1
|
Woo SJ, Han JY. Epigenetic programming of chicken germ cells: a comparative review. Poult Sci 2024; 103:103977. [PMID: 38970845 PMCID: PMC11269908 DOI: 10.1016/j.psj.2024.103977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 05/26/2024] [Accepted: 06/10/2024] [Indexed: 07/08/2024] Open
Abstract
Chicken embryos serve as an important model for investigating germ cells due to their ease of accessibility and manipulation within the egg. Understanding the development of germ cells is particularly crucial, as they are the only cell types capable of transmitting genetic information to the next generation. Therefore, gene expression regulation in germ cells is important for genomic function. Epigenetic programming is a crucial biological process for the regulation of gene expression without altering the genome sequence. Although epigenetic programming is evolutionarily conserved, several differences between chickens and mammals have been revealed. In this review, we compared the epigenetic regulation of germ cells in chickens and mammals (mainly mice as a representative species). In mammals, migrating primordial germ cells (precursors for germ cells [PGCs]) undergo global DNA demethylation and persist until sexual differentiation, while in chickens, DNA is demethylated until reaching the gonad but remethylated when sexually differentiated. Prospermatogonia is methylated at the onset of mitotic arrest in mammals, while DNA is demethylated at mitotic arrest in chickens. Furthermore, genomic imprinting and inactivation of sex chromosomes are differentially regulated through DNA methylation in chickens and mammals. Chickens and mammals exhibit different patterns of histone modifications during germ cell development, and non-coding RNA, which is not involved in PGC differentiation in mice, plays an important role in chicken PGC development. Additionally, several chicken-specific non-coding RNAs have been identified. In conclusion, we summarized current knowledge of epigenetic gene regulation of chicken germ cells, comparing that of mammals, and highlighted notable differences between them.
Collapse
Affiliation(s)
- Seung Je Woo
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Jae Yong Han
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea.
| |
Collapse
|
2
|
Wen C, Cao L, Wang S, Xu W, Yu Y, Zhao S, Yang F, Chen ZJ, Zhao S, Yang Y, Qin Y. MCM8 interacts with DDX5 to promote R-loop resolution. EMBO J 2024; 43:3044-3071. [PMID: 38858601 PMCID: PMC11251167 DOI: 10.1038/s44318-024-00134-0] [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: 08/12/2023] [Revised: 05/17/2024] [Accepted: 05/21/2024] [Indexed: 06/12/2024] Open
Abstract
MCM8 has emerged as a core gene in reproductive aging and is crucial for meiotic homologous recombination repair. It also safeguards genome stability by coordinating the replication stress response during mitosis, but its function in mitotic germ cells remains elusive. Here we found that disabling MCM8 in mice resulted in proliferation defects of primordial germ cells (PGCs) and ultimately impaired fertility. We further demonstrated that MCM8 interacted with two known helicases DDX5 and DHX9, and loss of MCM8 led to R-loop accumulation by reducing the retention of these helicases at R-loops, thus inducing genome instability. Cells expressing premature ovarian insufficiency-causative mutants of MCM8 with decreased interaction with DDX5 displayed increased R-loop levels. These results show MCM8 interacts with R-loop-resolving factors to prevent R-loop-induced DNA damage, which may contribute to the maintenance of genome integrity of PGCs and reproductive reserve establishment. Our findings thus reveal an essential role for MCM8 in PGC development and improve our understanding of reproductive aging caused by genome instability in mitotic germ cells.
Collapse
Affiliation(s)
- Canxin Wen
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive Medicine, Institute of Women, Children and Reproductive Health, Shandong University, Jinan, Shandong, 250012, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, 250012, China
- Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, Shandong, 250012, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250012, China
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences (No.2021RU001), Jinan, Shandong, 250012, China
| | - Lili Cao
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive Medicine, Institute of Women, Children and Reproductive Health, Shandong University, Jinan, Shandong, 250012, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, 250012, China
- Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, Shandong, 250012, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250012, China
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences (No.2021RU001), Jinan, Shandong, 250012, China
| | - Shuhan Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive Medicine, Institute of Women, Children and Reproductive Health, Shandong University, Jinan, Shandong, 250012, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, 250012, China
- Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, Shandong, 250012, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250012, China
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences (No.2021RU001), Jinan, Shandong, 250012, China
| | - Weiwei Xu
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive Medicine, Institute of Women, Children and Reproductive Health, Shandong University, Jinan, Shandong, 250012, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, 250012, China
- Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, Shandong, 250012, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250012, China
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences (No.2021RU001), Jinan, Shandong, 250012, China
| | - Yongze Yu
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive Medicine, Institute of Women, Children and Reproductive Health, Shandong University, Jinan, Shandong, 250012, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, 250012, China
- Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, Shandong, 250012, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250012, China
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences (No.2021RU001), Jinan, Shandong, 250012, China
| | - Simin Zhao
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive Medicine, Institute of Women, Children and Reproductive Health, Shandong University, Jinan, Shandong, 250012, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, 250012, China
- Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, Shandong, 250012, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250012, China
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences (No.2021RU001), Jinan, Shandong, 250012, China
| | - Fan Yang
- Advanced Medical Research Institute, Meili Lake Translational Research Park, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong, 250012, China
| | - Zi-Jiang Chen
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive Medicine, Institute of Women, Children and Reproductive Health, Shandong University, Jinan, Shandong, 250012, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, 250012, China
- Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, Shandong, 250012, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, 250012, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250012, China
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences (No.2021RU001), Jinan, Shandong, 250012, China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, China
- Department of Reproductive Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shidou Zhao
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive Medicine, Institute of Women, Children and Reproductive Health, Shandong University, Jinan, Shandong, 250012, China.
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, 250012, China.
- Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, Shandong, 250012, China.
- Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, 250012, China.
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, 250012, China.
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250012, China.
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences (No.2021RU001), Jinan, Shandong, 250012, China.
| | - Yajuan Yang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive Medicine, Institute of Women, Children and Reproductive Health, Shandong University, Jinan, Shandong, 250012, China.
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, 250012, China.
- Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, Shandong, 250012, China.
- Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, 250012, China.
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, 250012, China.
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250012, China.
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences (No.2021RU001), Jinan, Shandong, 250012, China.
| | - Yingying Qin
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive Medicine, Institute of Women, Children and Reproductive Health, Shandong University, Jinan, Shandong, 250012, China.
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, 250012, China.
- Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, Shandong, 250012, China.
- Shandong Technology Innovation Center for Reproductive Health, Jinan, Shandong, 250012, China.
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, 250012, China.
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250012, China.
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences (No.2021RU001), Jinan, Shandong, 250012, China.
| |
Collapse
|
3
|
Ito T, Kubiura-Ichimaru M, Miura F, Tajima S, Surani MA, Ito T, Yamaguchi S, Tada M. DNMT1 can induce primary germ layer differentiation through de novo DNA methylation. Genes Cells 2024; 29:549-566. [PMID: 38811355 DOI: 10.1111/gtc.13130] [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: 02/17/2024] [Revised: 05/12/2024] [Accepted: 05/14/2024] [Indexed: 05/31/2024]
Abstract
DNA methyltransferases and Ten-Eleven Translocation (TET) proteins regulate the DNA methylation and demethylation cycles during mouse embryonic development. Although DNMT1 mainly plays a role in the maintenance of DNA methylation after DNA replication, it is also reported to possess de novo methyltransferase capacity. However, its physiological significance remains unclear. Here, we demonstrate that full-length DNMT1 (FL) and a mutant lacking the N-terminus necessary for its maintenance activity (602) confer the differentiation potential of mouse Dnmt1, Dnmt3a, and Dnmt3b (Dnmts-TKO) embryonic stem cells (ESCs). Both FL and 602 inhibit the spontaneous differentiation of Dnmts-TKO ESCs in the undifferentiated state. Dnmts-TKO ESCs showed loss of DNA methylation and de-repression of primitive endoderm-related genes, but these defects were partially restored in Dnmts-TKO + FL and Dnmts-TKO + 602 ESCs. Upon differentiation, Dnmts-TKO + FL ESCs show increased 5mC and 5hmC levels across chromosomes, including pericentromeric regions. In contrast, Dnmts-TKO + 602 ESCs didn't accumulate 5mC, and sister chromatids showed 5hmC asynchronously. Furthermore, in comparison with DNMT1_602, DNMT1_FL effectively promoted commitment to the epiblast-like cells and beyond, driving cell-autonomous mesendodermal and germline differentiation through embryoid body-based methods. With precise target selectivity achieved by its N-terminal region, DNMT1 may play a role in gene regulation leading to germline development.
Collapse
Affiliation(s)
- Takamasa Ito
- Stem Cells & Reprogramming Laboratory, Department of Biology, Faculty of Science, Toho University, Chiba, Japan
| | - Musashi Kubiura-Ichimaru
- Stem Cells & Reprogramming Laboratory, Department of Biology, Faculty of Science, Toho University, Chiba, Japan
| | - Fumihito Miura
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Shoji Tajima
- Laboratory of Epigenetics Institute for Protein Research, Osaka University, Suita, Japan
| | - M Azim Surani
- Wellcome Trust Cancer Research UK Gurdon Institute, Tennis Court Road, University of Cambridge, Cambridge, UK
| | - Takashi Ito
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Shinpei Yamaguchi
- Stem Cells & Reprogramming Laboratory, Department of Biology, Faculty of Science, Toho University, Chiba, Japan
| | - Masako Tada
- Stem Cells & Reprogramming Laboratory, Department of Biology, Faculty of Science, Toho University, Chiba, Japan
| |
Collapse
|
4
|
Kress C, Jouneau L, Pain B. Reinforcement of repressive marks in the chicken primordial germ cell epigenetic signature: divergence from basal state resetting in mammals. Epigenetics Chromatin 2024; 17:11. [PMID: 38671530 PMCID: PMC11046797 DOI: 10.1186/s13072-024-00537-7] [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: 12/12/2023] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND In mammals, primordial germ cells (PGCs), the embryonic precursors of the germline, arise from embryonic or extra-embryonic cells upon induction by the surrounding tissues during gastrulation, according to mechanisms which are elucidated in mice but remain controversial in primates. They undergo genome-wide epigenetic reprogramming, consisting of extensive DNA demethylation and histone post-translational modification (PTM) changes, toward a basal, euchromatinized state. In contrast, chicken PGCs are specified by preformation before gastrulation based on maternally-inherited factors. They can be isolated from the bloodstream during their migration to the genital ridges. Our prior research highlighted differences in the global epigenetic profile of cultured chicken PGCs compared with chicken somatic cells and mammalian PGCs. This study investigates the acquisition and evolution of this profile during development. RESULTS Quantitative analysis of global DNA methylation and histone PTMs, including their distribution, during key stages of chicken early development revealed divergent PGC epigenetic changes compared with mammals. Unlike mammalian PGCs, chicken PGCs do not undergo genome-wide DNA demethylation or exhibit a decrease in histone H3 lysine 9 dimethylation. However, chicken PGCs show 5‑hydroxymethylcytosine loss, macroH2A redistribution, and chromatin decompaction, mirroring mammalian processes. Chicken PGCs initiate their epigenetic signature during migration, progressively accumulating high global levels of H3K9me3, with preferential enrichment in inactive genome regions. Despite apparent global chromatin decompaction, abundant heterochromatin marks, including repressive histone PTMs, HP1 variants, and DNA methylation, persists in chicken PGCs, contrasting with mammalian PGCs. CONCLUSIONS Chicken PGCs' epigenetic signature does not align with the basal chromatin state observed in mammals, suggesting a departure from extensive epigenetic reprogramming. Despite disparities in early PGC development, the persistence of several epigenetic features shared with mammals implies their involvement in chromatin-regulated germ cell properties, with the distinctive elevation of chicken-specific H3K9me3 potentially participating in these processes.
