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Scatturice LA, Vázquez N, Strobl-Mazzulla PH. miR-137 confers robustness to the territorial restriction of the neural plate border. Development 2024; 151:dev202344. [PMID: 38828854 DOI: 10.1242/dev.202344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 05/20/2024] [Indexed: 06/05/2024]
Abstract
The neural plate border (NPB) of vertebrate embryos is segregated from the neural plate (NP) and epidermal regions, and comprises an intermingled group of progenitors with multiple fate potential. Recent studies have shown that, during the gastrula stage, TFAP2A acts as a pioneer factor in remodeling the epigenetic landscape required to activate components of the NPB induction program. Here, we show that chick Tfap2a has two highly conserved binding sites for miR-137, and both display a reciprocal expression pattern at the NPB and NP, respectively. In addition, ectopic miR-137 expression reduced TFAP2A, whereas its functional inhibition expanded their territorial distribution overlapping with PAX7. Furthermore, we demonstrate that loss of the de novo DNA methyltransferase DNMT3A expanded miR-137 expression to the NPB. Bisulfite sequencing revealed a markedly elevated presence of non-canonical CpH methylation within the miR-137 promoter region when comparing NPB and NP samples. Our findings show that miR-137 contributes to the robustness of NPB territorial restriction in vertebrate development.
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Affiliation(s)
- Luciana A Scatturice
- Laboratory of Developmental Biology, Instituto Tecnológico de Chascomús (CONICET-UNSAM). Escuela de Bio y Nanotecnologías (UNSAM), Chascomús, Buenos Aires 7130, Argentina
| | - Nicolás Vázquez
- Laboratory of Developmental Biology, Instituto Tecnológico de Chascomús (CONICET-UNSAM). Escuela de Bio y Nanotecnologías (UNSAM), Chascomús, Buenos Aires 7130, Argentina
| | - Pablo H Strobl-Mazzulla
- Laboratory of Developmental Biology, Instituto Tecnológico de Chascomús (CONICET-UNSAM). Escuela de Bio y Nanotecnologías (UNSAM), Chascomús, Buenos Aires 7130, Argentina
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Toriyama K, Au Yeung WK, Inoue A, Kurimoto K, Yabuta Y, Saitou M, Nakamura T, Nakano T, Sasaki H. DPPA3 facilitates genome-wide DNA demethylation in mouse primordial germ cells. BMC Genomics 2024; 25:344. [PMID: 38580899 PMCID: PMC10996186 DOI: 10.1186/s12864-024-10192-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 03/05/2024] [Indexed: 04/07/2024] Open
Abstract
BACKGROUND Genome-wide DNA demethylation occurs in mammalian primordial germ cells (PGCs) as part of the epigenetic reprogramming important for gametogenesis and resetting the epigenetic information for totipotency. Dppa3 (also known as Stella or Pgc7) is highly expressed in mouse PGCs and oocytes and encodes a factor essential for female fertility. It prevents excessive DNA methylation in oocytes and ensures proper gene expression in preimplantation embryos: however, its role in PGCs is largely unexplored. In the present study, we investigated whether or not DPPA3 has an impact on CG methylation/demethylation in mouse PGCs. RESULTS We show that DPPA3 plays a role in genome-wide demethylation in PGCs even before sex differentiation. Dppa3 knockout female PGCs show aberrant hypermethylation, most predominantly at H3K9me3-marked retrotransposons, which persists up to the fully-grown oocyte stage. DPPA3 works downstream of PRDM14, a master regulator of epigenetic reprogramming in embryonic stem cells and PGCs, and independently of TET1, an enzyme that hydroxylates 5-methylcytosine. CONCLUSIONS The results suggest that DPPA3 facilitates DNA demethylation through a replication-coupled passive mechanism in PGCs. Our study identifies DPPA3 as a novel epigenetic reprogramming factor in mouse PGCs.
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Affiliation(s)
- Keisuke Toriyama
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Wan Kin Au Yeung
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan.
| | - Azusa Inoue
- Laboratory for Epigenome Inheritance, Riken Center for Integrative Medical Sciences, Kanagawa, 230-0045, Japan
- Tokyo Metropolitan University, Tokyo, 192-0397, Japan
| | - Kazuki Kurimoto
- Department of Embryology, School of Medicine, Nara Medical University, 840 Shijo-Cho, Kashihara, Nara, 634-8521, Japan
| | - Yukihiro Yabuta
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Yoshida-Konoe- cho, Sakyo-ku, Kyoto, 606-8501, Japan
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Mitinori Saitou
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Yoshida-Konoe- cho, Sakyo-ku, Kyoto, 606-8501, Japan
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Toshinobu Nakamura
- Laboratory for Epigenetic Regulation, Department of Animal Bio-Science, Nagahama Institute of Bio-Science and Technology, Shiga, 526-0829, Japan
| | - Toru Nakano
- Graduate School of Frontier Biosciences, Osaka University, Osaka, 565-0871, Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan.
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Ashokan M, Jayanthi KV, Elango K, Sneha K, Ramesha KP, Reshma RS, Saravanan KA, Naveen KGS. Biological methylation: redefining the link between genotype and phenotype. Anim Biotechnol 2023; 34:3174-3186. [PMID: 35468300 DOI: 10.1080/10495398.2022.2065999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
The central dogma of molecular biology is responsible for the crucial flow of genetic information from DNA to protein through the transcription and translation process. Although the sequence of DNA is constant in all organs, the difference in protein and variation in the phenotype is mainly due to the quality and quantity of tissue-specific gene expression and methylation pattern. The term methylation has been defined and redefined by various scientists in the last fifty years. There is always huge excitement around this field because the inheritance of something is beyond its DNA sequence. Advanced gene methylation studies have redefined molecular genetics and these tools are considered de novo in alleviating challenges of animal disease and production. Recent emerging evidence has shown that the impact of DNA, RNA, and protein methylation is crucial for embryonic development, cell proliferation, cell differentiation, and phenotype production. Currently, many researchers are focusing their work on methylation to understand its significant role in expression, disease-resistant traits, productivity, and longevity. The main aim of the present review is to provide an overview of DNA, RNA, and protein methylation, current research output from different sources, methodologies, factors responsible for methylation of genes, and future prospects in animal genetics.
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Affiliation(s)
- M Ashokan
- Animal Genetics and Breeding Division, Veterinary College, Hassan, KVAFSU, Karnataka, India
| | - K V Jayanthi
- Animal Genetics and Breeding Division, Veterinary College, Hassan, KVAFSU, Karnataka, India
| | - K Elango
- Southern Regional Station, ICAR-National Dairy Research Institute, Bangalore, India
| | - Kadimetla Sneha
- Animal Genetics and Breeding Division, Veterinary College, Hassan, KVAFSU, Karnataka, India
| | - K P Ramesha
- Southern Regional Station, ICAR-National Dairy Research Institute, Bangalore, India
| | - Raj S Reshma
- Southern Regional Station, ICAR-National Dairy Research Institute, Bangalore, India
| | - K A Saravanan
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Kumar G S Naveen
- Animal Genetics and Breeding Division, Veterinary College, Hassan, KVAFSU, Karnataka, India
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4
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Uehara R, Au Yeung WK, Toriyama K, Ohishi H, Kubo N, Toh H, Suetake I, Shirane K, Sasaki H. The DNMT3A ADD domain is required for efficient de novo DNA methylation and maternal imprinting in mouse oocytes. PLoS Genet 2023; 19:e1010855. [PMID: 37527244 PMCID: PMC10393158 DOI: 10.1371/journal.pgen.1010855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 07/03/2023] [Indexed: 08/03/2023] Open
Abstract
Establishment of a proper DNA methylation landscape in mammalian oocytes is important for maternal imprinting and embryonic development. De novo DNA methylation in oocytes is mediated by the DNA methyltransferase DNMT3A, which has an ATRX-DNMT3-DNMT3L (ADD) domain that interacts with histone H3 tail unmethylated at lysine-4 (H3K4me0). The domain normally blocks the methyltransferase domain via intramolecular interaction and binding to histone H3K4me0 releases the autoinhibition. However, H3K4me0 is widespread in chromatin and the role of the ADD-histone interaction has not been studied in vivo. We herein show that amino-acid substitutions in the ADD domain of mouse DNMT3A cause dwarfism. Oocytes derived from homozygous females show mosaic loss of CG methylation and almost complete loss of non-CG methylation. Embryos derived from such oocytes die in mid-to-late gestation, with stochastic and often all-or-none-type CG-methylation loss at imprinting control regions and misexpression of the linked genes. The stochastic loss is a two-step process, with loss occurring in cleavage-stage embryos and regaining occurring after implantation. These results highlight an important role for the ADD domain in efficient, and likely processive, de novo CG methylation and pose a model for stochastic inheritance of epigenetic perturbations in germ cells to the next generation.
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Affiliation(s)
- Ryuji Uehara
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Wan Kin Au Yeung
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Keisuke Toriyama
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Hiroaki Ohishi
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- Division of Gene Expression Dynamics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Naoki Kubo
- 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
- Advanced Genomics Center, National Institute of Genetics, Mishima, Japan
| | - Isao Suetake
- Department of Nutrition Science, Nakamura Gakuen University, Fukuoka, Japan
| | - Kenjiro Shirane
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- Department of Genome Biology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
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5
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Wang J, Sun X, Yang Z, Li S, Wang Y, Ren R, Liu Z, Yu D. Epigenetic regulation in premature ovarian failure: A literature review. Front Physiol 2023; 13:998424. [PMID: 36685174 PMCID: PMC9846267 DOI: 10.3389/fphys.2022.998424] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 12/14/2022] [Indexed: 01/05/2023] Open
Abstract
Premature ovarian failure (POF), or premature ovarian insufficiency (POI), is a multifactorial and heterogeneous disease characterized by amenorrhea, decreased estrogen levels and increased female gonadotropin levels. The incidence of POF is increasing annually, and POF has become one of the main causes of infertility in women of childbearing age. The etiology and pathogenesis of POF are complex and have not yet been clearly elucidated. In addition to genetic factors, an increasing number of studies have revealed that epigenetic changes play an important role in the occurrence and development of POF. However, we found that very few papers have summarized epigenetic variations in POF, and a systematic analysis of this topic is therefore necessary. In this article, by reviewing and analyzing the most relevant literature in this research field, we expound on the relationship between DNA methylation, histone modification and non-coding RNA expression and the development of POF. We also analyzed how environmental factors affect POF through epigenetic modulation. Additionally, we discuss potential epigenetic biomarkers and epigenetic treatment targets for POF. We anticipate that our paper may provide new therapeutic clues for improving ovarian function and maintaining fertility in POF patients.
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Affiliation(s)
- Jing Wang
- Department of Reproductive Medicine, Department of Prenatal Diagnosis, Changchun, China
| | | | | | - Sijie Li
- Department of Breast Surgery, Changchun, China
| | - Yufeng Wang
- Public Research Platform, The First Hospital of Jilin University, Jilin, China
| | - Ruoxue Ren
- Public Research Platform, The First Hospital of Jilin University, Jilin, China
| | - Ziyue Liu
- Public Research Platform, The First Hospital of Jilin University, Jilin, China
| | - Dehai Yu
- Public Research Platform, The First Hospital of Jilin University, Jilin, China,*Correspondence: Dehai Yu,
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6
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Lopes JS, Ivanova E, Ruiz S, Andrews S, Kelsey G, Coy P. Effect of Superovulation Treatment on Oocyte's DNA Methylation. Int J Mol Sci 2022; 23:16158. [PMID: 36555801 PMCID: PMC9785075 DOI: 10.3390/ijms232416158] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/09/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Controlled ovarian stimulation is a necessary step in some assisted reproductive procedures allowing a higher collection of female gametes. However, consequences of this stimulation for the gamete or the offspring have been shown in several mammals. Most studies used comparisons between oocytes from different donors, which may contribute to different responses. In this work, we use the bovine model in which each animal serves as its own control. DNA methylation profiles were obtained by single-cell whole-genome bisulfite sequencing of oocytes from pre-ovulatory unstimulated follicles compared to oocytes from stimulated follicles. Results show that the global percentage of methylation was similar between groups, but the percentage of methylation was lower for non-stimulated oocytes in the imprinted genes APEG3, MEG3, and MEG9 and higher in TSSC4 when compared to stimulated oocytes. Differences were also found in CGI of imprinted genes: higher methylation was found among non-stimulated oocytes in MEST (PEG1), IGF2R, GNAS (SCG6), KvDMR1 ICR UMD, and IGF2. In another region around IGF2, the methylation percentage was lower for non-stimulated oocytes when compared to stimulated oocytes. Data drawn from this study might help to understand the molecular reasons for the appearance of certain syndromes in assisted reproductive technologies-derived offspring.
