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Yamazaki W, Tan SL, Taketo T. Role of the X and Y Chromosomes in the Female Germ Cell Line Development in the Mouse (Mus musculus). Sex Dev 2022:1-10. [PMID: 35235936 DOI: 10.1159/000521151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 11/18/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND In eutherian mammals, the sex chromosome complement, XX and XY, determines sexual differentiation of gonadal primordia into testes and ovaries, which in turn direct differentiation of germ cells into haploid sperm and oocytes, respectively. When gonadal sex is reversed, however, the germ cell sex becomes discordant with the chromosomal sex. XY females in humans are infertile, while XY females in the mouse (Mus musculus) are subfertile or infertile dependent on the cause of sex reversal and the genetic background. This article reviews publications to understand how the sex chromosome complement affects the fertility of XY oocytes by comparing with XX and monosomy X (XO) oocytes. SUMMARY The results highlight 2 folds disadvantage of XY oocytes over XX oocytes: (1) the X and Y chromosomes fail to pair during the meiotic prophase I, resulting in sex chromosome aneuploidy at the first meiotic division and (2) expression of the Y-linked genes during oocyte growth affects the transcriptome landscape and renders the ooplasmic component incompetent for embryonic development. Key Message: The XX chromosome complement gives the oocyte the highest competence for embryonic development.
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Affiliation(s)
- Wataru Yamazaki
- Department of Surgery, McGill University, Montreal, Québec, Canada.,Research Institute of McGill University Health Centre, Montreal, Québec, Canada
| | - Seang Lin Tan
- Department of Obstetrics and Gynecology, McGill University, Montreal, Québec, Canada.,Research Institute of McGill University Health Centre, Montreal, Québec, Canada.,OriginElle Fertility Clinic and Women's Health Centre, Montreal, Québec, Canada
| | - Teruko Taketo
- Department of Surgery, McGill University, Montreal, Québec, Canada.,Department of Obstetrics and Gynecology, McGill University, Montreal, Québec, Canada.,Department of Biology, McGill University, Montreal, Québec, Canada.,Research Institute of McGill University Health Centre, Montreal, Québec, Canada
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52
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Dean W. Pathways of DNA Demethylation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:211-238. [DOI: 10.1007/978-3-031-11454-0_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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53
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Pastor WA, Kwon SY. Distinctive aspects of the placental epigenome and theories as to how they arise. Cell Mol Life Sci 2022; 79:569. [PMID: 36287261 PMCID: PMC9606139 DOI: 10.1007/s00018-022-04568-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 08/18/2022] [Accepted: 09/21/2022] [Indexed: 11/26/2022]
Abstract
The placenta has a methylome dramatically unlike that of any somatic cell type. Among other distinctions, it features low global DNA methylation, extensive “partially methylated domains” packed in dense heterochromatin and methylation of hundreds of CpG islands important in somatic development. These features attract interest in part because a substantial fraction of human cancers feature the exact same phenomena, suggesting parallels between epigenome formation in placentation and cancer. Placenta also features an expanded set of imprinted genes, some of which come about by distinctive developmental pathways. Recent discoveries, some from far outside the placental field, shed new light on how the unusual placental epigenetic state may arise. Nonetheless, key questions remain unresolved.
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Affiliation(s)
- William A Pastor
- Department of Biochemistry, McGill University, Montreal, QC, H3G 1Y6, Canada.
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, QC, H3A 1A3, Canada.
| | - Sin Young Kwon
- Department of Biochemistry, McGill University, Montreal, QC, H3G 1Y6, Canada
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54
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WGBS combined with RNA-seq analysis revealed that Dnmt1 affects the methylation modification and gene expression changes during mouse oocyte vitrification. Theriogenology 2022; 177:11-21. [PMID: 34653792 DOI: 10.1016/j.theriogenology.2021.09.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 01/01/2023]
Abstract
Understanding the molecular level changes of oocyte cryopreservation and the subsequent warming process is essential for improving the oocyte cryopreservation technologies. Here, we collected the mature metaphase II (MII) oocytes from mice and vitrified. After thawing, single-cell whole-genome bisulphite sequencing (scWGBS) and single-cell RNA sequencing (scRNA-seq) were used to investigate the molecular attributes of this process. Compared to the fresh oocytes, the vitrified oocytes had lower global methylation and gene expression levels, and 1426 genes up-regulated and 3321 genes down-regulated. The 1426 up-regulated differentially expressed genes (DEGs) in the vitrified oocytes were mainly associated with the histone ubiquitination, while the 3321 down-regulated genes were mainly enriched in the mitochondrion organisation and ATP metabolism processes. The differentially methylated regions (DMRs) were mainly located in promoter, intron and exon region of genes, and the length of DMRs in the vitrified oocytes were also significantly lower than that of the fresh oocytes. Notably, there were no significant difference in the expression levels of DNA demethylases (Tet1, Tet2 and Tet3) and methyltransferases (Dnmt3a and Dnmt3b) between two treatments of oocytes. However, Dnmt1 and kcnq1ot1, which are responsible for maintaining DNA methylation, were significantly down regulated in the vitrified oocytes. Gene regulatory network (GRN) analysis showed the Dnmt1 and kcnq1ot1 play a core role in regulating methylation and expression levels of downstream genes. Moreover, some genes associated with oocyte quality were significantly down-regulated in the vitrified oocytes. The present data provides a new perspective for understanding the impact of vitrification on oocytes.
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55
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Ramakrishna NB, Murison K, Miska EA, Leitch HG. Epigenetic Regulation during Primordial Germ Cell Development and Differentiation. Sex Dev 2021; 15:411-431. [PMID: 34847550 DOI: 10.1159/000520412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/10/2021] [Indexed: 11/19/2022] Open
Abstract
Germline development varies significantly across metazoans. However, mammalian primordial germ cell (PGC) development has key conserved landmarks, including a critical period of epigenetic reprogramming that precedes sex-specific differentiation and gametogenesis. Epigenetic alterations in the germline are of unique importance due to their potential to impact the next generation. Therefore, regulation of, and by, the non-coding genome is of utmost importance during these epigenomic events. Here, we detail the key chromatin changes that occur during mammalian PGC development and how these interact with the expression of non-coding RNAs alongside broader epitranscriptomic changes. We identify gaps in our current knowledge, in particular regarding epigenetic regulation in the human germline, and we highlight important areas of future research.
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Affiliation(s)
- Navin B Ramakrishna
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Genome Institute of Singapore, A*STAR, Biopolis, Singapore, Singapore
| | - Keir Murison
- MRC London Institute of Medical Sciences, London, United Kingdom
- Institute of Clinical Sciences, Imperial College London, London, United Kingdom
| | - Eric A Miska
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - Harry G Leitch
- MRC London Institute of Medical Sciences, London, United Kingdom
- Institute of Clinical Sciences, Imperial College London, London, United Kingdom
- Centre for Paediatrics and Child Health, Faculty of Medicine, Imperial College London, London, United Kingdom
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56
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Allen MC, Moog NK, Buss C, Yen E, Gustafsson HC, Sullivan EL, Graham AM. Co-occurrence of preconception maternal childhood adversity and opioid use during pregnancy: Implications for offspring brain development. Neurotoxicol Teratol 2021; 88:107033. [PMID: 34601061 PMCID: PMC8578395 DOI: 10.1016/j.ntt.2021.107033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 09/20/2021] [Accepted: 09/24/2021] [Indexed: 12/11/2022]
Abstract
Understanding of the effects of in utero opioid exposure on neurodevelopment is a priority given the recent dramatic increase in opioid use among pregnant individuals. However, opioid abuse does not occur in isolation-pregnant individuals abusing opioids often have a significant history of adverse experiences in childhood, among other co-occurring factors. Understanding the specific pathways in which these frequently co-occurring factors may interact and cumulatively influence offspring brain development in utero represents a priority for future research in this area. We highlight maternal history of childhood adversity (CA) as one such co-occurring factor that is more prevalent among individuals using opioids during pregnancy and which is increasingly shown to affect offspring neurodevelopment through mechanisms beginning in utero. Despite the high incidence of CA history in pregnant individuals using opioids, we understand very little about the effects of comorbid prenatal opioid exposure and maternal CA history on fetal brain development. Here, we first provide an overview of current knowledge regarding effects of opioid exposure and maternal CA on offspring neurodevelopment that may occur during gestation. We then outline potential mechanistic pathways through which these factors might have interactive and cumulative influences on offspring neurodevelopment as a foundation for future research in this area.
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Affiliation(s)
- Madeleine C Allen
- Department of Psychiatry, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd., Portland, OR 97239, United States
| | - Nora K Moog
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Psychology, Luisenstrasse 57, 10117 Berlin, Germany
| | - Claudia Buss
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Psychology, Luisenstrasse 57, 10117 Berlin, Germany; Development, Health and Disease Research Program, University of California, Irvine, 837 Health Sciences Drive, Irvine, California 92697, United States
| | - Elizabeth Yen
- Department of Pediatrics, Tufts Medical Center, Boston, MA 02111, United States
| | - Hanna C Gustafsson
- Department of Psychiatry, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd., Portland, OR 97239, United States
| | - Elinor L Sullivan
- Department of Psychiatry, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd., Portland, OR 97239, United States; Division of Neuroscience, Oregon National Primate Research Center, 505 NW 185(th) Ave., Beaverton, OR 97006, United States; Department of Behavioral Neuroscience, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd., Portland, OR 97239, United States
| | - Alice M Graham
- Department of Psychiatry, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd., Portland, OR 97239, United States.
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57
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Chu C, Zhang W, Kang Y, Si C, Ji W, Niu Y, Zhang Y. Analysis of developmental imprinting dynamics in primates using SNP-free methods to identify imprinting defects in cloned placenta. Dev Cell 2021; 56:2826-2840.e7. [PMID: 34619096 DOI: 10.1016/j.devcel.2021.09.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 08/25/2021] [Accepted: 09/10/2021] [Indexed: 12/30/2022]
Abstract
Our knowledge of genomic imprinting in primates is lagging behind that of mice largely because of the difficulties of allelic analyses in outbred animals. To understand imprinting dynamics in primates, we profiled transcriptomes, DNA methylomes, and H3K27me3 in uniparental monkey embryos. We further developed single-nucleotide-polymorphism (SNP)-free methods, TARSII and CARSII, to identify germline differentially methylated regions (DMRs) in somatic tissues. Our comprehensive analyses showed that allelic DNA methylation, but not H3K27me3, is a major mark that correlates with paternal-biasedly expressed genes (PEGs) in uniparental monkey embryos. Interestingly, primate germline DMRs are different from PEG-associated DMRs in early embryos and are enriched in placenta. Strikingly, most placenta-specific germline DMRs are lost in placenta of cloned monkeys. Collectively, our study establishes SNP-free germline DMR identification methods, defines developmental imprinting dynamics in primates, and demonstrates imprinting defects in cloned monkey placenta, which provides important clues for improving primate cloning.
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Affiliation(s)
- Chu Chu
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China; Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Wenhao Zhang
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA.
| | - Yu Kang
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China; Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Chenyang Si
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China; Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Weizhi Ji
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China.
| | - Yuyu Niu
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China; Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China.
| | - Yi Zhang
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, WAB-149G, 200 Longwood Avenue, Boston, MA 02115, USA.