Collapse
Affiliation(s)
- Clémence Kress
- Univ Lyon, Université Lyon 1, INSERM, INRAE, U1208, USC1361, Stem Cell and Brain Research Institute, Bron, France.
| | - Luc Jouneau
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, 78350, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort, 94700, France
| | - Bertrand Pain
- Univ Lyon, Université Lyon 1, INSERM, INRAE, U1208, USC1361, Stem Cell and Brain Research Institute, Bron, France
| |
Collapse
|
5
|
Prasasya RD, Caldwell BA, Liu Z, Wu S, Leu NA, Fowler JM, Cincotta SA, Laird DJ, Kohli RM, Bartolomei MS. Iterative oxidation by TET1 is required for reprogramming of imprinting control regions and patterning of mouse sperm hypomethylated regions. Dev Cell 2024; 59:1010-1027.e8. [PMID: 38569549 PMCID: PMC11042979 DOI: 10.1016/j.devcel.2024.02.012] [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: 02/15/2023] [Revised: 12/07/2023] [Accepted: 02/29/2024] [Indexed: 04/05/2024]
Abstract
Ten-eleven translocation (TET) enzymes iteratively oxidize 5-methylcytosine (5mC) to generate 5-hydroxymethylcytosine (5hmC), 5-formylcytosine, and 5-carboxylcytosine to facilitate active genome demethylation. Whether these bases are required to promote replication-coupled dilution or activate base excision repair during mammalian germline reprogramming remains unresolved due to the inability to decouple TET activities. Here, we generated two mouse lines expressing catalytically inactive TET1 (Tet1-HxD) and TET1 that stalls oxidation at 5hmC (Tet1-V). Tet1 knockout and catalytic mutant primordial germ cells (PGCs) fail to erase methylation at select imprinting control regions and promoters of meiosis-associated genes, validating the requirement for the iterative oxidation of 5mC for complete germline reprogramming. TET1V and TET1HxD rescue most hypermethylation of Tet1-/- sperm, suggesting the role of TET1 beyond its oxidative capability. We additionally identify a broader class of hypermethylated regions in Tet1 mutant mouse sperm that depend on TET oxidation for reprogramming. Our study demonstrates the link between TET1-mediated germline reprogramming and sperm methylome patterning.
Collapse
Affiliation(s)
- Rexxi D Prasasya
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Blake A Caldwell
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Zhengfeng Liu
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Songze Wu
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - N Adrian Leu
- Department of Biomedical Sciences, Center for Animal Transgenesis and Germ Cell Research, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104, USA
| | - Johanna M Fowler
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Steven A Cincotta
- Department of Obstetrics, Gynecology and Reproductive Science, Center for Reproductive Sciences, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 84143, USA
| | - Diana J Laird
- Department of Obstetrics, Gynecology and Reproductive Science, Center for Reproductive Sciences, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 84143, USA
| | - Rahul M Kohli
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Marisa S Bartolomei
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|
6
|
Yang X, Ren S, Yang J, Pan Y, Zhou Z, Chen Q, Fang Y, Shang L, Zhang F, Zhang X, Wu Y. Rare variants in FANCJ induce premature ovarian insufficiency in humans and mice. J Genet Genomics 2024; 51:252-255. [PMID: 37062450 DOI: 10.1016/j.jgg.2023.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 03/20/2023] [Accepted: 03/29/2023] [Indexed: 04/18/2023]
Affiliation(s)
- Xi Yang
- State Key Laboratory of Genetic Engineering at School of Life Sciences, Human Phenome Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200438, China
| | - Shuting Ren
- State Key Laboratory of Genetic Engineering at School of Life Sciences, Human Phenome Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200438, China
| | - Jialin Yang
- State Key Laboratory of Genetic Engineering at School of Life Sciences, Human Phenome Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200438, China
| | - Yuncheng Pan
- State Key Laboratory of Genetic Engineering at School of Life Sciences, Human Phenome Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200438, China
| | - Zixue Zhou
- State Key Laboratory of Genetic Engineering at School of Life Sciences, Human Phenome Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200438, China
| | - Qing Chen
- State Key Laboratory of Genetic Engineering at School of Life Sciences, Human Phenome Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200438, China
| | - Yunzheng Fang
- State Key Laboratory of Genetic Engineering at School of Life Sciences, Human Phenome Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200438, China
| | - Lingyue Shang
- State Key Laboratory of Genetic Engineering at School of Life Sciences, Human Phenome Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200438, China
| | - Feng Zhang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, State Key Laboratory of Genetic Engineering at School of Life Sciences, Fudan University, Shanghai 200011, China; Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai 201203, China.
| | - Xiaojin Zhang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai 200011, China.
| | - Yanhua Wu
- State Key Laboratory of Genetic Engineering at School of Life Sciences, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200438, China; National Demonstration Center for Experimental Biology Education, School of Life Sciences, Fudan University, Shanghai 200433, China.
| |
Collapse
|
7
|
Le Clercq LS, Kotzé A, Grobler JP, Dalton DL. Biological clocks as age estimation markers in animals: a systematic review and meta-analysis. Biol Rev Camb Philos Soc 2023; 98:1972-2011. [PMID: 37356823 DOI: 10.1111/brv.12992] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 06/04/2023] [Accepted: 06/08/2023] [Indexed: 06/27/2023]
Abstract
Various biological attributes associated with individual fitness in animals change predictably over the lifespan of an organism. Therefore, the study of animal ecology and the work of conservationists frequently relies upon the ability to assign animals to functionally relevant age classes to model population fitness. Several approaches have been applied to determining individual age and, while these methods have proved useful, they are not without limitations and often lack standardisation or are only applicable to specific species. For these reasons, scientists have explored the potential use of biological clocks towards creating a universal age-determination method. Two biological clocks, tooth layer annulation and otolith layering have found universal appeal. Both methods are highly invasive and most appropriate for post-mortem age-at-death estimation. More recently, attributes of cellular ageing previously explored in humans have been adapted to studying ageing in animals for the use of less-invasive molecular methods for determining age. Here, we review two such methods, assessment of methylation and telomere length, describing (i) what they are, (ii) how they change with age, and providing (iii) a summary and meta-analysis of studies that have explored their utility in animal age determination. We found that both attributes have been studied across multiple vertebrate classes, however, telomere studies were used before methylation studies and telomere length has been modelled in nearly twice as many studies. Telomere length studies included in the review often related changes to stress responses and illustrated that telomere length is sensitive to environmental and social stressors and, in the absence of repair mechanisms such as telomerase or alternative lengthening modes, lacks the ability to recover. Methylation studies, however, while also detecting sensitivity to stressors and toxins, illustrated the ability to recover from such stresses after a period of accelerated ageing, likely due to constitutive expression or reactivation of repair enzymes such as DNA methyl transferases. We also found that both studied attributes have parentally heritable features, but the mode of inheritance differs among taxa and may relate to heterogamy. Our meta-analysis included more than 40 species in common for methylation and telomere length, although both analyses included at least 60 age-estimation models. We found that methylation outperforms telomere length in terms of predictive power evidenced from effect sizes (more than double that observed for telomeres) and smaller prediction intervals. Both methods produced age correlation models using similar sample sizes and were able to classify individuals into young, middle, or old age classes with high accuracy. Our review and meta-analysis illustrate that both methods are well suited to studying age in animals and do not suffer significantly from variation due to differences in the lifespan of the species, genome size, karyotype, or tissue type but rather that quantitative method, patterns of inheritance, and environmental factors should be the main considerations. Thus, provided that complex factors affecting the measured trait can be accounted for, both methylation and telomere length are promising targets to develop as biomarkers for age determination in animals.
Collapse
Affiliation(s)
- Louis-Stéphane Le Clercq
- South African National Biodiversity Institute, P.O. Box 754, Pretoria, 0001, South Africa
- Department of Genetics, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
| | - Antoinette Kotzé
- South African National Biodiversity Institute, P.O. Box 754, Pretoria, 0001, South Africa
- Department of Genetics, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
| | - J Paul Grobler
- Department of Genetics, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
| | - Desiré Lee Dalton
- School of Health and Life Sciences, Teesside University, Middlesbrough, TS1 3BA, UK
| |
Collapse
|
8
|
Dion C, Laberthonnière C, Magdinier F. [Epigenetics, principles and examples of applications]. Rev Med Interne 2023; 44:594-601. [PMID: 37438189 DOI: 10.1016/j.revmed.2023.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 06/20/2023] [Accepted: 06/20/2023] [Indexed: 07/14/2023]
Abstract
Since the discovery of DNA as the support of genetic information, the challenge for generations of life scientists was to understand the mechanisms underlying the process that translate the sequence of a gene to a phenotype. In the 1950s, the concept of epigenetics was defined by the British biologist Conrad H. Waddington as the study of "epigenesis" that governs the biological processes involved in the development of any organism. The term epigenetics, now best defined as "above the DNA sequence" reflects the gene-environment interactions by which genes determine traits. Since, its first description, studies underlying the mechanisms involved in these processes has led to an increasing understanding of the regulation all genome transactions such as transcription, replication, repair and the biological pathways coordinated by these mechanisms. We will discuss here the main principles regulating epigenetic processes, their roles in physiology, their evolution over the life time and their implications in medicine.
Collapse
Affiliation(s)
- C Dion
- Aix Marseille Univ, INSERM, Marseille Medical Genetics, 13000 Marseille, France; MRC London Institute of Medical Sciences (LMS), London, United Kingdom; Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, United Kingdom
| | - C Laberthonnière
- Aix Marseille Univ, INSERM, Marseille Medical Genetics, 13000 Marseille, France; Molecular Developmental Biology, Faculty of Science, Radboud University, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - F Magdinier
- Aix Marseille Univ, INSERM, Marseille Medical Genetics, 13000 Marseille, France.
| |
Collapse
|
9
|
Irie N, Lee SM, Lorenzi V, Xu H, Chen J, Inoue M, Kobayashi T, Sancho-Serra C, Drousioti E, Dietmann S, Vento-Tormo R, Song CX, Surani MA. DMRT1 regulates human germline commitment. Nat Cell Biol 2023; 25:1439-1452. [PMID: 37709822 PMCID: PMC10567552 DOI: 10.1038/s41556-023-01224-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 08/07/2023] [Indexed: 09/16/2023]
Abstract
Germline commitment following primordial germ cell (PGC) specification during early human development establishes an epigenetic programme and competence for gametogenesis. Here we follow the progression of nascent PGC-like cells derived from human embryonic stem cells in vitro. We show that switching from BMP signalling for PGC specification to Activin A and retinoic acid resulted in DMRT1 and CDH5 expression, the indicators of migratory PGCs in vivo. Moreover, the induction of DMRT1 and SOX17 in PGC-like cells promoted epigenetic resetting with striking global enrichment of 5-hydroxymethylcytosine and locus-specific loss of 5-methylcytosine at DMRT1 binding sites and the expression of DAZL representing DNA methylation-sensitive genes, a hallmark of the germline commitment programme. We provide insight into the unique role of DMRT1 in germline development for advances in human germ cell biology and in vitro gametogenesis.
Collapse
Affiliation(s)
- Naoko Irie
- Wellcome Trust/Cancer Research UK Gurdon Institute, Henry Wellcome Building of Cancer and Developmental Biology, Cambridge, UK.
- Metabolic Systems Laboratory, Live Imaging Center, Central Institute for Experimental Animals, Kanagawa, Japan.
| | - Sun-Min Lee
- Wellcome Trust/Cancer Research UK Gurdon Institute, Henry Wellcome Building of Cancer and Developmental Biology, Cambridge, UK
- Department of Physics, Konkuk University, Seoul, Republic of Korea
| | - Valentina Lorenzi
- Wellcome Sanger Institute, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Haiqi Xu
- Ludwig Institute for Cancer Research and Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jinfeng Chen
- Ludwig Institute for Cancer Research and Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Masato Inoue
- Ludwig Institute for Cancer Research and Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Toshihiro Kobayashi
- Division of Mammalian Embryology, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, Aichi, Japan
| | | | - Elena Drousioti
- Wellcome Trust/Cancer Research UK Gurdon Institute, Henry Wellcome Building of Cancer and Developmental Biology, Cambridge, UK
| | - Sabine Dietmann
- Department of Developmental Biology and Institute for Informatics, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Chun-Xiao Song
- Ludwig Institute for Cancer Research and Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - M Azim Surani
- Wellcome Trust/Cancer Research UK Gurdon Institute, Henry Wellcome Building of Cancer and Developmental Biology, Cambridge, UK.
- Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge, UK.
| |
Collapse
|
10
|
Huang Y, Li L, An G, Yang X, Cui M, Song X, Lin J, Zhang X, Yao Z, Wan C, Zhou C, Zhao J, Song K, Ren S, Xia X, Fu X, Lan Y, Hu X, Wang W, Wang M, Zheng Y, Miao K, Bai X, Hutchins AP, Chang G, Gao S, Zhao XY. Single-cell multi-omics sequencing of human spermatogenesis reveals a DNA demethylation event associated with male meiotic recombination. Nat Cell Biol 2023; 25:1520-1534. [PMID: 37723297 DOI: 10.1038/s41556-023-01232-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 08/15/2023] [Indexed: 09/20/2023]
Abstract
Human spermatogenesis is a highly ordered process; however, the roles of DNA methylation and chromatin accessibility in this process remain largely unknown. Here by simultaneously investigating the chromatin accessibility, DNA methylome and transcriptome landscapes using the modified single-cell chromatin overall omic-scale landscape sequencing approach, we revealed that the transcriptional changes throughout human spermatogenesis were correlated with chromatin accessibility changes. In particular, we identified a set of transcription factors and cis elements with potential functions. A round of DNA demethylation was uncovered upon meiosis initiation in human spermatogenesis, which was associated with male meiotic recombination and conserved between human and mouse. Aberrant DNA hypermethylation could be detected in leptotene spermatocytes of certain nonobstructive azoospermia patients. Functionally, the intervention of DNA demethylation affected male meiotic recombination and fertility. Our work provides multi-omics landscapes of human spermatogenesis at single-cell resolution and offers insights into the association between DNA demethylation and male meiotic recombination.
Collapse
Affiliation(s)
- Yaping Huang
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Lin Li
- Guangdong Provincial Key Laboratory of Proteomics, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Geng An
- Department of Reproductive Medicine Center, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
| | - Xinyan Yang
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Manman Cui
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Xiuling Song
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Jing Lin
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Xiaoling Zhang
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Zhaokai Yao
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Cong Wan
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Cai Zhou
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Jiexiang Zhao
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Ke Song
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Shaofang Ren
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Xinyu Xia
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Xin Fu
- Department of Reproductive Medicine Center, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
| | - Yu Lan
- Department of Reproductive Medicine Center, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
| | - Xuesong Hu
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Wen Wang
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Mei Wang
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Yi Zheng
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Kai Miao
- Centre for Precision Medicine Research and Training, Faculty of Health Sciences, University of Macau, Macau, P. R. China
| | - Xiaochun Bai
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Andrew P Hutchins
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, P. R. China
| | - Gang Chang
- Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen, P. R. China.
| | - Shuai Gao
- State Key Laboratory of Animal Biotech Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the MARA, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, P. R. China.
| | - Xiao-Yang Zhao
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China.
- Guangdong Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, P. R. China.
- Key Laboratory of Mental Health of the Ministry of Education, Guangzhou, P. R. China.
- Department of Gynecology, Zhujiang Hospital, Southern Medical University, Guangzhou, P. R. China.
- National Clinical Research Center for Kidney Disease, Guangzhou, P. R. China.
| |
Collapse
|
11
|
Abstract
Male germ cells undergo a complex sequence of developmental events throughout fetal and postnatal life that culminate in the formation of haploid gametes: the spermatozoa. Errors in these processes result in infertility and congenital abnormalities in offspring. Male germ cell development starts when pluripotent cells undergo specification to sexually uncommitted primordial germ cells, which act as precursors of both oocytes and spermatozoa. Male-specific development subsequently occurs in the fetal testes, resulting in the formation of spermatogonial stem cells: the foundational stem cells responsible for lifelong generation of spermatozoa. Although deciphering such developmental processes is challenging in humans, recent studies using various models and single-cell sequencing approaches have shed new insight into human male germ cell development. Here, we provide an overview of cellular, signaling and epigenetic cascades of events accompanying male gametogenesis, highlighting conserved features and the differences between humans and other model organisms.
Collapse
Affiliation(s)
- John Hargy
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104, USA
| | - Kotaro Sasaki
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| |
Collapse
|
12
|
Zhou Z, Yin H, Suye S, Ren Z, Yan L, Shi L, Fu C. Fance deficiency inhibits primordial germ cell proliferation associated with transcription-replication conflicts accumulate and DNA repair defects. J Ovarian Res 2023; 16:160. [PMID: 37563658 PMCID: PMC10416540 DOI: 10.1186/s13048-023-01252-9] [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: 06/06/2023] [Accepted: 08/01/2023] [Indexed: 08/12/2023] Open
Abstract
Fanconi anemia (FA) gene mutations are critical components in the genetic etiology of premature ovarian insufficiency (POI). Fance-/- mice detected meiotic arrest of primordial germ cells (PGCs) as early as embryonic day (E) 13.5 and exhibited decreased ovarian reserve after birth. However, the mechanism of Fance defect leading to dysgenesis of PGCs is unclear. We aimed to explore the effect of Fance defects on mitotic proliferation of PGCs. Combined with transcriptomic sequencing and validation, we examined the effect of Fance defects on cell cycle, transcription-replication conflicts (TRCs), and multiple DNA repair pathways in PGCs during active DNA replication at E11.5 and E12.5. Results showed Fance defects cause decreased numbers of PGCs during rapid mitosis at E11.5 and E12.5. Mitotic cell cycle progression of Fance-/- PGCs was blocked at E11.5 and E12.5, shown by decreased cell proportions in S and G2 phases and increased cell proportions in M phase. RNA-seq suggested the mechanisms involved in DNA replication and repair. We found Fance-/- PGCs accumulate TRCs during active DNA replication at E11.5 and E12.5. Fance-/- PGCs down-regulate multiple DNA repair pathways at E11.5 and E12.5 including the FA pathway, homologous recombination (HR) pathway, and base excision repair (BER) pathway. In conclusion, Fance defect impaired the mitotic proliferation of PGCs leading to rapidly decreased numbers and abnormal cell cycle distribution. Proliferation inhibition of Fance-/- PGCs was associated with accumulated TRCs and down-regulation of FA, HR, BER pathways. These provided a theoretical basis for identifying the inherited etiology and guiding potential fertility management for POI.
Collapse
Affiliation(s)
- Zhixian Zhou
- Department of Obstetrics and Gynecology, The Second Xiangya Hospital of Central South University, Changsha, 410000, China
| | - Huan Yin
- Department of Obstetrics and Gynecology, The Second Xiangya Hospital of Central South University, Changsha, 410000, China
| | - Suye Suye
- Department of Obstetrics and Gynecology, The Second Xiangya Hospital of Central South University, Changsha, 410000, China
| | - Zhen Ren
- Department of Obstetrics and Gynecology, The Second Xiangya Hospital of Central South University, Changsha, 410000, China
| | - Lei Yan
- Department of Obstetrics and Gynecology, The Second Xiangya Hospital of Central South University, Changsha, 410000, China
| | - Liye Shi
- Department of Obstetrics and Gynecology, The Second Xiangya Hospital of Central South University, Changsha, 410000, China
| | - Chun Fu
- Department of Obstetrics and Gynecology, The Second Xiangya Hospital of Central South University, Changsha, 410000, China.
| |
Collapse
|
13
|
Hsu FM, Wu QY, Fabyanic EB, Wei A, Wu H, Clark AT. TET1 facilitates specification of early human lineages including germ cells. iScience 2023; 26:107191. [PMID: 37456839 PMCID: PMC10345126 DOI: 10.1016/j.isci.2023.107191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/07/2023] [Accepted: 06/18/2023] [Indexed: 07/18/2023] Open
Abstract
Ten Eleven Translocation 1 (TET1) is a regulator of localized DNA demethylation through the conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). To examine DNA demethylation in human primordial germ cell-like cells (hPGCLCs) induced from human embryonic stem cells (hESCs), we performed bisulfite-assisted APOBEC coupled epigenetic sequencing (bACEseq) followed by integrated genomics analysis. Our data indicates that 5hmC enriches at hPGCLC-specific NANOG, SOX17 or TFAP2C binding sites on hPGCLC induction, and this is accompanied by localized DNA demethylation. Using CRISPR-Cas9, we show that deleting the catalytic domain of TET1 reduces hPGCLC competency when starting with hESC cultured on mouse embryonic fibroblasts, and this phenotype can be rescued after transitioning hESCs to defined media and a recombinant substrate. Taken together, our study demonstrates the importance of 5hmC in facilitating hPGCLC competency, and the role of hESC culture conditions in modulating this effect.
Collapse
Affiliation(s)
- Fei-Man Hsu
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Qiu Ya Wu
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Emily B. Fabyanic
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alex Wei
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hao Wu
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Amander T. Clark
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| |
Collapse
|
14
|
Zhao L, Xu H, Liu X, Cheng Y, Xie J. The role of TET2-mediated ROBO4 hypomethylation in the development of diabetic retinopathy. J Transl Med 2023; 21:455. [PMID: 37430272 DOI: 10.1186/s12967-023-04310-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 06/26/2023] [Indexed: 07/12/2023] Open
Abstract
BACKGROUND In diabetic retinopathy, increasing evidence points to a link between the pathogenesis of retinal microangiopathy and the endothelial cell-specific factor roundabout4 (ROBO4). According to earlier research, specificity protein 1 (SP1) enhances the binding to the ROBO4 promoter, increasing Robo4 expression and hastening the progression of diabetic retinopathy. To determine if this is related to aberrant epigenetic modifications of ROBO4, we examined the methylation level of the ROBO4 promoter and the corresponding regulatory mechanism during the course of diabetic retinopathy and explored the effect of this mechanism on retinal vascular leakage and neovascularization. METHODS The methylation level of CpG sites in the ROBO4 promoter was detected in human retinal endothelial cells (HRECs) cultured under hyperglycemic conditions and retinas from streptozotocin-induced diabetic mice. The effects of hyperglycemia on DNA methyltransferase 1, Tet methylcytosine dioxygenase 2 (TET2), 5-methylcytosine, 5-hydroxymethylcytosine, and the binding of TET2 and SP1 to the ROBO4 promoter, as well as the expression of ROBO4, zonula occludens 1 (ZO-1) and occludin were examined. Short hairpin RNA was used to suppress the expression of TET2 or ROBO4 and the structural and functional changes in the retinal microvascular system were assessed. RESULTS In HRECs cultured under hyperglycemic conditions, the ROBO4 promoter methylation level decreased. Hyperglycemia-induced TET2 overexpression caused active demethylation of ROBO4 by oxidizing 5-methylcytosine to 5-hydroxymethylcytosine, which enhanced the binding of SP1 to ROBO4, increased the expression of ROBO4, and decreased the expression of ZO-1 and occludin, leading to the abnormalities in monolayer permeability, migratory ability and angiogenesis of HRECs. The above pathway was also demonstrated in the retinas of diabetic mice, which caused leakage from retinal capillaries and neovascularization. Inhibition of TET2 or ROBO4 expression significantly ameliorated the dysfunction of HRECs and retinal vascular abnormalities. CONCLUSIONS In diabetes, TET2 can regulate the expression of ROBO4 and its downstream proteins by mediating active demethylation of the ROBO4 promoter, which accelerates the development of retinal vasculopathy. These findings suggest that TET2-induced ROBO4 hypomethylation is a potential therapeutic target, and anti- TET2/ROBO4 therapy is anticipated to emerge as a novel strategy for early intervention and delayed progression of diabetic retinopathy.
Collapse
Affiliation(s)
- Liangliang Zhao
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, Jilin, China
| | - Haitao Xu
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, Jilin, China
| | - Xin Liu
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, Jilin, China
| | - Yan Cheng
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, Jilin, China
| | - Jia'nan Xie
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, Jilin, China.
| |
Collapse
|
15
|
Wu GMJ, Chen ACH, Yeung WSB, Lee YL. Current progress on in vitro differentiation of ovarian follicles from pluripotent stem cells. Front Cell Dev Biol 2023; 11:1166351. [PMID: 37325555 PMCID: PMC10267358 DOI: 10.3389/fcell.2023.1166351] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/22/2023] [Indexed: 06/17/2023] Open
Abstract
Mammalian female reproduction requires a functional ovary. Competence of the ovary is determined by the quality of its basic unit-ovarian follicles. A normal follicle consists of an oocyte enclosed within ovarian follicular cells. In humans and mice, the ovarian follicles are formed at the foetal and the early neonatal stage respectively, and their renewal at the adult stage is controversial. Extensive research emerges recently to produce ovarian follicles in-vitro from different species. Previous reports demonstrated the differentiation of mouse and human pluripotent stem cells into germline cells, termed primordial germ cell-like cells (PGCLCs). The germ cell-specific gene expressions and epigenetic features including global DNA demethylation and histone modifications of the pluripotent stem cells-derived PGCLCs were extensively characterized. The PGCLCs hold potential for forming ovarian follicles or organoids upon cocultured with ovarian somatic cells. Intriguingly, the oocytes isolated from the organoids could be fertilized in-vitro. Based on the knowledge of in-vivo derived pre-granulosa cells, the generation of these cells from pluripotent stem cells termed foetal ovarian somatic cell-like cells was also reported recently. Despite successful in-vitro folliculogenesis from pluripotent stem cells, the efficiency remains low, mainly due to the lack of information on the interaction between PGCLCs and pre-granulosa cells. The establishment of in-vitro pluripotent stem cell-based models paves the way for understanding the critical signalling pathways and molecules during folliculogenesis. This article aims to review the developmental events during in-vivo follicular development and discuss the current progress of generation of PGCLCs, pre-granulosa and theca cells in-vitro.