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Affiliation(s)
- Jordana S. Lopes
- Physiology of Reproduction Group, Department of Physiology, Faculty of Veterinary, University of Murcia, 30100 Murcia, Spain
- Institute for Biomedical Research of Murcia, IMIB-Arrixaca, 30100 Murcia, Spain
| | - Elena Ivanova
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Salvador Ruiz
- Physiology of Reproduction Group, Department of Physiology, Faculty of Veterinary, University of Murcia, 30100 Murcia, Spain
- Institute for Biomedical Research of Murcia, IMIB-Arrixaca, 30100 Murcia, Spain
| | - Simon Andrews
- Bioinformatics Group, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Gavin Kelsey
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK
| | - Pilar Coy
- Physiology of Reproduction Group, Department of Physiology, Faculty of Veterinary, University of Murcia, 30100 Murcia, Spain
- Institute for Biomedical Research of Murcia, IMIB-Arrixaca, 30100 Murcia, Spain
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7
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DNA Methylation Malleability and Dysregulation in Cancer Progression: Understanding the Role of PARP1. Biomolecules 2022; 12:biom12030417. [PMID: 35327610 PMCID: PMC8946700 DOI: 10.3390/biom12030417] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/28/2022] [Accepted: 03/04/2022] [Indexed: 02/05/2023] Open
Abstract
Mammalian genomic DNA methylation represents a key epigenetic modification and its dynamic regulation that fine-tunes the gene expression of multiple pathways during development. It maintains the gene expression of one generation of cells; particularly, the mitotic inheritance of gene-expression patterns makes it the key governing mechanism of epigenetic change to the next generation of cells. Convincing evidence from recent discoveries suggests that the dynamic regulation of DNA methylation is accomplished by the enzymatic action of TET dioxygenase, which oxidizes the methyl group of cytosine and activates transcription. As a result of aberrant DNA modifications, genes are improperly activated or inhibited in the inappropriate cellular context, contributing to a plethora of inheritable diseases, including cancer. We outline recent advancements in understanding how DNA modifications contribute to tumor suppressor gene silencing or oncogenic-gene stimulation, as well as dysregulation of DNA methylation in cancer progression. In addition, we emphasize the function of PARP1 enzymatic activity or inhibition in the maintenance of DNA methylation dysregulation. In the context of cancer remediation, the impact of DNA methylation and PARP1 pharmacological inhibitors, and their relevance as a combination therapy are highlighted.
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8
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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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9
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Matsuzaki H, Miyajima Y, Fukamizu A, Tanimoto K. Orientation of mouse H19 ICR affects imprinted H19 gene expression through promoter methylation-dependent and -independent mechanisms. Commun Biol 2021; 4:1410. [PMID: 34921234 PMCID: PMC8683476 DOI: 10.1038/s42003-021-02939-9] [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: 06/14/2021] [Accepted: 11/30/2021] [Indexed: 11/19/2022] Open
Abstract
The mouse Igf2/H19 locus is regulated by genomic imprinting, in which the paternally methylated H19 imprinting control region (ICR) plays a critical role in mono-allelic expression of the genes in the locus. Although the maternal allele-specific insulator activity of the H19 ICR in regulating imprinted Igf2 expression has been well established, the detailed mechanism by which the H19 ICR controls mono-allelic H19 gene expression has not been fully elucidated. In this study, we evaluated the effect of H19 ICR orientation on imprinting regulation in mutant mice in which the H19 ICR sequence was inverted at the endogenous locus. When the inverted-ICR allele was paternally inherited, the methylation level of the H19 promoter was decreased and the H19 gene was derepressed, suggesting that methylation of the H19 promoter is essential for complete repression of H19 gene expression. Unexpectedly, when the inverted allele was maternally inherited, the expression level of the H19 gene was lower than that of the WT allele, even though the H19 promoter remained fully hypomethylated. These observations suggested that the polarity of the H19 ICR is involved in controlling imprinted H19 gene expression on each parental allele, dependent or independent on DNA methylation of the H19 promoter.
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Affiliation(s)
- Hitomi Matsuzaki
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan.
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki, Japan.
| | - Yu Miyajima
- Graduate school of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Akiyoshi Fukamizu
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Keiji Tanimoto
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki, Japan
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10
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Transposable Element Dynamics and Regulation during Zygotic Genome Activation in Mammalian Embryos and Embryonic Stem Cell Model Systems. Stem Cells Int 2021; 2021:1624669. [PMID: 34691189 PMCID: PMC8536462 DOI: 10.1155/2021/1624669] [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: 05/21/2021] [Revised: 08/31/2021] [Accepted: 09/08/2021] [Indexed: 12/25/2022] Open
Abstract
Transposable elements (TEs) are mobile genetic sequences capable of duplicating and reintegrating at new regions within the genome. A growing body of evidence has demonstrated that these elements play important roles in host genome evolution, despite being traditionally viewed as parasitic elements. To prevent ectopic activation of TE transposition and transcription, they are epigenetically silenced in most somatic tissues. Intriguingly, a specific class of TEs-retrotransposons-is transiently expressed at discrete phases during mammalian development and has been linked to the establishment of totipotency during zygotic genome activation (ZGA). While mechanisms controlling TE regulation in somatic tissues have been extensively studied, the significance underlying the unique transcriptional reactivation of retrotransposons during ZGA is only beginning to be uncovered. In this review, we summarize the expression dynamics of key retrotransposons during ZGA, focusing on findings from in vivo totipotent embryos and in vitro totipotent-like embryonic stem cells (ESCs). We then dissect the functions of retrotransposons and discuss how their transcriptional activities are finetuned during early stages of mammalian development.
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11
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Ramos KS, Bojang P, Bowers E. Role of long interspersed nuclear element-1 in the regulation of chromatin landscapes and genome dynamics. Exp Biol Med (Maywood) 2021; 246:2082-2097. [PMID: 34304633 PMCID: PMC8524765 DOI: 10.1177/15353702211031247] [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: 06/18/2021] [Accepted: 06/22/2021] [Indexed: 12/27/2022] Open
Abstract
LINE-1 retrotransposon, the most active mobile element of the human genome, is subject to tight regulatory control. Stressful environments and disease modify the recruitment of regulatory proteins leading to unregulated activation of LINE-1. The activation of LINE-1 influences genome dynamics through altered chromatin landscapes, insertion mutations, deletions, and modulation of cellular plasticity. To date, LINE-1 retrotransposition has been linked to various cancer types and may in fact underwrite the genetic basis of various other forms of chronic human illness. The occurrence of LINE-1 polymorphisms in the human population may define inter-individual differences in susceptibility to disease. This review is written in honor of Dr Peter Stambrook, a friend and colleague who carried out highly impactful cancer research over many years of professional practice. Dr Stambrook devoted considerable energy to helping others live up to their full potential and to navigate the complexities of professional life. He was an inspirational leader, a strong advocate, a kind mentor, a vocal supporter and cheerleader, and yes, a hard critic and tough friend when needed. His passionate stand on issues, his witty sense of humor, and his love for humanity have left a huge mark in our lives. We hope that that the knowledge summarized here will advance our understanding of the role of LINE-1 in cancer biology and expedite the development of innovative cancer diagnostics and treatments in the ways that Dr Stambrook himself had so passionately envisioned.
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Affiliation(s)
- Kenneth S Ramos
- Institute of Biosciences and Technology, Texas A&M Health, Houston, TX 77030, USA
| | - Pasano Bojang
- University of Kentucky College of Medicine, Lexington, KY 40506, USA
| | - Emma Bowers
- Institute of Biosciences and Technology, Texas A&M Health, Houston, TX 77030, USA
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12
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In vitro reconstitution of the whole male germ-cell development from mouse pluripotent stem cells. Cell Stem Cell 2021; 28:2167-2179.e9. [PMID: 34496297 DOI: 10.1016/j.stem.2021.08.005] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 06/25/2021] [Accepted: 08/09/2021] [Indexed: 01/08/2023]
Abstract
Mammalian male germ-cell development consists of three distinct phases: primordial germ cell (PGC) development, male germ-cell specification for spermatogonium development, and ensuing spermatogenesis. Here, we show an in vitro reconstitution of whole male germ-cell development by pluripotent stem cells (PSCs). Mouse embryonic stem cells (mESCs) are induced into PGC-like cells (mPGCLCs), which are expanded for epigenetic reprogramming. In reconstituted testes under an optimized condition, such mPGCLCs differentiate into spermatogonium-like cells with proper developmental transitions, gene expression, and cell-cycle dynamics and are expanded robustly as germline stem cell-like cells (GSCLCs) with an appropriate androgenetic epigenome. Importantly, GSCLCs show vigorous spermatogenesis, not only upon transplantation into testes in vivo but also under an in vitro culture of testis transplants, and the resultant spermatids contribute to fertile offspring. By uniting faithful recapitulations of the three phases of male germ-cell development, our study creates a paradigm for the in vitro male gametogenesis by PSCs.
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13
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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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14
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Veikkolainen V, Ali N, Doroszko M, Kiviniemi A, Miinalainen I, Ohlsson C, Poutanen M, Rahman N, Elenius K, Vainio SJ, Naillat F. Erbb4 regulates the oocyte microenvironment during folliculogenesis. Hum Mol Genet 2021; 29:2813-2830. [PMID: 32716031 DOI: 10.1093/hmg/ddaa161] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/17/2020] [Accepted: 07/17/2020] [Indexed: 12/16/2022] Open
Abstract
Polycystic ovary syndrome (PCOS) is one of the most common endocrine disorders leading to infertility in women affecting reproductive, endocrine and metabolic systems. Recent genomewide association studies on PCOS cohorts revealed a single nucleotide polymorphism (SNP) in the ERBB4 receptor tyrosine kinase 4 gene, but its role in ovary development or during folliculogenesis remains poorly understood. Since no genetic animal models mimicking all PCOS reproductive features are available, we conditionally deleted Erbb4 in murine granulosa cells (GCs) under the control of Amh promoter. While we have demonstrated that Erbb4 deletion displayed aberrant ovarian function by affecting the reproductive function (asynchronous oestrous cycle leading to few ovulations and subfertility) and metabolic function (obesity), their ovaries also present severe structural and functional abnormalities (impaired oocyte development). Hormone analysis revealed an up-regulation of serum luteinizing hormone, hyperandrogenism, increased production of ovarian and circulating anti-Müllerian hormone. Our data implicate that Erbb4 deletion in GCs leads to defective intercellular junctions between the GCs and oocytes, causing changes in the expression of genes regulating the local microenvironment of the follicles. In vitro culture assays reducing the level of Erbb4 via shRNAs confirm that Erbb4 is essential for regulating Amh level. In conclusion, our results indicate a functional role for Erbb4 in the ovary, especially during folliculogenesis and its reduced expression plays an important role in reproductive pathophysiology, such as PCOS development.
