51
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He QL, Zhang L, Liu SZ. Effects of Polychlorinated Biphenyls on Animal Reproductive Systems and Epigenetic Modifications. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2021; 107:398-405. [PMID: 34110444 DOI: 10.1007/s00128-021-03285-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 06/03/2021] [Indexed: 06/12/2023]
Abstract
Polychlorinated biphenyls (PCBs) are a group of highly toxic endocrine-disrupting chemicals comprising 209 homologs. PCBs are extensively found in the environment and can induce typical estrogenic and profound, long-lasting effects on animals. In this article, the introduction of PCB residues into the environment and the pathways of PCB enrichment in animals are described. PCBs are widely deposited and eventually accumulate in human tissues and body fluids through biomagnification. PCBs can significantly decrease animal fertility and interfere with endocrine processes, leading to the development of various diseases and even cancer. The effects of PCBs on the reproductive systems of animals can also be passed to their offspring, indicating that PCBs may affect the epigenetic modification process. There is currently no treatment to effectively inhibit the toxicity of PCBs in organisms; therefore, the severity of PCB toxicity needs to be widely recognized.
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Affiliation(s)
- Qi-Long He
- Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, 250014, China
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing, 100191, China
| | - Lin Zhang
- Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Shu-Zhen Liu
- Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, 250014, China.
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52
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St John JC. Epigenetic Regulation of the Nuclear and Mitochondrial Genomes: Involvement in Metabolism, Development, and Disease. Annu Rev Anim Biosci 2021; 9:203-224. [PMID: 33592161 DOI: 10.1146/annurev-animal-080520-083353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Our understanding of the interactions between the nuclear and mitochondrial genomes is becoming increasingly important as they are extensively involved in establishing early development and developmental progression. Evidence from various biological systems indicates the interdependency between the genomes, which requires a high degree of compatibility and synchrony to ensure effective cellular function throughout development and in the resultant offspring. During development, waves of DNA demethylation, de novo methylation, and maintenance methylation act on the nuclear genome and typify oogenesis and pre- and postimplantation development. At the same time, significant changes in mitochondrial DNA copy number influence the metabolic status of the developing organism in a typically cell-type-specific manner. Collectively, at any given stage in development, these actions establish genomic balance that ensures each developmental milestone is met and that the organism's program for life is established.
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Affiliation(s)
- Justin C St John
- Mitochondrial Genetics Group, Robinson Research Institute and School of Medicine, University of Adelaide, Adelaide, South Australia 5005, Australia;
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53
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Anvar Z, Chakchouk I, Demond H, Sharif M, Kelsey G, Van den Veyver IB. DNA Methylation Dynamics in the Female Germline and Maternal-Effect Mutations That Disrupt Genomic Imprinting. Genes (Basel) 2021; 12:genes12081214. [PMID: 34440388 PMCID: PMC8394515 DOI: 10.3390/genes12081214] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 11/16/2022] Open
Abstract
Genomic imprinting is an epigenetic marking process that results in the monoallelic expression of a subset of genes. Many of these ‘imprinted’ genes in mice and humans are involved in embryonic and extraembryonic growth and development, and some have life-long impacts on metabolism. During mammalian development, the genome undergoes waves of (re)programming of DNA methylation and other epigenetic marks. Disturbances in these events can cause imprinting disorders and compromise development. Multi-locus imprinting disturbance (MLID) is a condition by which imprinting defects touch more than one locus. Although most cases with MLID present with clinical features characteristic of one imprinting disorder. Imprinting defects also occur in ‘molar’ pregnancies-which are characterized by highly compromised embryonic development-and in other forms of reproductive compromise presenting clinically as infertility or early pregnancy loss. Pathogenic variants in some of the genes encoding proteins of the subcortical maternal complex (SCMC), a multi-protein complex in the mammalian oocyte, are responsible for a rare subgroup of moles, biparental complete hydatidiform mole (BiCHM), and other adverse reproductive outcomes which have been associated with altered imprinting status of the oocyte, embryo and/or placenta. The finding that defects in a cytoplasmic protein complex could have severe impacts on genomic methylation at critical times in gamete or early embryo development has wider implications beyond these relatively rare disorders. It signifies a potential for adverse maternal physiology, nutrition, or assisted reproduction to cause epigenetic defects at imprinted or other genes. Here, we review key milestones in DNA methylation patterning in the female germline and the embryo focusing on humans. We provide an overview of recent findings regarding DNA methylation deficits causing BiCHM, MLID, and early embryonic arrest. We also summarize identified SCMC mutations with regard to early embryonic arrest, BiCHM, and MLID.
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Affiliation(s)
- Zahra Anvar
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX 77030, USA; (Z.A.); (I.C.); (M.S.)
- Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Imen Chakchouk
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX 77030, USA; (Z.A.); (I.C.); (M.S.)
- Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Hannah Demond
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK;
| | - Momal Sharif
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX 77030, USA; (Z.A.); (I.C.); (M.S.)
- Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Gavin Kelsey
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK;
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK
- Correspondence: (G.K.); (I.B.V.d.V.); Tel.: +44-1223-496332 (G.K.); +832-824-8125 (I.B.V.d.V.)
| | - Ignatia B. Van den Veyver
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX 77030, USA; (Z.A.); (I.C.); (M.S.)
- Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Correspondence: (G.K.); (I.B.V.d.V.); Tel.: +44-1223-496332 (G.K.); +832-824-8125 (I.B.V.d.V.)
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54
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Pasquesi GIM, Perry BW, Vandewege MW, Ruggiero RP, Schield DR, Castoe TA. Vertebrate Lineages Exhibit Diverse Patterns of Transposable Element Regulation and Expression across Tissues. Genome Biol Evol 2021; 12:506-521. [PMID: 32271917 PMCID: PMC7211425 DOI: 10.1093/gbe/evaa068] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/02/2020] [Indexed: 12/11/2022] Open
Abstract
Transposable elements (TEs) comprise a major fraction of vertebrate genomes, yet little is known about their expression and regulation across tissues, and how this varies across major vertebrate lineages. We present the first comparative analysis integrating TE expression and TE regulatory pathway activity in somatic and gametic tissues for a diverse set of 12 vertebrates. We conduct simultaneous gene and TE expression analyses to characterize patterns of TE expression and TE regulation across vertebrates and examine relationships between these features. We find remarkable variation in the expression of genes involved in TE negative regulation across tissues and species, yet consistently high expression in germline tissues, particularly in testes. Most vertebrates show comparably high levels of TE regulatory pathway activity across gonadal tissues except for mammals, where reduced activity of TE regulatory pathways in ovarian tissues may be the result of lower relative germ cell densities. We also find that all vertebrate lineages examined exhibit remarkably high levels of TE-derived transcripts in somatic and gametic tissues, with recently active TE families showing higher expression in gametic tissues. Although most TE-derived transcripts originate from inactive ancient TE families (and are likely incapable of transposition), such high levels of TE-derived RNA in the cytoplasm may have secondary, unappreciated biological relevance.
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Affiliation(s)
- Giulia I M Pasquesi
- Department of Biology, University of Texas at Arlington.,Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder
| | - Blair W Perry
- Department of Biology, University of Texas at Arlington
| | | | | | - Drew R Schield
- Department of Biology, University of Texas at Arlington.,Department of Ecology and Evolutionary Biology, University of Colorado, Boulder
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington
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55
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Hitchler MJ, Domann FE. The epigenetic and morphogenetic effects of molecular oxygen and its derived reactive species in development. Free Radic Biol Med 2021; 170:70-84. [PMID: 33450377 PMCID: PMC8217084 DOI: 10.1016/j.freeradbiomed.2021.01.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 01/04/2021] [Accepted: 01/05/2021] [Indexed: 12/11/2022]
Abstract
The development of multicellular organisms involves the unpacking of a complex genetic program. Extensive characterization of discrete developmental steps has revealed the genetic program is controlled by an epigenetic state. Shifting the epigenome is a group of epigenetic enzymes that modify DNA and proteins to regulate cell type specific gene expression. While the role of these modifications in development has been established, the input(s) responsible for electing changes in the epigenetic state remains unknown. Development is also associated with dynamic changes in cellular metabolism, redox, free radical production, and oxygen availability. It has previously been postulated that these changes are causal in development by affecting gene expression. This suggests that oxygen is a morphogenic compound that impacts the removal of epigenetic marks. Likewise, metabolism and reactive oxygen species influence redox signaling through iron and glutathione to limit the availability of key epigenetic cofactors such as α-ketoglutarate, ascorbate, NAD+ and S-adenosylmethionine. Given the close relationship between these cofactors and epigenetic marks it seems likely that the two are linked. Here we describe how changing these inputs might affect the epigenetic state during development to drive gene expression. Combined, these cofactors and reactive oxygen species constitute the epigenetic landscape guiding cells along differing developmental paths.
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Affiliation(s)
- Michael J Hitchler
- Department of Radiation Oncology, Kaiser Permanente Los Angeles Medical Center, 4950 Sunset Blvd, Los Angeles, CA, 90027, USA.
| | - Frederick E Domann
- Department of Radiation Oncology, Free Radical and Radiation Biology Program, University of Iowa, Iowa City, IA, 52242, USA.
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56
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Özbek M, Hitit M, Kaya A, Jousan FD, Memili E. Sperm Functional Genome Associated With Bull Fertility. Front Vet Sci 2021; 8:610888. [PMID: 34250055 PMCID: PMC8262648 DOI: 10.3389/fvets.2021.610888] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 05/05/2021] [Indexed: 01/08/2023] Open
Abstract
Bull fertility is an important economic trait in sustainable cattle production, as infertile or subfertile bulls give rise to large economic losses. Current methods to assess bull fertility are tedious and not totally accurate. The massive collection of functional data analyses, including genomics, proteomics, metabolomics, transcriptomics, and epigenomics, helps researchers generate extensive knowledge to better understand the unraveling physiological mechanisms underlying subpar male fertility. This review focuses on the sperm phenomes of the functional genome and epigenome that are associated with bull fertility. Findings from multiple sources were integrated to generate new knowledge that is transferable to applied andrology. Diverse methods encompassing analyses of molecular and cellular dynamics in the fertility-associated molecules and conventional sperm parameters can be considered an effective approach to determine bull fertility for efficient and sustainable cattle production. In addition to gene expression information, we also provide methodological information, which is important for the rigor and reliability of the studies. Fertility is a complex trait influenced by several factors and has low heritability, although heritability of scrotal circumference is high and that it is a known fertility maker. There is a need for new knowledge on the expression levels and functions of sperm RNA, proteins, and metabolites. The new knowledge can shed light on additional fertility markers that can be used in combination with scrotal circumference to predict the fertility of breeding bulls. This review provides a comprehensive review of sperm functional characteristics or phenotypes associated with bull fertility.
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Affiliation(s)
- Memmet Özbek
- Department of Histology and Embryology, Faculty of Veterinary Medicine, Burdur Mehmet Akif Ersoy University, Burdur, Turkey
| | - Mustafa Hitit
- Department of Genetics, Faculty of Veterinary Medicine, Kastamonu University, Kastamonu, Turkey
| | - Abdullah Kaya
- Department of Artificial Insemination and Reproduction, Faculty of Veterinary Medicine, Selcuk University, Konya, Turkey
| | - Frank Dean Jousan
- Department of Animal and Dairy Sciences, Mississippi State University, Starkville, MS, United States
| | - Erdogan Memili
- Department of Animal and Dairy Sciences, Mississippi State University, Starkville, MS, United States
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57
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Sasaki K, Takaoka S, Obata Y. Oocyte-specific gene knockdown by intronic artificial microRNAs driven by Zp3 transcription in mice. J Reprod Dev 2021; 67:229-234. [PMID: 33716236 PMCID: PMC8238676 DOI: 10.1262/jrd.2020-146] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Conditional knockout technology is a powerful tool for investigating the spatiotemporal functions of target genes. However, generation of conditional knockout
mice involves complicated breeding programs and considerable time. A recent study has shown that artificially designed microRNAs (amiRNAs), inserted into an
intron of the constitutively expressed gene, induce knockdown of the targeted gene in mice, thus creating a simpler method to analyze the functions of target
genes in oocytes. Here, to establish an oocyte-specific knockdown system, amiRNA sequences against enhanced green fluorescent protein (EGFP) were knocked into
the intronic sites of the Zp3 gene. Knock-in mice were then bred with EGFP transgenic mice. Our results showed that
Zp3-derived amiRNA successfully reduced EGFP fluorescence in the oocytes in a size-dependent manner. Importantly, knockdown of EGFP did not
occur in somatic cells. Thus, we present our knockdown system as a tool for screening gene functions in mouse oocytes.
