocytes, but not by its removal in early embryos. Imprinting defect mice exhibit several traits often found in individuals with Angelman syndrome imprinting defects.
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Affiliation(s)
- Michael W Lewis
- Department of Molecular Genetics and Microbiology College of Medicine University of Florida, Gainsvile, FL, USA
| | - Dorianmarie Vargas-Franco
- Department of Molecular Genetics and Microbiology College of Medicine University of Florida, Gainsvile, FL, USA
| | - Deborah A Morse
- Department of Molecular Genetics and Microbiology College of Medicine University of Florida, Gainsvile, FL, USA
| | - James L Resnick
- Department of Molecular Genetics and Microbiology College of Medicine University of Florida, Gainsvile, FL, USA
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Cao Y, Li M, Liu F, Ni X, Wang S, Zhang H, Sui X, Huo R. Deletion of maternal UHRF1 severely reduces mouse oocyte quality and causes developmental defects in preimplantation embryos. FASEB J 2019; 33:8294-8305. [PMID: 30995416 DOI: 10.1096/fj.201801696rrrr] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The ubiquitin-like, containing PHD and RING finger domains, 1 (UHRF1) protein recognizes DNA methylation and histone modification and plays a critical role in epigenetic regulation. Recently, UHRF1 was shown to have a role in DNA methylation in oocytes and early embryos. Here, we reveal that maternal UHRF1 determines the quality of mouse oocytes. We generated oocyte-specific Uhrf1-knockout mice and found that females were sterile, and few maternal UHRF1-null embryos developed into blastocysts. The UHRF1-null oocytes had an increased incidence of aneuploidy and DNA damage. In addition to defective DNA methylation, histone modification was affected during oogenesis, with UHRF1-null germinal vesicle and metaphase II-stage oocytes exhibiting reduced global histone H3 lysine 9 dimethylation levels and elevated acetylation of histone H4 lysine 12. Taken together, our results suggest that UHRF1 plays an important role in determining oocyte quality and affects epigenetic regulation of oocyte maturation as a maternal protein, which is crucial for embryo developmental potential. Further exploration of the biologic function and underlying mechanisms of maternal UHRF1 will enhance our understanding of the maternal control of the oocyte and early embryonic development.-Cao, Y., Li, M., Liu, F., Ni, X., Wang, S., Zhang, H., Sui, X., Huo, R. Deletion of maternal UHRF1 severely reduces mouse oocyte quality and causes developmental defects in preimplantation embryos.
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Affiliation(s)
- Yumeng Cao
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Mingrui Li
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Fei Liu
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - XiaoBei Ni
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Shuai Wang
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Hao Zhang
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Xuesong Sui
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Ran Huo
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
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34
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Zeng Y, Chen T. DNA Methylation Reprogramming during Mammalian Development. Genes (Basel) 2019; 10:E257. [PMID: 30934924 PMCID: PMC6523607 DOI: 10.3390/genes10040257] [Citation(s) in RCA: 181] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 03/22/2019] [Accepted: 03/25/2019] [Indexed: 12/15/2022] Open
Abstract
DNA methylation (5-methylcytosine, 5mC) is a major form of DNA modification in the mammalian genome that plays critical roles in chromatin structure and gene expression. In general, DNA methylation is stably maintained in somatic tissues. However, DNA methylation patterns and levels show dynamic changes during development. Specifically, the genome undergoes two waves of global demethylation and remethylation for the purpose of producing the next generation. The first wave occurs in the germline, initiated with the erasure of global methylation in primordial germ cells (PGCs) and completed with the establishment of sex-specific methylation patterns during later stages of germ cell development. The second wave occurs after fertilization, including the erasure of most methylation marks inherited from the gametes and the subsequent establishment of the embryonic methylation pattern. The two waves of DNA methylation reprogramming involve both distinct and shared mechanisms. In this review article, we provide an overview of the key reprogramming events, focusing on the important players in these processes, including DNA methyltransferases (DNMTs) and ten-eleven translocation (TET) family of 5mC dioxygenases.
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Affiliation(s)
- Yang Zeng
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, 1808 Park Road 1C, Smithville, TX 78957, USA.
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.
- Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA.
| | - Taiping Chen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, 1808 Park Road 1C, Smithville, TX 78957, USA.
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.
- Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA.