Collapse
Affiliation(s)
- Genie Min Ju Wu
- Department of Obstetrics and Gynaecology, School of Clinical Medicine, The University of Hong Kong, Hong Kong, China
| | - Andy Chun Hang Chen
- Department of Obstetrics and Gynaecology, School of Clinical Medicine, The University of Hong Kong, Hong Kong, China
- Shenzhen Key Laboratory of Fertility Regulation, Reproductive Medicine Center, The University of Hong Kong—Shenzhen Hospital, Shenzhen, China
- Centre for Translational Stem Cell Biology, The Hong Kong Science and Technology Park, Hong Kong, China
| | - William Shu Biu Yeung
- Department of Obstetrics and Gynaecology, School of Clinical Medicine, The University of Hong Kong, Hong Kong, China
- Shenzhen Key Laboratory of Fertility Regulation, Reproductive Medicine Center, The University of Hong Kong—Shenzhen Hospital, Shenzhen, China
- Centre for Translational Stem Cell Biology, The Hong Kong Science and Technology Park, Hong Kong, China
| | - Yin Lau Lee
- Department of Obstetrics and Gynaecology, School of Clinical Medicine, The University of Hong Kong, Hong Kong, China
- Shenzhen Key Laboratory of Fertility Regulation, Reproductive Medicine Center, The University of Hong Kong—Shenzhen Hospital, Shenzhen, China
- Centre for Translational Stem Cell Biology, The Hong Kong Science and Technology Park, Hong Kong, China
| |
Collapse
|
16
|
Sasaki K, Sangrithi M. Developmental origins of mammalian spermatogonial stem cells: New perspectives on epigenetic regulation and sex chromosome function. Mol Cell Endocrinol 2023:111949. [PMID: 37201564 DOI: 10.1016/j.mce.2023.111949] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 04/28/2023] [Accepted: 05/08/2023] [Indexed: 05/20/2023]
Abstract
Male and female germ cells undergo genome-wide reprogramming during their development, and execute sex-specific programs to complete meiosis and successfully generate healthy gametes. While sexually dimorphic germ cell development is fundamental, similarities and differences exist in the basic processes governing normal gametogenesis. At the simplest level, male gamete generation in mammals is centred on the activity of spermatogonial stem cells (SSCs), and an equivalent cell state is not present in females. Maintaining this unique SSC epigenetic state, while keeping to germ cell-intrinsic developmental programs, poses challenges for the correct completion of spermatogenesis. In this review, we highlight the origins of spermatogonia, comparing and contrasting them with female germline development to emphasize specific developmental processes that are required for their function as germline stem cells. We identify gaps in our current knowledge about human SSCs and further discuss the impact of the unique regulation of the sex chromosomes during spermatogenesis, and the roles of X-linked genes in SSCs.
Collapse
Affiliation(s)
- Kotaro Sasaki
- Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, United States.
| | - Mahesh Sangrithi
- King's College London, Centre for Gene Therapy and Regenerative Medicine, 28th Floor, Tower Wing, Guy's Hospital, Great Maze Pond, London, SE1 9RT, UK.
| |
Collapse
|
17
|
Strange A, Alberio R. Review: A barnyard in the lab: prospect of generating animal germ cells for breeding and conservation. Animal 2023; 17 Suppl 1:100753. [PMID: 37567650 DOI: 10.1016/j.animal.2023.100753] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 02/14/2023] [Accepted: 02/20/2023] [Indexed: 08/13/2023] Open
Abstract
In vitro gametogenesis (IVG) offers broad opportunities for gaining detailed new mechanistic knowledge of germ cell biology that will enable progress in the understanding of human infertility, as well as for applications in the conservation of endangered species and for accelerating genetic selection of livestock. The realisation of this potential depends on overcoming key technical challenges and of gaining more detailed knowledge of the ontogeny and developmental programme in different species. Important differences in the molecular mechanisms of germ cell determination and epigenetic reprogramming between mice and other animals have been elucidated in recent years. These must be carefully considered when developing IVG protocols, as cellular kinetics in mice may not accurately reflect mechanisms in other mammals. Similarly, diverse stem cell models with potential for germ cell differentiation may reflect alternative routes to successful IVG. In conclusion, the fidelity of the developmental programme recapitulated during IVG must be assessed against reference information from each species to ensure the production of healthy animals using these methods, as well as for developing genuine models of gametogenesis.
Collapse
Affiliation(s)
- A Strange
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, LE12 5RD, UK
| | - R Alberio
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, LE12 5RD, UK.
| |
Collapse
|
18
|
Ma Y, Wu W, Zhang Y, Wang X, Wei J, Guo X, Xue M, Zhu G. The Synchronized Progression from Mitosis to Meiosis in Female Primordial Germ Cells between Layers and Broilers. Genes (Basel) 2023; 14:genes14040781. [PMID: 37107539 PMCID: PMC10137798 DOI: 10.3390/genes14040781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/20/2023] [Accepted: 03/22/2023] [Indexed: 04/29/2023] Open
Abstract
Layer and broiler hens show a dramatic difference in the volume and frequency of egg production. However, it is unclear whether the intrinsic competency of oocyte generation is also different between the two types of chicken. All oocytes were derived from the primordial germ cells (PGC) in the developing embryo, and female PGC proliferation (mitosis) and the subsequent differentiation (meiosis) determine the ultimate ovarian pool of germ cells available for future ovulation. In this study, we systematically compared the cellular phenotype and gene expression patterns during PGC mitosis (embryonic day 10, E10) and meiosis (E14) between female layers and broilers to determine whether the early germ cell development is also subjected to the selective breeding of egg production traits. We found that PGCs from E10 showed much higher activity in cell propagation and were enriched in cell proliferation signaling pathways than PGCs from E14 in both types of chicken. A common set of genes, namely insulin-like growth factor 2 (IGF2) and E2F transcription factor 4 (E2F4), were identified as the major regulators of cell proliferation in E10 PGCs of both strains. In addition, we found that E14 PGCs from both strains showed an equal ability to initiate meiosis, which was associated with the upregulation of key genes for meiotic initiation. The intrinsic cellular dynamics during the transition from proliferation to differentiation of female germ cells were conserved between layers and broilers. Hence, we surmise that other non-cell autonomous mechanisms involved in germ-somatic cell interactions would contribute to the divergence of egg production performance between layers and broilers.
Collapse
Affiliation(s)
- Yuxiao Ma
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai'an 271000, China
| | - Wenhui Wu
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai'an 271000, China
| | - Yun Zhang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai'an 271000, China
| | - Xuzhao Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai'an 271000, China
| | - Jiahui Wei
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai'an 271000, China
| | - Xiaotong Guo
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai'an 271000, China
| | - Man Xue
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai'an 271000, China
| | - Guiyu Zhu
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai'an 271000, China
| |
Collapse
|
19
|
Yu Y, Xu W, Wen C, Zhao S, Li G, Liu R, Chen ZJ, Qin Y, Ma J, Yang Y, Zhao S. UBE2T resolves transcription-replication conflicts and protects common fragile sites in primordial germ cells. Cell Mol Life Sci 2023; 80:92. [PMID: 36928776 PMCID: PMC11072727 DOI: 10.1007/s00018-023-04733-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 02/04/2023] [Accepted: 02/22/2023] [Indexed: 03/18/2023]
Abstract
The proper development of primordial germ cells (PGCs) is an essential prerequisite for gametogenesis and mammalian fertility. The Fanconi anemia (FA) pathway functions in maintaining the development of PGCs. FANCT/UBE2T serves as an E2 ubiquitin-conjugating enzyme that ubiquitylates the FANCD2-FANCI complex to activate the FA pathway, but its role in the development of PGCs is not clear. In this study, we found that Ube2t knockout mice showed defects in PGC proliferation, leading to severe loss of germ cells after birth. Deletion of UBE2T exacerbated DNA damage and triggered the activation of the p53 pathway. We further demonstrated that UBE2T counteracted transcription-replication conflicts by resolving R-loops and stabilizing replication forks, and also protected common fragile sites by resolving R-loops in large genes and promoting mitotic DNA synthesis to maintain the genome stability of PGCs. Overall, these results provide new insights into the function and regulatory mechanisms of the FA pathway ensuring normal development of PGCs.
Collapse
Affiliation(s)
- Yongze Yu
- Center for Reproductive Medicine, Shandong University, Jinan, 250012, Shandong, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China
- Shandong Key Laboratory of Reproductive Medicine, Jinan, 250012, Shandong, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, 250012, Shandong, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, 250012, Shandong, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, 250012, Shandong, China
| | - Weiwei Xu
- Center for Reproductive Medicine, Shandong University, Jinan, 250012, Shandong, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China
- Shandong Key Laboratory of Reproductive Medicine, Jinan, 250012, Shandong, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, 250012, Shandong, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, 250012, Shandong, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, 250012, Shandong, China
| | - Canxin Wen
- Center for Reproductive Medicine, Shandong University, Jinan, 250012, Shandong, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China
- Shandong Key Laboratory of Reproductive Medicine, Jinan, 250012, Shandong, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, 250012, Shandong, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, 250012, Shandong, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, 250012, Shandong, China
| | - Simin Zhao
- Center for Reproductive Medicine, Shandong University, Jinan, 250012, Shandong, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China
- Shandong Key Laboratory of Reproductive Medicine, Jinan, 250012, Shandong, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, 250012, Shandong, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, 250012, Shandong, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, 250012, Shandong, China
| | - Guangyu Li
- Center for Reproductive Medicine, Shandong University, Jinan, 250012, Shandong, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China
- Shandong Key Laboratory of Reproductive Medicine, Jinan, 250012, Shandong, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, 250012, Shandong, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, 250012, Shandong, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, 250012, Shandong, China
| | - Ran Liu
- Center for Reproductive Medicine, Shandong University, Jinan, 250012, Shandong, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China
- Shandong Key Laboratory of Reproductive Medicine, Jinan, 250012, Shandong, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, 250012, Shandong, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, 250012, Shandong, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, 250012, Shandong, China
| | - Zi-Jiang Chen
- Center for Reproductive Medicine, Shandong University, Jinan, 250012, Shandong, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China
- Shandong Key Laboratory of Reproductive Medicine, Jinan, 250012, Shandong, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, 250012, Shandong, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, 250012, Shandong, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, 250012, Shandong, China
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences, Jinan, 250021, Shandong, China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, 200135, China
- Center for Reproductive Medicine, School of Medicine, Ren Ji Hospital, Shanghai Jiao Tong University, Shanghai, 200135, China
| | - Yingying Qin
- Center for Reproductive Medicine, Shandong University, Jinan, 250012, Shandong, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China
- Shandong Key Laboratory of Reproductive Medicine, Jinan, 250012, Shandong, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, 250012, Shandong, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, 250012, Shandong, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, 250012, Shandong, China
| | - Jinlong Ma
- Center for Reproductive Medicine, Shandong University, Jinan, 250012, Shandong, China.
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China.
- Shandong Key Laboratory of Reproductive Medicine, Jinan, 250012, Shandong, China.
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, 250012, Shandong, China.
- Shandong Technology Innovation Center for Reproductive Health, Jinan, 250012, Shandong, China.
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, 250012, Shandong, China.
| | - Yajuan Yang
- Center for Reproductive Medicine, Shandong University, Jinan, 250012, Shandong, China.
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China.