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Affiliation(s)
- Ville Veikkolainen
- Institute of Biomedicine and MediCity Research Laboratory, University of Turku, FI-20520 Turku, Finland
| | - Nsrein Ali
- Organogenesis Laboratory, Department of Medical Biochemistry and Molecular Biology, Biocenter Oulu, University of Oulu, FI-90014 Oulu, Finland
| | - Milena Doroszko
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, University of Turku, FI-20520 Turku, Finland.,Department of Immunology Genetics and Pathology, Section for Neuro-oncology, Uppsala University, 752 36 Uppsala, Sweden
| | - Antti Kiviniemi
- Organogenesis Laboratory, Department of Medical Biochemistry and Molecular Biology, Biocenter Oulu, University of Oulu, FI-90014 Oulu, Finland
| | - Ilkka Miinalainen
- Electron Microscopy Unit, Biocenter Oulu, University of Oulu, FI-90220 Oulu, Finland
| | - Claes Ohlsson
- Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, SE-41345 Gothenburg, Sweden
| | - Matti Poutanen
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, University of Turku, FI-20520 Turku, Finland.,Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, SE-41345 Gothenburg, Sweden
| | - Nafis Rahman
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, University of Turku, FI-20520 Turku, Finland
| | - Klaus Elenius
- Institute of Biomedicine and MediCity Research Laboratory, University of Turku, FI-20520 Turku, Finland.,Department of Oncology, Turku University Hospital, FI-20520 Turku, Finland
| | - Seppo J Vainio
- Department of Immunology Genetics and Pathology, Section for Neuro-oncology, Uppsala University, 752 36 Uppsala, Sweden.,InfoTech Oulu, Oulu University and Biobank Borealis of Northern Finland, Oulu University Hospital, University of Oulu, FI-90014 Oulu, FINLAND
| | - Florence Naillat
- Organogenesis Laboratory, Department of Medical Biochemistry and Molecular Biology, Biocenter Oulu, University of Oulu, FI-90014 Oulu, Finland
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15
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Taguchi J, Shibata H, Kabata M, Kato M, Fukuda K, Tanaka A, Ohta S, Ukai T, Mitsunaga K, Yamada Y, Nagaoka SI, Yamazawa S, Ohnishi K, Woltjen K, Ushiku T, Ozawa M, Saitou M, Shinkai Y, Yamamoto T, Yamada Y. DMRT1-mediated reprogramming drives development of cancer resembling human germ cell tumors with features of totipotency. Nat Commun 2021; 12:5041. [PMID: 34413299 PMCID: PMC8377058 DOI: 10.1038/s41467-021-25249-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 07/29/2021] [Indexed: 11/23/2022] Open
Abstract
In vivo reprogramming provokes a wide range of cell fate conversion. Here, we discover that in vivo induction of higher levels of OSKM in mouse somatic cells leads to increased expression of primordial germ cell (PGC)-related genes and provokes genome-wide erasure of genomic imprinting, which takes place exclusively in PGCs. Moreover, the in vivo OSKM reprogramming results in development of cancer that resembles human germ cell tumors. Like a subgroup of germ cell tumors, propagated tumor cells can differentiate into trophoblasts. Moreover, these tumor cells give rise to induced pluripotent stem cells (iPSCs) with expanded differentiation potential into trophoblasts. Remarkably, the tumor-derived iPSCs are able to contribute to non-neoplastic somatic cells in adult mice. Mechanistically, DMRT1, which is expressed in PGCs, drives the reprogramming and propagation of the tumor cells in vivo. Furthermore, the DMRT1-related epigenetic landscape is associated with trophoblast competence of the reprogrammed cells and provides a therapeutic target for germ cell tumors. These results reveal an unappreciated route for somatic cell reprogramming and underscore the impact of reprogramming in development of germ cell tumors.
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Affiliation(s)
- Jumpei Taguchi
- Division of Stem Cell Pathology, Center for Experimental Medicine and Systems Biology, Institute of Medical Science, The University of Tokyo, Minoto-ku, Tokyo, Japan
| | - Hirofumi Shibata
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto, Japan
- Department of Otolaryngology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Mio Kabata
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Masaki Kato
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, Wako-shi, Saitama, Japan
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kei Fukuda
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, Wako-shi, Saitama, Japan
| | - Akito Tanaka
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Sho Ohta
- Division of Stem Cell Pathology, Center for Experimental Medicine and Systems Biology, Institute of Medical Science, The University of Tokyo, Minoto-ku, Tokyo, Japan
| | - Tomoyo Ukai
- Division of Stem Cell Pathology, Center for Experimental Medicine and Systems Biology, Institute of Medical Science, The University of Tokyo, Minoto-ku, Tokyo, Japan
| | - Kanae Mitsunaga
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Yosuke Yamada
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto, Japan
- Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto, Japan
| | - So I Nagaoka
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, Japan
- Department of Embryology, Nara Medical University, Nara, Japan
| | - Sho Yamazawa
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kotaro Ohnishi
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto, Japan
- Department of Gastroenterology/Internal Medicine, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Knut Woltjen
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Tetsuo Ushiku
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Manabu Ozawa
- Laboratory of Reproductive Systems Biology, Center for Experimental Medicine and Systems Biology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Mitinori Saitou
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto, Japan
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, Japan
| | - Yoichi Shinkai
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, Wako-shi, Saitama, Japan
| | - Takuya Yamamoto
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, Japan
- Medical-risk Avoidance Based on iPS Cells Team, RIKEN Center for Advanced Intelligence Project (AIP), Kyoto, Japan
- AMED-CREST, AMED 1-7-1 Otemachi, Chiyodaku, Tokyo, Japan
| | - Yasuhiro Yamada
- Division of Stem Cell Pathology, Center for Experimental Medicine and Systems Biology, Institute of Medical Science, The University of Tokyo, Minoto-ku, Tokyo, Japan.
- AMED-CREST, AMED 1-7-1 Otemachi, Chiyodaku, Tokyo, Japan.
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16
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Ramasamy D, Deva Magendhra Rao AK, Rajkumar T, Mani S. Non-CpG methylation-a key epigenetic modification in cancer. Brief Funct Genomics 2021; 20:304-311. [PMID: 34318313 DOI: 10.1093/bfgp/elab035] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/28/2021] [Accepted: 07/02/2021] [Indexed: 12/17/2022] Open
Abstract
The methylation of cytosine residues that precede adenine/thymine or other cytosine nucleotides instead of guanine in DNA is known as non-CpG methylation. It is a pronounced epigenetic modification with a central role in gene regulation similar to CpG methylation. Due to technological limitations, the locus-specific role of non-CpG methylation was scarcely understood. At present, high-throughput analyses and improved enrichment methods can elucidate the role of genome-wide non-CpG methylation distributions. Although the functional basis of non-CpG methylation in regulating gene expression control is known, its role in cancer development is yet to be ascertained. This review sheds light on the possible mechanism of non-CpG methylation in embryos and developed tissues with a special focus on cancer development and progression. In particular, the maintenance and alteration of non-CpG methylation levels and the crucial factors that determine this level of non-CpG methylation and its functional role in cancer are discussed.
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17
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Liu R, Long Q, Zou X, Wang Y, Pei Y. DNA methylation occurring in Cre-expressing cells inhibits loxP recombination and silences loxP-sandwiched genes. THE NEW PHYTOLOGIST 2021; 231:210-224. [PMID: 33742463 DOI: 10.1111/nph.17353] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 03/12/2021] [Indexed: 06/12/2023]
Abstract
The low DNA recombination efficiency of site-specific recombinase systems in plants limits their application; however, the underlying mechanism is unknown. We evaluate the gene deletion performance of four recombinase systems (Cre/loxP, Flp/FRT, KD/KDRT and B3/B3RT) in tobacco where the recombinases are under the control of germline-specific promoters. We find that the expression of these recombinases results mostly in gene silencing rather than gene deletion. Using the Cre/loxP system as a model, we reveal that the region flanked by loxP sites (floxed) is hypermethylated, which prevents floxed genes from deletion while silencing the expression of the genes. We further show CG methylation alone in the recombinase binding element of the loxP site is unable to impede gene deletion; instead, CHH methylation in the crossover region is required to inhibit loxP recombination. Our study illustrates the important role of recombinase-induced DNA methylation in the inhibition of site-specific DNA recombination and uncovers the mechanism underlying recombinase-associated gene silence in plants.
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Affiliation(s)
- Ruochen Liu
- Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops; Biotechnology Research Center, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing, 400715, China
| | - Qin Long
- Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops; Biotechnology Research Center, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing, 400715, China
| | - Xiuping Zou
- Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops; Biotechnology Research Center, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing, 400715, China
| | - You Wang
- Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops; Biotechnology Research Center, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing, 400715, China
| | - Yan Pei
- Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops; Biotechnology Research Center, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing, 400715, China
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18
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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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19
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Chang S, Wang Y, Xin Y, Wang S, Luo Y, Wang L, Zhang H, Li J. DNA methylation abnormalities of imprinted genes in congenital heart disease: a pilot study. BMC Med Genomics 2021; 14:4. [PMID: 33407475 PMCID: PMC7789576 DOI: 10.1186/s12920-020-00848-0] [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] [Received: 11/22/2020] [Accepted: 12/03/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Congenital heart disease (CHD) is resulted from the interaction of genetic aberration and environmental factors. Imprinted genes, which are regulated by epigenetic modifications, are essential for the normal embryonic development. However, the role of imprinted genes in the etiology of CHD remains unclear. METHODS After the samples were treated with bisulfate salt, imprinted genes methylation were measured by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. T test and One-way ANOVA were performed to evaluate the differences among groups. Odds ratios (ORs) were performed to evaluate the incidence risk of CHD in relation to methylation levels. RESULTS We investigated the alterations of imprinted gene germline differential methylation regions (gDMRs) methylation in patients with CHD. Eighteen imprinted genes that are known to affect early embryonic development were selected and the methylation modification genes were detected by massarray in 27 CHD children and 28 healthy children. Altered gDMR methylation level of 8 imprinted genes was found, including 2 imprinted genes with hypermethylation of GRB10 and MEST and 6 genes with hypomethylation of PEG10, NAP1L5, INPP5F, PLAGL1, NESP and MEG3. Stratified analysis showed that the methylation degree of imprinted genes was different in different types of CHD. Risk analysis showed that 6 imprinted genes, except MEST and NAP1L5, within a specific methylation level range were the risk factors for CHD CONCLUSION: Altered methylation of imprinted genes is associated with CHD and varies in different types of CHD. Further experiments are warranted to identify the methylation characteristics of imprinted genes in different types of CHD and clarify the etiologies of imprinted genes in CHD.
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Affiliation(s)
- Shaoyan Chang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Yubo Wang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Yu Xin
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Shuangxing Wang
- Department of Cardiac Surgery, Children's Hospital Affiliated to Capital Institute of Pediatrics, No. 2 Yabao Road, Chao Yang District, Beijing, 100020, China
| | - Yi Luo
- Department of Cardiac Surgery, Children's Hospital Affiliated to Capital Institute of Pediatrics, No. 2 Yabao Road, Chao Yang District, Beijing, 100020, China
| | - Li Wang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Hui Zhang
- Department of Cardiac Surgery, Children's Hospital Affiliated to Capital Institute of Pediatrics, No. 2 Yabao Road, Chao Yang District, Beijing, 100020, China.
| | - Jia Li
- Clinical Physiology Laboratory, Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, No. 9 Jinsui Road, Tianhe District, Guangzhou City, 510000, Guangdong Province, China.
- Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510000, Guangdong Province, China.