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Affiliation(s)
- Keisuke Sasaki
- Department of Bioscience, Tokyo University of Agriculture, Tokyo 156-8502, Japan.,Research Fellow of Japan Society for the Promotion of Science, Tokyo 102-0083, Japan
| | - Saaya Takaoka
- Department of Bioscience, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Yayoi Obata
- Department of Bioscience, Tokyo University of Agriculture, Tokyo 156-8502, Japan
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58
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LncRNAs induce oxidative stress and spermatogenesis by regulating endoplasmic reticulum genes and pathways. Aging (Albany NY) 2021; 13:13764-13787. [PMID: 34001678 PMCID: PMC8202879 DOI: 10.18632/aging.202971] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 11/08/2020] [Indexed: 12/17/2022]
Abstract
Oligozoospermia or low sperm count is a leading cause of male infertility worldwide. Despite decades of work on non-coding RNAs (ncRNAs) as regulators of spermatogenesis, fertilization, and male fertility, the literature on the function of long non-coding RNAs (lncRNAs) in human oligozoospermia is scarce. We integrated lncRNA and mRNA sequencing data from 12 human normozoospermic and oligozoospermic samples and comprehensively analyzed the function of differentially expressed lncRNAs (DE lncRNAs) and mRNAs (DE mRNAs) in male infertility. The target genes of DE lncRNAs were identified using a Gaussian graphical model. Gene ontology terms and Kyoto Encyclopedia of Genes and Genomes pathways were primarily enriched in protein transport and localization to the endoplasmic reticulum (ER). The lncRNA–mRNA co-expression network revealed cis- and trans-regulated target genes of lncRNAs. The transcriptome data implicated DE lncRNAs and DE mRNAs and their target genes in the accumulation of unfolded proteins in sperm ER, PERK-EIF2 pathway-induced ER stress, oxidative stress, and sperm cell apoptosis in individuals with oligozoospermia. These findings suggest that the identified lncRNAs and pathways could serve as effective therapeutic targets for male infertility.
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59
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Environmental pollutants exposure and male reproductive toxicity: The role of epigenetic modifications. Toxicology 2021; 456:152780. [PMID: 33862174 DOI: 10.1016/j.tox.2021.152780] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 03/20/2021] [Accepted: 04/08/2021] [Indexed: 02/07/2023]
Abstract
Male fertility rates have shown a progressive decrease in recent decades. There is a growing concern about the male reproductive dysfunction caused by environmental pollutants exposure, however the underlying molecular mechanisms are still not well understood. Epigenetic modifications play a key role in the biological responses to external stressors. Therefore, this review discusses the roles of epigenetic modifications in male reproductive toxicity induced by environmental pollutants, with a particular emphasis on DNA methylation, histone modifications and miRNAs. The available literature proposed that environmental pollutants can directly or cause oxidative stress and DNA damage to induce a variety of epigenetic changes, which lead to gene dysregulation, mitochondrial dysfunction and consequent male reproductive toxicity. However, future studies focusing on more kinds of epigenetic modifications and their crosstalk as well as epidemiological data are still required to fill in the current research gaps. In addition, the intrinsic links between pollutants-mediated epigenetic regulations and male reproduction-related physiological responses deserve to be further explored.
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60
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The regulation mechanisms and the Lamarckian inheritance property of DNA methylation in animals. Mamm Genome 2021; 32:135-152. [PMID: 33860357 DOI: 10.1007/s00335-021-09870-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 04/05/2021] [Indexed: 12/19/2022]
Abstract
DNA methylation is a stable and heritable epigenetic mechanism, of which the main functions are stabilizing the transcription of genes and promoting genetic conservation. In animals, the direct molecular inducers of DNA methylation mainly include histone covalent modification and non-coding RNA, whereas the fundamental regulators of DNA methylation are genetic and environmental factors. As is well known, competition is present everywhere in life systems, and will finally strike a balance that is optimal for the animal's survival and reproduction. The same goes for the regulation of DNA methylation. Genetic and environmental factors, respectively, are responsible for the programmed and plasticity changes of DNA methylation, and keen competition exists between genetically influenced procedural remodeling and environmentally influenced plastic alteration. In this process, genetic and environmental factors collaboratively decide the methylation patterns of corresponding loci. DNA methylation alterations induced by environmental factors can be transgenerationally inherited, and exhibit the characteristic of Lamarckian inheritance. Further research on regulatory mechanisms and the environmental plasticity of DNA methylation will provide strong support for understanding the biological function and evolutionary effects of DNA methylation.
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61
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Arora I, Tollefsbol TO. Computational methods and next-generation sequencing approaches to analyze epigenetics data: Profiling of methods and applications. Methods 2021; 187:92-103. [PMID: 32941995 PMCID: PMC7914156 DOI: 10.1016/j.ymeth.2020.09.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/08/2020] [Accepted: 09/10/2020] [Indexed: 12/20/2022] Open
Abstract
Epigenetics is mainly comprised of features that regulate genomic interactions thereby playing a crucial role in a vast array of biological processes. Epigenetic mechanisms such as DNA methylation and histone modifications influence gene expression by modulating the packaging of DNA in the nucleus. A plethora of studies have emphasized the importance of analyzing epigenetics data through genome-wide studies and high-throughput approaches, thereby providing key insights towards epigenetics-based diseases such as cancer. Recent advancements have been made towards translating epigenetics research into a high throughput approach such as genome-scale profiling. Amongst all, bioinformatics plays a pivotal role in achieving epigenetics-related computational studies. Despite significant advancements towards epigenomic profiling, it is challenging to understand how various epigenetic modifications such as chromatin modifications and DNA methylation regulate gene expression. Next-generation sequencing (NGS) provides accurate and parallel sequencing thereby allowing researchers to comprehend epigenomic profiling. In this review, we summarize different computational methods such as machine learning and other bioinformatics tools, publicly available databases and resources to identify key modifications associated with epigenetic machinery. Additionally, the review also focuses on understanding recent methodologies related to epigenome profiling using NGS methods ranging from library preparation, different sequencing platforms and analytical techniques to evaluate various epigenetic modifications such as DNA methylation and histone modifications. We also provide detailed information on bioinformatics tools and computational strategies responsible for analyzing large scale data in epigenetics.
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Affiliation(s)
- Itika Arora
- Department of Biology, University of Alabama at Birmingham, 1300 University Boulevard, Birmingham, AL 35294, USA.
| | - Trygve O Tollefsbol
- Department of Biology, University of Alabama at Birmingham, 1300 University Boulevard, Birmingham, AL 35294, USA; Comprehensive Center for Healthy Aging, University of Alabama Birmingham, 1530 3rd Avenue South, Birmingham, AL 35294, USA; Comprehensive Cancer Center, University of Alabama Birmingham, 1802 6th Avenue South, Birmingham, AL 35294, USA; Nutrition Obesity Research Center, University of Alabama Birmingham, 1675 University Boulevard, Birmingham, AL 35294, USA; Comprehensive Diabetes Center, University of Alabama Birmingham, 1825 University Boulevard, Birmingham, AL 35294, USA.
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62
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Wu X, Lu M, Yun D, Gao S, Chen S, Hu L, Wu Y, Wang X, Duan E, Cheng CY, Sun F. Single cell ATAC-Seq reveals cell type-specific transcriptional regulation and unique chromatin accessibility in human spermatogenesis. Hum Mol Genet 2021; 31:321-333. [PMID: 33438010 DOI: 10.1093/hmg/ddab006] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/25/2020] [Accepted: 01/04/2021] [Indexed: 11/13/2022] Open
Abstract
During human spermatogenesis, germ cells undergo dynamic changes in chromatin organization/re-packaging and in transcriptomes. In order to better understand the underlying mechanism(s), scATAC-Seq of 5376 testicular cells from 3 normal men were performed. Data were analyzed in parallel with the scRNA-Seq data of human testicular cells. Ten germ cell types associated with spermatogenesis and 6 testicular somatic cell types were identified, along with 142 024 peaks located in promoter, genebody and CpG Island. We had examined chromatin accessibility of all chromosomes, with chromosomes 19 and 17 emerged as the leading chromosomes that displayed high chromatin accessibility. In accessible chromatin regions, transcription factor (TF)-binding sites were identified and specific motifs with high frequencies at different spermatogenesis stages were detected, including CTCF, BORIS, NFY, DMRT6, EN1, ISL1 and GLI3. Two most notable observations were noted. First, TLE3 was specifically expressed in differentiating spermatogonia. Second, PFN4 was found to be involved in actin cytoskeletal organization during meiosis. More important, unique regions upstream of PFN4 and TLE3 were shown to display high accessibility, illustrating their significance in supporting human spermatogenesis.
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Affiliation(s)
- Xiaolong Wu
- Medical School, Institute of Reproductive Medicine, Nantong University, Nantong 226001, Jiangsu, China
| | - Mujun Lu
- International Peace Maternity and Child Health Hospital, Shanghai Key Laboratory for Reproductive Medicine, School of Medicine, Shanghai Jiaotong University, Shanghai 200030, China
| | - Damin Yun
- Medical School, Institute of Reproductive Medicine, Nantong University, Nantong 226001, Jiangsu, China
| | - Sheng Gao
- Medical School, Institute of Reproductive Medicine, Nantong University, Nantong 226001, Jiangsu, China
| | - Shitao Chen
- Department of Urology and Andrology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200001, China
| | - Longfei Hu
- Singleron Biotechnologies Ltd., 211 Pubin Road, Nanjing, Jiangsu, China
| | - Yunhao Wu
- Medical School, Institute of Reproductive Medicine, Nantong University, Nantong 226001, Jiangsu, China
| | - Xiaorong Wang
- Medical School, Institute of Reproductive Medicine, Nantong University, Nantong 226001, Jiangsu, China
| | - Enkui Duan
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - C Yan Cheng
- The Mary M. Wohlford Laboratory for Male Contraceptive Research, Center for Biomedical Research, Population Council, 1230 York Ave, New York, NY 10065
| | - Fei Sun
- Medical School, Institute of Reproductive Medicine, Nantong University, Nantong 226001, Jiangsu, China
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63
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Xia W, Xie W. Rebooting the Epigenomes during Mammalian Early Embryogenesis. Stem Cell Reports 2020; 15:1158-1175. [PMID: 33035464 PMCID: PMC7724468 DOI: 10.1016/j.stemcr.2020.09.005] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 09/10/2020] [Accepted: 09/11/2020] [Indexed: 02/08/2023] Open
Abstract
Upon fertilization, terminally differentiated gametes are transformed to a totipotent zygote, which gives rise to an embryo. How parental epigenetic memories are inherited and reprogrammed to accommodate parental-to-zygotic transition remains a fundamental question in developmental biology, epigenetics, and stem cell biology. With the rapid advancement of ultra-sensitive or single-cell epigenome analysis methods, unusual principles of epigenetic reprogramming begin to be unveiled. Emerging data reveal that in many species, the parental epigenome undergoes dramatic reprogramming followed by subsequent re-establishment of the embryo epigenome, leading to epigenetic "rebooting." Here, we discuss recent progress in understanding epigenetic reprogramming and their functions during mammalian early development. We also highlight the conserved and species-specific principles underlying diverse regulation of the epigenome in early embryos during evolution.
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Affiliation(s)
- Weikun Xia
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China.
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64
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The methylation status in GNAS clusters May Be an epigenetic marker for oocyte quality. Biochem Biophys Res Commun 2020; 533:586-591. [PMID: 32980117 DOI: 10.1016/j.bbrc.2020.09.055] [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: 09/04/2020] [Accepted: 09/15/2020] [Indexed: 11/20/2022]
Abstract
During follicle growth, DNA methylation is gradually established, which is important for oocyte developmental competence. Due to the facts that oocytes from prepubertal individuals show reduced developmental outcomes when compared to those from sexually mature individuals, and the fact that oocytes derived from in vitro follicle culture have much lower developmental competence, it is worth exploring whether prepubertal superovulation and in vitro follicle culture will cause changes in DNA methylation imprinting status in oocytes. In this study, we found that the CpG island in maternally imprinted GNAS clusters was hypermethylated in the MII-stage oocytes from sexually mature mice, but was hypomethylated in oocytes from prepuberty individuals. The GNAS clusters in the MII-stage oocytes obtained by in vitro follicle culture showed heterogeneous methylation levels, indicating different qualities of oocytes, however, three other maternally imprinted genes, Peg1, Lot1 and Impact, were all hypermethylated in the MII-stage oocytes derived from both prepubertal superovulation and in vitro follicle culture. Taken together, the findings suggest that the methylation status in GNAS clusters may potentially represent a novel epigenetic marker for oocyte quality detection.