- Shandong Key Laboratory of Reproductive Medicine, Jinan, 250012, Shandong, China.
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, 250012, Shandong, China.
- Shandong Technology Innovation Center for Reproductive Health, Jinan, 250012, Shandong, China.
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, 250012, Shandong, China.
| | - Shidou Zhao
- Center for Reproductive Medicine, Shandong University, Jinan, 250012, Shandong, China.
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China.
- Shandong Key Laboratory of Reproductive Medicine, Jinan, 250012, Shandong, China.
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, 250012, Shandong, China.
- Shandong Technology Innovation Center for Reproductive Health, Jinan, 250012, Shandong, China.
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, 250012, Shandong, China.
| |
Collapse
|
20
|
Prasasya RD, Caldwell BA, Liu Z, Wu S, Leu NA, Fowler JM, Cincotta SA, Laird DJ, Kohli RM, Bartolomei MS. TET1 Catalytic Activity is Required for Reprogramming of Imprinting Control Regions and Patterning of Sperm-Specific Hypomethylated Regions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.21.529426. [PMID: 36865267 PMCID: PMC9980038 DOI: 10.1101/2023.02.21.529426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
DNA methylation erasure is required for mammalian primordial germ cell reprogramming. TET enzymes iteratively oxidize 5-methylcytosine to generate 5-hyroxymethylcytosine (5hmC), 5-formylcytosine, and 5-carboxycytosine to facilitate active genome demethylation. Whether these bases are required to promote replication-coupled dilution or activate base excision repair during germline reprogramming remains unresolved due to the lack of genetic models that decouple TET activities. Here, we generated two mouse lines expressing catalytically inactive TET1 ( Tet1-HxD ) and TET1 that stalls oxidation at 5hmC ( Tet1-V ). Tet1 -/- , Tet1 V/V , and Tet1 HxD/HxD sperm methylomes show that TET1 V and TET1 HxD rescue most Tet1 -/- hypermethylated regions, demonstrating the importance of TET1’s extra-catalytic functions. Imprinted regions, in contrast, require iterative oxidation. We further reveal a broader class of hypermethylated regions in sperm of Tet1 mutant mice that are excluded from de novo methylation during male germline development and depend on TET oxidation for reprogramming. Our study underscores the link between TET1-mediated demethylation during reprogramming and sperm methylome patterning.
Collapse
|
21
|
Seita Y, Cheng K, McCarrey JR, Yadu N, Cheeseman IH, Bagwell A, Ross CN, Santana Toro I, Yen LH, Vargas S, Navara CS, Hermann BP, Sasaki K. Efficient generation of marmoset primordial germ cell-like cells using induced pluripotent stem cells. eLife 2023; 12:e82263. [PMID: 36719274 PMCID: PMC9937652 DOI: 10.7554/elife.82263] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 01/31/2023] [Indexed: 02/01/2023] Open
Abstract
Reconstitution of germ cell fate from pluripotent stem cells provides an opportunity to understand the molecular underpinnings of germ cell development. Here, we established robust methods for induced pluripotent stem cell (iPSC) culture in the common marmoset (Callithrix jacchus [cj]), allowing stable propagation in an undifferentiated state. Notably, iPSCs cultured on a feeder layer in the presence of a WNT signaling inhibitor upregulated genes related to ubiquitin-dependent protein catabolic processes and enter a permissive state that enables differentiation into primordial germ cell-like cells (PGCLCs) bearing immunophenotypic and transcriptomic similarities to pre-migratory cjPGCs in vivo. Induction of cjPGCLCs is accompanied by transient upregulation of mesodermal genes, culminating in the establishment of a primate-specific germline transcriptional network. Moreover, cjPGCLCs can be expanded in monolayer while retaining the germline state. Upon co-culture with mouse testicular somatic cells, these cells acquire an early prospermatogonia-like phenotype. Our findings provide a framework for understanding and reconstituting marmoset germ cell development in vitro, thus providing a comparative tool and foundation for a preclinical modeling of human in vitro gametogenesis.
Collapse
Affiliation(s)
- Yasunari Seita
- Department of Biomedical Sciences, University of Pennsylvania, School of Veterinary MedicinePhiladelphiaUnited States
- Institute for Regenerative Medicine, University of PennsylvaniaPhiladelphiaUnited States
- Bell Research Center for Reproductive Health and CancerNagoyaJapan
| | - Keren Cheng
- Department of Biomedical Sciences, University of Pennsylvania, School of Veterinary MedicinePhiladelphiaUnited States
- Institute for Regenerative Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - John R McCarrey
- Department of Neuroscience, Developmental and Regenerative Biology, The University of Texas at San AntonioSan AntonioUnited States
| | - Nomesh Yadu
- Department of Neuroscience, Developmental and Regenerative Biology, The University of Texas at San AntonioSan AntonioUnited States
| | - Ian H Cheeseman
- Texas Biomedical Research InstituteSan AntonioUnited States
- Southwest National Primate Research CenterSan AntonioUnited States
| | - Alec Bagwell
- Texas Biomedical Research InstituteSan AntonioUnited States
- Southwest National Primate Research CenterSan AntonioUnited States
| | - Corinna N Ross
- Texas Biomedical Research InstituteSan AntonioUnited States
- Southwest National Primate Research CenterSan AntonioUnited States
| | - Isamar Santana Toro
- Department of Neuroscience, Developmental and Regenerative Biology, The University of Texas at San AntonioSan AntonioUnited States
| | - Li-hua Yen
- Department of Neuroscience, Developmental and Regenerative Biology, The University of Texas at San AntonioSan AntonioUnited States
| | - Sean Vargas
- Genomics Core, The University of Texas at San AntonioSan AntonioUnited States
| | - Christopher S Navara
- Department of Neuroscience, Developmental and Regenerative Biology, The University of Texas at San AntonioSan AntonioUnited States
| | - Brian P Hermann
- Department of Neuroscience, Developmental and Regenerative Biology, The University of Texas at San AntonioSan AntonioUnited States
- Genomics Core, The University of Texas at San AntonioSan AntonioUnited States
| | - Kotaro Sasaki
- Department of Biomedical Sciences, University of Pennsylvania, School of Veterinary MedicinePhiladelphiaUnited States
- Institute for Regenerative Medicine, University of PennsylvaniaPhiladelphiaUnited States
- Department of Pathology and Laboratory Medicine, University of PennsylvaniaPhiladelphiaUnited States
| |
Collapse
|
22
|
DNA repair protein FANCD2 has both ubiquitination-dependent and ubiquitination-independent functions during germ cell development. J Biol Chem 2023; 299:102905. [PMID: 36642183 PMCID: PMC9971320 DOI: 10.1016/j.jbc.2023.102905] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 12/30/2022] [Accepted: 01/04/2023] [Indexed: 01/14/2023] Open
Abstract
When DNA interstrand crosslink lesions occur, a core complex of Fanconi anemia proteins promotes the ubiquitination of FANCD2 and FANCI, which recruit downstream factors to repair the lesion. However, FANCD2 maintains genome stability not only through its ubiquitination-dependent but also its ubiquitination-independent functions in various DNA damage response pathways. Increasing evidence suggests that FANCD2 is essential for fertility, but its ubiquitination-dependent and ubiquitination-independent roles during germ cell development are not well characterized. In this study, we analyzed germ cell development in Fancd2 KO and ubiquitination-deficient mutant (Fancd2K559R/K559R) mice. We showed that in the embryonic stage, both the ubiquitination-dependent and ubiquitination-independent functions of FANCD2 were required for the expansion of primordial germ cells and establishment of the reproductive reserve by reducing transcription-replication conflicts and thus maintaining genome stability in primordial germ cells. Furthermore, we found that during meiosis in spermatogenesis, FANCD2 promoted chromosome synapsis and regulated crossover formation independently of its ubiquitination, but that both ubiquitinated and nonubiquitinated FANCD2 functioned in programmed double strand break repair. Finally, we revealed that on meiotic XY chromosomes, H3K4me2 accumulation required ubiquitination-independent functionality of FANCD2, while the regulation of H3K9me2 and H3K9me3 depended on FANCD2 ubiquitination. Taken together, our findings suggest that FANCD2 has distinct functions that are both dependent on and independent of its ubiquitination during germ cell development.
Collapse
|
23
|
Wei A, Wu H. Mammalian DNA methylome dynamics: mechanisms, functions and new frontiers. Development 2022; 149:dev182683. [PMID: 36519514 PMCID: PMC10108609 DOI: 10.1242/dev.182683] [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] [Indexed: 12/23/2022]
Abstract
DNA methylation is a highly conserved epigenetic modification that plays essential roles in mammalian gene regulation, genome stability and development. Despite being primarily considered a stable and heritable epigenetic silencing mechanism at heterochromatic and repetitive regions, whole genome methylome analysis reveals that DNA methylation can be highly cell-type specific and dynamic within proximal and distal gene regulatory elements during early embryonic development, stem cell differentiation and reprogramming, and tissue maturation. In this Review, we focus on the mechanisms and functions of regulated DNA methylation and demethylation, highlighting how these dynamics, together with crosstalk between DNA methylation and histone modifications at distinct regulatory regions, contribute to mammalian development and tissue maturation. We also discuss how recent technological advances in single-cell and long-read methylome sequencing, along with targeted epigenome-editing, are enabling unprecedented high-resolution and mechanistic dissection of DNA methylome dynamics.
Collapse
Affiliation(s)
- Alex Wei
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hao Wu
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Institute of Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| |
Collapse
|
24
|
Farini D, De Felici M. The Beginning of Meiosis in Mammalian Female Germ Cells: A Never-Ending Story of Intrinsic and Extrinsic Factors. Int J Mol Sci 2022; 23:ijms232012571. [PMID: 36293427 PMCID: PMC9604137 DOI: 10.3390/ijms232012571] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/06/2022] [Accepted: 10/18/2022] [Indexed: 11/16/2022] Open
Abstract
Meiosis is the unique division of germ cells resulting in the recombination of the maternal and paternal genomes and the production of haploid gametes. In mammals, it begins during the fetal life in females and during puberty in males. In both cases, entering meiosis requires a timely switch from the mitotic to the meiotic cell cycle and the transition from a potential pluripotent status to meiotic differentiation. Revealing the molecular mechanisms underlying these interrelated processes represents the essence in understanding the beginning of meiosis. Meiosis facilitates diversity across individuals and acts as a fundamental driver of evolution. Major differences between sexes and among species complicate the understanding of how meiosis begins. Basic meiotic research is further hindered by a current lack of meiotic cell lines. This has been recently partly overcome with the use of primordial-germ-cell-like cells (PGCLCs) generated from pluripotent stem cells. Much of what we know about this process depends on data from model organisms, namely, the mouse; in mice, the process, however, appears to differ in many aspects from that in humans. Identifying the mechanisms and molecules controlling germ cells to enter meiosis has represented and still represents a major challenge for reproductive medicine. In fact, the proper execution of meiosis is essential for fertility, for maintaining the integrity of the genome, and for ensuring the normal development of the offspring. The main clinical consequences of meiotic defects are infertility and, probably, increased susceptibility to some types of germ-cell tumors. In the present work, we report and discuss data mainly concerning the beginning of meiosis in mammalian female germ cells, referring to such process in males only when pertinent. After a brief account of this process in mice and humans and an historical chronicle of the major hypotheses and progress in this topic, the most recent results are reviewed and discussed.
Collapse
|
25
|
The Mutagenic Consequences of DNA Methylation within and across Generations. EPIGENOMES 2022; 6:epigenomes6040033. [PMID: 36278679 PMCID: PMC9624357 DOI: 10.3390/epigenomes6040033] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/20/2022] [Accepted: 09/28/2022] [Indexed: 12/28/2022] Open
Abstract
DNA methylation is an epigenetic modification with wide-ranging consequences across the life of an organism. This modification can be stable, persisting through development despite changing environmental conditions. However, in other contexts, DNA methylation can also be flexible, underlying organismal phenotypic plasticity. One underappreciated aspect of DNA methylation is that it is a potent mutagen; methylated cytosines mutate at a much faster rate than other genetic motifs. This mutagenic property of DNA methylation has been largely ignored in eco-evolutionary literature, despite its prevalence. Here, we explore how DNA methylation induced by environmental and other factors could promote mutation and lead to evolutionary change at a more rapid rate and in a more directed manner than through stochastic genetic mutations alone. We argue for future research on the evolutionary implications of DNA methylation driven mutations both within the lifetime of organisms, as well as across timescales.