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58
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Keshet G, Benvenisty N. Large-scale analysis of imprinting in naive human pluripotent stem cells reveals recurrent aberrations and a potential link to FGF signaling. Stem Cell Reports 2021; 16:2520-2533. [PMID: 34597600 PMCID: PMC8514966 DOI: 10.1016/j.stemcr.2021.09.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 09/01/2021] [Accepted: 09/02/2021] [Indexed: 01/21/2023] Open
Abstract
Genomic imprinting is a parent-of-origin dependent monoallelic expression of genes. Previous studies showed that conversion of primed human pluripotent stem cells (hPSCs) into naive pluripotency is accompanied by genome-wide loss of methylation that includes imprinted loci. However, the extent of aberrant biallelic expression of imprinted genes is still unknown. Here, we analyze loss of imprinting (LOI) in a large cohort of both bulk and single-cell RNA sequencing samples of naive and primed hPSCs. We show that naive hPSCs exhibit high levels of non-random LOI, with bias toward paternally methylated imprinting control regions. Importantly, we show that different protocols used for the primed to naive conversion led to different extents of LOI, tightly correlated to FGF signaling. This analysis sheds light on the process of LOI occurring during the conversion to naive pluripotency and highlights the importance of these events when modeling disease and development or when utilizing the cells for therapy.
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Affiliation(s)
- Gal Keshet
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel
| | - Nissim Benvenisty
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel.
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59
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Newkirk SJ, An W. UHRF1: a jack of all trades, and a master epigenetic regulator during spermatogenesis. Biol Reprod 2021; 102:1147-1152. [PMID: 32101289 DOI: 10.1093/biolre/ioaa026] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 02/26/2020] [Indexed: 01/03/2023] Open
Affiliation(s)
- Simon J Newkirk
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD, USA
| | - Wenfeng An
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD, USA
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60
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Ruiz de la Cruz M, de la Cruz Montoya AH, Rojas Jiménez EA, Martínez Gregorio H, Díaz Velásquez CE, Paredes de la Vega J, de la Cruz Hernández-Hernández F, Vaca Paniagua F. Cis-Acting Factors Causing Secondary Epimutations: Impact on the Risk for Cancer and Other Diseases. Cancers (Basel) 2021; 13:cancers13194807. [PMID: 34638292 PMCID: PMC8508567 DOI: 10.3390/cancers13194807] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/09/2021] [Accepted: 08/15/2021] [Indexed: 12/25/2022] Open
Abstract
Epigenetics affects gene expression and contributes to disease development by alterations known as epimutations. Hypermethylation that results in transcriptional silencing of tumor suppressor genes has been described in patients with hereditary cancers and without pathogenic variants in the coding region of cancer susceptibility genes. Although somatic promoter hypermethylation of these genes can occur in later stages of the carcinogenic process, constitutional methylation can be a crucial event during the first steps of tumorigenesis, accelerating tumor development. Primary epimutations originate independently of changes in the DNA sequence, while secondary epimutations are a consequence of a mutation in a cis or trans-acting factor. Secondary epimutations have a genetic basis in cis of the promoter regions of genes involved in familial cancers. This highlights epimutations as a novel carcinogenic mechanism whose contribution to human diseases is underestimated by the scarcity of the variants described. In this review, we provide an overview of secondary epimutations and present evidence of their impact on cancer. We propose the necessity for genetic screening of loci associated with secondary epimutations in familial cancer as part of prevention programs to improve molecular diagnosis, secondary prevention, and reduce the mortality of these diseases.
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Affiliation(s)
- Miguel Ruiz de la Cruz
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla 54090, Mexico; (M.R.d.l.C.); (E.A.R.J.); (H.M.G.); (C.E.D.V.); (J.P.d.l.V.)
- Avenida Instituto Politécnico Nacional # 2508, Colonia San Pedro Zacatenco, Delegación Gustavo A. Madero, C.P. Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Mexico City 07360, Mexico;
| | | | - Ernesto Arturo Rojas Jiménez
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla 54090, Mexico; (M.R.d.l.C.); (E.A.R.J.); (H.M.G.); (C.E.D.V.); (J.P.d.l.V.)
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla 54090, Mexico;
| | - Héctor Martínez Gregorio
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla 54090, Mexico; (M.R.d.l.C.); (E.A.R.J.); (H.M.G.); (C.E.D.V.); (J.P.d.l.V.)
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla 54090, Mexico;
| | - Clara Estela Díaz Velásquez
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla 54090, Mexico; (M.R.d.l.C.); (E.A.R.J.); (H.M.G.); (C.E.D.V.); (J.P.d.l.V.)
| | - Jimena Paredes de la Vega
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla 54090, Mexico; (M.R.d.l.C.); (E.A.R.J.); (H.M.G.); (C.E.D.V.); (J.P.d.l.V.)
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla 54090, Mexico;
| | - Fidel de la Cruz Hernández-Hernández
- Avenida Instituto Politécnico Nacional # 2508, Colonia San Pedro Zacatenco, Delegación Gustavo A. Madero, C.P. Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Mexico City 07360, Mexico;
| | - Felipe Vaca Paniagua
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla 54090, Mexico; (M.R.d.l.C.); (E.A.R.J.); (H.M.G.); (C.E.D.V.); (J.P.d.l.V.)
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla 54090, Mexico;
- Subdirección de Investigación Básica, Instituto Nacional de Cancerología, Ciudad de México 14080, Mexico
- Correspondence: ; Tel.: +52-55-5623-1333 (ext. 39788)
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61
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Wang F, Qin Z, Li Z, Yang S, Gao T, Sun L, Wang D. Dnmt3aa but Not Dnmt3ab Is Required for Maintenance of Gametogenesis in Nile Tilapia ( Oreochromis niloticus). Int J Mol Sci 2021; 22:ijms221810170. [PMID: 34576333 PMCID: PMC8469005 DOI: 10.3390/ijms221810170] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 12/20/2022] Open
Abstract
Dnmt3a, a de novo methyltransferase, is essential for mammalian germ line DNA methylation. Only one Dnmt3a is identified in mammals, and homozygous mutants of Dnmt3a are lethal, while two Dnmt3a paralogs, dnmt3aa and dnmt3ab, are identified in teleosts due to the third round of genome duplication, and homozygous mutants of dnmt3aa and dnmt3ab are viable in zebrafish. The expression patterns and roles of dnmt3aa and dnmt3ab in gonadal development remain poorly understood in teleosts. In this study, we elucidated the precise expression patterns of dnmt3aa and dnmt3ab in tilapia gonads. Dnmt3aa was highly expressed in oogonia, phase I and II oocytes and granulosa cells in ovaries and spermatogonia and spermatocytes in testes, while dnmt3ab was mainly expressed in ovarian granulosa cells and testicular spermatocytes. The mutation of dnmt3aa and dnmt3ab was achieved by CRISPR/Cas9 in tilapia. Lower gonadosomatic index (GSI), increased apoptosis of oocytes and spermatocytes and significantly reduced sperm quality were observed in dnmt3aa−/− mutants, while normal gonadal development was observed in dnmt3ab−/− mutants. Consistently, the expression of apoptotic genes was significantly increased in dnmt3aa−/− mutants. In addition, the 5-methylcytosine (5-mC) level in dnmt3aa−/− gonads was decreased significantly, compared with that of dnmt3ab−/− and wild type (WT) gonads. Taken together, our results suggest that dnmt3aa, not dnmt3ab, plays important roles in maintaining gametogenesis in teleosts.
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Affiliation(s)
| | | | | | | | | | - Lina Sun
- Correspondence: (L.S.); (D.W.); Tel.: +86-23-6825-3702 (D.W.)
| | - Deshou Wang
- Correspondence: (L.S.); (D.W.); Tel.: +86-23-6825-3702 (D.W.)
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62
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Kinoshita M, Li MA, Barber M, Mansfield W, Dietmann S, Smith A. Disabling de novo DNA methylation in embryonic stem cells allows an illegitimate fate trajectory. Proc Natl Acad Sci U S A 2021; 118:e2109475118. [PMID: 34518230 PMCID: PMC8463881 DOI: 10.1073/pnas.2109475118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/18/2021] [Indexed: 12/13/2022] Open
Abstract
Genome remethylation is essential for mammalian development but specific reasons are unclear. Here we examined embryonic stem (ES) cell fate in the absence of de novo DNA methyltransferases. We observed that ES cells deficient for both Dnmt3a and Dnmt3b are rapidly eliminated from chimeras. On further investigation we found that in vivo and in vitro the formative pluripotency transition is derailed toward production of trophoblast. This aberrant trajectory is associated with failure to suppress activation of Ascl2Ascl2 encodes a bHLH transcription factor expressed in the placenta. Misexpression of Ascl2 in ES cells provokes transdifferentiation to trophoblast-like cells. Conversely, Ascl2 deletion rescues formative transition of Dnmt3a/b mutants and improves contribution to chimeric epiblast. Thus, de novo DNA methylation safeguards against ectopic activation of Ascl2 However, Dnmt3a/b-deficient cells remain defective in ongoing embryogenesis. We surmise that multiple developmental transitions may be secured by DNA methylation silencing potentially disruptive genes.
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Affiliation(s)
- Masaki Kinoshita
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, United Kingdom
| | - Meng Amy Li
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, United Kingdom
| | - Michael Barber
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, United Kingdom
| | - William Mansfield
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, United Kingdom
| | - Sabine Dietmann
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, United Kingdom
| | - Austin Smith
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, United Kingdom;
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
- Living Systems Institute, University of Exeter, Exeter EX4 4QD, United Kingdom
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63
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Ben Maamar M, Nilsson EE, Skinner MK. Epigenetic transgenerational inheritance, gametogenesis and germline development†. Biol Reprod 2021; 105:570-592. [PMID: 33929020 PMCID: PMC8444706 DOI: 10.1093/biolre/ioab085] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/12/2021] [Accepted: 04/22/2021] [Indexed: 12/14/2022] Open
Abstract
One of the most important developing cell types in any biological system is the gamete (sperm and egg). The transmission of phenotypes and optimally adapted physiology to subsequent generations is in large part controlled by gametogenesis. In contrast to genetics, the environment actively regulates epigenetics to impact the physiology and phenotype of cellular and biological systems. The integration of epigenetics and genetics is critical for all developmental biology systems at the cellular and organism level. The current review is focused on the role of epigenetics during gametogenesis for both the spermatogenesis system in the male and oogenesis system in the female. The developmental stages from the initial primordial germ cell through gametogenesis to the mature sperm and egg are presented. How environmental factors can influence the epigenetics of gametogenesis to impact the epigenetic transgenerational inheritance of phenotypic and physiological change in subsequent generations is reviewed.
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Affiliation(s)
- Millissia Ben Maamar
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Eric E Nilsson
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Michael K Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, USA
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64
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Production of functional oocytes requires maternally expressed PIWI genes and piRNAs in golden hamsters. Nat Cell Biol 2021; 23:1002-1012. [PMID: 34489571 DOI: 10.1038/s41556-021-00745-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 07/27/2021] [Indexed: 02/06/2023]
Abstract
Many animals have a conserved adaptive genome defence system known as the Piwi-interacting RNA (piRNA) pathway, which is essential for germ cell development and function. Disruption of individual mouse Piwi genes results in male but not female sterility, leading to the assumption that PIWI genes play little or no role in mammalian oocytes. Here, we report the generation of PIWI-defective golden hamsters, which have defects in the production of functional oocytes. The mechanisms involved vary among the hamster PIWI genes, whereby the lack of PIWIL1 has a major impact on gene expression, including hamster-specific young transposon de-silencing, whereas PIWIL3 deficiency has little impact on gene expression in oocytes, although DNA methylation was reduced to some extent in PIWIL3-deficient oocytes. Our findings serve as the foundation for developing useful models to study the piRNA pathway in mammalian oocytes, including humans.