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20
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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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21
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Koganti P, Yao J, Cleveland BM. Molecular Mechanisms Regulating Muscle Plasticity in Fish. Animals (Basel) 2020; 11:ani11010061. [PMID: 33396941 PMCID: PMC7824542 DOI: 10.3390/ani11010061] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 12/24/2020] [Accepted: 12/25/2020] [Indexed: 12/12/2022] Open
Abstract
Growth rates in fish are largely dependent on genetic and environmental factors, of which the latter can be highly variable throughout development. For this reason, muscle growth in fish is particularly dynamic as muscle structure and function can be altered by environmental conditions, a concept referred to as muscle plasticity. Myogenic regulatory factors (MRFs) like Myogenin, MyoD, and Pax7 control the myogenic mechanisms regulating quiescent muscle cell maintenance, proliferation, and differentiation, critical processes central for muscle plasticity. This review focuses on recent advancements in molecular mechanisms involving microRNAs (miRNAs) and DNA methylation that regulate the expression and activity of MRFs in fish. Findings provide overwhelming support that these mechanisms are significant regulators of muscle plasticity, particularly in response to environmental factors like temperature and nutritional challenges. Genetic variation in DNA methylation and miRNA expression also correlate with variation in body weight and growth, suggesting that genetic markers related to these mechanisms may be useful for genomic selection strategies. Collectively, this knowledge improves the understanding of mechanisms regulating muscle plasticity and can contribute to the development of husbandry and breeding strategies that improve growth performance and the ability of the fish to respond to environmental challenges.
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Affiliation(s)
- Prasanthi Koganti
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506-6108, USA; (P.K.); (J.Y.)
| | - Jianbo Yao
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506-6108, USA; (P.K.); (J.Y.)
| | - Beth M. Cleveland
- USDA ARS National Center for Cool and Cold Water Aquaculture, Kearneysville, WV 25430, USA
- Correspondence: ; Tel.: +1-304-724-8340 (ext. 2133)
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22
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Castillo‐Fernandez J, Herrera‐Puerta E, Demond H, Clark SJ, Hanna CW, Hemberger M, Kelsey G. Increased transcriptome variation and localised DNA methylation changes in oocytes from aged mice revealed by parallel single-cell analysis. Aging Cell 2020; 19:e13278. [PMID: 33201571 PMCID: PMC7744954 DOI: 10.1111/acel.13278] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/27/2020] [Accepted: 10/18/2020] [Indexed: 01/08/2023] Open
Abstract
Advancing maternal age causes a progressive reduction in fertility. The decline in developmental competence of the oocyte with age is likely to be a consequence of multiple contributory factors. Loss of epigenetic quality of the oocyte could impair early developmental events or programme adverse outcomes in offspring that manifest only later in life. Here, we undertake joint profiling of the transcriptome and DNA methylome of individual oocytes from reproductively young and old mice undergoing natural ovulation. We find reduced complexity as well as increased variance in the transcriptome of oocytes from aged females. This transcriptome heterogeneity is reflected in the identification of discrete sub‐populations. Oocytes with a transcriptome characteristic of immature chromatin configuration (NSN) clustered into two groups: one with reduced developmental competence, as indicated by lower expression of maternal effect genes, and one with a young‐like transcriptome. Oocytes from older females had on average reduced CpG methylation, but the characteristic bimodal methylation landscape of the oocyte was preserved. Germline differentially methylated regions of imprinted genes were appropriately methylated irrespective of age. For the majority of differentially expressed transcripts, the absence of correlated methylation changes suggests a post‐transcriptional basis for most age‐related effects on the transcriptome. However, we did find differences in gene body methylation at which there were corresponding changes in gene expression, indicating age‐related effects on transcription that translate into methylation differences. Interestingly, oocytes varied in expression and methylation of these genes, which could contribute to variable competence of oocytes or penetrance of maternal age‐related phenotypes in offspring.
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Affiliation(s)
| | - Erika Herrera‐Puerta
- Epigenetics Programme Babraham Institute Cambridge UK
- Science and Biotechnology Faculty, Biology Program CES University Medellin Colombia
| | - Hannah Demond
- Epigenetics Programme Babraham Institute Cambridge UK
| | | | - Courtney W. Hanna
- Epigenetics Programme Babraham Institute Cambridge UK
- Centre for Trophoblast Research University of Cambridge Cambridge UK
| | - Myriam Hemberger
- Epigenetics Programme Babraham Institute Cambridge UK
- Centre for Trophoblast Research University of Cambridge Cambridge UK
- Departments of Biochemistry & Molecular Biology and Medical Genetics Cumming School of Medicine University of Calgary Calgary AL Canada
- Alberta Children’s Hospital Research InstituteUniversity of Calgary Calgary AL Canada
| | - Gavin Kelsey
- Epigenetics Programme Babraham Institute Cambridge UK
- Centre for Trophoblast Research University of Cambridge Cambridge UK
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23
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Deshpande SS, Nemani H, Arumugam G, Ravichandran A, Balasinor NH. High-fat diet-induced and genetically inherited obesity differentially alters DNA methylation profile in the germline of adult male rats. Clin Epigenetics 2020; 12:179. [PMID: 33213487 PMCID: PMC7678167 DOI: 10.1186/s13148-020-00974-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 11/10/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Paternal obesity has been associated with reduced live birth rates. It could lead to inheritance of metabolic disturbances to the offspring through epigenetic mechanisms. However, obesity is a multifactorial disorder with genetic or environmental causes. Earlier we had demonstrated differential effects of high-fat diet-induced obesity (DIO) and genetically inherited obesity (GIO) on metabolic, hormonal profile, male fertility, and spermatogenesis using two rat models. The present study aimed to understand the effect of DIO and GIO on DNA methylation in male germline, and its subsequent effects on the resorbed (post-implantation embryo loss) and normal embryos. First, we assessed the DNA methylation enzymatic machinery in the testis by Real-Time PCR, followed global DNA methylation levels in spermatozoa and testicular cells by ELISA and flow cytometry, respectively. Further, we performed Methylation Sequencing in spermatozoa for both the groups. Sequencing data in spermatozoa from both the groups were validated using Pyrosequencing. Expression of the differentially methylated genes was assessed in the resorbed and normal embryos sired by the DIO group using Real-Time PCR for functional validation. RESULTS We noted a significant decrease in Dnmt transcript and global DNA methylation levels in the DIO group and an increase in the GIO group. Sequencing analysis showed 16,966 and 9113 differentially methylated regions in the spermatozoa of the DIO and GIO groups, respectively. Upon pathway analysis, we observed genes enriched in pathways involved in embryo growth and development namely Wnt, Hedgehog, TGF-beta, and Notch in spermatozoa for both the groups, the methylation status of which partially correlated with the gene expression pattern in resorbed and normal embryos sired by the DIO group. CONCLUSION Our study reports the mechanism by which diet-induced and genetically inherited obesity causes differential effects on the DNA methylation in the male germline that could be due to a difference in the white adipose tissue accumulation. These differences could either lead to embryo loss or transmit obesity-related traits to the offspring in adult life.
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Affiliation(s)
- Sharvari S. Deshpande
- Department of Neuroendocrinology, ICMR-National Institute for Research in Reproductive Health, Jehangir Merwanji Street, Parel, Mumbai 400012 India
| | - Harishankar Nemani
- National Institute of Nutrition Animal Facility, ICMR-National Institute of Nutrition, Jamai-Osmania PO, Hyderabad 500 007 India
| | - Gandhimathi Arumugam
- Genome Informatics Department, Genotypic Technologies Pvt. Ltd., #2/13, Balaji Complex, Poojari Layout, 80 Feet Road, R.M.V. 2nd stage, Bengaluru, India
| | - Avinash Ravichandran
- Genome Informatics Department, Genotypic Technologies Pvt. Ltd., #2/13, Balaji Complex, Poojari Layout, 80 Feet Road, R.M.V. 2nd stage, Bengaluru, India
| | - Nafisa H. Balasinor
- Department of Neuroendocrinology, ICMR-National Institute for Research in Reproductive Health, Jehangir Merwanji Street, Parel, Mumbai 400012 India
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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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25
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NSD1-deposited H3K36me2 directs de novo methylation in the mouse male germline and counteracts Polycomb-associated silencing. Nat Genet 2020; 52:1088-1098. [PMID: 32929285 DOI: 10.1038/s41588-020-0689-z] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/10/2020] [Indexed: 12/12/2022]
Abstract
De novo DNA methylation (DNAme) in mammalian germ cells is dependent on DNMT3A and DNMT3L. However, oocytes and spermatozoa show distinct patterns of DNAme. In mouse oocytes, de novo DNAme requires the lysine methyltransferase (KMTase) SETD2, which deposits H3K36me3. We show here that SETD2 is dispensable for de novo DNAme in the male germline. Instead, the lysine methyltransferase NSD1, which broadly deposits H3K36me2 in euchromatic regions, plays a critical role in de novo DNAme in prospermatogonia, including at imprinted genes. However, males deficient in germline NSD1 show a more severe defect in spermatogenesis than Dnmt3l-/- males. Notably, unlike DNMT3L, NSD1 safeguards a subset of genes against H3K27me3-associated transcriptional silencing. In contrast, H3K36me2 in oocytes is predominantly dependent on SETD2 and coincides with H3K36me3. Furthermore, females with NSD1-deficient oocytes are fertile. Thus, the sexually dimorphic pattern of DNAme in mature mouse gametes is orchestrated by distinct profiles of H3K36 methylation.
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The Absence of C-5 DNA Methylation in Leishmania donovani Allows DNA Enrichment from Complex Samples. Microorganisms 2020; 8:microorganisms8081252. [PMID: 32824654 PMCID: PMC7463849 DOI: 10.3390/microorganisms8081252] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 08/12/2020] [Accepted: 08/12/2020] [Indexed: 11/21/2022] Open
Abstract
Cytosine C5 methylation is an important epigenetic control mechanism in a wide array of eukaryotic organisms and generally carried out by proteins of the C-5 DNA methyltransferase family (DNMTs). In several protozoans, the status of this mechanism remains elusive, such as in Leishmania, the causative agent of the disease leishmaniasis in humans and a wide array of vertebrate animals. In this work, we showed that the Leishmania donovani genome contains a C-5 DNA methyltransferase (DNMT) from the DNMT6 subfamily, whose function is still unclear, and verified its expression at the RNA level. We created viable overexpressor and knock-out lines of this enzyme and characterized their genome-wide methylation patterns using whole-genome bisulfite sequencing, together with promastigote and amastigote control lines. Interestingly, despite the DNMT6 presence, we found that methylation levels were equal to or lower than 0.0003% at CpG sites, 0.0005% at CHG sites, and 0.0126% at CHH sites at the genomic scale. As none of the methylated sites were retained after manual verification, we conclude that there is no evidence for DNA methylation in this species. We demonstrated that this difference in DNA methylation between the parasite (no detectable DNA methylation) and the vertebrate host (DNA methylation) allowed enrichment of parasite vs. host DNA using methyl-CpG-binding domain columns, readily available in commercial kits. As such, we depleted methylated DNA from mixes of Leishmania promastigote and amastigote DNA with human DNA, resulting in average Leishmania:human enrichments from 62× up to 263×. These results open a promising avenue for unmethylated DNA enrichment as a pre-enrichment step before sequencing Leishmania clinical samples.