Collapse
|
26
|
Ashapkin V, Suvorov A, Pilsner JR, Krawetz SA, Sergeyev O. Age-associated epigenetic changes in mammalian sperm: implications for offspring health and development. Hum Reprod Update 2022; 29:24-44. [PMID: 36066418 PMCID: PMC9825272 DOI: 10.1093/humupd/dmac033] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 08/05/2022] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Modern reproductive behavior in most developed countries is characterized by delayed parenthood. Older gametes are generally less fertile, accumulating and compounding the effects of varied environmental exposures that are modified by lifestyle factors. Clinicians are primarily concerned with advanced maternal age, while the influence of paternal age on fertility, early development and offspring health remains underappreciated. There is a growing trend to use assisted reproductive technologies for couples of advanced reproductive age. Thus, the number of children born from older gametes is increasing. OBJECTIVE AND RATIONALE We review studies reporting age-associated epigenetic changes in mammals and humans in sperm, including DNA methylation, histone modifications and non-coding RNAs. The interplay between environment, fertility, ART and age-related epigenetic signatures is explored. We focus on the association of sperm epigenetics on epigenetic and phenotype events in embryos and offspring. SEARCH METHODS Peer-reviewed original and review articles over the last two decades were selected using PubMed and the Web of Science for this narrative review. Searches were performed by adopting the two groups of main terms. The first group included 'advanced paternal age', 'paternal age', 'postponed fatherhood', 'late fatherhood', 'old fatherhood' and the second group included 'sperm epigenetics', 'sperm', 'semen', 'epigenetic', 'inheritance', 'DNA methylation', 'chromatin', 'non-coding RNA', 'assisted reproduction', 'epigenetic clock'. OUTCOMES Age is a powerful factor in humans and rodent models associated with increased de novo mutations and a modified sperm epigenome. Age affects all known epigenetic mechanisms, including DNA methylation, histone modifications and profiles of small non-coding (snc)RNA. While DNA methylation is the most investigated, there is a controversy about the direction of age-dependent changes in differentially hypo- or hypermethylated regions with advanced age. Successful development of the human sperm epigenetic clock based on cross-sectional data and four different methods for DNA methylation analysis indicates that at least some CpG exhibit a linear relationship between methylation levels and age. Rodent studies show a significant overlap between genes regulated through age-dependent differentially methylated regions and genes targeted by age-dependent sncRNA. Both age-dependent epigenetic mechanisms target gene networks enriched for embryo developmental, neurodevelopmental, growth and metabolic pathways. Thus, age-dependent changes in the sperm epigenome cannot be described as a stochastic accumulation of random epimutations and may be linked with autism spectrum disorders. Chemical and lifestyle exposures and ART techniques may affect the epigenetic aging of sperm. Although most epigenetic modifications are erased in the early mammalian embryo, there is growing evidence that an altered offspring epigenome and phenotype is linked with advanced paternal age due to the father's sperm accumulating epigenetic changes with time. It has been hypothesized that age-induced changes in the sperm epigenome are profound, physiological and dynamic over years, yet stable over days and months, and likely irreversible. WIDER IMPLICATIONS This review raises a concern about delayed fatherhood and age-associated changes in the sperm epigenome that may compromise reproductive health of fathers and transfer altered epigenetic information to subsequent generations. Prospective studies using healthy males that consider confounders are recommended. We suggest a broader discussion focused on regulation of the father's age in natural and ART conceptions is needed. The professional community should be informed and should raise awareness in the population and when counseling older men.
Collapse
Affiliation(s)
| | | | - J Richard Pilsner
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Stephen A Krawetz
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA,Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
| | - Oleg Sergeyev
- Correspondence address. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskye Gory, House 1, Building 40, Room 322, Moscow 119992, Russia. E-mail: https://orcid.org/0000-0002-5745-3348
| |
Collapse
|
27
|
Transcription-replication conflicts in primordial germ cells necessitate the Fanconi anemia pathway to safeguard genome stability. Proc Natl Acad Sci U S A 2022; 119:e2203208119. [PMID: 35969748 PMCID: PMC9407672 DOI: 10.1073/pnas.2203208119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Germ cells are capable of preserving their genetic information with high fidelity. We report that rapidly dividing mouse primordial germ cells (PGCs) are faced with high levels of endogenous replication stress due to frequent occurrence of transcription–replication conflicts (TRCs). Thus, PGCs have an increased requirement for the replication-coupled Fanconi anemia (FA) pathway to counteract TRC-induced replication stress, enabling their rapid proliferation to establish a sufficient reproductive reserve. This work provides insights into the unique genome feature of developing PGCs and helps to explain the reproductive defects in FA individuals. Preserving a high degree of genome integrity and stability in germ cells is of utmost importance for reproduction and species propagation. However, the regulatory mechanisms of maintaining genome stability in the developing primordial germ cells (PGCs), in which rapid proliferation is coupled with global hypertranscription, remain largely unknown. Here, we find that mouse PGCs encounter a constitutively high frequency of transcription–replication conflicts (TRCs), which lead to R-loop accumulation and impose endogenous replication stress on PGCs. We further demonstrate that the Fanconi anemia (FA) pathway is activated by TRCs and has a central role in the coordination between replication and transcription in the rapidly proliferating PGCs, as disabling the FA pathway leads to TRC and R-loop accumulation, replication fork destabilization, increased DNA damage, dramatic loss of mitotically dividing mouse PGCs, and consequent sterility of both sexes. Overall, our findings uncover the unique source and resolving mechanism of endogenous replication stress during PGC proliferation, provide a biological explanation for reproductive defects in individuals with FA, and improve our understanding of the monitoring strategies for genome stability during germ cell development.
Collapse
|
28
|
Shirane K. The dynamic chromatin landscape and mechanisms of DNA methylation during mouse germ cell development. Gene 2022; 97:3-14. [PMID: 35431282 DOI: 10.1266/ggs.21-00069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Epigenetic marks including DNA methylation (DNAme) play a critical role in the transcriptional regulation of genes and retrotransposons. Defects in DNAme are detected in infertility, imprinting disorders and congenital diseases in humans, highlighting the broad importance of this epigenetic mark in both development and disease. While DNAme in terminally differentiated cells is stably propagated following cell division by the maintenance DNAme machinery, widespread erasure and subsequent de novo establishment of this epigenetic mark occur early in embryonic development as well as in germ cell development. Combined with deep sequencing, low-input methods that have been developed in the past several years have enabled high-resolution and genome-wide mapping of both DNAme and histone post-translational modifications (PTMs) in rare cell populations including developing germ cells. Epigenome studies using these novel methods reveal an unprecedented view of the dynamic chromatin landscape during germ cell development. Furthermore, integrative analysis of chromatin marks in normal germ cells and in those deficient in chromatin-modifying enzymes uncovers a critical interplay between histone PTMs and de novo DNAme in the germline. This review discusses work on mechanisms of the erasure and subsequent de novo DNAme in mouse germ cells as well as the outstanding questions relating to the regulation of the dynamic chromatin landscape in germ cells.
Collapse
Affiliation(s)
- Kenjiro Shirane
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University
| |
Collapse
|
29
|
L M, C H, V V, J L, M M, E Q, T C, M DN, F M. A plant-based diet differentially affects the global hepatic methylome in rainbow trout depending on genetic background. Epigenetics 2022; 17:1726-1737. [PMID: 35345978 PMCID: PMC9621033 DOI: 10.1080/15592294.2022.2058226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Replacing fish meal and oil in trout diets with plant-derived ingredients is a contemporary challenge to move towards more sustainable aquaculture practices. However, such dietary replacement causes hepatic metabolic changes that have not yet been elucidated. Here, we aimed to decipher the effect of a 100% plant-based diet on the hepatic global DNA methylation landscape in trout and assess whether changes depend on fish genetic background. We analysed the global methylome and the expression of DNA (de)methylation-related genes of three isogenic lines that exhibit similar growth when fed a marine resource-based diet (M diet), but differ in their responses to a plant-based diet (V diet). Our results revealed that the V diet induced a decrease in 5-cytosine combined with an increase in 5-hydroxymethylcytosine in two of the three analysed lines. For one of these 2 affected lines, when fed the M diet but at the same feed intake of the V diet (MR), no methylome differences were highlighted between M and MR or between MR and V-fed trout whereas for the other affected line, M fed trout displayed a divergent methylome profile from MR and V fed fish. DNA (de)methylation-related genes were also affected by the V or MR diets. Our findings showed that the global hepatic methylome of trout is affected by a V diet, depending on genetic background. This latter effect seems to be due to either a decreased feed intake alone or combined with the effect of the dietary composition per se.
Collapse
Affiliation(s)
- Marandel L
- INRAE, Univ Pau & Pays Adour, E2S UPPA, UMR 1419, Nutrition, Métabolisme, Aquaculture, Saint Pée sur Nivelle, France
| | - Heraud C
- INRAE, Univ Pau & Pays Adour, E2S UPPA, UMR 1419, Nutrition, Métabolisme, Aquaculture, Saint Pée sur Nivelle, France
| | - Véron V
- INRAE, Univ Pau & Pays Adour, E2S UPPA, UMR 1419, Nutrition, Métabolisme, Aquaculture, Saint Pée sur Nivelle, France
| | - Laithier J
- INRAE, Univ Pau & Pays Adour, E2S UPPA, UMR 1419, Nutrition, Métabolisme, Aquaculture, Saint Pée sur Nivelle, France
| | - Marchand M
- INRAE, Univ Pau & Pays Adour, E2S UPPA, UMR 1419, Nutrition, Métabolisme, Aquaculture, Saint Pée sur Nivelle, France
| | - Quillet E
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Callet T
- INRAE, Univ Pau & Pays Adour, E2S UPPA, UMR 1419, Nutrition, Métabolisme, Aquaculture, Saint Pée sur Nivelle, France
| | - Dupont-Nivet M
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Médale F
- INRAE, Univ Pau & Pays Adour, E2S UPPA, UMR 1419, Nutrition, Métabolisme, Aquaculture, Saint Pée sur Nivelle, France
| |
Collapse
|
30
|
Spiller C, Bowles J. Instructing Mouse Germ Cells to Adopt a Female Fate. Sex Dev 2022:1-13. [PMID: 35320803 DOI: 10.1159/000523763] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 02/20/2022] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Germ cells are critical for the survival of our species. They are the only cells that undergo meiosis - the reductive form of cell division that is necessary for genetic reassortment of chromosomes and production of the haploid gametes, the sperm and eggs. Remarkably, the initial female/male fate decision in fetal germ cells does not depend on whether they are chromosomally XX or XY; rather, initial sexual fate is imposed by influences from the surrounding tissue. In mammals, the female germline is particularly precious: despite recent suggestions that germline stem cells exist in the ovary, it is still generally accepted that the ovarian reserve is finite, and its size is dependant on germ cells of the fetal ovary initiating meiosis in a timely manner. SUMMARY Prior to 2006, evidence suggested that gonadal germ cells initiate meiotic prophase I by default, but more recent data support a key role for the signalling molecule retinoic acid (RA) in instructing female germ cell fate. Newer findings also support a key meiosis-inducing role for another signalling molecule, bone morphogenic protein (BMP). Nonetheless, many questions remain. KEY MESSAGES Here, we review knowledge thus far regarding extrinsic and intrinsic determinants of a female germ cell fate, focusing on the mouse model.