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65
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Zhao ZH, Schatten H, Sun QY. High-throughput sequencing reveals landscapes of female germ cell development. Mol Hum Reprod 2021; 26:738-747. [PMID: 32866227 DOI: 10.1093/molehr/gaaa059] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/09/2020] [Indexed: 12/11/2022] Open
Abstract
Female germ cell development is a highly complex process that includes meiosis initiation, oocyte growth recruitment, oocyte meiosis retardation and resumption and final meiotic maturation. A series of coordinated molecular signaling factors ensure successful oogenesis. The recent rapid development of high-throughput sequencing technologies allows for the dynamic omics in female germ cells, which is essential for further understanding the regulatory mechanisms of molecular events comprehensively. In this review, we summarize the current literature of multi-omics sequenced by epigenome-, transcriptome- and proteome-associated technologies, which provide valuable information for understanding the regulation of key events during female germ cell development.
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Affiliation(s)
- Zheng-Hui Zhao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Heide Schatten
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, USA
| | - Qing-Yuan Sun
- Fertility Preservation Lab, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, China
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66
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Kobayashi H. Canonical and Non-canonical Genomic Imprinting in Rodents. Front Cell Dev Biol 2021; 9:713878. [PMID: 34422832 PMCID: PMC8375499 DOI: 10.3389/fcell.2021.713878] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 07/16/2021] [Indexed: 11/13/2022] Open
Abstract
Genomic imprinting is an epigenetic phenomenon that results in unequal expression of homologous maternal and paternal alleles. This process is initiated in the germline, and the parental epigenetic memories can be maintained following fertilization and induce further allele-specific transcription and chromatin modifications of single or multiple neighboring genes, known as imprinted genes. To date, more than 260 imprinted genes have been identified in the mouse genome, most of which are controlled by imprinted germline differentially methylated regions (gDMRs) that exhibit parent-of-origin specific DNA methylation, which is considered primary imprint. Recent studies provide evidence that a subset of gDMR-less, placenta-specific imprinted genes is controlled by maternal-derived histone modifications. To further understand DNA methylation-dependent (canonical) and -independent (non-canonical) imprints, this review summarizes the loci under the control of each type of imprinting in the mouse and compares them with the respective homologs in other rodents. Understanding epigenetic systems that differ among loci or species may provide new models for exploring genetic regulation and evolutionary divergence.
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Affiliation(s)
- Hisato Kobayashi
- Department of Embryology, Nara Medical University, Kashihara, Japan
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67
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Du Z, Zhang K, Xie W. Epigenetic Reprogramming in Early Animal Development. Cold Spring Harb Perspect Biol 2021; 14:cshperspect.a039677. [PMID: 34400552 DOI: 10.1101/cshperspect.a039677] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Dramatic nuclear reorganization occurs during early development to convert terminally differentiated gametes to a totipotent zygote, which then gives rise to an embryo. Aberrant epigenome resetting severely impairs embryo development and even leads to lethality. How the epigenomes are inherited, reprogrammed, and reestablished in this critical developmental period has gradually been unveiled through the rapid development of technologies including ultrasensitive chromatin analysis methods. In this review, we summarize the latest findings on epigenetic reprogramming in gametogenesis and embryogenesis, and how it contributes to gamete maturation and parental-to-zygotic transition. Finally, we highlight the key questions that remain to be answered to fully understand chromatin regulation and nuclear reprogramming in early development.
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Affiliation(s)
- Zhenhai Du
- 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
| | - Ke Zhang
- 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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68
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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: 19] [Impact Index Per Article: 6.3] [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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69
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Xu J, Shu Y, Yao G, Zhang Y, Niu W, Zhang Y, Ma X, Jin H, Zhang F, Shi S, Wang Y, Song W, Dai S, Cheng L, Zhang X, Xie W, J Hsueh A, Sun Y. Parental methylome reprogramming in human uniparental blastocysts reveals germline memory transition. Genome Res 2021; 31:1519-1530. [PMID: 34330789 PMCID: PMC8415376 DOI: 10.1101/gr.273318.120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 07/22/2021] [Indexed: 11/24/2022]
Abstract
Uniparental embryos derived from only the mother (gynogenetic [GG]) or the father (androgenetic [AG]) are unique models for studying genomic imprinting and parental contributions to embryonic development. Human parthenogenetic embryos can be obtained following artificial activation of unfertilized oocytes, but the production of AG embryos by injection of two sperm into one denucleated oocyte leads to an extra centriole, resulting in multipolar spindles, abnormal cell division, and developmental defects. Here, we improved androgenote production by transferring the male pronucleus from one zygote into another haploid androgenote to prevent extra centrioles and successfully generated human diploid AG embryos capable of developing into blastocysts with an identifiable inner cell mass (ICM) and trophectoderm (TE). The GG embryos were also generated. The zygotic genome was successfully activated in both the AG and GG embryos. DNA methylome analysis showed that the GG blastocysts partially retain the oocyte transcription-dependent methylation pattern, whereas the AG blastocyst methylome showed more extensive demethylation. The methylation states of most known imprinted differentially methylated regions (DMRs) were recapitulated in the AG and GG blastocysts. Novel candidate imprinted DMRs were also identified. The production of uniparental human embryos followed by transcriptome and methylome analysis is valuable for identifying parental contributions and epigenome memory transitions during early human development.
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Affiliation(s)
- Jiawei Xu
- The First Affiliated Hospital of Zhengzhou University, Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics;
| | - Yimin Shu
- Stanford University School of Medicine
| | - Guidong Yao
- The First Affiliated Hospital of Zhengzhou University, Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics
| | - Yu Zhang
- Tsinghua University, Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Center for Life Sciences
| | - Wenbin Niu
- The First Affiliated Hospital of Zhengzhou University, Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics
| | - Yile Zhang
- The First Affiliated Hospital of Zhengzhou University, Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics
| | - Xueshan Ma
- The First Affiliated Hospital of Zhengzhou University, Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics
| | - Haixia Jin
- The First Affiliated Hospital of Zhengzhou University, Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics
| | - Fuli Zhang
- The First Affiliated Hospital of Zhengzhou University, Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics
| | - Senlin Shi
- The First Affiliated Hospital of Zhengzhou University, Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics
| | - Yang Wang
- The First Affiliated Hospital of Zhengzhou University, Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics
| | - Wenyan Song
- The First Affiliated Hospital of Zhengzhou University, Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics
| | - Shanjun Dai
- The First Affiliated Hospital of Zhengzhou University, Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics
| | - Luyao Cheng
- The First Affiliated Hospital of Zhengzhou University, Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics
| | - Xiangyang Zhang
- The First Affiliated Hospital of Zhengzhou University, Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics
| | - Wei Xie
- Tsinghua University, Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Center for Life Sciences
| | | | - Yingpu Sun
- The First Affiliated Hospital of Zhengzhou University, Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics
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70
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Naillat F, Saadeh H, Nowacka-Woszuk J, Gahurova L, Santos F, Tomizawa SI, Kelsey G. Oxygen concentration affects de novo DNA methylation and transcription in in vitro cultured oocytes. Clin Epigenetics 2021; 13:132. [PMID: 34183052 PMCID: PMC8240245 DOI: 10.1186/s13148-021-01116-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 06/15/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Reproductive biology methods rely on in vitro follicle cultures from mature follicles obtained by hormonal stimulation for generating metaphase II oocytes to be fertilised and developed into a healthy embryo. Such techniques are used routinely in both rodent and human species. DNA methylation is a dynamic process that plays a role in epigenetic regulation of gametogenesis and development. In mammalian oocytes, DNA methylation establishment regulates gene expression in the embryos. This regulation is particularly important for a class of genes, imprinted genes, whose expression patterns are crucial for the next generation. The aim of this work was to establish an in vitro culture system for immature mouse oocytes that will allow manipulation of specific factors for a deeper analysis of regulatory mechanisms for establishing transcription regulation-associated methylation patterns. RESULTS An in vitro culture system was developed from immature mouse oocytes that were grown to germinal vesicles (GV) under two different conditions: normoxia (20% oxygen, 20% O2) and hypoxia (5% oxygen, 5% O2). The cultured oocytes were sorted based on their sizes. Reduced representative bisulphite sequencing (RRBS) and RNA-seq libraries were generated from cultured and compared to in vivo-grown oocytes. In the in vitro cultured oocytes, global and CpG-island (CGI) methylation increased gradually along with oocyte growth, and methylation of the imprinted genes was similar to in vivo-grown oocytes. Transcriptomes of the oocytes grown in normoxia revealed chromatin reorganisation and enriched expression of female reproductive genes, whereas in the 5% O2 condition, transcripts were biased towards cellular stress responses. To further confirm the results, we developed a functional assay based on our model for characterising oocyte methylation using drugs that reduce methylation and transcription. When histone methylation and transcription processes were reduced, DNA methylation at CGIs from gene bodies of grown oocytes presented a lower methylation profile. CONCLUSIONS Our observations reveal changes in DNA methylation and transcripts between oocytes cultured in vitro with different oxygen concentrations and in vivo-grown murine oocytes. Oocytes grown under 20% O2 had a higher correlation with in vivo oocytes for DNA methylation and transcription demonstrating that higher oxygen concentration is beneficial for the oocyte maturation in ex vivo culture condition. Our results shed light on epigenetic mechanisms for the development of oocytes from an immature to GV oocyte in an in vitro culture model.
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Affiliation(s)
- Florence Naillat
- Epigenetics Program, Babraham Institute, Cambridge, CB22 3AT, UK. .,Diseases Network Research Unit, Faculty of Biochemistry and Molecular Medicine, Oulu University, Oulu, Finland.
| | - Heba Saadeh
- Epigenetics Program, Babraham Institute, Cambridge, CB22 3AT, UK.,Department of Computer Science, King Abdullah II School of Information Technology, The University of Jordan, Amman, Jordan
| | - Joanna Nowacka-Woszuk
- Epigenetics Program, Babraham Institute, Cambridge, CB22 3AT, UK.,Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Poznan, Poland
| | - Lenka Gahurova
- Epigenetics Program, Babraham Institute, Cambridge, CB22 3AT, UK.,Laboratory of Early Mammalian Development, Department of Molecular Biology and Genetics, University of South Bohemia, 37005, České Budějovice, Czech Republic
| | - Fatima Santos
- Epigenetics Program, Babraham Institute, Cambridge, CB22 3AT, UK
| | - Shin-Ichi Tomizawa
- Epigenetics Program, Babraham Institute, Cambridge, CB22 3AT, UK.,School of Medicine, Yokohama City University, Yokohama, Japan
| | - Gavin Kelsey
- Epigenetics Program, Babraham Institute, Cambridge, CB22 3AT, UK. .,Centre for Trophoblast Research, University of Cambridge, Cambridge, CB2 3EG, UK.
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71
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Au Yeung WK, Maruyama O, Sasaki H. A convolutional neural network-based regression model to infer the epigenetic crosstalk responsible for CG methylation patterns. BMC Bioinformatics 2021; 22:341. [PMID: 34162326 PMCID: PMC8220828 DOI: 10.1186/s12859-021-04272-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 06/15/2021] [Indexed: 12/02/2022] Open
Abstract
Background Epigenetic modifications, including CG methylation (a major form of DNA methylation) and histone modifications, interact with each other to shape their genomic distribution patterns. However, the entire picture of the epigenetic crosstalk regulating the CG methylation pattern is unknown especially in cells that are available only in a limited number, such as mammalian oocytes. Most machine learning approaches developed so far aim at finding DNA sequences responsible for the CG methylation patterns and were not tailored for studying the epigenetic crosstalk.