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35
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Kawabata Y, Kamio A, Jincho Y, Sakashita A, Takashima T, Kobayashi H, Matsui Y, Kono T. Sex-specific histone modifications in mouse fetal and neonatal germ cells. Epigenomics 2019; 11:543-561. [PMID: 30667280 DOI: 10.2217/epi-2018-0193] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
AIMS Epigenetic signatures of germline cells are dynamically reprogrammed to induce appropriate differentiation, development and sex specification. We investigated sex-specific epigenetic changes in mouse fetal germ cells (FGCs) and neonatal germ cells. MATERIALS & METHODS Six histone marks in mouse E13.5 FGCs and P1 neonatal germ cells were analyzed by chromatin immunoprecipitation and sequencing. These datasets were compared with transposase-accessible chromatin sites, DNA methylation and transcriptome. RESULTS Different patterns of each histone mark were detected in female and male FGCs, and H3K4me3/H3K27me3 bivalent marks were enriched in different chromosomal regions of female and male FGCs. CONCLUSION Our results suggest that histone modifications may affect FGC gene expression following DNA methylation erasure, contributing to the differentiation into female and male germ cells.
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Affiliation(s)
- Yukiko Kawabata
- Department of Bioscience, Tokyo University of Agriculture, Setagaya, Tokyo, Japan
| | - Asuka Kamio
- Department of Bioscience, Tokyo University of Agriculture, Setagaya, Tokyo, Japan.,NODAI Genome Research Centre, Tokyo University of Agriculture, Setagaya, Tokyo, Japan
| | - Yuko Jincho
- Department of Bioscience, Tokyo University of Agriculture, Setagaya, Tokyo, Japan
| | - Akihiko Sakashita
- Department of Bioscience, Tokyo University of Agriculture, Setagaya, Tokyo, Japan
| | - Tomoya Takashima
- Department of Bioscience, Tokyo University of Agriculture, Setagaya, Tokyo, Japan
| | - Hisato Kobayashi
- NODAI Genome Research Centre, Tokyo University of Agriculture, Setagaya, Tokyo, Japan
| | - Yasuhisa Matsui
- Cell Resource Centre for Biomedical Research, Institute of Development, Aging & Cancer, Tohoku University, Sendai, Miyagi, Japan
| | - Tomohiro Kono
- Department of Bioscience, Tokyo University of Agriculture, Setagaya, Tokyo, Japan
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36
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Larose H, Shami AN, Abbott H, Manske G, Lei L, Hammoud SS. Gametogenesis: A journey from inception to conception. Curr Top Dev Biol 2019; 132:257-310. [PMID: 30797511 PMCID: PMC7133493 DOI: 10.1016/bs.ctdb.2018.12.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Gametogenesis, the process of forming mature germ cells, is an integral part of both an individual's and a species' health and well-being. This chapter focuses on critical male and female genetic and epigenetic processes underlying normal gamete formation through their differentiation to fertilization. Finally, we explore how knowledge gained from this field has contributed to progress in areas with great clinical promise, such as in vitro gametogenesis.
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Affiliation(s)
- Hailey Larose
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, United States
| | | | - Haley Abbott
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Gabriel Manske
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Lei Lei
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, United States; Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI, United States.
| | - Saher Sue Hammoud
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, United States; Department of Obstetrics and Gynecology, University of Michigan Medical School, Ann Arbor, MI, United States; Department of Urology, University of Michigan Medical School, Ann Arbor, MI, United States.
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37
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Marshall KL, Wang J, Ji T, Rivera RM. The effects of biological aging on global DNA methylation, histone modification, and epigenetic modifiers in the mouse germinal vesicle stage oocyte. Anim Reprod 2018; 15:1253-1267. [PMID: 34221140 PMCID: PMC8203117 DOI: 10.21451/1984-3143-ar2018-0087] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
A cultural trend in developed countries is favoring a delay in maternal age at first childbirth.
In mammals fertility and chronological age show an inverse correlation. Oocyte quality is
a contributing factor to this multifactorial phenomenon that may be influenced by age-related
changes in the oocyte epigenome. Based on previous reports, we hypothesized that advanced
maternal age would lead to alterations in the oocyte’s epigenome. We tested our hypothesis
by determining protein levels of various epigenetic modifications and modifiers in fully-grown
(≥70 µm), germinal vesicle (GV) stage oocytes of young (10-13 weeks) and aged
(69-70 weeks) mice. Our results demonstrate a significant increase in protein amounts of
the maintenance DNA methyltransferase DNMT1 (P = 0.003) and a trend toward increased global
DNA methylation (P = 0.09) with advanced age. MeCP2, a methyl DNA binding domain protein, recognizes
methylated DNA and induces chromatin compaction and silencing. We hypothesized that chromatin
associated MeCP2 would be increased similarly to DNA methylation in oocytes of aged female
mice. However, we detected a significant decrease (P = 0.0013) in protein abundance of MeCP2
between GV stage oocytes from young and aged females. Histone posttranslational modifications
can also alter chromatin conformation. Di-methylation of H3K9 (H3K9me2) is associated with
permissive heterochromatin while acetylation of H4K5 (H4K5ac) is associated with euchromatin.