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65
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Singh PB, Belyakin SN, Laktionov PP. Biology and Physics of Heterochromatin- Like Domains/Complexes. Cells 2020; 9:E1881. [PMID: 32796726 PMCID: PMC7465696 DOI: 10.3390/cells9081881] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 07/29/2020] [Accepted: 08/04/2020] [Indexed: 11/17/2022] Open
Abstract
The hallmarks of constitutive heterochromatin, HP1 and H3K9me2/3, assemble heterochromatin-like domains/complexes outside canonical constitutively heterochromatic territories where they regulate chromatin template-dependent processes. Domains are more than 100 kb in size; complexes less than 100 kb. They are present in the genomes of organisms ranging from fission yeast to human, with an expansion in size and number in mammals. Some of the likely functions of domains/complexes include silencing of the donor mating type region in fission yeast, preservation of DNA methylation at imprinted germline differentially methylated regions (gDMRs) and regulation of the phylotypic progression during vertebrate development. Far cis- and trans-contacts between micro-phase separated domains/complexes in mammalian nuclei contribute to the emergence of epigenetic compartmental domains (ECDs) detected in Hi-C maps. A thermodynamic description of micro-phase separation of heterochromatin-like domains/complexes may require a gestalt shift away from the monomer as the "unit of incompatibility" that determines the sign and magnitude of the Flory-Huggins parameter, χ. Instead, a more dynamic structure, the oligo-nucleosomal "clutch", consisting of between 2 and 10 nucleosomes is both the long sought-after secondary structure of chromatin and its unit of incompatibility. Based on this assumption we present a simple theoretical framework that enables an estimation of χ for domains/complexes flanked by euchromatin and thereby an indication of their tendency to phase separate. The degree of phase separation is specified by χN, where N is the number of "clutches" in a domain/complex. Our approach could provide an additional tool for understanding the biophysics of the 3D genome.
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Affiliation(s)
- Prim B. Singh
- Nazarbayev University School of Medicine, Nur-Sultan City 010000, Kazakhstan
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
| | - Stepan N. Belyakin
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
- Genomics laboratory, Institute of molecular and cellular biology SD RAS, Lavrentyev ave, 8/2, 630090 Novosibirsk, Russia; (S.N.B.); (P.P.L.)
| | - Petr P. Laktionov
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
- Genomics laboratory, Institute of molecular and cellular biology SD RAS, Lavrentyev ave, 8/2, 630090 Novosibirsk, Russia; (S.N.B.); (P.P.L.)
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66
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Abstract
Genomic imprinting is a parent-of-origin dependent phenomenon that restricts transcription to predominantly one parental allele. Since the discovery of the first long noncoding RNA (lncRNA), which notably was an imprinted lncRNA, a body of knowledge has demonstrated pivotal roles for imprinted lncRNAs in regulating parental-specific expression of neighboring imprinted genes. In this Review, we will discuss the multiple functionalities attributed to lncRNAs and how they regulate imprinted gene expression. We also raise unresolved questions about imprinted lncRNA function, which may lead to new avenues of investigation. This Review is dedicated to the memory of Denise Barlow, a giant in the field of genomic imprinting and functional lncRNAs. With her passion for understanding the inner workings of science, her indominable spirit and her consummate curiosity, Denise blazed a path of scientific investigation that made many seminal contributions to genomic imprinting and the wider field of epigenetic regulation, in addition to inspiring future generations of scientists.
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Affiliation(s)
- William A. MacDonald
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Rangos Research Center, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Mellissa R. W. Mann
- Department of Obstetrics, Gynaecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Magee-Womens Research Institute, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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67
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Abstract
Mammalian fertilization begins with the fusion of two specialized gametes, followed by major epigenetic remodeling leading to the formation of a totipotent embryo. During the development of the pre-implantation embryo, precise reprogramming progress is a prerequisite for avoiding developmental defects or embryonic lethality, but the underlying molecular mechanisms remain elusive. For the past few years, unprecedented breakthroughs have been made in mapping the regulatory network of dynamic epigenomes during mammalian early embryo development, taking advantage of multiple advances and innovations in low-input genome-wide chromatin analysis technologies. The aim of this review is to highlight the most recent progress in understanding the mechanisms of epigenetic remodeling during early embryogenesis in mammals, including DNA methylation, histone modifications, chromatin accessibility and 3D chromatin organization.
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68
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Global changes in epigenomes during mouse spermatogenesis: possible relation to germ cell apoptosis. Histochem Cell Biol 2020; 154:123-134. [PMID: 32653936 DOI: 10.1007/s00418-020-01900-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2020] [Indexed: 12/11/2022]
Abstract
Mammalian spermatogenesis is characterized by disproportionate germ cell apoptosis. The high frequency of apoptosis is considered a safety mechanism that serves to avoid unfavorable transmission of paternal aberrant genetic information to the offspring as well as elimination mechanism for removal of overproduced immature or damaged spermatogenic cells. The molecular mechanisms involved in the induction of germ cell apoptosis include both intrinsic mitochondrial Bcl-2/Bax and extrinsic Fas/FasL pathways. However, little is known about the nuclear trigger of those systems. Recent studies indicate that epigenomes are essential in the regulation of gene expression through remodeling of the chromatin structure, and are genome-like transmission materials that reflect the effects of various environmental factors. In spermatogenesis, epigenetic errors can act as the trigger for elimination of germ cells with abnormal chromatin structure, abnormal gene expression and/or morphological defects (disordered differentiation). In this review, we focus on the relationship between global changes in epigenetic parameters and germ cell apoptosis in mice and other mammals.
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69
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Huo Y, Yan ZQ, Yuan P, Qin M, Kuo Y, Li R, Yan LY, Feng HL, Qiao J. Single-cell DNA methylation sequencing reveals epigenetic alterations in mouse oocytes superovulated with different dosages of gonadotropins. Clin Epigenetics 2020; 12:75. [PMID: 32487258 PMCID: PMC7268365 DOI: 10.1186/s13148-020-00866-w] [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: 12/21/2019] [Accepted: 05/19/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Epigenetic abnormalities caused by superovulation have recently attracted increasing attention. Superovulation with exogenous hormones may prevent oocytes from establishing an appropriate epigenetic state, and this effect may extend to the methylation programming in preimplantation embryos, as de novo DNA methylation is a function of developmental stage of follicles and oocyte size. Follicle-stimulating hormone (FSH) and human menopausal gonadotropin (hMG) are common gonadotropins used for superovulation, and appropriate concentrations of these gonadotropins might be necessary. However, no systematic study on the effects of DNA methylation alterations in oocytes associated with superovulation with different dosages of FSH/hMG at the single-cell level has yet been reported. In the current study, different dosages of FSH/hMG combined with human chorionic gonadotropin (hCG) were used in female mice to generate experimental groups, while naturally matured oocytes and oocytes superovulated with only hCG were respectively used as controls. Single-cell level DNA methylation sequencing was carried out on all these matured oocytes. RESULTS In this study, we revealed that the genome-wide methylation pattern and CG methylation level of the maternal imprinting control regions of all mature oocytes were globally conserved and stable. However, methylation alterations associated with superovulation were found at a specific set of loci, and the differentially methylated regions (DMRs) mainly occurred in regions other than promoters. Furthermore, some of the annotated genes in the DMRs were involved in biological processes such as glucose metabolism, nervous system development, cell cycle, cell proliferation, and embryo implantation and were altered in all dosages of FSH/hMG group (for example, Gfod2 and SYF2). Other genes were impaired only after high gonadotropin dosages (for instance, Sox17 and Phactr4). CONCLUSIONS In conclusion, the current study addressed the effects of superovulation on DNA methylation from the perspective of different dosages of gonadotropins at the single-cell level. We found that the genome-wide DNA methylation landscape was globally preserved irrespective of superovulation or of the kind and dosage of gonadotropins used, whereas the methylation alterations associated with superovulation occurred at a specific set of loci. These observed effects reflect that superovulation recruits oocytes that would not normally be ovulated or that have not undergone complete epigenetic maturation. Our results provide an important reference for the safety assessment of superovulation with different dosages of gonadotropins. However, it should be noted that this study has some limitations, as the sample number and library coverage of analyzed oocytes were relatively low. Future studies with larger sample sizes and high-coverage libraries that examine the effects of superovulation on embryo development and offspring health as well as the underlying mechanisms are still needed.
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Affiliation(s)
- Ying Huo
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49 North HuaYuan Road, Hai Dian District, Beijing, 100191, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, No. 49 North HuaYuan Road, Hai Dian District, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, No. 49 North HuaYuan Road, Hai Dian District, Beijing, 100191, China.,Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, No. 38 XueYuan Road, Haidian District, Beijing, 100191, China
| | - Zhi Qiang Yan
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49 North HuaYuan Road, Hai Dian District, Beijing, 100191, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, No. 49 North HuaYuan Road, Hai Dian District, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, No. 49 North HuaYuan Road, Hai Dian District, Beijing, 100191, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Peng Yuan
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49 North HuaYuan Road, Hai Dian District, Beijing, 100191, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, No. 49 North HuaYuan Road, Hai Dian District, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, No. 49 North HuaYuan Road, Hai Dian District, Beijing, 100191, China
| | - Meng Qin
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49 North HuaYuan Road, Hai Dian District, Beijing, 100191, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, No. 49 North HuaYuan Road, Hai Dian District, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, No. 49 North HuaYuan Road, Hai Dian District, Beijing, 100191, China
| | - Ying Kuo
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49 North HuaYuan Road, Hai Dian District, Beijing, 100191, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, No. 49 North HuaYuan Road, Hai Dian District, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, No. 49 North HuaYuan Road, Hai Dian District, Beijing, 100191, China
| | - Rong Li
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49 North HuaYuan Road, Hai Dian District, Beijing, 100191, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, No. 49 North HuaYuan Road, Hai Dian District, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, No. 49 North HuaYuan Road, Hai Dian District, Beijing, 100191, China.,National Clinical Research Center of Obstetrics and Gynecology, No. 49 North HuaYuan Road, Hai Dian District, Beijing, 100191, China
| | - Li Ying Yan
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49 North HuaYuan Road, Hai Dian District, Beijing, 100191, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, No. 49 North HuaYuan Road, Hai Dian District, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, No. 49 North HuaYuan Road, Hai Dian District, Beijing, 100191, China.,National Clinical Research Center of Obstetrics and Gynecology, No. 49 North HuaYuan Road, Hai Dian District, Beijing, 100191, China
| | - Huai Liang Feng
- The New York Fertility Center, New York Hospital Queens, Weill Medical College of Cornell University, New York, NY, USA.
| | - Jie Qiao
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49 North HuaYuan Road, Hai Dian District, Beijing, 100191, China. .,Key Laboratory of Assisted Reproduction, Ministry of Education, No. 49 North HuaYuan Road, Hai Dian District, Beijing, 100191, China. .,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, No. 49 North HuaYuan Road, Hai Dian District, Beijing, 100191, China. .,Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, No. 38 XueYuan Road, Haidian District, Beijing, 100191, China. .,National Clinical Research Center of Obstetrics and Gynecology, No. 49 North HuaYuan Road, Hai Dian District, Beijing, 100191, China.
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70
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Bina M. Discovering candidate imprinted genes and imprinting control regions in the human genome. BMC Genomics 2020; 21:378. [PMID: 32475352 PMCID: PMC7262774 DOI: 10.1186/s12864-020-6688-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 03/18/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Genomic imprinting is a process thereby a subset of genes is expressed in a parent-of-origin specific manner. This evolutionary novelty is restricted to mammals and controlled by genomic DNA segments known as Imprinting Control Regions (ICRs) and germline Differentially Methylated Regions (gDMRs). Previously, I showed that in the mouse genome, the fully characterized ICRs/gDMRs often includes clusters of 2 or more of a set of composite-DNA-elements known as ZFBS-morph overlaps. RESULTS Because of the importance of the ICRs to regulating parent-of-origin specific gene expression, I developed a genome-wide strategy for predicting their positions in the human genome. My strategy consists of creating plots to display the density of ZFBS-morph overlaps along the entire chromosomal DNA sequences. In initial evaluations, I found that peaks in these plots pinpointed several of the known ICRs/gDMRs along the DNA in chromosomal bands. I deduced that in density-plots, robust peaks corresponded to actual or candidate ICRs in the DNA. By locating the genes in the vicinity of candidate ICRs, I could discover potential imprinting genes. Additionally, my assessments revealed a connection between several of the potential imprinted genes and human developmental anomalies. Examples include Leber congenital amaurosis 11, Coffin-Siris syndrome, progressive myoclonic epilepsy-10, microcephalic osteodysplastic primordial dwarfism type II, and microphthalmia, cleft lip and palate, and agenesis of the corpus callosum. CONCLUSION With plots displaying the density of ZFBS-morph overlaps, researchers could locate candidate ICRs and imprinted genes. Since the datafiles are available for download and display at the UCSC genome browser, it is possible to examine the plots in the context of Single nucleotide polymorphisms (SNPs) to design experiments to discover novel ICRs and imprinted genes in the human genome.