Results We built a machine learning model named epiNet to predict CG methylation patterns based on other epigenetic features, such as histone modifications, but not DNA sequence. Using epiNet, we identified biologically relevant epigenetic crosstalk between histone H3K36me3, H3K4me3, and CG methylation in mouse oocytes. This model also predicted the altered CG methylation pattern of mutant oocytes having perturbed histone modification, was applicable to cross-species prediction of the CG methylation pattern of human oocytes, and identified the epigenetic crosstalk potentially important in other cell types. Conclusions Our findings provide insight into the epigenetic crosstalk regulating the CG methylation pattern in mammalian oocytes and other cells. The use of epiNet should help to design or complement biological experiments in epigenetics studies. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04272-8.
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Affiliation(s)
- Wan Kin Au Yeung
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan.
| | - Osamu Maruyama
- Faculty of Design, Kyushu University, Fukuoka, 815-0032, Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan.
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72
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Bellver-Sanchis A, Pallàs M, Griñán-Ferré C. The Contribution of Epigenetic Inheritance Processes on Age-Related Cognitive Decline and Alzheimer's Disease. EPIGENOMES 2021; 5:epigenomes5020015. [PMID: 34968302 PMCID: PMC8594669 DOI: 10.3390/epigenomes5020015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/15/2021] [Accepted: 06/17/2021] [Indexed: 12/15/2022] Open
Abstract
During the last years, epigenetic processes have emerged as important factors for many neurodegenerative diseases, such as Alzheimer’s disease (AD). These complex diseases seem to have a heritable component; however, genome-wide association studies failed to identify the genetic loci involved in the etiology. So, how can these changes be transmitted from one generation to the next? Answering this question would allow us to understand how the environment can affect human populations for multiple generations and explain the high prevalence of neurodegenerative diseases, such as AD. This review pays particular attention to the relationship among epigenetics, cognition, and neurodegeneration across generations, deepening the understanding of the relevance of heritability in neurodegenerative diseases. We highlight some recent examples of EI induced by experiences, focusing on their contribution of processes in learning and memory to point out new targets for therapeutic interventions. Here, we first describe the prominent role of epigenetic factors in memory processing. Then, we briefly discuss aspects of EI. Additionally, we summarize evidence of how epigenetic marks inherited by experience and/or environmental stimuli contribute to cognitive status offspring since better knowledge of EI can provide clues in the appearance and development of age-related cognitive decline and AD.
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73
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Defective folate metabolism causes germline epigenetic instability and distinguishes Hira as a phenotype inheritance biomarker. Nat Commun 2021; 12:3714. [PMID: 34140513 PMCID: PMC8211854 DOI: 10.1038/s41467-021-24036-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 05/29/2021] [Indexed: 02/02/2023] Open
Abstract
The mechanism behind transgenerational epigenetic inheritance is unclear, particularly through the maternal grandparental line. We previously showed that disruption of folate metabolism in mice by the Mtrr hypomorphic mutation results in transgenerational epigenetic inheritance of congenital malformations. Either maternal grandparent can initiate this phenomenon, which persists for at least four wildtype generations. Here, we use genome-wide approaches to reveal genetic stability in the Mtrr model and genome-wide differential DNA methylation in the germline of Mtrr mutant maternal grandfathers. We observe that, while epigenetic reprogramming occurs, wildtype grandprogeny and great grandprogeny exhibit transcriptional changes that correlate with germline methylation defects. One region encompasses the Hira gene, which is misexpressed in embryos for at least three wildtype generations in a manner that distinguishes Hira transcript expression as a biomarker of maternal phenotypic inheritance.
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74
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Chen Y, Gao Y, Jia J, Chang L, Liu P, Qiao J, Tang F, Wen L, Huang J. DNA methylome reveals cellular origin of cell-free DNA in spent medium of human preimplantation embryos. J Clin Invest 2021; 131:e146051. [PMID: 34128477 DOI: 10.1172/jci146051] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 04/28/2021] [Indexed: 02/03/2023] Open
Abstract
The discovery of embryonic cell-free DNA (cfDNA) in spent embryo culture media (SECM) has brought hope for noninvasive preimplantation genetic testing. However, the cellular origins of SECM cfDNA are not sufficiently understood, and methods for determining maternal DNA contamination are limited. Here, we performed whole-genome DNA methylation sequencing for SECM cfDNA. Our results demonstrated that SECM cfDNA was derived from blastocysts, cumulus cells, and polar bodies. We identified the cumulus-specific differentially methylated regions (DMRs) and oocyte/polar body-specific DMRs, and established an algorithm for deducing the cumulus, polar body, and net maternal DNA contamination ratios in SECM. We showed that DNA methylation sequencing accurately detected chromosome aneuploidy in SECM and distinguished SECM samples with low and high false negative rates and gender discordance rates, after integrating the origin analysis. Our work provides insights into the characterization of embryonic DNA in SECM and provides a perspective for noninvasive preimplantation genetic testing in reproductive medicine.
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Affiliation(s)
- Yidong Chen
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology, and.,Biomedical Pioneering Innovation Center and Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Yuan Gao
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology, and.,Biomedical Pioneering Innovation Center and Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Jialin Jia
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology, and.,Biomedical Pioneering Innovation Center and Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China.,Key Laboratory of Assisted Reproduction and Key Laboratory of Cell Proliferation and Differentiation, Ministry of Education, Beijing, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
| | - Liang Chang
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology, and.,Biomedical Pioneering Innovation Center and Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China.,Key Laboratory of Assisted Reproduction and Key Laboratory of Cell Proliferation and Differentiation, Ministry of Education, Beijing, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
| | - Ping Liu
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology, and.,Biomedical Pioneering Innovation Center and Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China.,Key Laboratory of Assisted Reproduction and Key Laboratory of Cell Proliferation and Differentiation, Ministry of Education, Beijing, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
| | - Jie Qiao
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology, and.,Biomedical Pioneering Innovation Center and Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.,Key Laboratory of Assisted Reproduction and Key Laboratory of Cell Proliferation and Differentiation, Ministry of Education, Beijing, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
| | - Fuchou Tang
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology, and.,Biomedical Pioneering Innovation Center and Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Lu Wen
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology, and.,Biomedical Pioneering Innovation Center and Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China
| | - Jin Huang
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology, and.,Biomedical Pioneering Innovation Center and Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China.,Key Laboratory of Assisted Reproduction and Key Laboratory of Cell Proliferation and Differentiation, Ministry of Education, Beijing, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
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75
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Abstract
Genomic imprinting is the monoallelic expression of a gene based on parent of origin and is a consequence of differential epigenetic marking between the male and female germlines. Canonically, genomic imprinting is mediated by allelic DNA methylation. However, recently it has been shown that maternal H3K27me3 can result in DNA methylation-independent imprinting, termed "noncanonical imprinting." In this review, we compare and contrast what is currently known about the underlying mechanisms, the role of endogenous retroviral elements, and the conservation of canonical and noncanonical genomic imprinting.
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Affiliation(s)
- Courtney W Hanna
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom
| | - Gavin Kelsey
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom
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76
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Kibe K, Shirane K, Ohishi H, Uemura S, Toh H, Sasaki H. The DNMT3A PWWP domain is essential for the normal DNA methylation landscape in mouse somatic cells and oocytes. PLoS Genet 2021; 17:e1009570. [PMID: 34048432 PMCID: PMC8162659 DOI: 10.1371/journal.pgen.1009570] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/30/2021] [Indexed: 12/28/2022] Open
Abstract
DNA methylation at CG sites is important for gene regulation and embryonic development. In mouse oocytes, de novo CG methylation requires preceding transcription-coupled histone mark H3K36me3 and is mediated by a DNA methyltransferase DNMT3A. DNMT3A has a PWWP domain, which recognizes H3K36me2/3, and heterozygous mutations in this domain, including D329A substitution, cause aberrant CG hypermethylation of regions marked by H3K27me3 in somatic cells, leading to a dwarfism phenotype. We herein demonstrate that D329A homozygous mice show greater CG hypermethylation and severer dwarfism. In oocytes, D329A substitution did not affect CG methylation of H3K36me2/3-marked regions, including maternally methylated imprinting control regions; rather, it caused aberrant hypermethylation in regions lacking H3K36me2/3, including H3K27me3-marked regions. Thus, the role of the PWWP domain in CG methylation seems similar in somatic cells and oocytes; however, there were cell-type-specific differences in affected regions. The major satellite repeat was also hypermethylated in mutant oocytes. Contrary to the CA hypomethylation in somatic cells, the mutation caused hypermethylation at CH sites, including CA sites. Surprisingly, oocytes expressing only the mutated protein could support embryonic and postnatal development. Our study reveals that the DNMT3A PWWP domain is important for suppressing aberrant CG hypermethylation in both somatic cells and oocytes but that D329A mutation has little impact on the developmental potential of oocytes.
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Affiliation(s)
- Kanako Kibe
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Kenjiro Shirane
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hiroaki Ohishi
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- Graduate School of Integrated Science for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Shuhei Uemura
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Hidehiro Toh
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- * E-mail:
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77
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Unraveling the Balance between Genes, Microbes, Lifestyle and the Environment to Improve Healthy Reproduction. Genes (Basel) 2021; 12:genes12040605. [PMID: 33924000 PMCID: PMC8073673 DOI: 10.3390/genes12040605] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/08/2021] [Accepted: 04/17/2021] [Indexed: 12/16/2022] Open
Abstract
Humans’ health is the result of a complex and balanced interplay between genetic factors, environmental stimuli, lifestyle habits, and the microbiota composition. The knowledge about their single contributions, as well as the complex network linking each to the others, is pivotal to understand the mechanisms underlying the onset of many diseases and can provide key information for their prevention, diagnosis and therapy. This applies also to reproduction. Reproduction, involving almost 10% of our genetic code, is one of the most critical human’s functions and is a key element to assess the well-being of a population. The last decades revealed a progressive decline of reproductive outcomes worldwide. As a consequence, there is a growing interest in unveiling the role of the different factors involved in human reproduction and great efforts have been carried out to improve its outcomes. As for many other diseases, it is now clear that the interplay between the underlying genetics, our commensal microbiome, the lifestyle habits and the environment we live in can either exacerbate the outcome or mitigate the adverse effects. Here, we aim to analyze how each of these factors contribute to reproduction highlighting their individual contribution and providing supporting evidence of how to modify their impact and overall contribution to a healthy reproductive status.