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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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28
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The role and mechanisms of DNA methylation in the oocyte. Essays Biochem 2020; 63:691-705. [PMID: 31782490 PMCID: PMC6923320 DOI: 10.1042/ebc20190043] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/29/2019] [Accepted: 10/29/2019] [Indexed: 12/27/2022]
Abstract
Epigenetic information in the mammalian oocyte has the potential to be transmitted to the next generation and influence gene expression; this occurs naturally in the case of imprinted genes. Therefore, it is important to understand how epigenetic information is patterned during oocyte development and growth. Here, we review the current state of knowledge of de novo DNA methylation mechanisms in the oocyte: how a distinctive gene-body methylation pattern is created, and the extent to which the DNA methylation machinery reads chromatin states. Recent epigenomic studies building on advances in ultra-low input chromatin profiling methods, coupled with genetic studies, have started to allow a detailed interrogation of the interplay between DNA methylation establishment and chromatin states; however, a full mechanistic description awaits.
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29
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Histone H3K9 Methyltransferase G9a in Oocytes Is Essential for Preimplantation Development but Dispensable for CG Methylation Protection. Cell Rep 2020; 27:282-293.e4. [PMID: 30943408 DOI: 10.1016/j.celrep.2019.03.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 01/07/2019] [Accepted: 02/27/2019] [Indexed: 01/02/2023] Open
Abstract
Mammalian histone methyltransferase G9a (also called EHMT2) deposits H3K9me2 on chromatin and is essential for postimplantation development. However, its role in oogenesis and preimplantation development remains poorly understood. We show that H3K9me2-enriched chromatin domains in mouse oocytes are generally depleted of CG methylation, contrasting with their association in embryonic stem and somatic cells. Oocyte-specific disruption of G9a results in reduced H3K9me2 enrichment and impaired reorganization of heterochromatin in oocytes, but only a modest reduction in CG methylation is detected. Furthermore, in both oocytes and 2-cell embryos, G9a depletion has limited impact on the expression of genes and retrotransposons. Although their CG methylation is minimally affected, preimplantation embryos derived from such oocytes show abnormal chromosome segregation and frequent developmental arrest. Our findings illuminate the functional importance of G9a independent of CG methylation in preimplantation development and call into question the proposed role for H3K9me2 in CG methylation protection in zygotes.
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30
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Ivanova E, Canovas S, Garcia-Martínez S, Romar R, Lopes JS, Rizos D, Sanchez-Calabuig MJ, Krueger F, Andrews S, Perez-Sanz F, Kelsey G, Coy P. DNA methylation changes during preimplantation development reveal inter-species differences and reprogramming events at imprinted genes. Clin Epigenetics 2020; 12:64. [PMID: 32393379 PMCID: PMC7216732 DOI: 10.1186/s13148-020-00857-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 04/23/2020] [Indexed: 02/08/2023] Open
Abstract
Preimplantation embryos experience profound resetting of epigenetic information inherited from the gametes. Genome-wide analysis at single-base resolution has shown similarities but also species differences between human and mouse preimplantation embryos in DNA methylation patterns and reprogramming. Here, we have extended such analysis to two key livestock species, the pig and the cow. We generated genome-wide DNA methylation and whole-transcriptome datasets from gametes to blastocysts in both species. In oocytes from both species, a distinctive bimodal methylation landscape is present, with hypermethylated domains prevalent over hypomethylated domains, similar to human, while in the mouse the proportions are reversed.An oocyte-like pattern of methylation persists in the cleavage stages, albeit with some reduction in methylation level, persisting to blastocysts in cow, while pig blastocysts have a highly hypomethylated landscape. In the pig, there was evidence of transient de novo methylation at the 8-16 cell stages of domains unmethylated in oocytes, revealing a complex dynamic of methylation reprogramming. The methylation datasets were used to identify germline differentially methylated regions (gDMRs) of known imprinted genes and for the basis of detection of novel imprinted loci. Strikingly in the pig, we detected a consistent reduction in gDMR methylation at the 8-16 cell stages, followed by recovery to the blastocyst stage, suggesting an active period of imprint stabilization in preimplantation embryos. Transcriptome analysis revealed absence of expression in oocytes of both species of ZFP57, a key factor in the mouse for gDMR methylation maintenance, but presence of the alternative imprint regulator ZNF445. In conclusion, our study reveals species differences in DNA methylation reprogramming and suggests that porcine or bovine models may be closer to human in key aspects than in the mouse model.
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Affiliation(s)
- Elena Ivanova
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Sebastian Canovas
- Physiology of Reproduction Group, Departamento de Fisiología, Universidad de Murcia, Campus Mare Nostrum, 30100, Murcia, Spain
- Instituto Murciano de Investigación Biosanitaria, IMIB-Arrixaca-UMU, 30120, Murcia, Spain
| | - Soledad Garcia-Martínez
- Physiology of Reproduction Group, Departamento de Fisiología, Universidad de Murcia, Campus Mare Nostrum, 30100, Murcia, Spain
| | - Raquel Romar
- Physiology of Reproduction Group, Departamento de Fisiología, Universidad de Murcia, Campus Mare Nostrum, 30100, Murcia, Spain
- Instituto Murciano de Investigación Biosanitaria, IMIB-Arrixaca-UMU, 30120, Murcia, Spain
| | - Jordana S Lopes
- Physiology of Reproduction Group, Departamento de Fisiología, Universidad de Murcia, Campus Mare Nostrum, 30100, Murcia, Spain
| | | | | | - Felix Krueger
- Bioinformatics Group, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Simon Andrews
- Bioinformatics Group, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Fernando Perez-Sanz
- Instituto Murciano de Investigación Biosanitaria, IMIB-Arrixaca-UMU, 30120, Murcia, Spain
| | - Gavin Kelsey
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK.
- Centre for Trophoblast Research, University of Cambridge, Cambridge, CB2 3EG, UK.
| | - Pilar Coy
- Physiology of Reproduction Group, Departamento de Fisiología, Universidad de Murcia, Campus Mare Nostrum, 30100, Murcia, Spain.
- Instituto Murciano de Investigación Biosanitaria, IMIB-Arrixaca-UMU, 30120, Murcia, Spain.
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Active Demethylation of Non-CpG Moieties in Animals: A Neglected Research Area. Int J Mol Sci 2019; 20:ijms20246272. [PMID: 31842376 PMCID: PMC6940975 DOI: 10.3390/ijms20246272] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 12/09/2019] [Accepted: 12/10/2019] [Indexed: 11/17/2022] Open
Abstract
The functional role of cytosine methylation in the CpG moieties of DNA, is well established in several biological functions. The interplay between CpG methylation and hypomethylation is a well-known mechanism of modulation of gene expression. However, the role of non-CpG methylation and active dynamics of demethylation is not clearly recognized. Although some evidence exists of a role of active non-CpG demethylation in the fast dynamics of transcriptional activation in animals, few studies deal with this topic. At present, active demethylation of non-CpG moieties is a neglected research area, in spite of the promise of significant novelties.
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32
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Coronado-Posada N, Olivero-Verbel J. In silico evaluation of pesticides as potential modulators of human DNA methyltransferases. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2019; 30:865-878. [PMID: 31595789 DOI: 10.1080/1062936x.2019.1666165] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 09/06/2019] [Indexed: 06/10/2023]
Abstract
DNA methylations are carried out by DNA methyltransferases (DNMTs) that are key enzymes during gene expression. Many chemicals, including pesticides, have shown modulation of epigenetic functions by inhibiting DNMTs. In this work, human DNMTs were evaluated as a potential target for pesticides through virtual screening of 1038 pesticides on DNMT1 (3SWR) and DNMT3A (2QRV). Molecular docking calculations for DNMTs-pesticide complexes were performed using AutoDock Vina. Binding-affinity values and contact patterns were employed as selection criteria of pesticides as virtual hits for DNMTs. The best three DNMT-pesticides complexes selected according to their high absolute affinity values (kcal/mol), for both DNMT1 and DNMT3A, were flocoumafen (-12.5; -9.9), brodifacoum (-12.4; -8.4) and difenacoum (-12.1; -8.7). These chemicals belong to second-generation rodenticides. The most frequent predicted interacting residues for DNMT1-pesticide complexes were Trp1170A, Phe1145A, Asn1578A, Arg1574A and Pro1225A; whereas for DNMT3A those were Arg271B, Lys740A, and Glu303B. These results suggest that rodenticides used for pest control are potential DNMT ligands and therefore, may modulate DNA methylations. This finding has important environmental and clinical implications, as epigenetic pathways are critical in many biochemical processes leading to diseases.
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Affiliation(s)
- N Coronado-Posada
- Environmental and Computational Chemistry Group, School of Pharmaceutical Sciences, University of Cartagena, Cartagena, Colombia
| | - J Olivero-Verbel
- Environmental and Computational Chemistry Group, School of Pharmaceutical Sciences, University of Cartagena, Cartagena, Colombia
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Jiang Z, Lin J, Dong H, Zheng X, Marjani SL, Duan J, Ouyang Z, Chen J, Tian XC. DNA methylomes of bovine gametes and in vivo produced preimplantation embryos. Biol Reprod 2019; 99:949-959. [PMID: 29912291 DOI: 10.1093/biolre/ioy138] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Accepted: 06/12/2018] [Indexed: 12/13/2022] Open
Abstract
DNA methylation is an important epigenetic modification that undergoes dynamic changes in mammalian embryogenesis, during which both parental genomes are reprogrammed. Despite the many immunostaining studies that have assessed global methylation, the gene-specific DNA methylation patterns in bovine preimplantation embryos are unknown. Using reduced representation bisulfite sequencing, we determined genome-scale DNA methylation of bovine sperm and individual in vivo developed oocytes and preimplantation embryos. We show that (1) the major wave of genome-wide demethylation was completed by the 8-cell stage; (2) promoter methylation was significantly and inversely correlated with gene expression at the 8-cell and blastocyst stages; (3) sperm and oocytes have numerous differentially methylated regions (DMRs)-DMRs specific for sperm were strongly enriched in long terminal repeats and rapidly lost methylation in embryos; while the oocyte-specific DMRs were more frequently localized in exons and CpG islands (CGIs) and demethylated gradually across cleavage stages; (4) DMRs were also found between in vivo and in vitro matured oocytes; and (5) differential methylation between bovine gametes was confirmed in some but not all known imprinted genes. Our data provide insights into the complex epigenetic reprogramming of bovine early embryos, which serve as an important model for human preimplantation development.
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Affiliation(s)
- Zongliang Jiang
- School of Animal Sciences, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA
| | - Jianan Lin
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA.,Department of Biomedical Engineering, University of Connecticut, Storrs, Connecticut, USA.,Department of Genetics and Genome Sciences and Institute for System Genomics, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Hong Dong
- Xinjiang Academy of Animal Science, Urumqi, Xinjiang, PR China
| | - Xinbao Zheng
- Xinjiang Academy of Animal Science, Urumqi, Xinjiang, PR China
| | - Sadie L Marjani
- Department of Biology, Central Connecticut State University, New Britain, Connecticut, USA
| | - Jingyue Duan
- Department of Animal Science, University of Connecticut, Storrs, Connecticut, USA
| | - Zhengqing Ouyang
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA.,Department of Biomedical Engineering, University of Connecticut, Storrs, Connecticut, USA.,Department of Genetics and Genome Sciences and Institute for System Genomics, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Jingbo Chen
- Xinjiang Academy of Animal Science, Urumqi, Xinjiang, PR China
| | - Xiuchun Cindy Tian
- Department of Animal Science, University of Connecticut, Storrs, Connecticut, USA
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Seelan RS, Pisano M, Greene RM. Nucleic acid methylation and orofacial morphogenesis. Birth Defects Res 2019; 111:1593-1610. [PMID: 31385455 DOI: 10.1002/bdr2.1564] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 07/17/2019] [Accepted: 07/19/2019] [Indexed: 12/19/2022]
Abstract
In this review, we highlight the current state of knowledge of the diverse roles nucleic acid methylation plays in the embryonic development of the orofacial region and how aberrant methylation may contribute to orofacial clefts. We also consider the role of methylation in the regulation of neural crest cell function as it pertains to orofacial ontogeny. Changes in DNA methylation, as a consequence of environmental effects, have been observed in the regulatory regions of several genes, potentially identifying new candidate genes for orofacial clefting and opening promising new avenues for further research. While the focus of this review is primarily on the nonsyndromic forms of orofacial clefting, syndromic forms are briefly discussed in the context of aberrant nucleic acid methylation.