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Affiliation(s)
- Minou Bina
- Department of Chemistry, Purdue University, 560 Oval Dr., West Lafayette, IN, 47907, USA.
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71
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Zhang GW, Wang L, Chen H, Guan J, Wu Y, Zhao J, Luo Z, Huang W, Zuo F. Promoter hypermethylation of PIWI/piRNA pathway genes associated with diminished pachytene piRNA production in bovine hybrid male sterility. Epigenetics 2020; 15:914-931. [PMID: 32141383 DOI: 10.1080/15592294.2020.1738026] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
Hybrid male sterility (HMS) is a postzygotic reproductive isolation mechanism that enforces speciation. A bovine example of HMS is the yattle (also called dzo), an interspecies hybrid of taurine cattle (Bos taurus) and yak (Bos grunniens). The molecular mechanisms underlying HMS of yattle are not well understood. Epigenetic modifications of DNA methylation and P-element induced wimpy testis (PIWI)-interacting RNA (piRNAs) are important regulators in spermatogenesis. In this study, we investigated DNA methylation patterns and piRNA expression in adult testes in hybrid infertile yattle bulls and fertile cattle and yak bulls using whole genome bisulphite-seq and small RNA-seq. Promoter hypermethylation in yattle were associated with DNA methylation involved in gamete generation, piRNA metabolic processes, spermatogenesis, and spermatid development (P < 2.6 × 10-5). Male infertility in yattle was associated with the promoter hypermethylation-associated silencing of PIWI/piRNA pathway genes including PIWIL1, DDX4, PLD6, MAEL, FKBP6, TDRD1 and TDRD5. The downstream effects of silencing these genes were diminished production of 29- to 31- nucleotide pachytene piRNAs in yattle testes. Hypermethylation events at transposable element loci (LINEs, SINEs, and LTRs) were found in yattle. LINE-derived prepachytene piRNAs increased and SINE-derived prepachytene piRNAs were reduced in yattle testes. Our data suggests that DNA methylation affects the PIWI/piRNA pathway and is involved in gene expression and pachytene piRNA production during spermatogenesis in bovine HMS. DNA hypermethylation and disruption of piRNA production contributed to unsuccessful germ cell development that may drive bovine HMS.
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Affiliation(s)
- Gong-Wei Zhang
- College of Animal Science, Southwest University , Chongqing, China.,Beef Cattle Engineering and Technology Research Center of Chongqing, Southwest University , Chongqing, China
| | - Ling Wang
- College of Animal Science, Southwest University , Chongqing, China.,Beef Cattle Engineering and Technology Research Center of Chongqing, Southwest University , Chongqing, China
| | - Huiyou Chen
- College of Animal Science, Southwest University , Chongqing, China.,Beef Cattle Engineering and Technology Research Center of Chongqing, Southwest University , Chongqing, China
| | - Jiuqiang Guan
- Yak Research Institution, Sichuan Academy of Grassland Science , Chengdu, Sichuan, China
| | - Yuhui Wu
- College of Animal Science, Southwest University , Chongqing, China.,Beef Cattle Engineering and Technology Research Center of Chongqing, Southwest University , Chongqing, China
| | - Jianjun Zhao
- College of Animal Science, Southwest University , Chongqing, China.,Beef Cattle Engineering and Technology Research Center of Chongqing, Southwest University , Chongqing, China
| | - Zonggang Luo
- College of Animal Science, Southwest University , Chongqing, China.,Beef Cattle Engineering and Technology Research Center of Chongqing, Southwest University , Chongqing, China
| | - Wenming Huang
- College of Animal Science, Southwest University , Chongqing, China.,Beef Cattle Engineering and Technology Research Center of Chongqing, Southwest University , Chongqing, China
| | - Fuyuan Zuo
- College of Animal Science, Southwest University , Chongqing, China.,Beef Cattle Engineering and Technology Research Center of Chongqing, Southwest University , Chongqing, China
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72
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Kiefer H, Perrier JP. DNA methylation in bull spermatozoa: evolutionary impacts, interindividual variability, and contribution to the embryo. CANADIAN JOURNAL OF ANIMAL SCIENCE 2020. [DOI: 10.1139/cjas-2019-0071] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The DNA methylome of spermatozoa results from a unique epigenetic reprogramming crucial for chromatin compaction and the protection of the paternal genetic heritage. Although bull semen is widely used for artificial insemination (AI), little is known about the sperm epigenome in cattle. The purpose of this review is to synthetize recent work on the bull sperm methylome in light of the knowledge accumulated in humans and model species. We will address sperm-specific DNA methylation features and their potential evolutionary impacts, with particular emphasis on hypomethylated regions and repetitive elements. We will review recent examples of interindividual variability and intra-individual plasticity of the bull sperm methylome as related to fertility and age, respectively. Finally, we will address paternal methylome reprogramming after fertilization, as well as the mechanisms potentially involved in epigenetic inheritance, and provide some examples of disturbances that alter the dynamics of reprogramming in cattle. Because the selection of AI bulls is closely based on their genotypes, we will also discuss the complex interplay between sequence polymorphism and DNA methylation, which represents both a difficulty in addressing the role of DNA methylation in shaping phenotypes and an opportunity to better understand genome plasticity.
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Affiliation(s)
- Hélène Kiefer
- UMR BDR, INRA, ENVA, Université Paris Saclay, 78350 Jouy en-Josas, France
- UMR BDR, INRA, ENVA, Université Paris Saclay, 78350 Jouy en-Josas, France
| | - Jean-Philippe Perrier
- UMR BDR, INRA, ENVA, Université Paris Saclay, 78350 Jouy en-Josas, France
- UMR BDR, INRA, ENVA, Université Paris Saclay, 78350 Jouy en-Josas, France
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73
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Du Z, Zheng H, Kawamura YK, Zhang K, Gassler J, Powell S, Xu Q, Lin Z, Xu K, Zhou Q, Ozonov EA, Véron N, Huang B, Li L, Yu G, Liu L, Au Yeung WK, Wang P, Chang L, Wang Q, He A, Sun Y, Na J, Sun Q, Sasaki H, Tachibana K, Peters AHFM, Xie W. Polycomb Group Proteins Regulate Chromatin Architecture in Mouse Oocytes and Early Embryos. Mol Cell 2020; 77:825-839.e7. [PMID: 31837995 DOI: 10.1016/j.molcel.2019.11.011] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/03/2019] [Accepted: 11/08/2019] [Indexed: 11/18/2022]
Abstract
In mammals, chromatin organization undergoes drastic reorganization during oocyte development. However, the dynamics of three-dimensional chromatin structure in this process is poorly characterized. Using low-input Hi-C (genome-wide chromatin conformation capture), we found that a unique chromatin organization gradually appears during mouse oocyte growth. Oocytes at late stages show self-interacting, cohesin-independent compartmental domains marked by H3K27me3, therefore termed Polycomb-associating domains (PADs). PADs and inter-PAD (iPAD) regions form compartment-like structures with strong inter-domain interactions among nearby PADs. PADs disassemble upon meiotic resumption from diplotene arrest but briefly reappear on the maternal genome after fertilization. Upon maternal depletion of Eed, PADs are largely intact in oocytes, but their reestablishment after fertilization is compromised. By contrast, depletion of Polycomb repressive complex 1 (PRC1) proteins attenuates PADs in oocytes, which is associated with substantial gene de-repression in PADs. These data reveal a critical role of Polycomb in regulating chromatin architecture during mammalian oocyte growth and early development.
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Affiliation(s)
- Zhenhai Du
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Hui Zheng
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yumiko K Kawamura
- Friedrich Miescher Institute for Biomedical Research, Basel 4058, Switzerland
| | - Ke Zhang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Johanna Gassler
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Sean Powell
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Qianhua Xu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zili Lin
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Kai Xu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qian Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Evgeniy A Ozonov
- Friedrich Miescher Institute for Biomedical Research, Basel 4058, Switzerland
| | - Nathalie Véron
- Friedrich Miescher Institute for Biomedical Research, Basel 4058, Switzerland
| | - Bo Huang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Lijia Li
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Guang Yu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ling Liu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Wan Kin Au Yeung
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Peizhe Wang
- Center for Stem Cell Biology and Regenerative Medicine, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Lei Chang
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Qiujun Wang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Aibin He
- Institute of Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China
| | - Yujie Sun
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Jie Na
- Center for Stem Cell Biology and Regenerative Medicine, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Qingyuan Sun
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Kikuë Tachibana
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria; Department of Totipotency, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Antoine H F M Peters
- Friedrich Miescher Institute for Biomedical Research, Basel 4058, Switzerland; Faculty of Sciences, University of Basel, Basel 4056, Switzerland.
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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Li H, Zhang P, Zhao Y, Zhang H. Low doses of carbendazim and chlorothalonil synergized to impair mouse spermatogenesis through epigenetic pathways. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 188:109908. [PMID: 31706243 DOI: 10.1016/j.ecoenv.2019.109908] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 10/29/2019] [Accepted: 10/31/2019] [Indexed: 06/10/2023]
Abstract
Pesticides have been extensively produced and used to help the agricultural production which leads to the contamination of the environment, soil, groundwater sources, and even foodstuffs. Fungicides carbendazim (CBZ) and chlorothalonil (Chl) are widely applied in agriculture and other aspects. CBZ or Chl have been reported to disrupt spermatogenesis and decrease semen quality. However, it is not understood the effects of pubertal exposure to low doses of CBZ and Chl together, and the underlying mechanisms. Therefore, the aim of current investigation was to explore the negative impacts of pubertal exposure to low doses of CBZ and Chl together on spermatogenesis and the role of epigenetic modifications in the process. We demonstrated that CBZ and Chl together synergize to decrease sperm motility in vitro (CBZ 1.0 + Chl 0.1, CBZ 10.0 + CHl 1.0, CBZ 100.0 + Chl 10 μM in incubation medium for 24 h) and sperm concentration and motility in vivo with ICR mice (CBZ 0.1 + Chl 0.1, CBZ 1.0 + CHl 1.0, CBZ 10.0 + Chl 10 mg/kg body weight; oral gavage for five weeks). CBZ + Chl significantly increase reactive oxygen species (ROS) and apoptosis by the increase in the protein level of caspase 8 in vitro. Moreover, CBZ + Chl synergized to disrupt mouse spermatogenesis with the disturbance in sperm production proteins and sperm proteins (VASA, A-Myb, STK31, AR, Acrosin). CBZ + Chl synergized to decrease the protein level of estrogen receptor alpha and the protein level of DNA methylation marker 5 mC in Leydig cells, and to increase the protein levels of histone methylation marker H3K9 and the methylation enzyme G9a in germ cells. Therefore, greater attention should be paid to the use of CBZ and Chl as pesticides to minimise their adverse impacts on spermatogenesis.
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Affiliation(s)
- Huatao Li
- College of Veterinary Sciences, Qingdao Agricultural University, Qingdao, 266109, PR China
| | - Pengfei Zhang
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, PR China
| | - Yong Zhao
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, PR China; State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, PR China.
| | - Hongfu Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, PR China.
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75
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76
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Thamban T, Agarwaal V, Khosla S. Role of genomic imprinting in mammalian development. J Biosci 2020; 45:20. [PMID: 31965998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Non-mendelian inheritance refers to the group of phenomena and observations related to the inheritance of genetic information that cannot be merely explained by Mendel's laws of inheritance. Phenomenon including Genomic imprinting, X-chromosome Inactivation, Paramutations are some of the best studied examples of non-mendelian inheritance. Genomic imprinting is a process that reversibly marks one of the two homologous loci, chromosome or chromosomal sets during development, resulting in functional non-equivalence of gene expression. Genomic imprinting is known to occur in a few insect species, plants, and placental mammals. Over the years, studies on imprinted genes have contributed immensely to highlighting the role of epigenetic modifications and the epigenetic circuitry during gene expression and development. In this review, we discuss the phenomenon of genomic imprinting in mammals and the role it plays especially during fetoplacental growth and early development.
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Affiliation(s)
- Thushara Thamban
- Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
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77
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Wen L, Liu Q, Xu J, Liu X, Shi C, Yang Z, Zhang Y, Xu H, Liu J, Yang H, Huang H, Qiao J, Tang F, Chen ZJ. Recent advances in mammalian reproductive biology. SCIENCE CHINA. LIFE SCIENCES 2020; 63:18-58. [PMID: 31813094 DOI: 10.1007/s11427-019-1572-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 10/22/2019] [Indexed: 01/05/2023]
Abstract
Reproductive biology is a uniquely important topic since it is about germ cells, which are central for transmitting genetic information from generation to generation. In this review, we discuss recent advances in mammalian germ cell development, including preimplantation development, fetal germ cell development and postnatal development of oocytes and sperm. We also discuss the etiologies of female and male infertility and describe the emerging technologies for studying reproductive biology such as gene editing and single-cell technologies.