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78
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The prolonged disease state of infertility is associated with embryonic epigenetic dysregulation. Fertil Steril 2021; 116:309-318. [PMID: 33745724 DOI: 10.1016/j.fertnstert.2021.01.040] [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] [Received: 11/04/2020] [Revised: 01/20/2021] [Accepted: 01/21/2021] [Indexed: 11/22/2022]
Abstract
OBJECTIVE To evaluate the epigenetic consequence of a prolonged disease state of infertility in euploid blastocysts. DESIGN Methylome analysis as well as targeted imprinted methylation and expression analysis on individual human euploid blastocysts examined in association with duration of patient infertility and time to live birth. SETTING Research study. PATIENT(S) One hundred four surplus cryopreserved euploid blastocysts of transferrable-quality were donated with informed patient consent and grouped based on time to pregnancy (TTP). INTERVENTION(S) None MAIN OUTCOME MEASURE(S): The Methyl Maxi-Seq platform (Zymo Research) was used to determine genome-wide methylation, while targeted methylation and expression analyses were performed by pyrosequencing and quantitative real-time polymerase chain reaction, respectively. Statistical analyses used Student's t test, 1-way ANOVA, Fisher's exact test, and pairwise-fixed reallocation randomization test, where appropriate. RESULT(S) The methylome analysis of individual blastocysts revealed significant alterations at 6,609 CpG sites associated with prolonged infertility (≥60 months) compared with those of fertile controls (0 months). Significant CpG alterations were localized to numerous imprinting control regions and imprinted genes, and several signaling pathways were highly represented among genes that were differentially methylated. Targeted imprinting methylation analysis uncovered significant hypomethylation at KvDMR and MEST imprinting control regions, with significant decreases in the gene expression levels upon extended TTP (≥36 months) compared to minimal TTP (≤24 months). CONCLUSION(S) The prolonged disease state of infertility correlates with an altered methylome in euploid blastocysts, with particular emphasis on genomic imprinting regulation, compared with assisted reproductive technologies alone.
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79
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Zhu H, Sun H, Yu D, Li T, Hai T, Liu C, Zhang Y, Chen Y, Dai X, Li Z, Li W, Liu R, Feng G, Zhou Q. Transcriptome and DNA Methylation Profiles of Mouse Fetus and Placenta Generated by Round Spermatid Injection. Front Cell Dev Biol 2021; 9:632183. [PMID: 33796527 PMCID: PMC8009284 DOI: 10.3389/fcell.2021.632183] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/24/2021] [Indexed: 02/05/2023] Open
Abstract
Low birth efficiency and developmental abnormalities in embryos derived using round spermatid injection (ROSI) limit the clinical application of this method. Further, the underlying molecular mechanisms remain elusive and warrant further in-depth study. In this study, the embryonic day (E) 11.5 mouse fetuses and corresponding placentas derived upon using ROSI, intracytoplasmic sperm injection (ICSI), and natural in vivo fertilized (control) embryos were collected. Transcriptome and DNA methylation profiles were analyzed and compared using RNA-sequencing (RNA-seq) and whole-genome bisulfite sequencing, respectively. RNA-seq results revealed similar gene expression profiles in the ROSI, ICSI, and control fetuses and placentas. Compared with the other two groups, seven differentially expressed genes (DEGs) were identified in ROSI fetuses, and ten DEGs were identified in the corresponding placentas. However, no differences in CpG methylation were observed in fetuses and placentas from the three groups. Imprinting control region methylation and imprinted gene expression were the same between the three fetus and placenta groups. Although 49 repetitive DNA sequences (RS) were abnormally activated in ROSI fetuses, RS DNA methylation did not differ between the three groups. Interestingly, abnormal hypermethylation in promoter regions and low expression of Fggy and Rec8 were correlated with a crown-rump length less than 6 mm in one ROSI fetus. Our study demonstrates that the transcriptome and DNA methylation in ROSI-derived E11.5 mouse fetuses and placentas were comparable with those in the other two groups. However, some abnormally expressed genes in the ROSI fetus and placenta warrant further investigation to elucidate their effect on the development of ROSI-derived embryos.
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Affiliation(s)
- Haibo Zhu
- Center of Reproductive Medicine, Center of Prenatal Diagnosis, First Hospital, Jilin University, Changchun, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, First Hospital, Jilin University, Changchun, China
| | - Hao Sun
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute of Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China
| | - Dawei Yu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute of Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China
| | - Tianda Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute of Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China
| | - Tang Hai
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute of Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China
| | - Chao Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute of Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China
| | - Ying Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute of Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China
| | - Yurong Chen
- Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, First Hospital, Jilin University, Changchun, China
| | - Xiangpeng Dai
- Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, First Hospital, Jilin University, Changchun, China
| | - Ziyi Li
- Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, First Hospital, Jilin University, Changchun, China
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute of Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ruizhi Liu
- Center of Reproductive Medicine, Center of Prenatal Diagnosis, First Hospital, Jilin University, Changchun, China
| | - Guihai Feng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute of Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China
| | - Qi Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, First Hospital, Jilin University, Changchun, China
- Institute of Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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80
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Ansere VA, Ali-Mondal S, Sathiaseelan R, Garcia DN, Isola JVV, Henseb JD, Saccon TD, Ocañas SR, Tooley KB, Stout MB, Schneider A, Freeman WM. Cellular hallmarks of aging emerge in the ovary prior to primordial follicle depletion. Mech Ageing Dev 2021; 194:111425. [PMID: 33383072 PMCID: PMC8279026 DOI: 10.1016/j.mad.2020.111425] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/02/2020] [Accepted: 12/22/2020] [Indexed: 01/10/2023]
Abstract
Decline in ovarian reserve with advancing age is associated with reduced fertility and the emergence of metabolic disturbances, osteoporosis, and neurodegeneration. Recent studies have provided insight into connections between ovarian insufficiency and systemic aging, although the basic mechanisms that promote ovarian reserve depletion remain unknown. Here, we sought to determine if chronological age is linked to changes in ovarian cellular senescence, transcriptomic, and epigenetic mechanisms in a mouse model. Histological assessments and transcriptional analyses revealed the accumulation of lipofuscin aggresomes and senescence-related transcripts (Cdkn1a, Cdkn2a, Pai-1 and Hmgb1) significantly increased with advancing age. Transcriptomic profiling and pathway analyses following RNA sequencing, revealed an upregulation of genes related to pro-inflammatory stress and cell-cycle inhibition, whereas genes involved in cell-cycle progression were downregulated; which could be indicative of senescent cell accumulation. The emergence of these senescence-related markers preceded the dramatic decline in primordial follicle reserve observed. Whole Genome Oxidative Bisulfite Sequencing (WGoxBS) found no genome-wide or genomic context-specific DNA methylation and hydroxymethylation changes with advancing age. These findings suggest that cellular senescence may contribute to ovarian aging, and thus, declines in ovarian follicular reserve. Cell-type-specific analyses across the reproductive lifespan are needed to fully elucidate the mechanisms that promote ovarian insufficiency.
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Affiliation(s)
- Victor A Ansere
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Oklahoma Center for Geroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Samim Ali-Mondal
- Oklahoma Center for Geroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Department of Nutritional Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Roshini Sathiaseelan
- Oklahoma Center for Geroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Department of Nutritional Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Driele N Garcia
- Department of Nutritional Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - José V V Isola
- Department of Nutritional Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Jéssica D Henseb
- Faculdade de Nutrição, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Tatiana D Saccon
- Faculdade de Nutrição, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Sarah R Ocañas
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Oklahoma Center for Geroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Kyla B Tooley
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Oklahoma Center for Geroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Michael B Stout
- Oklahoma Center for Geroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Department of Nutritional Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Augusto Schneider
- Faculdade de Nutrição, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Willard M Freeman
- Oklahoma Center for Geroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA; Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Oklahoma City Veterans Affairs Medical Center, Oklahoma City, OK, USA.
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81
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KŠiŇanovÁ M, KovaŘÍkovÁ V, ŠefČÍkovÁ Z, ŠpirkovÁ A, ČikoŠ Š, Pisko J, Fabian D. Different response of embryos originating from control and obese mice to insulin in vitro. J Reprod Dev 2021; 67:25-34. [PMID: 33250503 PMCID: PMC7902211 DOI: 10.1262/jrd.2020-096] [Citation(s) in RCA: 3] [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: 07/17/2020] [Accepted: 10/28/2020] [Indexed: 12/11/2022] Open
Abstract
The aim of the present work was to investigate the impact of maternal obesity on DNA methylation in ovulated oocytes, and to compare the response of in vitro-developing preimplantation embryos originating from control and obese mice to insulin. An intergenerational, diet-induced obesity model was used to produce outbred mice with an increased body weight and body fat. Two-cell and eight-cell embryos recovered from obese and control mice were cultured in a medium supplemented with 1 or 10 ng/ml insulin until blastocyst formation. In the derived blastocysts, cell proliferation, differentiation, and death rates were determined. The results of immunochemical visualization of 5-methylcytosine indicated a slightly higher DNA methylation in ovulated metaphase II oocytes recovered from obese females; however, the difference between groups did not reach statistical significance. Expanded blastocysts developed from embryos provided by control dams showed increased mean cell numbers (two and eight-cell embryos exposed to 10 ng/ml), an increased inner-cell-mass/trophectoderm ratio (two-cell embryos exposed to 1 ng/ml and eight-cell embryos exposed to 10 ng/ml), and a reduced level of apoptosis (two and eight-cell embryos exposed to 10 ng/ml). In contrast, embryos originating from obese mice were significantly less sensitive to insulin; indeed, no difference was recorded in any tested variable between the embryos exposed to insulin and those cultured in insulin-free medium. Real-time RT-PCR analysis showed a significant increase in the amount of insulin receptor transcripts in blastocysts recovered from obese dams. These results suggest that maternal obesity might modulate the mitogenic and antiapoptotic responses of preimplantation embryos to insulin.
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Affiliation(s)
- Martina KŠiŇanovÁ
- Institute of Animal Physiology, Centre of Biosciences, Slovak Academy of Sciences, 040 01 Košice, Slovak Republic
| | - Veronika KovaŘÍkovÁ
- Institute of Animal Physiology, Centre of Biosciences, Slovak Academy of Sciences, 040 01 Košice, Slovak Republic
| | - Zuzana ŠefČÍkovÁ
- Institute of Animal Physiology, Centre of Biosciences, Slovak Academy of Sciences, 040 01 Košice, Slovak Republic
| | - Alexandra ŠpirkovÁ
- Institute of Animal Physiology, Centre of Biosciences, Slovak Academy of Sciences, 040 01 Košice, Slovak Republic
| | - Štefan ČikoŠ
- Institute of Animal Physiology, Centre of Biosciences, Slovak Academy of Sciences, 040 01 Košice, Slovak Republic
| | - Jozef Pisko
- Institute of Animal Physiology, Centre of Biosciences, Slovak Academy of Sciences, 040 01 Košice, Slovak Republic
| | - Dušan Fabian
- Institute of Animal Physiology, Centre of Biosciences, Slovak Academy of Sciences, 040 01 Košice, Slovak Republic
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82
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Kohlrausch FB, Berteli TS, Wang F, Navarro PA, Keefe DL. Control of LINE-1 Expression Maintains Genome Integrity in Germline and Early Embryo Development. Reprod Sci 2021; 29:328-340. [PMID: 33481218 DOI: 10.1007/s43032-021-00461-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 01/06/2021] [Indexed: 11/28/2022]
Abstract
Maintenance of genome integrity in the germline and in preimplantation embryos is crucial for mammalian development. Epigenetic remodeling during primordial germ cell (PGC) and preimplantation embryo development may contribute to genomic instability in these cells, since DNA methylation is an important mechanism to silence retrotransposons. Long interspersed elements 1 (LINE-1 or L1) are the most common autonomous retrotransposons in mammals, corresponding to approximately 17% of the human genome. Retrotransposition events are more frequent in germ cells and in early stages of embryo development compared with somatic cells. It has been shown that L1 activation and expression occurs in germline and is essential for preimplantation development. In this review, we focus on the role of L1 retrotransposon in mouse and human germline and early embryo development and discuss the possible relationship between L1 expression and genomic instability during these stages. Although several studies have addressed L1 expression at different stages of development, the developmental consequences of this expression remain poorly understood. Future research is still needed to highlight the relationship between L1 retrotransposition events and genomic instability during germline and early embryo development.