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Affiliation(s)
- Ratnam S Seelan
- Department of Oral Immunology and Infectious Diseases, Division of Craniofacial Development and Anomalies, University of Louisville School of Dentistry, Louisville, Kentucky
| | - Michele Pisano
- Department of Oral Immunology and Infectious Diseases, Division of Craniofacial Development and Anomalies, University of Louisville School of Dentistry, Louisville, Kentucky
| | - Robert M Greene
- Department of Oral Immunology and Infectious Diseases, Division of Craniofacial Development and Anomalies, University of Louisville School of Dentistry, Louisville, Kentucky
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Whyte JM, Ellis JJ, Brown MA, Kenna TJ. Best practices in DNA methylation: lessons from inflammatory bowel disease, psoriasis and ankylosing spondylitis. Arthritis Res Ther 2019; 21:133. [PMID: 31159831 PMCID: PMC6547594 DOI: 10.1186/s13075-019-1922-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Advances in genomic technology have enabled a greater understanding of the genetics of common immune-mediated diseases such as ankylosing spondylitis (AS), inflammatory bowel disease (IBD) and psoriasis. The substantial overlap in genetically identified pathogenic pathways has been demonstrated between these diseases. However, to date, gene discovery approaches have only mapped a minority of the heritability of these common diseases, and most disease-associated variants have been found to be non-coding, suggesting mechanisms of disease-association through transcriptional regulatory effects. Epigenetics is a major interface between genetic and environmental modifiers of disease and strongly influence transcription. DNA methylation is a well-characterised epigenetic mechanism, and a highly stable epigenetic marker, that is implicated in disease pathogenesis. DNA methylation is an under-investigated area in immune-mediated diseases, and many studies in the field are affected by experimental design limitations, related to study design, technical limitations of the methylation typing methods employed, and statistical issues. This has resulted in both sparsity of investigations into disease-related changes in DNA methylation, a paucity of robust findings, and difficulties comparing studies in the same disease. In this review, we cover the basics of DNA methylation establishment and control, and the methods used to examine it. We examine the current state of DNA methylation studies in AS, IBD and psoriasis; the limitations of previous studies; and the best practices for DNA methylation studies. The purpose of this review is to assist with proper experimental design and consistency of approach in future studies to enable a better understanding of the functional role of DNA methylation in immune-mediated disease.
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Affiliation(s)
- Jessica M Whyte
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Woolloongabba, Queensland, Australia
| | - Jonathan J Ellis
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Woolloongabba, Queensland, Australia
| | - Matthew A Brown
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Woolloongabba, Queensland, Australia. .,Translational Research Institute, Princess Alexandra Hospital, 37 Kent Street, Woolloongabba, Queensland, 4102, Australia.
| | - Tony J Kenna
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Woolloongabba, Queensland, Australia
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36
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Duan JE, Jiang ZC, Alqahtani F, Mandoiu I, Dong H, Zheng X, Marjani SL, Chen J, Tian XC. Methylome Dynamics of Bovine Gametes and in vivo Early Embryos. Front Genet 2019; 10:512. [PMID: 31191619 PMCID: PMC6546829 DOI: 10.3389/fgene.2019.00512] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 05/10/2019] [Indexed: 01/12/2023] Open
Abstract
DNA methylation undergoes drastic fluctuation during early mammalian embryogenesis. The dynamics of global DNA methylation in bovine embryos, however, have mostly been studied by immunostaining. We adopted the whole genome bisulfite sequencing (WGBS) method to characterize stage-specific genome-wide DNA methylation in bovine sperm, immature oocytes, oocytes matured in vivo and in vitro, as well as in vivo developed single embryos at the 2-, 4-, 8-, and 16-cell stages. We found that the major wave of genome-wide DNA demethylation was complete by the 8-cell stage when de novo methylation became prominent. Sperm and oocytes were differentially methylated in numerous regions (DMRs), which were primarily intergenic, suggesting that these non-coding regions may play important roles in gamete specification. DMRs were also identified between in vivo and in vitro matured oocytes, suggesting environmental effects on epigenetic modifications. In addition, virtually no (less than 1.5%) DNA methylation was found in mitochondrial DNA. Finally, by using RNA-seq data generated from embryos at the same developmental stages, we revealed a weak inverse correlation between gene expression and promoter methylation. This comprehensive analysis provides insight into the critical features of the bovine embryo methylome, and serves as an important reference for embryos produced in vitro, such as by in vitro fertilization and cloning. Lastly, these data can also provide a model for the epigenetic dynamics in human early embryos.
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Affiliation(s)
- Jingyue Ellie Duan
- Department of Animal Science, University of Connecticut, Storrs, CT, United States
| | - Zongliang Carl Jiang
- School of Animal Science, AgCenter, Louisiana State University, Baton Rouge, LA, United States
| | - Fahad Alqahtani
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, United States
| | - Ion Mandoiu
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, United States
| | - Hong Dong
- Institute of Animal Science, Xinjiang Academy of Animal Sciences, Ürümqi, China
| | - Xinbao Zheng
- Institute of Animal Science, Xinjiang Academy of Animal Sciences, Ürümqi, China
| | - Sadie L Marjani
- Department of Biology, Central Connecticut State University, New Britain, CT, United States
| | - Jingbo Chen
- Institute of Animal Science, Xinjiang Academy of Animal Sciences, Ürümqi, China
| | - Xiuchun Cindy Tian
- Department of Animal Science, University of Connecticut, Storrs, CT, United States
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Yagi M, Kabata M, Ukai T, Ohta S, Tanaka A, Shimada Y, Sugimoto M, Araki K, Okita K, Woltjen K, Hochedlinger K, Yamamoto T, Yamada Y. De Novo DNA Methylation at Imprinted Loci during Reprogramming into Naive and Primed Pluripotency. Stem Cell Reports 2019; 12:1113-1128. [PMID: 31056481 PMCID: PMC6524733 DOI: 10.1016/j.stemcr.2019.04.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 04/05/2019] [Accepted: 04/08/2019] [Indexed: 12/16/2022] Open
Abstract
CpG islands (CGIs) including those at imprinting control regions (ICRs) are protected from de novo methylation in somatic cells. However, many cancers often exhibit CGI hypermethylation, implying that the machinery is impaired in cancer cells. Here, we conducted a comprehensive analysis of CGI methylation during somatic cell reprogramming. Although most CGIs remain hypomethylated, a small subset of CGIs, particularly at several ICRs, was often de novo methylated in reprogrammed pluripotent stem cells (PSCs). Such de novo ICR methylation was linked with the silencing of reprogramming factors, which occurs at a late stage of reprogramming. The ICR-preferred CGI hypermethylation was similarly observed in human PSCs. Mechanistically, ablation of Dnmt3a prevented PSCs from de novo ICR methylation. Notably, the ICR-preferred CGI hypermethylation was observed in pediatric cancers, while adult cancers exhibit genome-wide CGI hypermethylation. These results may have important implications in the pathogenesis of pediatric cancers and the application of PSCs. Several ICRs are de novo methylated in reprogrammed PSCs De novo ICR methylation in iPSCs is linked with transgene silencing Depletion of Dnmt3a prevents reprogrammed PSCs from de novo ICR methylation Pediatric cancers exhibit reprogrammed PSC-like aberration in CGI methylation
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Affiliation(s)
- Masaki Yagi
- Division of Stem Cell Pathology, Center for Experimental Medicine and Systems Biology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan; Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Mio Kabata
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Tomoyo Ukai
- Division of Stem Cell Pathology, Center for Experimental Medicine and Systems Biology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan; Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Sho Ohta
- Division of Stem Cell Pathology, Center for Experimental Medicine and Systems Biology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Akito Tanaka
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Yui Shimada
- Division of Stem Cell Pathology, Center for Experimental Medicine and Systems Biology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan; Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Michihiko Sugimoto
- Institute of Resource Development and Analysis, Kumamoto University, Kumamoto 860-0811, Japan
| | - Kimi Araki
- Institute of Resource Development and Analysis, Kumamoto University, Kumamoto 860-0811, Japan
| | - Keisuke Okita
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Knut Woltjen
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan; Hakubi Center for Advanced Research, Kyoto University, Kyoto 606-8501, Japan
| | - Konrad Hochedlinger
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Takuya Yamamoto
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan; AMED-CREST, AMED 1-7-1 Otemachi, Chiyodaku, Tokyo 100-0004, Japan; Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan; Medical-risk Avoidance Based on iPS Cells Team, RIKEN Center for Advanced Intelligence Project (AIP), Kyoto 606-8507, Japan.
| | - Yasuhiro Yamada
- Division of Stem Cell Pathology, Center for Experimental Medicine and Systems Biology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan; Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan; AMED-CREST, AMED 1-7-1 Otemachi, Chiyodaku, Tokyo 100-0004, Japan.
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38
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Abstract
Mammalian oocytes carry specific nongenetic information, including DNA methylation to the next generation, which is important for development and disease. However, evaluation and manipulation of specific methylation for both functional analysis and therapeutic purposes remains challenging. Here, we demonstrate evaluation of specific methylation in single oocytes from its sibling first polar body (PB1) and manipulation of specific methylation in single oocytes by microinjection-mediated dCas9-based targeted methylation editing. We optimized a single-cell bisulfite sequencing approach with high efficiency and demonstrate that the PB1 carries similar methylation profiles at specific regions to its sibling oocyte. By bisulfite sequencing of a single PB1, the methylation information regarding agouti viable yellow (A vy )-related coat color, as well as imprinting linked parthenogenetic development competency, in a single oocyte can be efficiently evaluated. Microinjection-based dCas9-Tet/Dnmt-mediated methylation editing allows targeted manipulation of specific methylation in single oocytes. By targeted methylation editing, we were able to reverse A vy -related coat color, generate full-term development of bimaternal mice, and correct familial Angelman syndrome in a mouse model. Our work will facilitate the investigation of specific methylation events in oocytes and provides a strategy for prevention and correction of maternally transmitted nongenetic disease or disorders.
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39
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Li C, Xiong W, Liu X, Xiao W, Guo Y, Tan J, Li Y. Hypomethylation at non-CpG/CpG sites in the promoter of HIF-1α gene combined with enhanced H3K9Ac modification contribute to maintain higher HIF-1α expression in breast cancer. Oncogenesis 2019; 8:26. [PMID: 30940798 PMCID: PMC6445832 DOI: 10.1038/s41389-019-0135-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 02/26/2019] [Accepted: 03/18/2019] [Indexed: 02/06/2023] Open
Abstract
HIF-1α has a broad impact on tumors, including enhanced utilization of glucose, tumor cell stemness, migration, metastasis and so on. In pilot study, we found that the expression of HIF-1α significantly increased in breast cancer cell lines and tissue samples with higher malignant behaviors and decreased in luminal subtype breast cancer cells and tissue samples. We analyzed and found there is one large CpG island in HIF-1α promoter around transcription start site, and the hypermethylation occurred at these CpGs and their surrounding non-CpGs sites. Epigenetic events driving tumorigenesis has been characterized. However, knowledge is lacking on the non-CpGs methylation of HIF-1α promoter in breast cancer cells. We validated that non-CpGs methylation can directly regulate HIF-1α expression by luciferase activity assay. We also found DNMT3a and Mecp2 play vital role in methylation at non-CpGs and CpGs sites. In addition, we noticed that H3K9ac modification could promote the transcription of HIF-1α in MDA-MB-231 cells by binding to the region contained hypomethylated non-CpG and CpG sites. Taken together, the hypomethylation status at non-CpG and CpG loci in HIF-1α promoter and H3K9ac modification together contribute to maintain higher HIF-1αactivity in invasive breast cancer cells when compared with the non-invasive breast cancer cells, which may establish a tissue-specific epigenetic modification pattern and point to the new directions for future understanding breast cancer therapy.