Our results indicate a trend toward decreasing H3K9me2 (P = 0.077) with advanced female age
and no significant differences in levels of H4K5ac. These data demonstrate that physiologic
aging affects the mouse oocyte epigenome and provide a better understanding of the mechanisms
underlying the decrease in oocyte quality and reproductive potential of aged females.
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Affiliation(s)
- Kira Lynn Marshall
- Division of Animal Sciences.,Reproductive Sciences, San Diego Zoo Global Institute for Conservation Research, San Pasqual Valley Rd
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38
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Yarychkivska O, Shahabuddin Z, Comfort N, Boulard M, Bestor TH. BAH domains and a histone-like motif in DNA methyltransferase 1 (DNMT1) regulate de novo and maintenance methylation in vivo. J Biol Chem 2018; 293:19466-19475. [PMID: 30341171 DOI: 10.1074/jbc.ra118.004612] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 10/12/2018] [Indexed: 12/31/2022] Open
Abstract
DNA methyltransferase 1 (DNMT1) is a multidomain protein believed to be involved only in the passive transmission of genomic methylation patterns via maintenance methylation. The mechanisms that regulate DNMT1 activity and targeting are complex and poorly understood. We used embryonic stem (ES) cells to investigate the function of the uncharacterized bromo-adjacent homology (BAH) domains and the glycine-lysine (GK) repeats that join the regulatory and catalytic domains of DNMT1. We removed the BAH domains by means of a CRISPR/Cas9-mediated deletion within the endogenous Dnmt1 locus. The internally deleted protein failed to associate with replication foci during S phase in vivo and lost the ability to mediate maintenance methylation. The data indicate that ablation of the BAH domains causes DNMT1 to be excluded from replication foci even in the presence of the replication focus-targeting sequence (RFTS). The GK repeats resemble the N-terminal tails of histones H2A and H4 and are normally acetylated. Substitution of lysines within the GK repeats with arginines to prevent acetylation did not alter the maintenance activity of DNMT1 but unexpectedly activated de novo methylation of paternal imprinting control regions (ICRs) in mouse ES cells; maternal ICRs remained unmethylated. We propose a model under which DNMT1 deposits paternal imprints in male germ cells in an acetylation-dependent manner. These data reveal that DNMT1 responds to multiple regulatory inputs that control its localization as well as its activity and is not purely a maintenance methyltransferase but can participate in the de novo methylation of a small but essential compartment of the genome.
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Affiliation(s)
| | | | - Nicole Comfort
- Environmental Health Science, College of Physicians and Surgeons of Columbia University, New York, New York 10032, and
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39
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Generation of Bimaternal and Bipaternal Mice from Hypomethylated Haploid ESCs with Imprinting Region Deletions. Cell Stem Cell 2018; 23:665-676.e4. [PMID: 30318303 DOI: 10.1016/j.stem.2018.09.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Revised: 07/16/2018] [Accepted: 09/05/2018] [Indexed: 11/24/2022]
Abstract
Unisexual reproduction is widespread among lower vertebrates, but not in mammals. Deletion of the H19 imprinted region in immature oocytes produced bimaternal mice with defective growth; however, bipaternal reproduction has not been previously achieved in mammals. We found that cultured parthenogenetic and androgenetic haploid embryonic stem cells (haESCs) display DNA hypomethylation resembling that of primordial germ cells. Through MII oocyte injection or sperm coinjection with hypomethylated haploid ESCs carrying specific imprinted region deletions, we obtained live bimaternal and bipaternal mice. Deletion of 3 imprinted regions in parthenogenetic haploid ESCs restored normal growth of fertile bimaternal mice, whereas deletion of 7 imprinted regions in androgenetic haploid ESCs enabled production of live bipaternal mice that died shortly after birth. Phenotypic analyses of organ and body size of these mice support the genetic conflict theory of genomic imprinting. Taken together, our results highlight the factors necessary for crossing same-sex reproduction barriers in mammals.