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Affiliation(s)
- Fabiana B Kohlrausch
- Department of Obstetrics and Gynecology, New York University Langone Medical Center, 462 1st Avenue, New York, NY, 10016, USA.,Departamento de Biologia Geral, Instituto de Biologia, Universidade Federal Fluminense, Niterói, RJ, Brazil
| | - Thalita S Berteli
- Department of Obstetrics and Gynecology, New York University Langone Medical Center, 462 1st Avenue, New York, NY, 10016, USA.,Departamento de Ginecologia e Obstetrícia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Fang Wang
- Department of Obstetrics and Gynecology, New York University Langone Medical Center, 462 1st Avenue, New York, NY, 10016, USA
| | - Paula A Navarro
- Departamento de Ginecologia e Obstetrícia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - David L Keefe
- Department of Obstetrics and Gynecology, New York University Langone Medical Center, 462 1st Avenue, New York, NY, 10016, USA.
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83
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Tinarelli F, Ivanova E, Colombi I, Barini E, Balzani E, Garcia CG, Gasparini L, Chiappalone M, Kelsey G, Tucci V. Cell-cell coupling and DNA methylation abnormal phenotypes in the after-hours mice. Epigenetics Chromatin 2021; 14:1. [PMID: 33407878 PMCID: PMC7789812 DOI: 10.1186/s13072-020-00373-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 11/13/2020] [Indexed: 11/10/2022] Open
Abstract
Background DNA methylation has emerged as an important epigenetic regulator of brain processes, including circadian rhythms. However, how DNA methylation intervenes between environmental signals, such as light entrainment, and the transcriptional and translational molecular mechanisms of the cellular clock is currently unknown. Here, we studied the after-hours mice, which have a point mutation in the Fbxl3 gene and a lengthened circadian period. Methods In this study, we used a combination of in vivo, ex vivo and in vitro approaches. We measured retinal responses in Afh animals and we have run reduced representation bisulphite sequencing (RRBS), pyrosequencing and gene expression analysis in a variety of brain tissues ex vivo. In vitro, we used primary neuronal cultures combined to micro electrode array (MEA) technology and gene expression. Results We observed functional impairments in mutant neuronal networks, and a reduction in the retinal responses to light-dependent stimuli. We detected abnormalities in the expression of photoreceptive melanopsin (OPN4). Furthermore, we identified alterations in the DNA methylation pathways throughout the retinohypothalamic tract terminals and links between the transcription factor Rev-Erbα and Fbxl3. Conclusions The results of this study, primarily represent a contribution towards an understanding of electrophysiological and molecular phenotypic responses to external stimuli in the Afh model. Moreover, as DNA methylation has recently emerged as a new regulator of neuronal networks with important consequences for circadian behaviour, we discuss the impact of the Afh mutation on the epigenetic landscape of circadian biology.
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Affiliation(s)
- Federico Tinarelli
- Genetics and Epigenetics of Behaviour (GEB) Laboratory, Istituto Italiano Di Tecnologia, via Morego, 30, 16163, Genova, Italy.,BioMed X Innovation Center, Im Neuenheimer Feld 515, 69120, Heidelberg, Germany
| | - Elena Ivanova
- Epigenetics Programme, The Babraham Institute, Cambridge, UK
| | - Ilaria Colombi
- Neuroscience and Brain Technologies, Istituto Italiano Di Tecnologia, via Morego, 30, 16163, Genova, Italy.,Brain Development and Disease, NBT, Istituto Italiano Di Tecnologia, via Morego, 30, 16163, Genova, Italy
| | - Erica Barini
- Neurodevelopmental and Neurodegenerative Disease Laboratory, Istituto Italiano Di Tecnologia, via Morego, 30, 16163, Genova, Italy.,AbbVie Deutschland GmbH & Co, Knollstr, 67061, Ludwigshafen, Germany
| | - Edoardo Balzani
- Genetics and Epigenetics of Behaviour (GEB) Laboratory, Istituto Italiano Di Tecnologia, via Morego, 30, 16163, Genova, Italy.,Center for Neural Science, New York University, New York, NY, 10006, USA
| | - Celina Garcia Garcia
- Genetics and Epigenetics of Behaviour (GEB) Laboratory, Istituto Italiano Di Tecnologia, via Morego, 30, 16163, Genova, Italy
| | - Laura Gasparini
- Neurodevelopmental and Neurodegenerative Disease Laboratory, Istituto Italiano Di Tecnologia, via Morego, 30, 16163, Genova, Italy.,AbbVie Deutschland GmbH & Co, Knollstr, 67061, Ludwigshafen, Germany
| | - Michela Chiappalone
- Neuroscience and Brain Technologies, Istituto Italiano Di Tecnologia, via Morego, 30, 16163, Genova, Italy.,Rehab Technologies, Istituto Italiano Di Tecnologia, via Morego, 30, 16163, Genova, Italy
| | - Gavin Kelsey
- Epigenetics Programme, The Babraham Institute, Cambridge, UK
| | - Valter Tucci
- Genetics and Epigenetics of Behaviour (GEB) Laboratory, Istituto Italiano Di Tecnologia, via Morego, 30, 16163, Genova, Italy.
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84
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Zhu L, Marjani SL, Jiang Z. The Epigenetics of Gametes and Early Embryos and Potential Long-Range Consequences in Livestock Species-Filling in the Picture With Epigenomic Analyses. Front Genet 2021; 12:557934. [PMID: 33747031 PMCID: PMC7966815 DOI: 10.3389/fgene.2021.557934] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 02/04/2021] [Indexed: 12/31/2022] Open
Abstract
The epigenome is dynamic and forged by epigenetic mechanisms, such as DNA methylation, histone modifications, chromatin remodeling, and non-coding RNA species. Increasing lines of evidence support the concept that certain acquired traits are derived from environmental exposure during early embryonic and fetal development, i.e., fetal programming, and can even be "memorized" in the germline as epigenetic information and transmitted to future generations. Advances in technology are now driving the global profiling and precise editing of germline and embryonic epigenomes, thereby improving our understanding of epigenetic regulation and inheritance. These achievements open new avenues for the development of technologies or potential management interventions to counteract adverse conditions or improve performance in livestock species. In this article, we review the epigenetic analyses (DNA methylation, histone modification, chromatin remodeling, and non-coding RNAs) of germ cells and embryos in mammalian livestock species (cattle, sheep, goats, and pigs) and the epigenetic determinants of gamete and embryo viability. We also discuss the effects of parental environmental exposures on the epigenetics of gametes and the early embryo, and evidence for transgenerational inheritance in livestock.
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Affiliation(s)
- Linkai Zhu
- AgCenter, School of Animal Sciences, Louisiana State University, Baton Rouge, LA, United States
| | - Sadie L Marjani
- Department of Biology, Central Connecticut State University, New Britain, CT, United States
| | - Zongliang Jiang
- AgCenter, School of Animal Sciences, Louisiana State University, Baton Rouge, LA, United States
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85
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Hayashi K, Galli C, Diecke S, Hildebrandt TB. Artificially produced gametes in mice, humans and other species. Reprod Fertil Dev 2021; 33:91-101. [PMID: 38769675 DOI: 10.1071/rd20265] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024] Open
Abstract
The production of gametes from pluripotent stem cells in culture, also known as invitro gametogenesis, will make an important contribution to reproductive biology and regenerative medicine, both as a unique tool for understanding germ cell development and as an alternative source of gametes for reproduction. Invitro gametogenesis was developed using mouse pluripotent stem cells but is increasingly being applied in other mammalian species, including humans. In principle, the entire process of germ cell development is nearly reconstitutable in culture using mouse pluripotent stem cells, although the fidelity of differentiation processes and the quality of resultant gametes remain to be refined. The methodology in the mouse system is only partially applicable to other species, and thus it must be optimised for each species. In this review, we update the current status of invitro gametogenesis in mice, humans and other animals, and discuss challenges for further development of this technology.
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Affiliation(s)
- Katsuhiko Hayashi
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-0054, Japan; and Corresponding author
| | - Cesare Galli
- Avantea, Laboratory of Reproductive Technologies, 26100 Cremona, Italy; and Fondazione Avantea, 26100 Cremona, Italy
| | - Sebastian Diecke
- Max-Delbrueck-Center for Molecular Medicine, 13092 Berlin, Germany
| | - Thomas B Hildebrandt
- Leibniz Institute for Zoo and Wildlife Research, D-10315 Berlin, Germany; and Freie Universität Berlin, D-14195 Berlin, Germany
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86
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Mayne B, Korbie D, Kenchington L, Ezzy B, Berry O, Jarman S. A DNA methylation age predictor for zebrafish. Aging (Albany NY) 2020; 12:24817-24835. [PMID: 33353889 PMCID: PMC7803548 DOI: 10.18632/aging.202400] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 11/30/2020] [Indexed: 12/11/2022]
Abstract
Changes in DNA methylation at specific CpG sites have been used to build predictive models to estimate animal age, predominantly in mammals. Little testing for this effect has been conducted in other vertebrate groups, such as bony fish, the largest vertebrate class. The development of most age-predictive models has relied on a genome-wide sequencing method to obtain a DNA methylation level, which makes it costly to deploy as an assay to estimate age in many samples. Here, we have generated a reduced representation bisulfite sequencing data set of caudal fin tissue from a model fish species, zebrafish (Danio rerio), aged from 11.9-60.1 weeks. We identified changes in methylation at specific CpG sites that correlated strongly with increasing age. Using an optimised unique set of 26 CpG sites we developed a multiplex PCR assay that predicts age with an average median absolute error rate of 3.2 weeks in zebrafish between 10.9-78.1 weeks of age. We also demonstrate the use of multiplex PCR as an efficient quantitative approach to measure DNA methylation for the use of age estimation. This study highlights the potential further use of DNA methylation as an age estimation method in non-mammalian vertebrate species.
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Affiliation(s)
- Benjamin Mayne
- Environomics Future Science Platform, Indian Ocean Marine Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Crawley, Western Australia, Australia
| | - Darren Korbie
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia, Queensland, Australia
| | - Lisa Kenchington
- Western Australian Zebrafish Experimental Research Centre (WAZERC), University of Western Australia, Perth, Western Australia, Australia
| | - Ben Ezzy
- Western Australian Zebrafish Experimental Research Centre (WAZERC), University of Western Australia, Perth, Western Australia, Australia
| | - Oliver Berry
- Environomics Future Science Platform, Indian Ocean Marine Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Crawley, Western Australia, Australia
| | - Simon Jarman
- School of Biological Sciences, The University of Western Australia, Perth, Western Australia, Australia
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87
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Reconstitution of the oocyte transcriptional network with transcription factors. Nature 2020; 589:264-269. [PMID: 33328630 DOI: 10.1038/s41586-020-3027-9] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 10/28/2020] [Indexed: 02/08/2023]
Abstract
During female germline development, oocytes become a highly specialized cell type and form a maternal cytoplasmic store of crucial factors. Oocyte growth is triggered at the transition from primordial to primary follicle and is accompanied by dynamic changes in gene expression1, but the gene regulatory network that controls oocyte growth remains unknown. Here we identify a set of transcription factors that are sufficient to trigger oocyte growth. By investigation of the changes in gene expression and functional screening using an in vitro mouse oocyte development system, we identified eight transcription factors, each of which was essential for the transition from primordial to primary follicle. Notably, enforced expression of these transcription factors swiftly converted pluripotent stem cells into oocyte-like cells that were competent for fertilization and subsequent cleavage. These transcription-factor-induced oocyte-like cells were formed without specification of primordial germ cells, epigenetic reprogramming or meiosis, and demonstrate that oocyte growth and lineage-specific de novo DNA methylation are separable from the preceding epigenetic reprogramming in primordial germ cells. This study identifies a core set of transcription factors for orchestrating oocyte growth, and provides an alternative source of ooplasm, which is a unique material for reproductive biology and medicine.