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Affiliation(s)
- Chun Li
- The central laboratory, of Cancer Hospital of Shantou University Medical College, No.7 Raoping Road, Shantou, 515031, China
- Department of Pathology, of Cancer Hospital of Shantou University Medical College, No.7 Raoping Road, Shantou, 515031, China
| | - Wei Xiong
- The central laboratory, of Cancer Hospital of Shantou University Medical College, No.7 Raoping Road, Shantou, 515031, China
| | - Xiong Liu
- The central laboratory, of Cancer Hospital of Shantou University Medical College, No.7 Raoping Road, Shantou, 515031, China
| | - Wenjun Xiao
- The central laboratory, of Cancer Hospital of Shantou University Medical College, No.7 Raoping Road, Shantou, 515031, China
| | - Yuxian Guo
- The central laboratory, of Cancer Hospital of Shantou University Medical College, No.7 Raoping Road, Shantou, 515031, China
| | - Junyu Tan
- The central laboratory, of Cancer Hospital of Shantou University Medical College, No.7 Raoping Road, Shantou, 515031, China
| | - Yaochen Li
- The central laboratory, of Cancer Hospital of Shantou University Medical College, No.7 Raoping Road, Shantou, 515031, China.
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40
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Singh PB, Shloma VV, Belyakin SN. Maternal regulation of chromosomal imprinting in animals. Chromosoma 2019; 128:69-80. [PMID: 30719566 PMCID: PMC6536480 DOI: 10.1007/s00412-018-00690-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 12/24/2018] [Accepted: 12/28/2018] [Indexed: 11/29/2022]
Abstract
Chromosomal imprinting requires an epigenetic system that "imprints" one of the two parental chromosomes such that it results in a heritable (cell-to-cell) change in behavior of the "imprinted" chromosome. Imprinting takes place when the parental genomes are separate, which occurs during gamete formation in the respective germ-lines and post-fertilization during the period when the parental pro-nuclei lie separately within the ooplasm of the zygote. In the mouse, chromosomal imprinting is regulated by germ-line specific DNA methylation. But the methylation machinery in the respective germ-lines does not discriminate between imprinted and non-imprinted regions. As a consequence, the mouse oocyte nucleus contains over a thousand oocyte-specific germ-line differentially methylated regions (gDMRs). Upon fertilization, the sperm provides a few hundred sperm-specific gDMRs of its own. Combined, there are around 1600 imprinted and non-imprinted gDMRs in the pro-nuclei of the newly fertilized zygote. It is a remarkable fact that beginning in the maternal ooplasm, there are mechanisms that manage to preserve DNA methylation at ~ 26 known imprinted gDMRs in the face of the ongoing genome-wide DNA de-methylation that characterizes pre-implantation development. Specificity is achieved through the binding of KRAB-zinc finger proteins to their cognate recognition sequences within the gDMRs of imprinted genes. This in turn nucleates the assembly of localized heterochromatin-like complexes that preserve methylation at imprinted gDMRs through recruitment of the maintenance methyl transferase Dnmt1. These studies have shown that a germ-line imprint may cause parent-of-origin-specific behavior only if "licensed" by mechanisms that operate post-fertilization. Study of the germ-line and post-fertilization contributions to the imprinting of chromosomes in classical insect systems (Coccidae and Sciaridae) show that the ooplasm is the likely site where imprinting takes place. By comparing molecular and genetic studies across these three species, we suggest that mechanisms which operate post-fertilization play a key role in chromosomal imprinting phenomena in animals and conserved components of heterochromatin are shared by these mechanisms.
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Affiliation(s)
- Prim B Singh
- Nazarbayev University School of Medicine, 5/1 Kerei, Zhanibek Khandar Street, Astana, Z05K4F4, Kazakhstan.
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, Pirogov str. 2, Novosibirsk, 630090, Russian Federation.
| | - Victor V Shloma
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, Pirogov str. 2, Novosibirsk, 630090, Russian Federation
- Genomics Laboratory, Institute of Molecular and Cellular Biology SD RAS, Lavrentyev ave, 8/2, Novosibirsk, 630090, Russian Federation
| | - Stepan N Belyakin
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, Pirogov str. 2, Novosibirsk, 630090, Russian Federation
- Genomics Laboratory, Institute of Molecular and Cellular Biology SD RAS, Lavrentyev ave, 8/2, Novosibirsk, 630090, Russian Federation
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41
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Abstract
Textbook and scientific papers addressing DNA methylation usually still cite “DNA methylation occurs at CpG cytosines”. Methylation at cytosines outside the CpG nucleotide, the so-called “non-CpG methylation”, is usually considered a minor and not biologically relevant process. However, the technical improvements and additional studies in epigenetics have demonstrated that non-CpG methylation is present with frequency higher than previously thought and retains biological activity, potentially relevant to the understanding and the treatment of human diseases.
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42
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Unoki M, Funabiki H, Velasco G, Francastel C, Sasaki H. CDCA7 and HELLS mutations undermine nonhomologous end joining in centromeric instability syndrome. J Clin Invest 2018; 129:78-92. [PMID: 30307408 DOI: 10.1172/jci99751] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 10/04/2018] [Indexed: 02/06/2023] Open
Abstract
Mutations in CDCA7 and HELLS that respectively encode a CXXC-type zinc finger protein and an SNF2 family chromatin remodeler cause immunodeficiency, centromeric instability, and facial anomalies (ICF) syndrome types 3 and 4. Here, we demonstrate that the classical nonhomologous end joining (C-NHEJ) proteins Ku80 and Ku70, as well as HELLS, coimmunoprecipitated with CDCA7. The coimmunoprecipitation of the repair proteins was sensitive to nuclease treatment and an ICF3 mutation in CDCA7 that impairs its chromatin binding. The functional importance of these interactions was strongly suggested by the compromised C-NHEJ activity and significant delay in Ku80 accumulation at DNA damage sites in CDCA7- and HELLS-deficient HEK293 cells. Consistent with the repair defect, these cells displayed increased apoptosis, abnormal chromosome segregation, aneuploidy, centrosome amplification, and significant accumulation of γH2AX signals. Although less prominent, cells with mutations in the other ICF genes DNMT3B and ZBTB24 (responsible for ICF types 1 and 2, respectively) showed similar defects. Importantly, lymphoblastoid cells from ICF patients shared the same changes detected in the mutant HEK293 cells to varying degrees. Although the C-NHEJ defect alone did not cause CG hypomethylation, CDCA7 and HELLS are involved in maintaining CG methylation at centromeric and pericentromeric repeats. The defect in C-NHEJ may account for some common features of ICF cells, including centromeric instability, abnormal chromosome segregation, and apoptosis.
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Affiliation(s)
- Motoko Unoki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Hironori Funabiki
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, New York, USA
| | - Guillaume Velasco
- CNRS UMR7216, Epigenetics and Cell Fate, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Claire Francastel
- CNRS UMR7216, Epigenetics and Cell Fate, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
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43
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Watanabe T, Cui X, Yuan Z, Qi H, Lin H. MIWI2 targets RNAs transcribed from piRNA-dependent regions to drive DNA methylation in mouse prospermatogonia. EMBO J 2018; 37:e95329. [PMID: 30108053 PMCID: PMC6138435 DOI: 10.15252/embj.201695329] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 07/06/2018] [Accepted: 07/09/2018] [Indexed: 12/24/2022] Open
Abstract
Argonaute/Piwi proteins can regulate gene expression via RNA degradation and translational regulation using small RNAs as guides. They also promote the establishment of suppressive epigenetic marks on repeat sequences in diverse organisms. In mice, the nuclear Piwi protein MIWI2 and Piwi-interacting RNAs (piRNAs) are required for DNA methylation of retrotransposon sequences and some other sequences. However, its underlying molecular mechanisms remain unclear. Here, we show that piRNA-dependent regions are transcribed at the stage when piRNA-mediated DNA methylation takes place. MIWI2 specifically interacts with RNAs from these regions. In addition, we generated mice with deletion of a retrotransposon sequence either in a representative piRNA-dependent region or in a piRNA cluster. Both deleted regions were required for the establishment of DNA methylation of the piRNA-dependent region, indicating that piRNAs determine the target specificity of MIWI2-mediated DNA methylation. Our results indicate that MIWI2 affects the chromatin state through base-pairing between piRNAs and nascent RNAs, as observed in other organisms possessing small RNA-mediated epigenetic regulation.
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Affiliation(s)
- Toshiaki Watanabe
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Xiekui Cui
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Zhongyu Yuan
- Zhiyuan College, Shanghai Jiaotong University, Shanghai, China
| | - Hongying Qi
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Haifan Lin
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
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44
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Franczak A, Zglejc-Waszak K, Martyniak M, Waszkiewicz EM, Kotwica G. Peri-conceptional nutritional restriction alters transcriptomic profile in the peri-implantation pig embryos. Anim Reprod Sci 2018; 197:305-316. [PMID: 30197056 DOI: 10.1016/j.anireprosci.2018.08.045] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 08/17/2018] [Accepted: 08/29/2018] [Indexed: 12/12/2022]
Abstract
Restricted nutritional consumption during the peri-conceptional period affects the potential for DNA methylation and alters endometrial transcriptomic profile during the peri-implantation period. The restricted diet fed to females during the peri-conceptional period may affect the transcriptomic profile in peri-implantation embryos. In the present study, the transcriptome of embryos of normal-diet-fed gilts was determined and compared with that in embryos of restricted-diet-fed gilts during the peri-implantation period. The restricted-diet-fed gilts were fed forage, in which the dose of proteins and energy had been reduced by 30% compared to the normal diet (Polish Norms of Nutrition). To clarify the issue Agilent's Porcine (V2) Two-Color Gene Expression Microarray 4 × 44 was used. Analysis of the microarray data revealed that the expression of 787 genes with known biological function were consistently altered (496 up- and 291 down-regulated) in embryos. The accurately annotated genes were organized into five categories and 18 subcategories containing 62 biological pathways. The qPCR analysis of ten selected genes [i.e., 5 acid phosphatase, tartrate resistant (ACP5), high mobility group box 2 (HMGB2), prostaglandin-endoperoxide synthase 2 (PTGS2), arachidonate 12-lipoxygenase (ALOX12), adiponectin receptor 2 (ADIPOR2), DNA (cytosine-5)-methyltransferase 1 (DNMT1), steroidogenic acute regulatory protein (STAR), progesterone receptor membrane component 2 (PGRMC2), progestin and adipoQ receptor family member 7 (PAQR7) and serpin family A member 1 (SERPINA1)] confirmed altered gene expression in embryos of restricted-diet-fed gilts. The insight into embryonic transcriptome indicates that female under-nutrition during the peri-conceptional period may create alterations in the pattern of genes expressed in the peri-implantation embryos.
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Affiliation(s)
- Anita Franczak
- Department of Anatomy and Animal Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowski 1A, 10-719, Olsztyn, Poland.
| | - Kamila Zglejc-Waszak
- Department of Anatomy and Animal Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowski 1A, 10-719, Olsztyn, Poland.
| | - Marcin Martyniak
- Department of Anatomy and Animal Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowski 1A, 10-719, Olsztyn, Poland.
| | - Ewa Monika Waszkiewicz
- Department of Anatomy and Animal Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowski 1A, 10-719, Olsztyn, Poland.
| | - Genowefa Kotwica
- Department of Anatomy and Animal Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowski 1A, 10-719, Olsztyn, Poland.