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40
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Hanna CW, Demond H, Kelsey G. Epigenetic regulation in development: is the mouse a good model for the human? Hum Reprod Update 2018; 24:556-576. [PMID: 29992283 PMCID: PMC6093373 DOI: 10.1093/humupd/dmy021] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 05/20/2018] [Accepted: 06/05/2018] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Over the past few years, advances in molecular technologies have allowed unprecedented mapping of epigenetic modifications in gametes and during early embryonic development. This work is allowing a detailed genomic analysis, which for the first time can answer long-standing questions about epigenetic regulation and reprogramming, and highlights differences between mouse and human, the implications of which are only beginning to be explored. OBJECTIVE AND RATIONALE In this review, we summarise new low-cell molecular methods enabling the interrogation of epigenetic information in gametes and early embryos, the mechanistic insights these have provided, and contrast the findings in mouse and human. SEARCH METHODS Relevant studies were identified by PubMed search. OUTCOMES We discuss the levels of epigenetic regulation, from DNA modifications to chromatin organisation, during mouse gametogenesis, fertilisation and pre- and post-implantation development. The recently characterised features of the oocyte epigenome highlight its exceptionally unique regulatory landscape. The chromatin organisation and epigenetic landscape of both gametic genomes are rapidly reprogrammed after fertilisation. This extensive epigenetic remodelling is necessary for zygotic genome activation, but the mechanistic link remains unclear. While the vast majority of epigenetic information from the gametes is erased in pre-implantation development, new insights suggest that repressive histone modifications from the oocyte may mediate a novel mechanism of imprinting. To date, the characterisation of epigenetics in human development has been almost exclusively limited to DNA methylation profiling; these data reinforce that the global dynamics are conserved between mouse and human. However, as we look closer, it is becoming apparent that the mechanisms regulating these dynamics are distinct. These early findings emphasise the importance of investigations of fundamental epigenetic mechanisms in both mouse and humans. WIDER IMPLICATIONS Failures in epigenetic regulation have been implicated in human disease and infertility. With increasing maternal age and use of reproductive technologies in countries all over the world, it is becoming ever more important to understand the necessary processes required to establish a developmentally competent embryo. Furthermore, it is essential to evaluate the extent to which these epigenetic patterns are sensitive to such technologies and other adverse environmental exposures.
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Affiliation(s)
- Courtney W Hanna
- Epigenetics programme, Babraham Institute, Cambridge, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | - Hannah Demond
- Epigenetics programme, Babraham Institute, Cambridge, UK
| | - Gavin Kelsey
- Epigenetics programme, Babraham Institute, Cambridge, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
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41
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Mattern F, Heinzmann J, Herrmann D, Lucas-Hahn A, Haaf T, Niemann H. Gene-specific profiling of DNA methylation and mRNA expression in bovine oocytes derived from follicles of different size categories. Reprod Fertil Dev 2018; 29:2040-2051. [PMID: 28152377 DOI: 10.1071/rd16327] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 12/14/2016] [Indexed: 12/20/2022] Open
Abstract
Epigenetic changes, such as DNA methylation, play an essential role in the acquisition of full developmental competence by mammalian oocytes during the late follicular growth phase. Here we used the bovine model to investigate the DNA methylation profiles of seven candidate genes (imprinted: bH19, bSNRPN; non-imprinted: bZAR1, bDNMT3A, bOCT4, bDNMT3 Lo and bDNMT3 Ls) and the mRNA expression of nine candidate genes (imprinted: bSNRPN, bPEG3, bIGF2R; non-imprinted: bPRDX1, bDNMT1B, bDNMT3A, bZAR1, bHSF1 and bNLRP9) in oocytes from antral follicles of three different size classes (≤2mm, 3-5mm, ≥6mm) to unravel the epigenetic contribution to this process. We observed an increased number of aberrantly methylated alleles in bH19, bSNRPN and bDNMT3 Lo of oocytes from small antral follicles (≤2mm), correlating with lower developmental competence. Furthermore, we detected an increased frequency of CpG sites with an unclear methylation status for DNMT3 Ls, specifically in oocytes from follicles ≥6mm, predominantly at three CpG positions (CpG2, CpG7 and CpG8), of which CpG7 is a potential regulatory site. No major differences in mRNA expression were observed, indicating that the transcriptional machinery may not yet be active during the follicular growth phase. Our results support the notion that a follicle diameter of ~2mm is a critical stage for establishing DNA methylation profiles and indicate a link between DNA methylation and the acquisition of oocyte developmental competence.