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88
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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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89
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Abstract
A battery of chromatin modifying enzymes play essential roles in remodeling the epigenome in the zygote and cleavage stage embryos, when the maternal genome is the sole contributor. Here we identify an exemption. DOT1L methylates lysine 79 in the globular domain of histone H3 (H3K79). Dot1l is an essential gene, as homozygous null mutant mouse embryos exhibit multiple developmental abnormalities and die before 11.5 days of gestation. To test if maternally deposited DOT1L is required for embryo development, we carried out a conditional Dot1l knockout in growing oocytes using the Zona pellucida 3-Cre (Zp3-Cre) transgenic mice. We found that the resulting maternal mutant Dot1lmat−/+ offspring displayed normal development and fertility, suggesting that the expression of the paternally inherited copy of Dot1l in the embryo is sufficient to support development. In addition, Dot1l maternal deletion did not affect the parental allele-specific expression of imprinted genes, indicating that DOT1L is not needed for imprint establishment in the oocyte or imprint protection in the zygote. In summary, uniquely and as opposed to other histone methyltransferases and histone marks, maternal DOT1L deposition and H3K79 methylation in the zygote and in the preimplantation stage embryo is dispensable for mouse development.
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90
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Wang X, Lai F, Xiong J, Zhu W, Yuan B, Cheng H, Zhou R. DNA methylation modification is associated with gonadal differentiation in Monopterus albus. Cell Biosci 2020; 10:129. [PMID: 33292595 PMCID: PMC7654577 DOI: 10.1186/s13578-020-00490-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 10/29/2020] [Indexed: 02/07/2023] Open
Abstract
Background Both testis and ovary can be produced sequentially in an individual with the same genome when sex reversal occurs in the teleost Monopterus albus, and epigenetic modification is supposed to be involved in gonadal differentiation. However, DNA methylation regulation mechanism underlying the gonadal differentiation remains unclear. Results Here, we used liquid chromatography-electrospray ionization tandem mass spectrometry (LC–ESI–MS/MS) to simultaneously determine endogenous levels of both 5-methyl-2′-deoxycytidine (m5dC) and 5-hydroxymethyl-2′-deoxycytidine (hm5dC) during gonadal differentiation. Overall DNA methylation level was upregulated from ovary to testis via ovotestis. As a de novo methylase, dnmt3aa expression was also upregulated in the process. Notably, we determined transcription factor Foxa1 for dnmt3aa gene expression. Site-specific mutations and chromatin immunoprecipitation showed that Foxa1 can bind to and activate the dnmt3aa promoter. Furthermore, DNA methylation levels of key genes foxl2 (forkhead box L2) and cyp19a1a (cytochrome P450, family 19, subfamily A, polypeptide 1a) in regulation of female hormone synthesis were consistently upregulated during gonadal differentiation. Conclusions These data suggested that dynamic change of DNA methylation modification is associated with gonadal differentiation.
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Affiliation(s)
- Xin Wang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Fengling Lai
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jun Xiong
- Key Laboratory of Analytical Chemistry for Biology and Medicine of Ministry of Education, Department of Chemistry, Wuhan University, Wuhan, 430072, China
| | - Wang Zhu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Bifeng Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine of Ministry of Education, Department of Chemistry, Wuhan University, Wuhan, 430072, China
| | - Hanhua Cheng
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
| | - Rongjia Zhou
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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91
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Yu B, Doni Jayavelu N, Battle SL, Mar JC, Schimmel T, Cohen J, Hawkins RD. Single-cell analysis of transcriptome and DNA methylome in human oocyte maturation. PLoS One 2020; 15:e0241698. [PMID: 33152014 PMCID: PMC7643955 DOI: 10.1371/journal.pone.0241698] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 10/20/2020] [Indexed: 12/20/2022] Open
Abstract
Oocyte maturation is a coordinated process that is tightly linked to reproductive potential. A better understanding of gene regulation during human oocyte maturation will not only answer an important question in biology, but also facilitate the development of in vitro maturation technology as a fertility treatment. We generated single-cell transcriptome and used our previously published single-cell methylome data from human oocytes at different maturation stages to investigate how genes are regulated during oocyte maturation, focusing on the potential regulatory role of non-CpG methylation. DNMT3B, a gene encoding a key non-CpG methylation enzyme, is one of the 1,077 genes upregulated in mature oocytes, which may be at least partially responsible for the increased non-CpG methylation as oocytes mature. Non-CpG differentially methylated regions (DMRs) between mature and immature oocytes have multiple binding motifs for transcription factors, some of which bind with DNMT3B and may be important regulators of oocyte maturation through non-CpG methylation. Over 98% of non-CpG DMRs locate in transposable elements, and these DMRs are correlated with expression changes of the nearby genes. Taken together, this data indicates that global non-CpG hypermethylation during oocyte maturation may play an active role in gene expression regulation, potentially through the interaction with transcription factors.
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Affiliation(s)
- Bo Yu
- Department of OBGYN, University of Washington School of Medicine, Seattle, Washington, United States of America
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, United States of America
| | - Naresh Doni Jayavelu
- Departments of Medicine and Genome Sciences, University of Washington, School of Medicine, Seattle, Washington, United States of America
| | - Stephanie L. Battle
- Department of OBGYN, University of Washington School of Medicine, Seattle, Washington, United States of America
- Departments of Medicine and Genome Sciences, University of Washington, School of Medicine, Seattle, Washington, United States of America
| | - Jessica C. Mar
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Timothy Schimmel
- Reprogenetics LLC, Livingston, New Jersey, United States of America
| | - Jacques Cohen
- Reprogenetics LLC, Livingston, New Jersey, United States of America
| | - R. David Hawkins
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, United States of America
- Departments of Medicine and Genome Sciences, University of Washington, School of Medicine, Seattle, Washington, United States of America
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92
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Maternal DNMT3A-dependent de novo methylation of the paternal genome inhibits gene expression in the early embryo. Nat Commun 2020; 11:5417. [PMID: 33110091 PMCID: PMC7591512 DOI: 10.1038/s41467-020-19279-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 10/01/2020] [Indexed: 12/20/2022] Open
Abstract
De novo DNA methylation (DNAme) during mammalian spermatogenesis yields a densely methylated genome, with the exception of CpG islands (CGIs), which are hypomethylated in sperm. While the paternal genome undergoes widespread DNAme loss before the first S-phase following fertilization, recent mass spectrometry analysis revealed that the zygotic paternal genome is paradoxically also subject to a low level of de novo DNAme. However, the loci involved, and impact on transcription were not addressed. Here, we employ allele-specific analysis of whole-genome bisulphite sequencing data and show that a number of genomic regions, including several dozen CGI promoters, are de novo methylated on the paternal genome by the 2-cell stage. A subset of these promoters maintains DNAme through development to the blastocyst stage. Consistent with paternal DNAme acquisition, many of these loci are hypermethylated in androgenetic blastocysts but hypomethylated in parthenogenetic blastocysts. Paternal DNAme acquisition is lost following maternal deletion of Dnmt3a, with a subset of promoters, which are normally transcribed from the paternal allele in blastocysts, being prematurely transcribed at the 4-cell stage in maternal Dnmt3a knockout embryos. These observations uncover a role for maternal DNMT3A activity in post-fertilization epigenetic reprogramming and transcriptional silencing of the paternal genome. The paternal genome in mice undergoes widespread DNA methylation loss post-fertilization. Here, the authors apply allele-specific analysis of WGBS data to show that a number of genomic regions are simultaneously de novo methylated on the paternal genome dependent on maternal DNMT3A activity, which induces transcriptional silencing of this allele in the early embryo.
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93
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Li L, Zhu S, Shu W, Guo Y, Guan Y, Zeng J, Wang H, Han L, Zhang J, Liu X, Li C, Hou X, Gao M, Ge J, Ren C, Zhang H, Schedl T, Guo X, Chen M, Wang Q. Characterization of Metabolic Patterns in Mouse Oocytes during Meiotic Maturation. Mol Cell 2020; 80:525-540.e9. [PMID: 33068521 DOI: 10.1016/j.molcel.2020.09.022] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 08/07/2020] [Accepted: 09/21/2020] [Indexed: 12/16/2022]
Abstract
Well-balanced and timed metabolism is essential for making a high-quality egg. However, the metabolic framework that supports oocyte development remains poorly understood. Here, we obtained the temporal metabolome profiles of mouse oocytes during in vivo maturation by isolating large number of cells at key stages. In parallel, quantitative proteomic analyses were conducted to bolster the metabolomic data, synergistically depicting the global metabolic patterns in oocytes. In particular, we discovered the metabolic features during meiotic maturation, such as the fall in polyunsaturated fatty acids (PUFAs) level and the active serine-glycine-one-carbon (SGOC) pathway. Using functional approaches, we further identified the key targets mediating the action of PUFA arachidonic acid (ARA) on meiotic maturation and demonstrated the control of epigenetic marks in maturing oocytes by SGOC network. Our data serve as a broad resource on the dynamics occurring in metabolome and proteome during oocyte maturation.
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Affiliation(s)
- Ling Li
- State Key Laboratory of Reproductive Medicine, Suzhou Municipal Hospital, Nanjing Medical University, Nanjing 211166, China
| | - Shuai Zhu
- State Key Laboratory of Reproductive Medicine, Suzhou Municipal Hospital, Nanjing Medical University, Nanjing 211166, China
| | - Wenjie Shu
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Yueshuai Guo
- State Key Laboratory of Reproductive Medicine, Suzhou Municipal Hospital, Nanjing Medical University, Nanjing 211166, China
| | - Yusheng Guan
- State Key Laboratory of Reproductive Medicine, Suzhou Municipal Hospital, Nanjing Medical University, Nanjing 211166, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Juan Zeng
- State Key Laboratory of Reproductive Medicine, Suzhou Municipal Hospital, Nanjing Medical University, Nanjing 211166, China
| | - Haichao Wang
- State Key Laboratory of Reproductive Medicine, Suzhou Municipal Hospital, Nanjing Medical University, Nanjing 211166, China
| | - Longsen Han
- State Key Laboratory of Reproductive Medicine, Suzhou Municipal Hospital, Nanjing Medical University, Nanjing 211166, China
| | - Jiaqi Zhang
- State Key Laboratory of Reproductive Medicine, Suzhou Municipal Hospital, Nanjing Medical University, Nanjing 211166, China
| | - Xiaohui Liu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Chunling Li
- State Key Laboratory of Reproductive Medicine, Suzhou Municipal Hospital, Nanjing Medical University, Nanjing 211166, China
| | - Xiaojing Hou
- State Key Laboratory of Reproductive Medicine, Suzhou Municipal Hospital, Nanjing Medical University, Nanjing 211166, China
| | - Min Gao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Juan Ge
- State Key Laboratory of Reproductive Medicine, Suzhou Municipal Hospital, Nanjing Medical University, Nanjing 211166, China
| | - Chao Ren
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Hao Zhang
- State Key Laboratory of Reproductive Medicine, Suzhou Municipal Hospital, Nanjing Medical University, Nanjing 211166, China; Department of Histology and Embryology, Nanjing Medical University, Nanjing 211166, China
| | - Tim Schedl
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Xuejiang Guo
- State Key Laboratory of Reproductive Medicine, Suzhou Municipal Hospital, Nanjing Medical University, Nanjing 211166, China; Department of Histology and Embryology, Nanjing Medical University, Nanjing 211166, China.
| | - Minjian Chen
- State Key Laboratory of Reproductive Medicine, Suzhou Municipal Hospital, Nanjing Medical University, Nanjing 211166, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China.
| | - Qiang Wang
- State Key Laboratory of Reproductive Medicine, Suzhou Municipal Hospital, Nanjing Medical University, Nanjing 211166, China; Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China.