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45
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Pegoraro M, Marshall H, Lonsdale ZN, Mallon EB. Do social insects support Haig's kin theory for the evolution of genomic imprinting? Epigenetics 2018; 12:725-742. [PMID: 28703654 PMCID: PMC5739101 DOI: 10.1080/15592294.2017.1348445] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Although numerous imprinted genes have been described in several lineages, the phenomenon of genomic imprinting presents a peculiar evolutionary problem. Several hypotheses have been proposed to explain gene imprinting, the most supported being Haig's kinship theory. This theory explains the observed pattern of imprinting and the resulting phenotypes as a competition for resources between related individuals, but despite its relevance it has not been independently tested. Haig's theory predicts that gene imprinting should be present in eusocial insects in many social scenarios. These lineages are therefore ideal for testing both the theory's predictions and the mechanism of gene imprinting. Here we review the behavioral evidence of genomic imprinting in eusocial insects, the evidence of a mechanism for genomic imprinting and finally we evaluate recent results showing parent of origin allele specific expression in honeybees in the light of Haig's theory.
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Affiliation(s)
- Mirko Pegoraro
- a Department of Genetics and Genome Biology , University of Leicester , UK
| | - Hollie Marshall
- a Department of Genetics and Genome Biology , University of Leicester , UK
| | - Zoë N Lonsdale
- a Department of Genetics and Genome Biology , University of Leicester , UK
| | - Eamonn B Mallon
- a Department of Genetics and Genome Biology , University of Leicester , UK
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46
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Matoba S, Wang H, Jiang L, Lu F, Iwabuchi KA, Wu X, Inoue K, Yang L, Press W, Lee JT, Ogura A, Shen L, Zhang Y. Loss of H3K27me3 Imprinting in Somatic Cell Nuclear Transfer Embryos Disrupts Post-Implantation Development. Cell Stem Cell 2018; 23:343-354.e5. [PMID: 30033120 DOI: 10.1016/j.stem.2018.06.008] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 05/08/2018] [Accepted: 06/13/2018] [Indexed: 12/20/2022]
Abstract
Animal cloning can be achieved through somatic cell nuclear transfer (SCNT), although the live birth rate is relatively low. Recent studies have identified H3K9me3 in donor cells and abnormal Xist activation as epigenetic barriers that impede SCNT. Here we overcome these barriers using a combination of Xist knockout donor cells and overexpression of Kdm4 to achieve more than 20% efficiency of mouse SCNT. However, post-implantation defects and abnormal placentas were still observed, indicating that additional epigenetic barriers impede SCNT cloning. Comparative DNA methylome analysis of IVF and SCNT blastocysts identified abnormally methylated regions in SCNT embryos despite successful global reprogramming of the methylome. Strikingly, allelic transcriptomic and ChIP-seq analyses of pre-implantation SCNT embryos revealed complete loss of H3K27me3 imprinting, which may account for the postnatal developmental defects observed in SCNT embryos. Together, these results provide an efficient method for mouse cloning while paving the way for further improving SCNT efficiency.
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Affiliation(s)
- Shogo Matoba
- Howard Hughes Medical Institute; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; RIKEN Bioresource Research Center, Tsukuba, Ibaraki 305-0074, Japan; Cooperative Division of Veterinary Sciences, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Huihan Wang
- Life Sciences Institute and Stem Cell Institute, Zhejiang University, Hangzhou 310058, China
| | - Lan Jiang
- Howard Hughes Medical Institute; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Falong Lu
- Howard Hughes Medical Institute; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Kumiko A Iwabuchi
- Howard Hughes Medical Institute; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Xiaoji Wu
- Howard Hughes Medical Institute; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Kimiko Inoue
- RIKEN Bioresource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Lin Yang
- Howard Hughes Medical Institute; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - William Press
- Howard Hughes Medical Institute; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Jeannie T Lee
- Howard Hughes Medical Institute; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Atsuo Ogura
- RIKEN Bioresource Research Center, Tsukuba, Ibaraki 305-0074, Japan; RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Li Shen
- Howard Hughes Medical Institute; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Life Sciences Institute and Stem Cell Institute, Zhejiang University, Hangzhou 310058, China.
| | - Yi Zhang
- Howard Hughes Medical Institute; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Harvard Stem Cell Institute, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
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47
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Liu C, Jiao C, Wang K, Yuan N. DNA Methylation and Psychiatric Disorders. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 157:175-232. [PMID: 29933950 DOI: 10.1016/bs.pmbts.2018.01.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
DNA methylation has been an important area of research in the study of molecular mechanism to psychiatric disorders. Recent evidence has suggested that abnormalities in global methylation, methylation of genes, and pathways could play a role in the etiology of many forms of mental illness. In this article, we review the mechanisms of DNA methylation, including the genetic and environmental factors affecting methylation changes. We report and discuss major findings regarding DNA methylation in psychiatric patients, both within the context of global methylation studies and gene-specific methylation studies. Finally, we discuss issues surrounding data quality improvement, the limitations of current methylation analysis methods, and the possibility of using DNA methylation-based treatment for psychiatric disorders in the future.
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Affiliation(s)
- Chunyu Liu
- University of Illinois, Chicago, IL, United States; School of Life Science, Central South University, Changsha, China.
| | - Chuan Jiao
- School of Life Science, Central South University, Changsha, China
| | - Kangli Wang
- School of Life Science, Central South University, Changsha, China
| | - Ning Yuan
- Hunan Brain Hospital, Changsha, China
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Gaysinskaya V, Miller BF, De Luca C, van der Heijden GW, Hansen KD, Bortvin A. Transient reduction of DNA methylation at the onset of meiosis in male mice. Epigenetics Chromatin 2018; 11:15. [PMID: 29618374 PMCID: PMC5883305 DOI: 10.1186/s13072-018-0186-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 03/30/2018] [Indexed: 01/12/2023] Open
Abstract
Background Meiosis is a specialized germ cell cycle that generates haploid gametes. In the initial stage of meiosis, meiotic prophase I (MPI), homologous chromosomes pair and recombine. Extensive changes in chromatin in MPI raise an important question concerning the contribution of epigenetic mechanisms such as DNA methylation to meiosis. Interestingly, previous studies concluded that in male mice, genome-wide DNA methylation patters are set in place prior to meiosis and remain constant subsequently. However, no prior studies examined DNA methylation during MPI in a systematic manner necessitating its further investigation. Results In this study, we used genome-wide bisulfite sequencing to determine DNA methylation of adult mouse spermatocytes at all MPI substages, spermatogonia and haploid sperm. This analysis uncovered transient reduction of DNA methylation (TRDM) of spermatocyte genomes. The genome-wide scope of TRDM, its onset in the meiotic S phase and presence of hemimethylated DNA in MPI are all consistent with a DNA replication-dependent DNA demethylation. Following DNA replication, spermatocytes regain DNA methylation gradually but unevenly, suggesting that key MPI events occur in the context of hemimethylated genome. TRDM also uncovers the prior deficit of DNA methylation of LINE-1 retrotransposons in spermatogonia resulting in their full demethylation during TRDM and likely contributing to the observed mRNA and protein expression of some LINE-1 elements in early MPI. Conclusions Our results suggest that contrary to the prevailing view, chromosomes exhibit dynamic changes in DNA methylation in MPI. We propose that TRDM facilitates meiotic prophase processes and gamete quality control. Electronic supplementary material The online version of this article (10.1186/s13072-018-0186-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Valeriya Gaysinskaya
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, USA.,Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Brendan F Miller
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA.,Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Chiara De Luca
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, USA
| | - Godfried W van der Heijden
- Department of Obstetrics and Gynaecology, Erasmus MC, University Medical Center, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands
| | - Kasper D Hansen
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD, USA.,Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Alex Bortvin
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, USA.
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49
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Zhu Q, Stöger R, Alberio R. A Lexicon of DNA Modifications: Their Roles in Embryo Development and the Germline. Front Cell Dev Biol 2018; 6:24. [PMID: 29637072 PMCID: PMC5880922 DOI: 10.3389/fcell.2018.00024] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 02/27/2018] [Indexed: 12/12/2022] Open
Abstract
5-methylcytosine (5mC) on CpG dinucleotides has been viewed as the major epigenetic modification in eukaryotes for a long time. Apart from 5mC, additional DNA modifications have been discovered in eukaryotic genomes. Many of these modifications are thought to be solely associated with DNA damage. However, growing evidence indicates that some base modifications, namely 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), 5-carboxylcytosine (5caC), and N6-methadenine (6mA), may be of biological relevance, particularly during early stages of embryo development. Although abundance of these DNA modifications in eukaryotic genomes can be low, there are suggestions that they cooperate with other epigenetic markers to affect DNA-protein interactions, gene expression, defense of genome stability and epigenetic inheritance. Little is still known about their distribution in different tissues and their functions during key stages of the animal lifecycle. This review discusses current knowledge and future perspectives of these novel DNA modifications in the mammalian genome with a focus on their dynamic distribution during early embryonic development and their potential function in epigenetic inheritance through the germ line.
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Affiliation(s)
- Qifan Zhu
- School of Biosciences, University of Nottingham, Nottingham, United Kingdom
| | - Reinhard Stöger
- School of Biosciences, University of Nottingham, Nottingham, United Kingdom
| | - Ramiro Alberio
- School of Biosciences, University of Nottingham, Nottingham, United Kingdom
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50
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Carr CE, Ganugula R, Shikiya R, Soto AM, Marky LA. Effect of dC → d(m 5C) substitutions on the folding of intramolecular triplexes with mixed TAT and C +GC base triplets. Biochimie 2018; 146:156-165. [PMID: 29277568 PMCID: PMC5811340 DOI: 10.1016/j.biochi.2017.12.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 12/19/2017] [Indexed: 12/31/2022]
Abstract
Oligonucleotide-directed triple helix formation has been recognized as a potential tool for targeting genes with high specificity. Cystosine methylation in the 5' position is both ubiquitous and a stable regulatory modification, which could potentially stabilize triple helix formation. In this work, we have used a combination of calorimetric and spectroscopic techniques to study the intramolecular unfolding of four triplexes and two duplexes. We used the following triplex control sequence, named Control Tri, d(AGAGAC5TCTCTC5TCTCT), where C5 are loops of five cytosines. From this sequence, we studied three other sequences with dC → d(m5C) substitutions on the Hoogsteen strand (2MeH), Crick strand (2MeC) and both strands (4MeHC). Calorimetric studies determined that methylation does increase the thermal and enthalpic stability, leading to an overall favorable free energy, and that this increased stability is cumulative, i.e. methylation on both the Hoogsteen and Crick strands yields the largest favorable free energy. The differential uptake of protons, counterions and water was determined. It was found that methylation increases cytosine protonation by shifting the apparent pKa value to a higher pH; this increase in proton uptake coincides with a release of counterions during folding of the triplex, likely due to repulsion from the increased positive charge from the protonated cytosines. The immobilization of water was not affected for triplexes with methylated cytosines on their Hoogsteen or Crick strands, but was seen for the triplex where both strands are methylated. This may be due to the alignment in the major groove of the methyl groups on the cytosines with the methyl groups on the thymines which causes an increase in structural water along the spine of the triplex.
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Affiliation(s)
- Carolyn E Carr
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE, 68198-6025, USA
| | - Rajkumar Ganugula
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE, 68198-6025, USA
| | - Ronald Shikiya
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE, 68198-6025, USA
| | - Ana Maria Soto
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE, 68198-6025, USA
| | - Luis A Marky
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE, 68198-6025, USA.
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