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Affiliation(s)
- F Mattern
- Institute of Human Genetics, Julius Maximilians University, 97070 Würzburg, Germany
| | - J Heinzmann
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Federal Research Institute of Animal Health, Mariensee, 31535 Neustadt, Germany
| | - D Herrmann
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Federal Research Institute of Animal Health, Mariensee, 31535 Neustadt, Germany
| | - A Lucas-Hahn
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Federal Research Institute of Animal Health, Mariensee, 31535 Neustadt, Germany
| | - T Haaf
- Institute of Human Genetics, Julius Maximilians University, 97070 Würzburg, Germany
| | - H Niemann
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Federal Research Institute of Animal Health, Mariensee, 31535 Neustadt, Germany
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42
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Lee J, Matsuzawa A, Shiura H, Sutani A, Ishino F. Preferable in vitro condition for maintaining faithful DNA methylation imprinting in mouse embryonic stem cells. Genes Cells 2018; 23:146-160. [PMID: 29356242 DOI: 10.1111/gtc.12560] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 12/16/2017] [Indexed: 01/13/2023]
Abstract
Epigenetic properties of cultured embryonic stem cells (ESCs), including DNA methylation imprinting, are important because they affect the developmental potential. Here, we tested a variety of culture media, including knockout serum replacement (KSR) and fetal bovine serum (FBS) with or without inhibitors of Gsk3β and Mek1/2 (2i) at various time points. In addition to the previously known passage-dependent global changes, unexpected dynamic DNA methylation changes occurred in both maternal and paternal differentially methylated regions: under the widely used condition of KSR with 2i, a highly hypomethylated state occurred at early passages (P1-7) as well as P10, but DNA methylation increased over further passages in most conditions, except under KSR with 2i at P25. Dramatic DNA demethylation under KSR+2i until P25 was associated with upregulated Tet1 and Parp1, and their related genes, whereas 2i regulated the expressions of DNA methyltransferase-related genes for the change in DNA methylation during the cumulative number of passages. Although DNA methylation imprinting is more labile under KSR with and without 2i, it can be more faithfully maintained under condition of cooperative FBS and 2i. Thus, our study will provide the useful information for improved epigenetic control of ESCs and iPSCs in applications in regenerative medicine.
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Affiliation(s)
- Jiyoung Lee
- Department of Epigenetics, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Ayumi Matsuzawa
- Department of Epigenetics, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Hirosuke Shiura
- Department of Epigenetics, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Akito Sutani
- Department of Epigenetics, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan.,Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Fumitoshi Ishino
- Department of Epigenetics, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
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43
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Marshall KL, Rivera RM. The effects of superovulation and reproductive aging on the epigenome of the oocyte and embryo. Mol Reprod Dev 2018; 85:90-105. [PMID: 29280527 DOI: 10.1002/mrd.22951] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 12/14/2017] [Accepted: 12/19/2017] [Indexed: 12/26/2022]
Abstract
A societal preference of delaying maternal age at first childbirth has increased reliance on assisted reproductive technologies/therapies (ART) to conceive a child. Oocytes that have undergone physiologic aging (≥35 years for humans) are now commonly used for ART, yet evidence is building that suboptimal reproductive environments associated with aging negatively affect oocyte competence and embryo development-although the mechanisms underlying these relationship are not yet well understood. Epigenetic programming of the oocyte occurs during its growth within a follicle, so the ovarian stimulation protocols that administer exogenous hormones, as part of the first step for all ART procedures, may prevent the gamete from establishing an appropriate epigenetic state. Therefore, understanding how oocyte. Therefore, understanding how hormone stimulation and oocyte physiologic age independently and synergistically physiologic age independently and synergistically affect the epigenetic programming of these gametes, and how this may affect their developmental competence, are crucial to improved ART outcomes. Here, we review studies that measured the developmental outcomes affected by superovulation and aging, focusing on how the epigenome (i.e., global and imprinted DNA methylation, histone modifications, and epigenetic modifiers) of gametes and embryos acquired from females undergoing physiologic aging and exogenous ovarian stimulation is affected.
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Affiliation(s)
- Kira L Marshall
- Division of Animal Sciences, University of Missouri, Columbia, Missouri
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44
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Takahashi N, Gray D, Strogantsev R, Noon A, Delahaye C, Skarnes WC, Tate PH, Ferguson-Smith AC. ZFP57 and the Targeted Maintenance of Postfertilization Genomic Imprints. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2018; 80:177-87. [PMID: 27325708 DOI: 10.1101/sqb.2015.80.027466] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Epigenetic modifications play an important role in modulating genome function. In mammals, inappropriate epigenetic states can cause embryonic lethality and various acquired and inherited diseases; hence, it is important to understand how such states are formed and maintained in particular genomic contexts. Genomic imprinting is a process in which epigenetic states provide a sustained memory of parental origin and cause gene expression/repression from only one of the two parental chromosomes. Genomic imprinting is therefore a valuable model to decipher the principles and processes associated with the targeting and maintenance of epigenetic states in general. Krüppel-associated box zinc finger proteins (KRAB-ZFPs) are proteins that have the potential to mediate this. ZFP57, one of the best characterized proteins in this family, has been shown to target and maintain epigenetic states at imprinting control regions after fertilization. Its role in imprinting through the use of ZFP57 mutants in mouse and the wider implications of KRAB-ZFPs for the targeted maintenance of epigenetic states are discussed here.