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94
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Amoushahi M, Sunde L, Lykke-Hartmann K. The pivotal roles of the NOD-like receptors with a PYD domain, NLRPs, in oocytes and early embryo development†. Biol Reprod 2020; 101:284-296. [PMID: 31201414 DOI: 10.1093/biolre/ioz098] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 03/29/2019] [Accepted: 06/11/2019] [Indexed: 12/19/2022] Open
Abstract
Nucleotide-binding oligomerization domain (NOD)-like receptors with a pyrin domain (PYD), NLRPs, are pattern recognition receptors, well recognized for their important roles in innate immunity and apoptosis. However, several NLRPs have received attention for their new, specialized roles as maternally contributed genes important in reproduction and embryo development. Several NLRPs have been shown to be specifically expressed in oocytes and preimplantation embryos. Interestingly, and in line with divergent functions, NLRP genes reveal a complex evolutionary divergence. The most pronounced difference is the human-specific NLRP7 gene, not identified in rodents. However, mouse models have been extensively used to study maternally contributed NLRPs. The NLRP2 and NLRP5 proteins are components of the subcortical maternal complex (SCMC), which was recently identified as essential for mouse preimplantation development. The SCMC integrates multiple proteins, including KHDC3L, NLRP5, TLE6, OOEP, NLRP2, and PADI6. The NLRP5 (also known as MATER) has been extensively studied. In humans, inactivating variants in specific NLRP genes in the mother are associated with distinct phenotypes in the offspring, such as biparental hydatidiform moles (BiHMs) and preterm birth. Maternal-effect recessive mutations in KHDC3L and NLRP5 (and NLRP7) are associated with reduced reproductive outcomes, BiHM, and broad multilocus imprinting perturbations. The precise mechanisms of NLRPs are unknown, but research strongly indicates their pivotal roles in the establishment of genomic imprints and post-zygotic methylation maintenance, among other processes. Challenges for the future include translations of findings from the mouse model into human contexts and implementation in therapies and clinical fertility management.
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Affiliation(s)
| | - Lone Sunde
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.,Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Karin Lykke-Hartmann
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.,Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
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95
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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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96
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Rivera RM. Consequences of assisted reproductive techniques on the embryonic epigenome in cattle. Reprod Fertil Dev 2020; 32:65-81. [PMID: 32188559 DOI: 10.1071/rd19276] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Procedures used in assisted reproduction have been under constant scrutiny since their inception with the goal of improving the number and quality of embryos produced. However, invitro production of embryos is not without complications because many fertilised oocytes fail to become blastocysts, and even those that do often differ in the genetic output compared with their invivo counterparts. Thus only a portion of those transferred complete normal fetal development. An unwanted consequence of bovine assisted reproductive technology (ART) is the induction of a syndrome characterised by fetal overgrowth and placental abnormalities, namely large offspring syndrome; a condition associated with inappropriate control of the epigenome. Epigenetics is the study of chromatin and its effects on genetic output. Establishment and maintenance of epigenetic marks during gametogenesis and embryogenesis is imperative for the maintenance of cell identity and function. ARTs are implemented during times of vast epigenetic reprogramming; as a result, many studies have identified ART-induced deviations in epigenetic regulation in mammalian gametes and embryos. This review describes the various layers of epigenetic regulation and discusses findings pertaining to the effects of ART on the epigenome of bovine gametes and the preimplantation embryo.
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Affiliation(s)
- Rocío Melissa Rivera
- Division of Animal Science University of Missouri, Columbia, Missouri 65211, USA.
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97
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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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Barberet J, Barry F, Choux C, Guilleman M, Karoui S, Simonot R, Bruno C, Fauque P. What impact does oocyte vitrification have on epigenetics and gene expression? Clin Epigenetics 2020; 12:121. [PMID: 32778156 PMCID: PMC7418205 DOI: 10.1186/s13148-020-00911-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 07/21/2020] [Indexed: 02/07/2023] Open
Abstract
Children conceived by assisted reproductive technologies (ART) have a moderate risk for a number of adverse events and conditions. The question whether this additional risk is associated with specific procedures used in ART or whether it is related to the intrinsic biological factors associated with infertility remains unresolved. One of the main hypotheses is that laboratory procedures could have an effect on the epigenome of gametes and embryos. This suspicion is linked to the fact that ART procedures occur precisely during the period when there are major changes in the organization of the epigenome. Oocyte freezing protocols are generally considered safe; however, some evidence suggests that vitrification may be associated with modifications of the epigenetic marks. In this manuscript, after describing the main changes that occur during epigenetic reprogramming, we will provide current information regarding the impact of oocyte vitrification on epigenetic regulation and the consequences on gene expression, both in animals and humans. Overall, the literature suggests that epigenetic and transcriptomic profiles are sensitive to the stress induced by oocyte vitrification, and it also underlines the need to improve our knowledge in this field.
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Affiliation(s)
- Julie Barberet
- CHU Dijon Bourgogne, Laboratoire de Biologie de la Reproduction, CECOS, 14 rue Gaffarel, 21079 Dijon Cedex, France
| | - Fatima Barry
- CHU Dijon Bourgogne, Laboratoire de Biologie de la Reproduction, CECOS, 14 rue Gaffarel, 21079 Dijon Cedex, France
| | - Cécile Choux
- Gynécologie-Obstétrique, CHU Dijon Bourgogne, 14 rue Gaffarel, 21079 Dijon Cedex, France
| | - Magali Guilleman
- CHU Dijon Bourgogne, Laboratoire de Biologie de la Reproduction, CECOS, 14 rue Gaffarel, 21079 Dijon Cedex, France
| | - Sara Karoui
- CHU Dijon Bourgogne, Laboratoire de Biologie de la Reproduction, CECOS, 14 rue Gaffarel, 21079 Dijon Cedex, France
| | - Raymond Simonot
- CHU Dijon Bourgogne, Laboratoire de Biologie de la Reproduction, CECOS, 14 rue Gaffarel, 21079 Dijon Cedex, France
| | - Céline Bruno
- CHU Dijon Bourgogne, Laboratoire de Biologie de la Reproduction, CECOS, 14 rue Gaffarel, 21079 Dijon Cedex, France
| | - Patricia Fauque
- CHU Dijon Bourgogne, Laboratoire de Biologie de la Reproduction, CECOS, 14 rue Gaffarel, 21079 Dijon Cedex, France
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Wang J, Tian GG, Li X, Sun Y, Cheng L, Li Y, Shen Y, Chen X, Tang W, Tao S, Wu J. Integrated Glycosylation Patterns of Glycoproteins and DNA Methylation Landscapes in Mammalian Oogenesis and Preimplantation Embryo Development. Front Cell Dev Biol 2020; 8:555. [PMID: 32754589 PMCID: PMC7365846 DOI: 10.3389/fcell.2020.00555] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 06/11/2020] [Indexed: 12/19/2022] Open
Abstract
Glycosylation is one of the most fundamental post-translational modifications. However, the glycosylation patterns of glycoproteins have not been analyzed in mammalian preimplantation embryos, because of technical difficulties and scarcity of the required materials. Using high-throughput lectin microarrays of low-input cells and electrochemical techniques, an integration analysis of the DNA methylation and glycosylation landscapes of mammal oogenesis and preimplantation embryo development was performed. Highly noticeable changes occurred in the level of protein glycosylation during these events. Further analysis identified several stage-specific lectins including LEL, MNA-M, and MAL I. It was later confirmed that LEL was involved in mammalian oogenesis and preimplantation embryogenesis, and might be a marker of FGSC differentiation. Modified nanocomposite polyaniline/AuNPs were characterized by electron microscopy and modification on bare gold electrodes using layer-by-layer assembly technology. These nanoparticles were further subjected to accuracy measurements by analyzing the protein level of ten-eleven translocation protein (TET), which is an important enzyme in DNA demethylation that is regulated by O-glycosylation. Subsequent results showed that the variations in the glycosylation patterns of glycoproteins were opposite to those of the TET levels. Moreover, analysis of correlation between the changes in glyco-gene expression and female germline stem cell glycosylation profiles indicated that glycosylation was related to DNA methylation. Subsequent integration analysis showed that the trend in the variations of glycosylation patterns of glycoproteins was similar to that of DNA methylation and opposite to that of the TET protein levels during female germ cell and preimplantation embryo development. Our findings provide insight into the complex molecular mechanisms that regulate human embryo development, and a foundation for further elucidation of early embryonic development and informed reproductive medicine.
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Affiliation(s)
- Jian Wang
- Renji Hospital, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Geng G. Tian
- Renji Hospital, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoyong Li
- Renji Hospital, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yangyang Sun
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Li Cheng
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Yanfei Li
- Renji Hospital, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yue Shen
- Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, Ningxia Medical University, Yinchuan, China
| | - Xuejin Chen
- Department of Laboratory Animal Sciences, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wenwei Tang
- School of Chemistry Science and Technology, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai, China
| | - Shengce Tao
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Ji Wu
- Renji Hospital, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, Ningxia Medical University, Yinchuan, China
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100
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Żylicz JJ, Heard E. Molecular Mechanisms of Facultative Heterochromatin Formation: An X-Chromosome Perspective. Annu Rev Biochem 2020; 89:255-282. [PMID: 32259458 DOI: 10.1146/annurev-biochem-062917-012655] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Facultative heterochromatin (fHC) concerns the developmentally regulated heterochromatinization of different regions of the genome and, in the case of the mammalian X chromosome and imprinted loci, of only one allele of a homologous pair. The formation of fHC participates in the timely repression of genes, by resisting strong trans activators. In this review, we discuss the molecular mechanisms underlying the establishment and maintenance of fHC in mammals using a mouse model. We focus on X-chromosome inactivation (XCI) as a paradigm for fHC but also relate it to genomic imprinting and homeobox (Hox) gene cluster repression. A vital role for noncoding transcription and/or transcripts emerges as the general principle of triggering XCI and canonical imprinting. However, other types of fHC are established through an unknown mechanism, independent of noncoding transcription (Hox clusters and noncanonical imprinting). We also extensively discuss polycomb-group repressive complexes (PRCs), which frequently play a vital role in fHC maintenance.
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Affiliation(s)
- Jan J Żylicz
- Mammalian Developmental Epigenetics Group, Institut Curie, CNRS UMR 3215, INSERM U934, PSL University, 75248 Paris Cedex 05, France.,Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EL, United Kingdom
| | - Edith Heard
- Directors' Research, EMBL Heidelberg, 69117 Heidelberg, Germany;
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