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Affiliation(s)
- Lu Wen
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology Third Hospital, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Qiang Liu
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology Third Hospital, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Jingjing Xu
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China
| | - Xixi Liu
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology Third Hospital, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Chaoyi Shi
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China
| | - Zuwei Yang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China
| | - Yili Zhang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China
| | - Hong Xu
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China
| | - Jiang Liu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Hui Yang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Hefeng Huang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China.
| | - Jie Qiao
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology Third Hospital, College of Life Sciences, Peking University, Beijing, 100871, China.
| | - Fuchou Tang
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology Third Hospital, College of Life Sciences, Peking University, Beijing, 100871, China.
| | - Zi-Jiang Chen
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, 250021, China.
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Schrott R, Murphy SK. Cannabis use and the sperm epigenome: a budding concern? ENVIRONMENTAL EPIGENETICS 2020; 6:dvaa002. [PMID: 32211199 PMCID: PMC7081939 DOI: 10.1093/eep/dvaa002] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/04/2020] [Accepted: 02/06/2020] [Indexed: 05/13/2023]
Abstract
The United States is swiftly moving toward increased legalization of medical and recreational cannabis. Currently considered the most commonly used illicit psychoactive drug, recreational cannabis is legal in 11 states and Washington, DC, and male use is an important and understudied concern. Questions remain, however, about the potential long-term consequences of this exposure and how cannabis might impact the epigenetic integrity of sperm in such a way that could influence the health and development of offspring. This review summarizes cannabis use and potency in the USA, provides a brief overview of DNA methylation as an epigenetic mechanism that is vulnerable in sperm to environmental exposures including cannabis, and summarizes studies that have examined the effects of parental exposure to cannabis or delta-9 tetrahydrocannabinol (THC, the main psychoactive component of cannabis) on the epigenetic profile of the gametes and behavior of offspring. These studies have demonstrated significant changes to the sperm DNA methylome following cannabis use in humans, and THC exposure in rats. Furthermore, the use of rodent models has shown methylation and behavioral changes in rats born to fathers exposed to THC or synthetic cannabinoids, or to parents who were both exposed to THC. These data substantiate an urgent need for additional studies assessing the effects of cannabis exposure on childhood health and development. This is especially true given the current growing state of cannabis use in the USA.
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Affiliation(s)
- Rose Schrott
- Department of Obstetrics and Gynecology, Division of Reproductive Sciences, Duke University Medical Center, The Chesterfield, 701 W. Main Street, Suite 510, Durham, NC 27701 USA
- Integrated Toxicology and Environmental Health Program, Nicholas School of the Environment, Duke University, Circuit Dr, Durham, NC 27710 USA
| | - Susan K Murphy
- Department of Obstetrics and Gynecology, Division of Reproductive Sciences, Duke University Medical Center, The Chesterfield, 701 W. Main Street, Suite 510, Durham, NC 27701 USA
- Integrated Toxicology and Environmental Health Program, Nicholas School of the Environment, Duke University, Circuit Dr, Durham, NC 27710 USA
- Correspondence address: Duke University Medical Center, The Chesterfield, 701 W. Main Street, Suite 510, Durham, NC 27701, USA. Tel: 919-681-3423; Fax: 919-385-9358; E-mail:
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Saenz-de-Juano MD, Ivanova E, Billooye K, Herta AC, Smitz J, Kelsey G, Anckaert E. Genome-wide assessment of DNA methylation in mouse oocytes reveals effects associated with in vitro growth, superovulation, and sexual maturity. Clin Epigenetics 2019; 11:197. [PMID: 31856890 PMCID: PMC6923880 DOI: 10.1186/s13148-019-0794-y] [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: 09/04/2019] [Accepted: 12/03/2019] [Indexed: 12/27/2022] Open
Abstract
Background In vitro follicle culture (IFC), as applied in the mouse system, allows the growth and maturation of a large number of immature preantral follicles to become mature and competent oocytes. In the human oncofertility clinic, there is increasing interest in developing this technique as an alternative to ovarian cortical tissue transplantation and to preserve the fertility of prepubertal cancer patients. However, the effect of IFC and hormonal stimulation on DNA methylation in the oocyte is not fully known, and there is legitimate concern over epigenetic abnormalities that could be induced by procedures applied during assisted reproductive technology (ART). Results In this study, we present the first genome-wide analysis of DNA methylation in MII oocytes obtained after natural ovulation, after IFC and after superovulation. We also performed a comparison between prepubertal and adult hormonally stimulated oocytes. Globally, the distinctive methylation landscape of oocytes, comprising alternating hyper- and hypomethylated domains, is preserved irrespective of the procedure. The conservation of methylation extends to the germline differential methylated regions (DMRs) of imprinted genes, necessary for their monoallelic expression in the embryo. However, we do detect specific, consistent, and coherent differences in DNA methylation in IFC oocytes, and between oocytes obtained after superovulation from prepubertal compared with sexually mature females. Several methylation differences span entire transcription units. Among these, we found alterations in Tcf4, Sox5, Zfp521, and other genes related to nervous system development. Conclusions Our observations show that IFC is associated with altered methylation at specific set of loci. DNA methylation of superovulated prepubertal oocytes differs from that of superovulated adult oocytes, whereas oocytes from superovulated adult females differ very little from naturally ovulated oocytes. Importantly, we show that regions other than imprinted gDMRs are susceptible to methylation changes associated with superovulation, IFC, and/or sexual immaturity in mouse oocytes. Our results provide an important reference for the use of in vitro growth and maturation of oocytes, particularly from prepubertal females, in assisted reproductive treatments or fertility preservation.
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Affiliation(s)
- Maria Desemparats Saenz-de-Juano
- Follicle Biology Laboratory (FOBI), UZ Brussel, Vrije Universiteit Brussel, Laarbeeklaan, Brussels, Belgium.,Present Address: Animal Physiology, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Elena Ivanova
- Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT, UK
| | - Katy Billooye
- Follicle Biology Laboratory (FOBI), UZ Brussel, Vrije Universiteit Brussel, Laarbeeklaan, Brussels, Belgium
| | - Anamaria-Cristina Herta
- Follicle Biology Laboratory (FOBI), UZ Brussel, Vrije Universiteit Brussel, Laarbeeklaan, Brussels, Belgium
| | - Johan Smitz
- Follicle Biology Laboratory (FOBI), UZ Brussel, Vrije Universiteit Brussel, Laarbeeklaan, Brussels, Belgium
| | - Gavin Kelsey
- Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT, UK.,Centre for Trophoblast Research, University of Cambridge, Cambridge, CB2 3EG, UK
| | - Ellen Anckaert
- Follicle Biology Laboratory (FOBI), UZ Brussel, Vrije Universiteit Brussel, Laarbeeklaan, Brussels, Belgium.
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80
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Nie J, Xiao P, Wang X, Yang X, Xu H, Lu K, Lu S, Liang X. Melatonin prevents deterioration in quality by preserving epigenetic modifications of porcine oocytes after prolonged culture. Aging (Albany NY) 2019; 10:3897-3909. [PMID: 30530915 PMCID: PMC6326688 DOI: 10.18632/aging.101680] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 11/19/2018] [Indexed: 12/14/2022]
Abstract
Prolonged culture of metaphase II oocytes is an in vitro aging process that compromises oocyte quality. We tested whether melatonin preserves epigenetic modifications in oocytes after prolonged culture. The porcine oocytes were maturated in vitro for 44 h, and then metaphase II oocytes were continuously cultured in medium supplemented with or without melatonin for 24 h. We found that the parthenogenetic blastocyst formation rate of prolonged-culture oocytes was lower than in fresh oocytes. We further observed that methylation at H3K4me2 and H3K27me2 of oocytes enhanced after prolonged culture. However, 5mc fluorescence intensity was lower in prolonged-culture oocytes than in fresh oocytes. Moreover, the promoter of the imprinted gene NNAT exhibited a higher level of DNA methylation in prolonged-culture oocytes than in fresh oocytes, which was associated with a reduced expression level and glucose uptake capability. Conversely, melatonin improved blastocyst formation rate and preserved histone and DNA methylation modifications, as well as NNAT function in the oocytes after prolonged culture. Notably, DNA methyltransferase inhibitor 5-aza significantly attenuated the protective role of melatonin on genomic DNA methylation. In summary, our results revealed that epigenetic modifications are disrupted in oocytes after prolonged culture, but the changes are reversed by melatonin.
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Affiliation(s)
- Junyu Nie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, Guangxi 530004, PR China.,College of Animal Science and Technology, Guangxi University, Nanning, Guangxi 530004, PR China
| | - Peng Xiao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, Guangxi 530004, PR China.,College of Animal Science and Technology, Guangxi University, Nanning, Guangxi 530004, PR China
| | - Xuefang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, Guangxi 530004, PR China.,College of Animal Science and Technology, Guangxi University, Nanning, Guangxi 530004, PR China
| | - Xiaogan Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, Guangxi 530004, PR China.,College of Animal Science and Technology, Guangxi University, Nanning, Guangxi 530004, PR China
| | - Huiyan Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, Guangxi 530004, PR China.,College of Animal Science and Technology, Guangxi University, Nanning, Guangxi 530004, PR China
| | - Kehuan Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, Guangxi 530004, PR China.,College of Animal Science and Technology, Guangxi University, Nanning, Guangxi 530004, PR China
| | - Shengsheng Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, Guangxi 530004, PR China.,College of Animal Science and Technology, Guangxi University, Nanning, Guangxi 530004, PR China
| | - Xingwei Liang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, Guangxi 530004, PR China.,College of Animal Science and Technology, Guangxi University, Nanning, Guangxi 530004, PR China
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81
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Farhadova S, Gomez-Velazquez M, Feil R. Stability and Lability of Parental Methylation Imprints in Development and Disease. Genes (Basel) 2019; 10:genes10120999. [PMID: 31810366 PMCID: PMC6947649 DOI: 10.3390/genes10120999] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 11/25/2019] [Accepted: 11/27/2019] [Indexed: 02/06/2023] Open
Abstract
DNA methylation plays essential roles in mammals. Of particular interest are parental methylation marks that originate from the oocyte or the sperm, and bring about mono-allelic gene expression at defined chromosomal regions. The remarkable somatic stability of these parental imprints in the pre-implantation embryo—where they resist global waves of DNA demethylation—is not fully understood despite the importance of this phenomenon. After implantation, some methylation imprints persist in the placenta only, a tissue in which many genes are imprinted. Again here, the underlying epigenetic mechanisms are not clear. Mouse studies have pinpointed the involvement of transcription factors, covalent histone modifications, and histone variants. These and other features linked to the stability of methylation imprints are instructive as concerns their conservation in humans, in which different congenital disorders are caused by perturbed parental imprints. Here, we discuss DNA and histone methylation imprints, and why unravelling maintenance mechanisms is important for understanding imprinting disorders in humans.
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82
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Liu S, Fang L, Zhou Y, Santos DJA, Xiang R, Daetwyler HD, Chamberlain AJ, Cole JB, Li CJ, Yu Y, Ma L, Zhang S, Liu GE. Analyses of inter-individual variations of sperm DNA methylation and their potential implications in cattle. BMC Genomics 2019; 20:888. [PMID: 31752687 PMCID: PMC6873545 DOI: 10.1186/s12864-019-6228-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 10/28/2019] [Indexed: 12/18/2022] Open
Abstract
Background DNA methylation has been shown to be involved in many biological processes, including X chromosome inactivation in females, paternal genomic imprinting, and others. Results Based on the correlation patterns of methylation levels of neighboring CpG sites among 28 sperm whole genome bisulfite sequencing (WGBS) data (486 × coverage), we obtained 31,272 methylation haplotype blocks (MHBs). Among them, we defined conserved methylated regions (CMRs), variably methylated regions (VMRs) and highly variably methylated regions (HVMRs) among individuals, and showed that HVMRs might play roles in transcriptional regulation and function in complex traits variation and adaptive evolution by integrating evidence from traditional and molecular quantitative trait loci (QTL), and selection signatures. Using a weighted correlation network analysis (WGCNA), we also detected a co-regulated module of HVMRs that was significantly associated with reproduction traits, and enriched for glycosyltransferase genes, which play critical roles in spermatogenesis and fertilization. Additionally, we identified 46 VMRs significantly associated with reproduction traits, nine of which were regulated by cis-SNPs, implying the possible intrinsic relationships among genomic variations, DNA methylation, and phenotypes. These significant VMRs were co-localized (± 10 kb) with genes related to sperm motility and reproduction, including ZFP36L1, CRISP2 and HGF. We provided further evidence that rs109326022 within a predominant QTL on BTA18 might influence the reproduction traits through regulating the methylation level of nearby genes JOSD2 and ASPDH in sperm. Conclusion In summary, our results demonstrated associations of sperm DNA methylation with reproduction traits, highlighting the potential of epigenomic information in genomic improvement programs for cattle.