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Affiliation(s)
- Nozomi Takahashi
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Dionne Gray
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | | | - Angela Noon
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Celia Delahaye
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - William C Skarnes
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Peri H Tate
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
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45
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Whidden L, Martel J, Rahimi S, Chaillet JR, Chan D, Trasler JM. Compromised oocyte quality and assisted reproduction contribute to sex-specific effects on offspring outcomes and epigenetic patterning. Hum Mol Genet 2018; 25:4649-4660. [PMID: 28173052 DOI: 10.1093/hmg/ddw293] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 08/04/2016] [Accepted: 08/25/2016] [Indexed: 11/13/2022] Open
Abstract
Clinical studies have revealed an increased incidence of growth and genomic imprinting disorders in children conceived using assisted reproductive technologies (ARTs), and aberrant DNA methylation has been implicated. We propose that compromised oocyte quality associated with female infertility may make embryos more susceptible to the induction of epigenetic defects by ART. DNA methylation patterns in the preimplantation embryo are dependent on the oocyte-specific DNA methyltransferase 1o (DNMT1o), levels of which are decreased in mature oocytes of aging females. Here, we assessed the effects of maternal deficiency in DNMT1o (Dnmt1Δ1o/+) in combination with superovulation and embryo transfer on offspring DNA methylation and development. We demonstrated a significant increase in the rates of morphological abnormalities in offspring collected from Dnmt1Δ1o/+ females only when combined with ART. Together, maternal oocyte DNMT1o deficiency and ART resulted in an accentuation of placental imprinting defects and the induction of genome-wide DNA methylation alterations, which were exacerbated in the placenta compared to the embryo. Significant sex-specific trends were also apparent, with a preponderance of DNA hypomethylation in females. Among genic regions affected, a significant enrichment for neurodevelopmental pathways was observed. Taken together, our results demonstrate that oocyte DNMT1o-deficiency exacerbates genome-wide DNA methylation abnormalities induced by ART in a sex-specific manner and plays a role in mediating poor embryonic outcome.
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Affiliation(s)
- Laura Whidden
- Montreal Children's Hospital and Research Institute of the McGill University Health Centre, Montreal, QC, Canada.,Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada
| | - Josée Martel
- Montreal Children's Hospital and Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Sophia Rahimi
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - J Richard Chaillet
- Department of OB/GYN and Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Donovan Chan
- Montreal Children's Hospital and Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Jacquetta M Trasler
- Montreal Children's Hospital and Research Institute of the McGill University Health Centre, Montreal, QC, Canada.,Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada,Department of Human Genetics, McGill University, Montreal, QC, Canada,Department of Pediatrics, McGill University, Montreal, QC, Canada
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46
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Velker BAM, Denomme MM, Krafty RT, Mann MRW. Maintenance of Mest imprinted methylation in blastocyst-stage mouse embryos is less stable than other imprinted loci following superovulation or embryo culture. ENVIRONMENTAL EPIGENETICS 2017; 3:dvx015. [PMID: 29492315 PMCID: PMC5804554 DOI: 10.1093/eep/dvx015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 06/07/2017] [Accepted: 07/19/2017] [Indexed: 06/08/2023]
Abstract
Assisted reproductive technologies are fertility treatments used by subfertile couples to conceive their biological child. Although generally considered safe, these pregnancies have been linked to genomic imprinting disorders, including Beckwith-Wiedemann and Silver-Russell Syndromes. Silver-Russell Syndrome is a growth disorder characterized by pre- and post-natal growth retardation. The Mest imprinted domain is one candidate region on chromosome 7 implicated in Silver-Russell Syndrome. We have previously shown that maintenance of imprinted methylation was disrupted by superovulation or embryo culture during pre-implantation mouse development. For superovulation, this disruption did not originate in oogenesis as a methylation acquisition defect. However, in comparison to other genes, Mest exhibits late methylation acquisition kinetics, possibly making Mest more vulnerable to perturbation by environmental insult. In this study, we present a comprehensive evaluation of the effects of superovulation and in vitro culture on genomic imprinting at the Mest gene. Superovulation resulted in disruption of imprinted methylation at the maternal Mest allele in blastocysts with an equal frequency of embryos having methylation errors following low or high hormone treatment. This disruption was not due to a failure of imprinted methylation acquisition at Mest in oocytes. For cultured embryos, both the Fast and Slow culture groups experienced a significant loss of maternal Mest methylation compared to in vivo-derived controls. This loss of methylation was independent of development rates in culture. These results indicate that Mest is more susceptible to imprinted methylation maintenance errors compared to other imprinted genes.