Collapse
Affiliation(s)
- Cassy Spiller
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Josephine Bowles
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia
| |
Collapse
|
31
|
Aigner GP, Pittl V, Fiechtner B, Egger B, Šrut M, Höckner M. Common mechanisms cannot explain time- and dose-dependent DNA methylation changes in earthworms exposed to cadmium. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 812:151468. [PMID: 34742794 DOI: 10.1016/j.scitotenv.2021.151468] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/28/2021] [Accepted: 11/02/2021] [Indexed: 06/13/2023]
Abstract
DNA hypermethylation caused by environmental pollutants like cadmium (Cd) has already been demonstrated in many invertebrates, including earthworms. However, the exact epigenetic mechanisms that drive this hypermethylation are largely unknown and even basic DNA methylation and demethylation processes are hardly characterized. Therefore, we used an important bioindicator, the earthworm Lumbricus terrestris, as a model organism to determine time- and dose-dependent effects of Cd on global and gene-specific DNA methylation and its underlying mechanisms. We revealed Cd-induced adenine and cytosine hypermethylation using specific antibodies in dot blots and found that the methylation level of adenine compared to cytosine changed even to a bigger extent. However, the levels of hydroxymethylated cytosine did not differ between treatment groups. General methylation and demethylation components like methyltransferases (DNMT1 and 3), and ten-eleven translocation (TET) genes were confirmed in L. terrestris by quantitative RealTime PCR. However, neither gene expression, nor DNMT and TET enzyme activity showed significant differences in the Cd exposure groups. Using bisulfite conversion and sequencing, gene body methylation (gbm) of metallothionein 2 (MT2), one of the most important detoxification proteins, was characterized. Cd-dependent changes in MT2 gbm could, however, not be correlated to MT2 gene activity evaluated by quantitative RealTime PCR. Future directions as well as missing links are discussed in the present study hinting towards the importance of studying epigenetic marks and mechanistic insights in a broad variety of species to deepen our knowledge on the effects of changing environmental conditions.
Collapse
Affiliation(s)
- Gerhard P Aigner
- University of Innsbruck, Institute of Zoology, Center for Molecular Biosciences Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Verena Pittl
- University of Innsbruck, Institute of Zoology, Center for Molecular Biosciences Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Birgit Fiechtner
- University of Innsbruck, Institute of Zoology, Center for Molecular Biosciences Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Bernhard Egger
- University of Innsbruck, Institute of Zoology, Center for Molecular Biosciences Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Maja Šrut
- University of Innsbruck, Institute of Zoology, Center for Molecular Biosciences Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Martina Höckner
- University of Innsbruck, Institute of Zoology, Center for Molecular Biosciences Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria.
| |
Collapse
|
32
|
Kaneko-Ishino T, Ishino F. The Evolutionary Advantage in Mammals of the Complementary Monoallelic Expression Mechanism of Genomic Imprinting and Its Emergence From a Defense Against the Insertion Into the Host Genome. Front Genet 2022; 13:832983. [PMID: 35309133 PMCID: PMC8928582 DOI: 10.3389/fgene.2022.832983] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 02/11/2022] [Indexed: 12/30/2022] Open
Abstract
In viviparous mammals, genomic imprinting regulates parent-of-origin-specific monoallelic expression of paternally and maternally expressed imprinted genes (PEGs and MEGs) in a region-specific manner. It plays an essential role in mammalian development: aberrant imprinting regulation causes a variety of developmental defects, including fetal, neonatal, and postnatal lethality as well as growth abnormalities. Mechanistically, PEGs and MEGs are reciprocally regulated by DNA methylation of germ-line differentially methylated regions (gDMRs), thereby exhibiting eliciting complementary expression from parental genomes. The fact that most gDMR sequences are derived from insertion events provides strong support for the claim that genomic imprinting emerged as a host defense mechanism against the insertion in the genome. Recent studies on the molecular mechanisms concerning how the DNA methylation marks on the gDMRs are established in gametes and maintained in the pre- and postimplantation periods have further revealed the close relationship between genomic imprinting and invading DNA, such as retroviruses and LTR retrotransposons. In the presence of gDMRs, the monoallelic expression of PEGs and MEGs confers an apparent advantage by the functional compensation that takes place between the two parental genomes. Thus, it is likely that genomic imprinting is a consequence of an evolutionary trade-off for improved survival. In addition, novel genes were introduced into the mammalian genome via this same surprising and complex process as imprinted genes, such as the genes acquired from retroviruses as well as those that were duplicated by retropositioning. Importantly, these genes play essential/important roles in the current eutherian developmental system, such as that in the placenta and/or brain. Thus, genomic imprinting has played a critically important role in the evolutionary emergence of mammals, not only by providing a means to escape from the adverse effects of invading DNA with sequences corresponding to the gDMRs, but also by the acquisition of novel functions in development, growth and behavior via the mechanism of complementary monoallelic expression.
Collapse
Affiliation(s)
- Tomoko Kaneko-Ishino
- School of Medicine, Tokai University, Isehara, Japan
- *Correspondence: Tomoko Kaneko-Ishino, ; Fumitoshi Ishino,
| | - Fumitoshi Ishino
- Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
- *Correspondence: Tomoko Kaneko-Ishino, ; Fumitoshi Ishino,
| |
Collapse
|
33
|
Zhou S, Sakashita A, Yuan S, Namekawa SH. Retrotransposons in the Mammalian Male Germline. Sex Dev 2022:1-19. [PMID: 35231923 DOI: 10.1159/000520683] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 10/25/2021] [Indexed: 11/19/2022] Open
Abstract
Retrotransposons are a subset of DNA sequences that constitute a large part of the mammalian genome. They can translocate autonomously or non-autonomously, potentially jeopardizing the heritable germline genome. Retrotransposons coevolved with the host genome, and the germline is the prominent battlefield between retrotransposons and the host genome to maximize their mutual fitness. Host genomes have developed various mechanisms to suppress and control retrotransposons, including DNA methylation, histone modifications, and Piwi-interacting RNA (piRNA), for their own benefit. Thus, rapidly evolved retrotransposons often acquire positive functions, including gene regulation within the germline, conferring reproductive fitness in a species over the course of evolution. The male germline serves as an ideal model to examine the regulation and evolution of retrotransposons, resulting in genomic co-evolution with the host genome. In this review, we summarize and discuss the regulatory mechanisms of retrotransposons, stage-by-stage, during male germ cell development, with a particular focus on mice as an extensively studied mammalian model, highlighting suppression mechanisms and emerging functions of retrotransposons in the male germline.
Collapse
Affiliation(s)
- Shumin Zhou
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Akihiko Sakashita
- Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan
| | - Shuiqiao Yuan
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, China
| | - Satoshi H Namekawa
- Department of Microbiology and Molecular Genetics, University of California, Davis, California, USA
| |
Collapse
|
34
|
Aigner GP, Nenning P, Fiechtner B, Šrut M, Höckner M. DNA Methylation and Detoxification in the Earthworm Lumbricus terrestris Exposed to Cadmium and the DNA Demethylation Agent 5-aza-2'-deoxycytidine. TOXICS 2022; 10:100. [PMID: 35202286 PMCID: PMC8879108 DOI: 10.3390/toxics10020100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/14/2022] [Accepted: 02/18/2022] [Indexed: 01/27/2023]
Abstract
Earthworms are well-established model organisms for testing the effects of heavy metal pollution. How DNA methylation affects cadmium (Cd) detoxification processes such as the expression of metallothionein 2 (MT2), however, is largely unknown. We therefore exposed Lumbricus terrestris to 200 mg concentrations of Cd and 5-aza-2'-deoxycytidine (Aza), a demethylating agent, and sampled tissue and coelomocytes, cells of the innate immune system, for 48 h. MT2 transcription significantly increased in the Cd- and Cd-Aza-treated groups. In tissue samples, a significant decrease in MT2 in the Aza-treated group was detected, showing that Aza treatment inhibits basal MT2 gene activity but has no effect on Cd-induced MT2 levels. Although Cd repressed the gene expression of DNA-(cytosine-5)-methyltransferase-1 (DNMT1), which is responsible for maintaining DNA methylation, DNMT activity was unchanged, meaning that methylation maintenance was not affected in coelomocytes. The treatment did not influence DNMT3, which mediates de novo methylation, TET gene expression, which orchestrates demethylation, and global levels of hydroxymethylcytosine (5hmC), a product of the demethylation process. Taken together, this study indicates that Aza inhibits basal gene activity, in contrast to Cd-induced MT2 gene expression, but does not affect global DNA methylation. We therefore conclude that Cd detoxification based on the induction of MT2 does not relate to DNA methylation changes.
Collapse
Affiliation(s)
| | | | | | | | - Martina Höckner
- Department of Zoology, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria; (G.P.A.); (P.N.); (B.F.); (M.Š.)
| |
Collapse
|
35
|
Ben Maamar M, Beck D, Nilsson E, McCarrey JR, Skinner MK. Developmental alterations in DNA methylation during gametogenesis from primordial germ cells to sperm. iScience 2022; 25:103786. [PMID: 35146397 PMCID: PMC8819394 DOI: 10.1016/j.isci.2022.103786] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 12/21/2021] [Accepted: 01/14/2022] [Indexed: 02/08/2023] Open
Abstract
Because epigenetics is a critical component for gene expression, the hypothesis was tested that DNA methylation alterations are dynamic and continually change throughout gametogenesis to generate the mature sperm. Developmental alterations and stage-specific DNA methylation during gametogenesis from primordial germ cells (PGCs) to mature sperm are investigated. Individual developmental stage germ cells were isolated and analyzed for differential DNA methylation regions (DMRs). The number of DMRs was highest in the first three comparisons with mature PGCs, prospermatogonia, and spermatogonia. The most statistically significant DMRs were present at all stages of development and had variations involving both increases or decreases in DNA methylation. DMR-associated genes were identified and correlated with gene functional categories, pathways, and cellular processes. Observations identified a dynamic cascade of epigenetic changes during development that is dramatic during the early developmental stages. Complex epigenetic alterations are required to regulate genome biology and gene expression during gametogenesis. A dynamic cascade of epigenetic change throughout gametogenesis from PGC to sperm Most dramatic epigenetic alterations in PGC and spermatogenic stem cell stages Different DNA methylation regions between and within stages were identified Complex epigenetic alterations required for gene expression during gametogenesis
Collapse
Affiliation(s)
- Millissia Ben Maamar
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - Daniel Beck
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - Eric Nilsson
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - John R McCarrey
- Department of Biology, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Michael K Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| |
Collapse
|
36
|
Varela RB, Cararo JH, Tye SJ, Carvalho AF, Valvassori SS, Fries GR, Quevedo J. Contributions of epigenetic inheritance to the predisposition of major psychiatric disorders: theoretical framework, evidence, and implications. Neurosci Biobehav Rev 2022; 135:104579. [DOI: 10.1016/j.neubiorev.2022.104579] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 01/10/2022] [Accepted: 02/11/2022] [Indexed: 02/08/2023]
|
37
|
Liu J, Heraud C, Véron V, Laithier J, Burel C, Prézelin A, Panserat S, Marandel L. Hepatic Global DNA Hypomethylation Phenotype in Rainbow Trout Fed Diets Varying in Carbohydrate to Protein Ratio. J Nutr 2022; 152:29-39. [PMID: 34550380 DOI: 10.1093/jn/nxab343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 08/30/2021] [Accepted: 09/17/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND A high carbohydrate-low protein diet can induce hepatic global DNA hypomethylation in trout. The mechanisms remain unclear. OBJECTIVES We aimed to investigate whether an increase in dietary carbohydrates (dHCs) or a decrease in dietary proteins (dLPs) can cause hepatic global DNA hypomethylation, as well as explore the underlying mechanisms in trout. METHODS Two feeding trials were conducted on juvenile males, both of which involved a 4-d fasting and 4-d refeeding protocol. In trial 1, trout were fed either a high protein-no carbohydrate [HP-NC, protein 60% dry matter (DM), carbohydrates 0% DM] or a moderate protein-high carbohydrate (MP-HC, protein 40% DM, carbohydrates 30% DM) diet. In trial 2, fish were fed either a moderate protein-no carbohydrate (MP-NC, protein 40% DM, carbohydrates 0% DM), an MP-HC (protein 40% DM, carbohydrates 30% DM), or a low protein-no carbohydrate (LP-NC, protein 20% DM, carbohydrates 0% DM) diet to separate the effects of dHCs and dLPs on the hepatic methylome. Global CmCGG methylation, DNA demethylation derivative concentrations, and mRNA expression of DNA (de)methylation-related genes were measured. Differences were tested by 1-factor ANOVA when data were normally distributed or by Kruskal-Wallis nonparametric test if not. RESULTS In both trials, global CmCGG methylation concentrations remained unaffected, but the hepatic 5-mdC content decreased after refeeding (1-3%). The MP-HC group had 3.4-fold higher hepatic 5-hmdC and a similar 5-mdC concentration compared with the HP-NC group in trial 1. Both MP-HC and LP-NC diets lowered the hepatic 5-mdC content (1-2%), but only the LP-NC group had a significantly lower 5-hmdC concentration (P < 0.01) compared with MP-NC group in trial 2. CONCLUSIONS dHC and dLP independently induced hepatic global DNA demethylation in trout. The alterations in other methylation derivative concentrations indicated the demethylation process was achieved through an active demethylation pathway and probably occurred at non-CmCGG sites.