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Affiliation(s)
- Shuli Liu
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.,USDA-ARS, Animal Genomics and Improvement Laboratory, Beltsville, MD, 20705, USA
| | - Lingzhao Fang
- USDA-ARS, Animal Genomics and Improvement Laboratory, Beltsville, MD, 20705, USA.,Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA.,Medical Research Council Human Genetics Unit at the Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Yang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Education Ministry of China, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Daniel J A Santos
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA
| | - Ruidong Xiang
- Faculty of Veterinary & Agricultural Science, The University of Melbourne, Parkville, Victoria, 3052, Australia.,Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, Victoria, 3083, Australia
| | - Hans D Daetwyler
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, Victoria, 3083, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, 3083, Australia
| | - Amanda J Chamberlain
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, Victoria, 3083, Australia
| | - John B Cole
- USDA-ARS, Animal Genomics and Improvement Laboratory, Beltsville, MD, 20705, USA
| | - Cong-Jun Li
- USDA-ARS, Animal Genomics and Improvement Laboratory, Beltsville, MD, 20705, USA
| | - Ying Yu
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Li Ma
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA
| | - Shengli Zhang
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| | - George E Liu
- USDA-ARS, Animal Genomics and Improvement Laboratory, Beltsville, MD, 20705, USA.
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83
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Liu Y, Zhang Y, Yin J, Gao Y, Li Y, Bai D, He W, Li X, Zhang P, Li R, Zhang L, Jia Y, Zhang Y, Lin J, Zheng Y, Wang H, Gao S, Zeng W, Liu W. Distinct H3K9me3 and DNA methylation modifications during mouse spermatogenesis. J Biol Chem 2019; 294:18714-18725. [PMID: 31662436 DOI: 10.1074/jbc.ra119.010496] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 10/24/2019] [Indexed: 12/15/2022] Open
Abstract
DNA methylation and histone modifications critically regulate the expression of many genes and repeat regions during spermatogenesis. However, the molecular details of these processes in male germ cells remain to be addressed. Here, using isolated murine sperm cells, ultra-low-input native ChIP-Seq (ULI-NChIP-Seq), and whole genome bisulfite sequencing (WGBS), we investigated genome-wide DNA methylation patterns and histone 3 Lys-9 trimethylation (H3K9me3) modifications during mouse spermatogenesis. We found that DNA methylation and H3K9me3 have distinct sequence preferences and dynamics in promoters and repeat elements during spermatogenesis. H3K9me3 modifications in histones at gene promoters were highly enriched in round spermatids. H3K9me3 modification on long terminal repeats (LTRs) and long interspersed nuclear elements (LINEs) was involved in silencing active transcription from these regions in conjunction with reestablishment of DNA methylation. Furthermore, H3K9me3 remodeling on the X chromosome was involved in meiotic sex chromosome inactivation and in partial transcriptional reactivation of sex chromosomes in spermatids. Our findings also revealed the DNA methylation patterns and H3K9me3 modification profiles of paternal and maternal germline imprinting control regions (gICRs) during spermatogenesis. Taken together, our results provide a genome-wide map of H3K9me3 modifications during mouse spermatogenesis that may be helpful for understanding male reproductive disorders.
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Affiliation(s)
- Yingdong Liu
- College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yanping Zhang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Jiqing Yin
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yawei Gao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yanhe Li
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Dandan Bai
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Wenteng He
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Xueliang Li
- College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Pengfei Zhang
- College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Rongnan Li
- College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lingkai Zhang
- College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yanping Jia
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yalin Zhang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Jiaming Lin
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yi Zheng
- College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hong Wang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Shaorong Gao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.
| | - Wenxian Zeng
- College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Wenqiang Liu
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.
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84
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Genomic Balance: Two Genomes Establishing Synchrony to Modulate Cellular Fate and Function. Cells 2019; 8:cells8111306. [PMID: 31652817 PMCID: PMC6912345 DOI: 10.3390/cells8111306] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 10/17/2019] [Accepted: 10/22/2019] [Indexed: 01/21/2023] Open
Abstract
It is becoming increasingly apparent that cells require cooperation between the nuclear and mitochondrial genomes to promote effective function. However, it was long thought that the mitochondrial genome was under the strict control of the nuclear genome and the mitochondrial genome had little influence on cell fate unless it was extensively mutated, as in the case of the mitochondrial DNA diseases. However, as our understanding of the roles that epigenetic regulators, including DNA methylation, and metabolism play in cell fate and function, the role of the mitochondrial genome appears to have a greater influence than previously thought. In this review, I draw on examples from tumorigenesis, stem cells, and oocyte pre- and post-fertilisation events to discuss how modulating one genome affects the other and that this results in a compromise to produce functional mature cells. I propose that, during development, both of the genomes interact with each other through intermediaries to establish genomic balance and that establishing genomic balance is a key facet in determining cell fate and viability.
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85
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Franzago M, La Rovere M, Guanciali Franchi P, Vitacolonna E, Stuppia L. Epigenetics and human reproduction: the primary prevention of the noncommunicable diseases. Epigenomics 2019; 11:1441-1460. [PMID: 31596147 DOI: 10.2217/epi-2019-0163] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Epigenetic regulation of gene expression plays a key role in affecting human health and diseases with particular regard to human reproduction. The major concern in this field is represented by the epigenetic modifications in the embryo and the increased risk of long-life disorders induced by the use of assisted reproduction techniques, able to affect the epigenetic assessment in the first steps of embryo development. In this review, we analyze the correlation between epigenetic modifications and human reproduction, suggesting that the reversibility of the epigenetic processes could represent a novel resource for the treatment of the couple's infertility and that parental lifestyle in periconceptional period could be considered as an important issue of primary prevention.
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Affiliation(s)
- Marica Franzago
- Department of Medicine & Aging, School of Medicine & Health Sciences, 'G. d'Annunzio' University, Chieti-Pescara, Chieti, Italy.,Center for Aging Studies & Translational Medicine (CESI-MET), 'G. d'Annunzio' University of Chieti-Pescara, Chieti, Italy
| | - Marina La Rovere
- Department of Psychological, Health & Territorial Sciences, School of Medicine & Health Sciences, 'G. d'Annunzio' University of Chieti-Pescara, Chieti, Italy
| | - Paolo Guanciali Franchi
- Department of Medical, Oral & Biotechnological Sciences, School of Medicine & Health Sciences, 'G. d'Annunzio' University of Chieti-Pescara, Chieti, Italy
| | - Ester Vitacolonna
- Department of Medicine & Aging, School of Medicine & Health Sciences, 'G. d'Annunzio' University, Chieti-Pescara, Chieti, Italy
| | - Liborio Stuppia
- Center for Aging Studies & Translational Medicine (CESI-MET), 'G. d'Annunzio' University of Chieti-Pescara, Chieti, Italy.,Department of Psychological, Health & Territorial Sciences, School of Medicine & Health Sciences, 'G. d'Annunzio' University of Chieti-Pescara, Chieti, Italy
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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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Zhang P, Zhao Y, Zhang H, Liu J, Feng Y, Yin S, Cheng S, Sun X, Min L, Li L, Shen W. Low dose chlorothalonil impairs mouse spermatogenesis through the intertwining of Estrogen Receptor Pathways with histone and DNA methylation. CHEMOSPHERE 2019; 230:384-395. [PMID: 31112861 DOI: 10.1016/j.chemosphere.2019.05.029] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 04/23/2019] [Accepted: 05/03/2019] [Indexed: 06/09/2023]
Abstract
Recently, environment contaminants including pesticides, fungicides, mycotoxin and others chemicals have been suggested to be responsible for the decline in the human spermatozoa quality especially motility and the increase in infertility rate. Chlorothalonil is used widely for protection of vegetables and crops because it is a broad spectrum fungicide. It has been reported that chronic occupational exposure to fungicides was associated with poor spermatozoa morphology in young men. The pubertal period is very important for the male reproductive system development due to spermatogonial cell proliferation, the expansion of meiotic and haploid germ cells. Although some investigations have studied the male reproductive toxicity of chlorothalonil, almost no studies focused on spermatogenesis. The aim of our current investigation was to explore the impacts of chlorothalonil on spermatogenesis and the underlying mechanisms. It demonstrates: i) chlorothalonil decreased boar spermatozoa motility in vitro and increased the cell apoptosis; ii) chlorothalonil inhibited mouse spermatogenesis in vivo; iii) chlorothalonil disturbed spermatogenesis through the disruption of estrogen receptor signalling; iv) chlorothalonil disrupted histone methylation and DNA methylation which might be through estrogen signalling pathways. Due to the over use or incorrect use, chlorothalonil might cause serious problems to human health, especially spermatogenesis. Therefore we strongly recommend that greater attention should be paid to this fungicide to minimise its impact on human health especially spermatogenesis.
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Affiliation(s)
- Pengfei Zhang
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, PR China; College of Animal Sciences and Technology, Qingdao Agricultural University, Qingdao 266109, PR China
| | - Yong Zhao
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, PR China
| | - Hongfu Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Jing Liu
- University Research Core, Qingdao Agricultural University, Qingdao 266109, PR China
| | - Yanni Feng
- College of Veterinary Sciences, Qingdao Agricultural University, Qingdao 266109, PR China
| | - Shen Yin
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, PR China
| | - Shunfeng Cheng
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, PR China
| | - Xiaofeng Sun
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, PR China
| | - Lingjiang Min
- College of Animal Sciences and Technology, Qingdao Agricultural University, Qingdao 266109, PR China
| | - Lan Li
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, PR China
| | - Wei Shen
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, PR China.
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88
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Germ cell-mediated mechanisms of epigenetic inheritance. Semin Cell Dev Biol 2019; 97:116-122. [PMID: 31404658 DOI: 10.1016/j.semcdb.2019.07.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 07/15/2019] [Accepted: 07/25/2019] [Indexed: 01/07/2023]
Abstract
It is well established that lifestyle and other environmental factors have the potential to shape our own health and future. Research from the last two decades, however, provides mounting evidence that parental exposures or experiences such as dietary challenges, toxin exposure, or stress can impact the health and future of our offspring. There are indications that both the paternal and maternal germline are able to store information of the parental environment and pass certain information on to their progeny. These intergenerational effects are mediated by epigenetic mechanisms. This review summarizes and discusses insights into germline epigenetic plasticity caused by environmental stimuli and how such alterations are transmitted to induce a stable phenotype in the offspring.
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89
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Kerr K, McAneney H, Flanagan C, Maxwell AP, McKnight AJ. Differential methylation as a diagnostic biomarker of rare renal diseases: a systematic review. BMC Nephrol 2019; 20:320. [PMID: 31419951 PMCID: PMC6697952 DOI: 10.1186/s12882-019-1517-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 08/08/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The challenges in diagnosis of rare renal conditions can negatively impact patient prognosis, quality of life and result in significant healthcare costs. Differential methylation is emerging as an important biomarker for rare diseases and should be evaluated for rare renal conditions. METHODS A comprehensive systematic review of methylation and rare renal disorders was conducted by searching the electronic databases MEDLINE, EMBASE, PubMed, Cochrane Library, alongside grey literature from GreyLit and OpenGrey databases, for publications published before September 2018. Additionally, the reference lists of the included papers were searched. Data was extracted and appraised including the primary focus, measurement and methodological rigour of the source. Eligibility criteria were adapted using the inclusion criteria from 'The 100,000 Genomes Project' and The National Registry of Rare Kidney Diseases, with additional focus on methylation. RESULTS Thirteen full text articles were included in the review. Diseases analysed for differential methylation included glomerular disease, IgA nephropathy, ADPKD, rare causes of proteinuria, congenital renal agenesis, and membranous nephropathy. CONCLUSIONS Differential methylation has been observed for several rare renal diseases, highlighting its potential for improving molecular characterisation of these disorders. Further investigation of methylation following a standardised reporting structure is necessary to improve research quality. Multi-omic data will provide insights for improved diagnosis, prognosis and support for individuals living and working with rare renal diseases.
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Affiliation(s)
- Katie Kerr
- Centre for Public Health, Queen's University Belfast, c/o Regional Genetics Centre, Level A, Tower Block, Belfast City Hospital, Lisburn Road, BT9 7AB, Belfast, Northern Ireland
| | - Helen McAneney
- Centre for Public Health, Queen's University Belfast, c/o Regional Genetics Centre, Level A, Tower Block, Belfast City Hospital, Lisburn Road, BT9 7AB, Belfast, Northern Ireland
| | - Cheryl Flanagan
- 100,000 Genomes Project Team, Belfast Health and Social Care Trust, Belfast, Northern Ireland
| | | | - Amy Jayne McKnight
- Centre for Public Health, Queen's University Belfast, c/o Regional Genetics Centre, Level A, Tower Block, Belfast City Hospital, Lisburn Road, BT9 7AB, Belfast, Northern Ireland.