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Affiliation(s)
- Brenna A. M. Velker
- Department of Obstetrics & Gynecology, University of Western Ontario, Schulich School of Medicine and Dentistry, London, ON, Canada
- Department of Biochemistry, University of Western Ontario, Schulich School of Medicine and Dentistry, London, ON, Canada
- Children’s Health Research Institute, London, ON, Canada
| | - Michelle M. Denomme
- Department of Obstetrics & Gynecology, University of Western Ontario, Schulich School of Medicine and Dentistry, London, ON, Canada
- Department of Biochemistry, University of Western Ontario, Schulich School of Medicine and Dentistry, London, ON, Canada
- Children’s Health Research Institute, London, ON, Canada
- Fertility Laboratories Of Colorado, 10290 Ridgegate Circle, Lonetree, CO 80124 USA
| | - Robert T. Krafty
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Mellissa R. W. Mann
- Magee-Womens Research Institute, Pittsburgh, PA, USA
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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Singh VB, Sribenja S, Wilson KE, Attwood KM, Hillman JC, Pathak S, Higgins MJ. Blocked transcription through KvDMR1 results in absence of methylation and gene silencing resembling Beckwith-Wiedemann syndrome. Development 2017; 144:1820-1830. [PMID: 28428215 PMCID: PMC5450836 DOI: 10.1242/dev.145136] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 03/23/2017] [Indexed: 12/30/2022]
Abstract
The maternally methylated KvDMR1 ICR regulates imprinted expression of a cluster of maternally expressed genes on human chromosome 11p15.5. Disruption of imprinting leads to Beckwith-Wiedemann syndrome (BWS), an overgrowth and cancer predisposition condition. In the majority of individuals with BWS, maternal-specific methylation at KvDMR1 is absent and genes under its control are repressed. We analyzed a mouse model carrying a poly(A) truncation cassette inserted to prevent RNA transcripts from elongation through KvDMR1. Maternal inheritance of this mutation resulted in absence of DNA methylation at KvDMR1, which led to biallelic expression of Kcnq1ot1 and suppression of maternally expressed genes. This study provides further evidence that transcription is required for establishment of methylation at maternal gametic DMRs. More importantly, this mouse model recapitulates the molecular phenotypic characteristics of the most common form of BWS, including loss of methylation at KvDMR1 and biallelic repression of Cdkn1c, suggesting that deficiency of maternal transcription through KvDMR1 may be an underlying cause of some BWS cases.
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Affiliation(s)
- Vir B Singh
- Departments of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Sirinapa Sribenja
- Departments of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Kayla E Wilson
- Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Kristopher M Attwood
- Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Joanna C Hillman
- Departments of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Shilpa Pathak
- Departments of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Michael J Higgins
- Departments of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
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48
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Gahurova L, Tomizawa SI, Smallwood SA, Stewart-Morgan KR, Saadeh H, Kim J, Andrews SR, Chen T, Kelsey G. Transcription and chromatin determinants of de novo DNA methylation timing in oocytes. Epigenetics Chromatin 2017; 10:25. [PMID: 28507606 PMCID: PMC5429541 DOI: 10.1186/s13072-017-0133-5] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 05/02/2017] [Indexed: 12/30/2022] Open
Abstract
Background Gametogenesis in mammals entails profound re-patterning of the epigenome. In the female germline, DNA methylation is acquired late in oogenesis from an essentially unmethylated baseline and is established largely as a consequence of transcription events. Molecular and functional studies have shown that imprinted genes become methylated at different times during oocyte growth; however, little is known about the kinetics of methylation gain genome wide and the reasons for asynchrony in methylation at imprinted loci. Results Given the predominant role of transcription, we sought to investigate whether transcription timing is rate limiting for de novo methylation and determines the asynchrony of methylation events. Therefore, we generated genome-wide methylation and transcriptome maps of size-selected, growing oocytes to capture the onset and progression of methylation. We find that most sequence elements, including most classes of transposable elements, acquire methylation at similar rates overall. However, methylation of CpG islands (CGIs) is delayed compared with the genome average and there are reproducible differences amongst CGIs in onset of methylation. Although more highly transcribed genes acquire methylation earlier, the major transitions in the oocyte transcriptome occur well before the de novo methylation phase, indicating that transcription is generally not rate limiting in conferring permissiveness to DNA methylation. Instead, CGI methylation timing negatively correlates with enrichment for histone 3 lysine 4 (H3K4) methylation and dependence on the H3K4 demethylases KDM1A and KDM1B, implicating chromatin remodelling as a major determinant of methylation timing. We also identified differential enrichment of transcription factor binding motifs in CGIs acquiring methylation early or late in oocyte growth. By combining these parameters into multiple regression models, we were able to account for about a fifth of the variation in methylation timing of CGIs. Finally, we show that establishment of non-CpG methylation, which is prevalent in fully grown oocytes, and methylation over non-transcribed regions, are later events in oogenesis. Conclusions These results do not support a major role for transcriptional transitions in the time of onset of DNA methylation in the oocyte, but suggest a model in which sequences least dependent on chromatin remodelling are the earliest to become permissive for methylation. Electronic supplementary material The online version of this article (doi:10.1186/s13072-017-0133-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lenka Gahurova
- Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT UK.,Laboratory of Developmental Biology and Genetics, Department of Molecular Biology, University of South Bohemia, 37005 Ceske Budejovice, Czech Republic
| | - Shin-Ichi Tomizawa
- Department of Histology and Cell Biology, School of Medicine, Yokohama City University, Yokohama, 236-0004 Japan
| | - Sébastien A Smallwood
- Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT UK.,Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Kathleen R Stewart-Morgan
- Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT UK.,Biotech Research and Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark
| | - Heba Saadeh
- Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT UK.,Computer Science Department, KASIT, University of Jordan, Amman, Jordan
| | - Jeesun Kim
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Smithville, TX 77030 USA
| | - Simon R Andrews
- Bioinformatics Group, Babraham Institute, Cambridge, CB22 3AT UK
| | - Taiping Chen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Smithville, TX 77030 USA
| | - Gavin Kelsey
- Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT UK.,Centre for Trophoblast Research, University of Cambridge, Cambridge, CB2 3EG UK
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49
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Anckaert E, Fair T. DNA methylation reprogramming during oogenesis and interference by reproductive technologies: Studies in mouse and bovine models. Reprod Fertil Dev 2017; 27:739-54. [PMID: 25976160 DOI: 10.1071/rd14333] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 04/01/2015] [Indexed: 12/24/2022] Open
Abstract
The use of assisted reproductive technology (ART) to overcome fertility problems has continued to increase since the birth of the first baby conceived by ART over 30 years ago. Similarly, embryo transfer is widely used as a mechanism to advance genetic gain in livestock. Despite repeated optimisation of ART treatments, pre- and postnatal outcomes remain compromised. Epigenetic mechanisms play a fundamental role in successful gametogenesis and development. The best studied of these is DNA methylation; the appropriate establishment of DNA methylation patterns in gametes and early embryos is essential for healthy development. Superovulation studies in the mouse indicate that specific ARTs are associated with normal imprinting establishment in oocytes, but abnormal imprinting maintenance in embryos. A similar limited impact of ART on oocytes has been reported in cattle, whereas the majority of embryo-focused studies have used cloned embryos, which do exhibit aberrant DNA methylation. The present review discusses the impact of ART on oocyte and embryo DNA methylation with regard to data available from mouse and bovine models.
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Affiliation(s)
- Ellen Anckaert
- Follicle Biology Laboratory and Center for Reproductive Medicine, UZ Brussel, Vrije Universiteit Brussel, Laarbeeklaan 101, Brussels 1090, Belgium
| | - Trudee Fair
- School of Agriculture and Food Sciences, University College Dublin, Belfield, Dublin 4, Ireland
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50
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Xu GF, Liao Y, Li JY, Liu YF, Huang Y, Wu YQ, Liu J, Lv PP, Zhang RJ, Zhang D. Ovarian stimulation perturbs methylation status of placental imprinting genes and reduces blood pressure in the second generation offspring. Eur J Obstet Gynecol Reprod Biol 2017; 211:140-145. [PMID: 28259006 DOI: 10.1016/j.ejogrb.2017.02.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Revised: 02/03/2017] [Accepted: 02/17/2017] [Indexed: 10/20/2022]
Abstract
OBJECTIVE(S) Assisted reproductive technology (ART) is associated with DNA methylation dysfunction of offspring. However, it is unclear whether ovarian stimulation (OS) is responsible for DNA methylation dysfunction of offspring STUDY DESIGN: We built the first-generation (F1) and second-generation (F2) offspring mice model of ovarian stimulation. Bodyweight of F1 and F2 were measured. Expression levels of several imprinted genes (Impact, H19, Igf2, Plagl1, Mest, and Snrpn) in F1 placenta were tested. Methylation status of Plagl1 and H19 promoters was examined with bisulfite sequencing. Glucose tolerance, blood pressure, and heart rate were evaluated in F2 mice. RESULTS The OS F1 showed elevated bodyweights in the 2nd, 3rd and 4th weeks, but the difference disappeared in the 5th week. Plagl1 was down-regulated in OS F1. Promoters of Plagl1 and H19 were also hypermethylated in OS F1. F2 of OS mice had the similar bodyweight and glucose tolerance compared with the control F2. However, F2 of OS ♂F1+OS♀ F1 showed the decreased systolic pressure, diastolic pressure, and heart rate. CONCLUSIONS Ovarian stimulation perturbs expression levels and methylation status of imprinted genes in offspring. The effect of ovarian stimulation may be passed to F2.
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Affiliation(s)
- Gu-Feng Xu
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, China
| | - Yun Liao
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jing-Yi Li
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, China
| | - Yi-Feng Liu
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, China
| | - Yun Huang
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, China
| | - Yi-Qing Wu
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Juan Liu
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, China
| | - Ping-Ping Lv
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, China
| | - Run-Jv Zhang
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, China
| | - Dan Zhang
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, China.
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