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90
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Gao Y, Zhao Y, Zhang H, Zhang P, Liu J, Feng Y, Men Y, Li L, Shen W, Sun Z, Min L. Pubertal exposure to low doses of zearalenone disrupting spermatogenesis through ERα related genetic and epigenetic pathways. Toxicol Lett 2019; 315:31-38. [PMID: 31419471 DOI: 10.1016/j.toxlet.2019.08.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 08/06/2019] [Accepted: 08/08/2019] [Indexed: 12/21/2022]
Abstract
Endocrine disruptor zearalenone (ZEA) has been found to damage the reproductive system especially spermatogenesis. In our previous report, we have found that low dose (lower than No-Observed Effect Level, NOEL) ZEA exposure disturbed mouse spermatogenesis and diminished mouse semen quality. The purpose of current investigation was to explore the underlying mechanisms of pubertal low dose ZEA exposure upsetting spermatogenesis. And it was demonstrated that pubertal low dose ZEA exposure disrupted the meiosis process and the important genetic pathways to inhibit the spermatogenesis and even to diminish the semen quality with the decrease in spermatozoa motility and concentration. The DNA methylation markers 5mC and 5hmC were decreased, the histone methylation marker H3K27 was increased, at the same time estrogen receptor alpha was diminished in mouse testis after pubertal low dose ZEA exposure. The data indicate that the disruption in spermatogenesis by pubertal low dose ZEA exposure may be through the alterations in genetic and epigenetic pathways, and the interactions with estrogen receptor signaling pathway. Therefore, we should pay great attention on ZEA exposure to reduce its adverse impacts on male reproductive health.
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Affiliation(s)
- Yishan Gao
- College of Animal Sciences and Technology, Qingdao Agricultural University, Qingdao 266109, PR China
| | - Yong Zhao
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, PR China
| | - Hongfu Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Pengfei Zhang
- College of Animal Sciences and Technology, Qingdao Agricultural University, Qingdao 266109, PR China; College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, PR China
| | - Jing Liu
- University research core, Qingdao Agricultural University, Qingdao 266109, PR China
| | - Yanni Feng
- College of Veterinary Sciences, Qingdao Agricultural University, Qingdao 266109, PR China
| | - Yuhao Men
- College of Animal Sciences and Technology, Qingdao Agricultural University, Qingdao 266109, PR China
| | - Lan Li
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, PR China
| | - Wei Shen
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, PR China
| | - Zhongyi Sun
- Center for Reproductive Medicine, Shenzhen Hospital, Peking University, Shenzhen 518036, PR China
| | - Lingjiang Min
- College of Animal Sciences and Technology, Qingdao Agricultural University, Qingdao 266109, PR China.
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91
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ZFP57 regulation of transposable elements and gene expression within and beyond imprinted domains. Epigenetics Chromatin 2019; 12:49. [PMID: 31399135 PMCID: PMC6688207 DOI: 10.1186/s13072-019-0295-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 07/18/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND KRAB zinc finger proteins (KZFPs) represent one of the largest families of DNA-binding proteins in vertebrate genomes and appear to have evolved to silence transposable elements (TEs) including endogenous retroviruses through sequence-specific targeting of repressive chromatin states. ZFP57 is required to maintain the post-fertilization DNA methylation memory of parental origin at genomic imprints. Here we conduct RNA-seq and ChIP-seq analyses in normal and ZFP57 mutant mouse ES cells to understand the relative importance of ZFP57 at imprints, unique and repetitive regions of the genome. RESULTS Over 80% of ZFP57 targets are TEs, however, ZFP57 is not essential for their repression. The remaining targets lie within unique imprinted and non-imprinted sequences. Though the loss of ZFP57 influences imprinted genes as expected, the majority of unique gene targets lose H3K9me3 with little effect on DNA methylation and very few exhibit alterations in expression. Comparison of ZFP57 mutants with DNA methyltransferase-deleted ES cells (TKO) identifies a remarkably similar pattern of H3K9me3 loss across the genome. These data define regions where H3K9me3 is secondary to DNA methylation and we propose that ZFP57 is the principal if not sole methylation-sensitive KZFP in mouse ES cells. Finally, we examine dynamics of DNA and H3K9 methylation during pre-implantation development and show that sites bound by ZFP57 in ES cells maintain DNA methylation and H3K9me3 at imprints and at non-imprinted regions on the maternally inherited chromosome throughout preimplantation development. CONCLUSION Our analyses suggest the evolution of a rare DNA methylation-sensitive KZFP that is not essential for repeat silencing, but whose primary function is to maintain DNA methylation and repressive histone marks at germline-derived imprinting control regions.
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Mitochondria and Female Germline Stem Cells-A Mitochondrial DNA Perspective. Cells 2019; 8:cells8080852. [PMID: 31398797 PMCID: PMC6721711 DOI: 10.3390/cells8080852] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 08/06/2019] [Accepted: 08/06/2019] [Indexed: 02/06/2023] Open
Abstract
Mitochondria and mitochondrial DNA have important roles to play in development. In primordial germ cells, they progress from small numbers to populate the maturing oocyte with high numbers to support post-fertilization events. These processes take place under the control of significant changes in DNA methylation and other epigenetic modifiers, as well as changes to the DNA methylation status of the nuclear-encoded mitochondrial DNA replication factors. Consequently, the differentiating germ cell requires significant synchrony between the two genomes in order to ensure that they are fit for purpose. In this review, I examine these processes in the context of female germline stem cells that are isolated from the ovary and those derived from embryonic stem cells and reprogrammed somatic cells. Although our knowledge is limited in this respect, I provide predictions based on other cellular systems of what is expected and provide insight into how these cells could be used in clinical medicine.
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93
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Liu J, Zhang P, Zhao Y, Zhang H. Low dose carbendazim disrupts mouse spermatogenesis might Be through estrogen receptor related histone and DNA methylation. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 176:242-249. [PMID: 30939404 DOI: 10.1016/j.ecoenv.2019.03.103] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 03/20/2019] [Accepted: 03/25/2019] [Indexed: 06/09/2023]
Abstract
Pesticides, fungicides are reportedly involved in a decline in spermatozoa quality, especially motility, and a consequent increase in the rate of infertility. Fungicide carbendazim (CBZ) is widely used in agriculture and other aspects. Although CBZ is known to disrupt spermatogenesis, causing a decrease in spermatozoa concentration and motility, the mechanisms are not fully understood. We aimed to further explore the underlying mechanisms of CBZ disruption of spermatogenesis. Pubertal mice were exposed to low doses (0.1, 1 and 10 mg/kg body weight) of CBZ for 5 weeks, then many factors related to spermatogenesis have been explored. It was found that 0.1-10 mg/kg body weight of CBZ exposure decreased mouse sperm motility and concentration, diminished the important protein factors (VASA, PGK2, B-Amy and CREM) for spermatogenesis, reduced sperm protein acrosin level, disrupted very vital epigenetic factors H3K27, 5 mC and 5 hmC. Furthermore, CBZ exposure damaged estrogen receptor alpha (ERα) pathway by decreased the protein levels of ERα and its targets PI3K and AKT. In summary low doses of CBZ exposure disrupted mouse spermatogenesis through estrogen receptor signaling; and that histone methylation and DNA methylation might play vital roles in CBZ disturbance of spermatogenesis through intertwining with estrogen signaling pathways. CBZ from the contamination in environment or food chain poses a serious threat to the normal development of spermatozoa. Therefore we strongly recommend to minimise the use of CBZ since it causes the severe issues on spermatogenesis.
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Affiliation(s)
- Jing Liu
- University Research Core, Qingdao Agricultural University, Qingdao, 266109, PR China
| | - Pengfei Zhang
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, PR China; College of Animal Sciences and Technology, Qingdao Agricultural University, Qingdao, 266109, PR China
| | - Yong Zhao
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, PR China
| | - Hongfu Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, PR China.
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Cocero MJ, Marigorta P, Novillo F, Folch J, Sánchez P, Alabart JL, Lahoz B. Ovine oocytes display a similar germinal vesicle configuration and global DNA methylation at prepubertal and adult ages. Theriogenology 2019; 138:154-163. [PMID: 31357118 DOI: 10.1016/j.theriogenology.2019.07.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 06/20/2019] [Accepted: 07/16/2019] [Indexed: 12/22/2022]
Abstract
Epigenetic mechanisms are thought to be involved in the reduced developmental capacity of early prepubertal ewe oocytes compared to their adult counterparts. In this study, we have analyzed the global DNA methylation pattern and in vitro meiotic and developmental competence of oocytes at the germinal vesicle (GV) stage obtained from adult and 3-month-old donors. All oocytes were aspirated from antral follicles with a diameter ≥3 mm, and DNA methylation on 5-methylcytosine was detected by immunofluorescence using an anti-methyl cytosine antibody. The main global chromatin configuration pattern shown by both prepubertal and adult ovine oocytes corresponded to condensed chromatin localized close to the nuclear envelope (the SNE pattern). Immunofluorescence showed that a global bright nuclear staining of 5-methylcytosine (5-mC) occurred in all germinal vesicle stage oocytes and matched the propidium iodide staining pattern. The total fluorescence intensity values of lamb GVs were not lower than those observed in adult GVs. The meiotic competence and cleavage rates were similar in adult and prepubertal oocytes, however, the developmental competence of embryos to reach blastocysts was higher for adult oocytes than lamb oocytes (p<0.0001). In conclusion, our results indicate that adult-size oocytes derived from 3 to 4 month old prepubertal ewes show similar GV morphology and DNA methylation staining patterns to those obtained from adult animals, despite exhibiting a lower developmental competence.
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Affiliation(s)
- María J Cocero
- Departamento de Reproducción Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Avenida Puerta de Hierro 12 local 10, 28040, Madrid, Spain.
| | - Pilar Marigorta
- Departamento de Reproducción Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Avenida Puerta de Hierro 12 local 10, 28040, Madrid, Spain
| | - Fernando Novillo
- Departamento de Reproducción Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Avenida Puerta de Hierro 12 local 10, 28040, Madrid, Spain
| | - José Folch
- Unidad de Producción y Sanidad Animal, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Gobierno de Aragón, Av. Montañana 930, 50059, Zaragoza, Spain; Instituto Agroalimentario de Aragón - IA2 (CITA-Universidad de Zaragoza), Spain
| | - Pilar Sánchez
- Unidad de Producción y Sanidad Animal, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Gobierno de Aragón, Av. Montañana 930, 50059, Zaragoza, Spain; Instituto Agroalimentario de Aragón - IA2 (CITA-Universidad de Zaragoza), Spain
| | - José L Alabart
- Unidad de Producción y Sanidad Animal, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Gobierno de Aragón, Av. Montañana 930, 50059, Zaragoza, Spain; Instituto Agroalimentario de Aragón - IA2 (CITA-Universidad de Zaragoza), Spain
| | - Belén Lahoz
- Unidad de Producción y Sanidad Animal, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Gobierno de Aragón, Av. Montañana 930, 50059, Zaragoza, Spain; Instituto Agroalimentario de Aragón - IA2 (CITA-Universidad de Zaragoza), Spain
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Viluksela M, Pohjanvirta R. Multigenerational and Transgenerational Effects of Dioxins. Int J Mol Sci 2019; 20:E2947. [PMID: 31212893 PMCID: PMC6627869 DOI: 10.3390/ijms20122947] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 06/12/2019] [Accepted: 06/13/2019] [Indexed: 12/12/2022] Open
Abstract
Dioxins are ubiquitous and persistent environmental contaminants whose background levels are still reason for concern. There is mounting evidence from both epidemiological and experimental studies that paternal exposure to the most potent congener of dioxins, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), can lower the male/female ratio of offspring. Moreover, in laboratory rodents and zebrafish, TCDD exposure of parent animals has been reported to result in reduced reproductive performance along with other adverse effects in subsequent generations, foremost through the paternal but also via the maternal germline. These impacts have been accompanied by epigenetic alterations in placenta and/or sperm cells, including changes in methylation patterns of imprinted genes. Here, we review recent key studies in this field with an attempt to provide an up-to-date picture of the present state of knowledge to the reader. These studies provide biological plausibility for the potential of dioxin exposure at a critical time-window to induce epigenetic alterations across multiple generations and the significance of aryl hydrocarbon receptor (AHR) in mediating these effects. Currently available data do not allow to accurately estimate the human health implications of these findings, although epidemiological evidence on lowered male/female ratio suggests that this effect may take place at realistic human exposure levels.
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Affiliation(s)
- Matti Viluksela
- School of Pharmacy and Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland.
- Environmental Health Unit, National Institute for Health and Welfare, P.O. Box 95, FI-70701 Kuopio, Finland.
| | - Raimo Pohjanvirta
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, P.O. Box 66, FI-00014 Helsinki, Finland.
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96
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Men Y, Zhao Y, Zhang P, Zhang H, Gao Y, Liu J, Feng Y, Li L, Shen W, Sun Z, Min L. Gestational exposure to low-dose zearalenone disrupting offspring spermatogenesis might be through epigenetic modifications. Basic Clin Pharmacol Toxicol 2019; 125:382-393. [PMID: 31058416 DOI: 10.1111/bcpt.13243] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 04/24/2019] [Indexed: 12/12/2022]
Abstract
Zearalenone (ZEA), a F-2 mycotoxin produced by Fusarium, has been found to be an endocrine disruptor through oestrogen receptor signalling pathway to impair spermatogenesis. The disruption on reproductive systems by ZEA exposure might be transgenerational. In our previous report, we have found that low dose (lower than no-observed effect level, NOEL) of ZEA impaired mouse spermatogenesis and decreased mouse semen quality. The purpose of the current investigation was to explore the impacts of low-dose ZEA on spermatogenesis in the offspring after prenatal exposure and the underlying mechanisms. And it demonstrated that prenatal low-dose ZEA exposure disrupted the meiosis process to inhibit the spermatogenesis in offspring and even to diminish the semen quality by the decrease in spermatozoa motility and concentration. The DNA methylation marker 5hmC was decreased, the histone methylation markers H3K9 and H3K27 were elevated, and oestrogen receptor alpha was reduced in the offspring testis after prenatal low-dose ZEA exposure. The data suggest that the disruption in spermatogenesis by prenatal low-dose ZEA exposure may be through the modifications on epigenetic pathways (DNA methylation and histone methylation) and the interactions with oestrogen receptor signalling pathway. Moreover, in the current study, the male offspring were indirectly exposed to low-dose ZEA through placenta and the spermatogenesis in offspring was disrupted which suggested that the toxicity of ZEA on reproductive systems was very severe. Therefore, we strongly recommend that greater attention should be paid to this mycotoxin to minimize its adverse impact on human spermatogenesis.
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Affiliation(s)
- Yuhao Men
- College of Animal Sciences and Technology, Qingdao Agricultural University, Qingdao, China
| | - Yong Zhao
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Pengfei Zhang
- College of Animal Sciences and Technology, Qingdao Agricultural University, Qingdao, China.,College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Hongfu Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yishan Gao
- College of Animal Sciences and Technology, Qingdao Agricultural University, Qingdao, China
| | - Jing Liu
- University Research Core, Qingdao Agricultural University, Qingdao, China
| | - Yanni Feng
- College of Veterinary Sciences, Qingdao Agricultural University, Qingdao, China
| | - Lan Li
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Wei Shen
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Zhongyi Sun
- Center for Reproductive Medicine, Shenzhen Hospital, Peking University, Shenzhen, China
| | - Lingjiang Min
- College of Animal Sciences and Technology, Qingdao Agricultural University, Qingdao, China
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97
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Duan JE, Jiang ZC, Alqahtani F, Mandoiu I, Dong H, Zheng X, Marjani SL, Chen J, Tian XC. Methylome Dynamics of Bovine Gametes and in vivo Early Embryos. Front Genet 2019; 10:512. [PMID: 31191619 PMCID: PMC6546829 DOI: 10.3389/fgene.2019.00512] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 05/10/2019] [Indexed: 01/12/2023] Open
Abstract
DNA methylation undergoes drastic fluctuation during early mammalian embryogenesis. The dynamics of global DNA methylation in bovine embryos, however, have mostly been studied by immunostaining. We adopted the whole genome bisulfite sequencing (WGBS) method to characterize stage-specific genome-wide DNA methylation in bovine sperm, immature oocytes, oocytes matured in vivo and in vitro, as well as in vivo developed single embryos at the 2-, 4-, 8-, and 16-cell stages. We found that the major wave of genome-wide DNA demethylation was complete by the 8-cell stage when de novo methylation became prominent. Sperm and oocytes were differentially methylated in numerous regions (DMRs), which were primarily intergenic, suggesting that these non-coding regions may play important roles in gamete specification. DMRs were also identified between in vivo and in vitro matured oocytes, suggesting environmental effects on epigenetic modifications. In addition, virtually no (less than 1.5%) DNA methylation was found in mitochondrial DNA. Finally, by using RNA-seq data generated from embryos at the same developmental stages, we revealed a weak inverse correlation between gene expression and promoter methylation. This comprehensive analysis provides insight into the critical features of the bovine embryo methylome, and serves as an important reference for embryos produced in vitro, such as by in vitro fertilization and cloning. Lastly, these data can also provide a model for the epigenetic dynamics in human early embryos.
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Affiliation(s)
- Jingyue Ellie Duan
- Department of Animal Science, University of Connecticut, Storrs, CT, United States
| | - Zongliang Carl Jiang
- School of Animal Science, AgCenter, Louisiana State University, Baton Rouge, LA, United States
| | - Fahad Alqahtani
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, United States
| | - Ion Mandoiu
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, United States
| | - Hong Dong
- Institute of Animal Science, Xinjiang Academy of Animal Sciences, Ürümqi, China
| | - Xinbao Zheng
- Institute of Animal Science, Xinjiang Academy of Animal Sciences, Ürümqi, China
| | - Sadie L Marjani
- Department of Biology, Central Connecticut State University, New Britain, CT, United States
| | - Jingbo Chen
- Institute of Animal Science, Xinjiang Academy of Animal Sciences, Ürümqi, China
| | - Xiuchun Cindy Tian
- Department of Animal Science, University of Connecticut, Storrs, CT, United States
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98
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Oblette A, Rondeaux J, Dumont L, Delessard M, Saulnier J, Rives A, Rives N, Rondanino C. DNA methylation and histone post-translational modifications in the mouse germline following in-vitro maturation of fresh or cryopreserved prepubertal testicular tissue. Reprod Biomed Online 2019; 39:383-401. [PMID: 31315814 DOI: 10.1016/j.rbmo.2019.05.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 04/22/2019] [Accepted: 05/09/2019] [Indexed: 02/07/2023]
Abstract
RESEARCH QUESTION Do cryopreservation and in-vitro culture procedures affect the expression of DNA methyltransferases (DNMT) and histone-modifying enzymes, as well as the establishment of DNA methylation and histone post-translational modifications (PTM) in germ cells in prepubertal mouse testicular tissue? DESIGN This study investigated the expression of epigenetic modification enzymes, DNA methylation and histone PTM, and the spermatogenic progression after in-vitro maturation of fresh or cryopreserved mouse prepubertal testicular tissue. Fresh or cryopreserved testicular fragments from 6-7 days post-partum mice were cultured for 30 days in the presence of retinol with or without FSH. RESULTS The in-vitro maturation of fresh or cryopreserved tissue allowed the differentiation of spermatogonia into spermatozoa. Differences in the levels of transcripts encoding epigenetic modification enzymes (Dnmt1, Dnmt3a, Jarid1b, Src1, Sirt1, Hdac1) were found between 30-day tissue cultures and age-matched in-vivo controls. DNMT1/DNMT3a expression and the presence of 5-methylcytosine (5mC) were detected in spermatogonia and leptotene/zygotene spermatocytes in cultures. The relative 5mC fluorescence intensity was similar in spermatozoa produced in cultures of cryopreserved tissues or in vivo. H3K4me3, H3K9ac and H4K8ac were present in all germ cell types but differences in the proportion of germ cells containing these epigenetic marks were found after cultures. CONCLUSIONS Despite differences with the in-vivo situation, DNA methylation and histone methylation and acetylation occur in the mouse germline in in-vitro matured fresh or cryopreserved mouse prepubertal testicular tissue, and the expression of the enzymes catalysing these epigenetic modifications are maintained in vitro.
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Affiliation(s)
- Antoine Oblette
- Normandie University, UNIROUEN, EA 4308 'Gametogenesis and Gamete Quality', Rouen University Hospital, Department of Reproductive Biology-CECOS, Rouen F 76000, France
| | - Julie Rondeaux
- Normandie University, UNIROUEN, EA 4308 'Gametogenesis and Gamete Quality', Rouen University Hospital, Department of Reproductive Biology-CECOS, Rouen F 76000, France
| | - Ludovic Dumont
- Normandie University, UNIROUEN, EA 4308 'Gametogenesis and Gamete Quality', Rouen University Hospital, Department of Reproductive Biology-CECOS, Rouen F 76000, France
| | - Marion Delessard
- Normandie University, UNIROUEN, EA 4308 'Gametogenesis and Gamete Quality', Rouen University Hospital, Department of Reproductive Biology-CECOS, Rouen F 76000, France
| | - Justine Saulnier
- Normandie University, UNIROUEN, EA 4308 'Gametogenesis and Gamete Quality', Rouen University Hospital, Department of Reproductive Biology-CECOS, Rouen F 76000, France
| | - Aurélie Rives
- Normandie University, UNIROUEN, EA 4308 'Gametogenesis and Gamete Quality', Rouen University Hospital, Department of Reproductive Biology-CECOS, Rouen F 76000, France
| | - Nathalie Rives
- Normandie University, UNIROUEN, EA 4308 'Gametogenesis and Gamete Quality', Rouen University Hospital, Department of Reproductive Biology-CECOS, Rouen F 76000, France
| | - Christine Rondanino
- Normandie University, UNIROUEN, EA 4308 'Gametogenesis and Gamete Quality', Rouen University Hospital, Department of Reproductive Biology-CECOS, Rouen F 76000, France.
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Abstract
Germ cells undergo epigenome reprogramming for proper development of the next generation. The achievement of in vitro germ cell derivation from human and mouse pluripotent stem cells and further differentiation in a plane culture and in aggregation with gonadal somatic cells offers unprecedented opportunities for investigation of the germ cell development. Moreover, advances in low-input/single-cell genomics have enabled detailed investigation of epigenome dynamics during germ cell development. These technologies have advanced our knowledge of epigenome reprogramming during the specification and development of primordial germ cells, their sex differentiation, and gametogenesis. Key findings include details of chromatin remodeling and transcriptional regulation, progressive and comprehensive DNA demethylation, and tight links between DNA demethylation and histone marks during the development of primordial germ cells, acquisition of unique totipotent epigenome during oogenesis (e.g., broad H3K4me3 domains and low-level three-dimensional genomic organization), and unexpected organization of the sperm genome. Moreover, these studies suggest the importance of epigenome analyses for in-depth evaluations of in vitro gametogenesis.
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Affiliation(s)
- Kazuki Kurimoto
- Department of Embryology, Nara Medical University, Nara, Japan.
| | - Mitinori Saitou
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan; Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan; Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
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100
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Gheldof A, Mackay DJG, Cheong Y, Verpoest W. Genetic diagnosis of subfertility: the impact of meiosis and maternal effects. J Med Genet 2019; 56:271-282. [PMID: 30728173 PMCID: PMC6581078 DOI: 10.1136/jmedgenet-2018-105513] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Revised: 12/24/2018] [Accepted: 12/27/2018] [Indexed: 02/06/2023]
Abstract
During reproductive age, approximately one in seven couples are confronted with fertility problems. While the aetiology is diverse, including infections, metabolic diseases, hormonal imbalances and iatrogenic effects, it is becoming increasingly clear that genetic factors have a significant contribution. Due to the complex nature of infertility that often hints at a multifactorial cause, the search for potentially causal gene mutations in idiopathic infertile couples has remained difficult. Idiopathic infertility patients with a suspicion of an underlying genetic cause can be expected to have mutations in genes that do not readily affect general health but are only essential in certain processes connected to fertility. In this review, we specifically focus on genes involved in meiosis and maternal-effect processes, which are of critical importance for reproduction and initial embryonic development. We give an overview of genes that have already been linked to infertility in human, as well as good candidates which have been described in other organisms. Finally, we propose a phenotypic range in which we expect an optimal diagnostic yield of a meiotic/maternal-effect gene panel.
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Affiliation(s)
- Alexander Gheldof
- Center for Medical Genetics, Universitair Ziekenhuis Brussel, Brussels, Belgium
- Reproduction and Genetics Department, Vrije Universiteit Brussel, Brussels, Belgium
| | - Deborah J G Mackay
- Faculty of Medicine, University of Southampton, Southampton University Hospital, Southampton, UK
| | - Ying Cheong
- Complete Fertility, Human Development of Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Willem Verpoest
- Reproduction and Genetics Department, Vrije Universiteit Brussel, Brussels, Belgium
- Center for Reproductive Medicine, Universitair Ziekenhuis Brussel, Brussels, Belgium
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