Collapse
Affiliation(s)
- Jingwei Liu
- INRAE, Univ Pau & Pays de l'Adour, E2S UPPA, UMR1419 Nutrition Metabolism and Aquaculture, Aquapôle, Saint-Pée-sur-Nivelle, France
| | - Cécile Heraud
- INRAE, Univ Pau & Pays de l'Adour, E2S UPPA, UMR1419 Nutrition Metabolism and Aquaculture, Aquapôle, Saint-Pée-sur-Nivelle, France
| | - Vincent Véron
- INRAE, Univ Pau & Pays de l'Adour, E2S UPPA, UMR1419 Nutrition Metabolism and Aquaculture, Aquapôle, Saint-Pée-sur-Nivelle, France
| | - Jésabel Laithier
- INRAE, Univ Pau & Pays de l'Adour, E2S UPPA, UMR1419 Nutrition Metabolism and Aquaculture, Aquapôle, Saint-Pée-sur-Nivelle, France
| | - Christine Burel
- INRAE, Univ Pau & Pays de l'Adour, E2S UPPA, UMR1419 Nutrition Metabolism and Aquaculture, Aquapôle, Saint-Pée-sur-Nivelle, France
| | - Audrey Prézelin
- Université Paris Saclay, UVSQ, INRAE, BREED, Jouy en Josas, France.,Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort, France
| | - Stéphane Panserat
- INRAE, Univ Pau & Pays de l'Adour, E2S UPPA, UMR1419 Nutrition Metabolism and Aquaculture, Aquapôle, Saint-Pée-sur-Nivelle, France
| | - Lucie Marandel
- INRAE, Univ Pau & Pays de l'Adour, E2S UPPA, UMR1419 Nutrition Metabolism and Aquaculture, Aquapôle, Saint-Pée-sur-Nivelle, France
| |
Collapse
|
38
|
Genetic Studies on Mammalian DNA Methyltransferases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:111-136. [PMID: 36350508 PMCID: PMC9815518 DOI: 10.1007/978-3-031-11454-0_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Cytosine methylation at the C5-position-generating 5-methylcytosine (5mC)-is a DNA modification found in many eukaryotic organisms, including fungi, plants, invertebrates, and vertebrates, albeit its levels vary greatly in different organisms. In mammals, cytosine methylation occurs predominantly in the context of CpG dinucleotides, with the majority (60-80%) of CpG sites in their genomes being methylated. DNA methylation plays crucial roles in the regulation of chromatin structure and gene expression and is essential for mammalian development. Aberrant changes in DNA methylation and genetic alterations in enzymes and regulators involved in DNA methylation are associated with various human diseases, including cancer and developmental disorders. In mammals, DNA methylation is mediated by two families of DNA methyltransferases (Dnmts), namely Dnmt1 and Dnmt3 proteins. Over the last three decades, genetic manipulations of these enzymes, as well as their regulators, in mice have greatly contributed to our understanding of the biological functions of DNA methylation in mammals. In this chapter, we discuss genetic studies on mammalian Dnmts, focusing on their roles in embryogenesis, cellular differentiation, genomic imprinting, and human diseases.
Collapse
|
39
|
UNOKI M, SASAKI H. The UHRF protein family in epigenetics, development, and carcinogenesis. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2022; 98:401-415. [PMID: 36216533 PMCID: PMC9614205 DOI: 10.2183/pjab.98.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 06/14/2022] [Indexed: 05/31/2023]
Abstract
The UHRF protein family consists of multidomain regulatory proteins that sense modification status of DNA and/or proteins and catalyze the ubiquitylation of target proteins. Through their functional domains, they interact with other molecules and serve as a hub for regulatory networks of several important biological processes, including maintenance of DNA methylation and DNA damage repair. The UHRF family is conserved in vertebrates and plants but is missing from fungi and many nonvertebrate animals. Mammals commonly have UHRF1 and UHRF2, but, despite their high structural similarity, the two paralogues appear to have distinct functions. Furthermore, UHRF1 and UHRF2 show different expression patterns and different outcomes in gene knockout experiments. In this review, we summarize the current knowledge on the molecular function of the UHRF family in various biological pathways and discuss their roles in epigenetics, development, gametogenesis, and carcinogenesis, with a focus on the mammalian UHRF proteins.
Collapse
Affiliation(s)
- Motoko UNOKI
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- Department of Human Genetics, School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki SASAKI
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| |
Collapse
|
40
|
Generation of developmentally competent oocytes and fertile mice from parthenogenetic embryonic stem cells. Protein Cell 2021; 12:947-964. [PMID: 34845589 PMCID: PMC8674391 DOI: 10.1007/s13238-021-00865-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 06/20/2021] [Indexed: 12/11/2022] Open
Abstract
Parthenogenetic embryos, created by activation and diploidization of oocytes, arrest at mid-gestation for defective paternal imprints, which impair placental development. Also, viable offspring has not been obtained without genetic manipulation from parthenogenetic embryonic stem cells (pESCs) derived from parthenogenetic embryos, presumably attributable to their aberrant imprinting. We show that an unlimited number of oocytes can be derived from pESCs and produce healthy offspring. Moreover, normal expression of imprinted genes is found in the germ cells and the mice. pESCs exhibited imprinting consistent with exclusively maternal lineage, and higher X-chromosome activation compared to female ESCs derived from the same mouse genetic background. pESCs differentiated into primordial germ cell-like cells (PGCLCs) and formed oocytes following in vivo transplantation into kidney capsule that produced fertile pups and reconstituted ovarian endocrine function. The transcriptome and methylation of imprinted and X-linked genes in pESC-PGCLCs closely resembled those of in vivo produced PGCs, consistent with efficient reprogramming of methylation and genomic imprinting. These results demonstrate that amplification of germ cells through parthenogenesis faithfully maintains maternal imprinting, offering a promising route for deriving functional oocytes and having potential in rebuilding ovarian endocrine function.
Collapse
|
41
|
Ramakrishna NB, Murison K, Miska EA, Leitch HG. Epigenetic Regulation during Primordial Germ Cell Development and Differentiation. Sex Dev 2021; 15:411-431. [PMID: 34847550 DOI: 10.1159/000520412] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/10/2021] [Indexed: 11/19/2022] Open
Abstract
Germline development varies significantly across metazoans. However, mammalian primordial germ cell (PGC) development has key conserved landmarks, including a critical period of epigenetic reprogramming that precedes sex-specific differentiation and gametogenesis. Epigenetic alterations in the germline are of unique importance due to their potential to impact the next generation. Therefore, regulation of, and by, the non-coding genome is of utmost importance during these epigenomic events. Here, we detail the key chromatin changes that occur during mammalian PGC development and how these interact with the expression of non-coding RNAs alongside broader epitranscriptomic changes. We identify gaps in our current knowledge, in particular regarding epigenetic regulation in the human germline, and we highlight important areas of future research.
Collapse
Affiliation(s)
- Navin B Ramakrishna
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Genome Institute of Singapore, A*STAR, Biopolis, Singapore, Singapore
| | - Keir Murison
- MRC London Institute of Medical Sciences, London, United Kingdom
- Institute of Clinical Sciences, Imperial College London, London, United Kingdom
| | - Eric A Miska
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - Harry G Leitch
- MRC London Institute of Medical Sciences, London, United Kingdom
- Institute of Clinical Sciences, Imperial College London, London, United Kingdom
- Centre for Paediatrics and Child Health, Faculty of Medicine, Imperial College London, London, United Kingdom
| |
Collapse
|
42
|
Bend family proteins mark chromatin boundaries and synergistically promote early germ cell differentiation. Protein Cell 2021; 13:721-741. [PMID: 34731408 PMCID: PMC9233729 DOI: 10.1007/s13238-021-00884-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 09/19/2021] [Indexed: 12/30/2022] Open
Abstract
Understanding the regulatory networks for germ cell fate specification is necessary to developing strategies for improving the efficiency of germ cell production in vitro. In this study, we developed a coupled screening strategy that took advantage of an arrayed bi-molecular fluorescence complementation (BiFC) platform for protein-protein interaction screens and epiblast-like cell (EpiLC)-induction assays using reporter mouse embryonic stem cells (mESCs). Investigation of candidate interaction partners of core human pluripotent factors OCT4, NANOG, KLF4 and SOX2 in EpiLC differentiation assays identified novel primordial germ cell (PGC)-inducing factors including BEN-domain (BEND/Bend) family members. Through RNA-seq, ChIP-seq, and ATAC-seq analyses, we showed that Bend5 worked together with Bend4 and helped mark chromatin boundaries to promote EpiLC induction in vitro. Our findings suggest that BEND/Bend proteins represent a new family of transcriptional modulators and chromatin boundary factors that participate in gene expression regulation during early germline development.
Collapse
|
43
|
Abstract
[Figure: see text].
Collapse
Affiliation(s)
- Mitinori Saitou
- Institute for the Advanced Study of Human Biology (WPI-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
| | - Katsuhiko Hayashi
- Department of Developmental Stem Cell Biology, Faculty of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan.,Department of Germline Genetics, Graduate School of Medicine, Osaka University, 2-2 Yamada-oka, Suita, Osaka 565-0871, Japan
| |
Collapse
|
44
|
Newkirk SJ, An W. UHRF1: a jack of all trades, and a master epigenetic regulator during spermatogenesis. Biol Reprod 2021; 102:1147-1152. [PMID: 32101289 DOI: 10.1093/biolre/ioaa026] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 02/26/2020] [Indexed: 01/03/2023] Open
Affiliation(s)
- Simon J Newkirk
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD, USA
| | - Wenfeng An
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD, USA
| |
Collapse
|
45
|
Ben Maamar M, Nilsson EE, Skinner MK. Epigenetic transgenerational inheritance, gametogenesis and germline development†. Biol Reprod 2021; 105:570-592. [PMID: 33929020 PMCID: PMC8444706 DOI: 10.1093/biolre/ioab085] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/12/2021] [Accepted: 04/22/2021] [Indexed: 12/14/2022] Open
Abstract
One of the most important developing cell types in any biological system is the gamete (sperm and egg). The transmission of phenotypes and optimally adapted physiology to subsequent generations is in large part controlled by gametogenesis. In contrast to genetics, the environment actively regulates epigenetics to impact the physiology and phenotype of cellular and biological systems. The integration of epigenetics and genetics is critical for all developmental biology systems at the cellular and organism level. The current review is focused on the role of epigenetics during gametogenesis for both the spermatogenesis system in the male and oogenesis system in the female. The developmental stages from the initial primordial germ cell through gametogenesis to the mature sperm and egg are presented. How environmental factors can influence the epigenetics of gametogenesis to impact the epigenetic transgenerational inheritance of phenotypic and physiological change in subsequent generations is reviewed.
Collapse
Affiliation(s)
- Millissia Ben Maamar
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Eric E Nilsson
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Michael K Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, USA
| |
Collapse
|
46
|
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: 75] [Impact Index Per Article: 25.0] [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.
Collapse
|
47
|
Nishiyama A, Nakanishi M. Navigating the DNA methylation landscape of cancer. Trends Genet 2021; 37:1012-1027. [PMID: 34120771 DOI: 10.1016/j.tig.2021.05.002] [Citation(s) in RCA: 307] [Impact Index Per Article: 102.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 05/06/2021] [Accepted: 05/11/2021] [Indexed: 12/11/2022]
Abstract
DNA methylation is a chemical modification that defines cell type and lineage through the control of gene expression and genome stability. Disruption of DNA methylation control mechanisms causes a variety of diseases, including cancer. Cancer cells are characterized by aberrant DNA methylation (i.e., genome-wide hypomethylation and site-specific hypermethylation), mainly targeting CpG islands in gene expression regulatory elements. In particular, the early findings that a variety of tumor suppressor genes (TSGs) are targets of DNA hypermethylation in cancer led to the proposal of a model in which aberrant DNA methylation promotes cellular oncogenesis through TSGs silencing. However, recent genome-wide analyses have revealed that this classical model needs to be reconsidered. In this review, we will discuss the molecular mechanisms of DNA methylation abnormalities in cancer as well as their therapeutic potential.
Collapse
Affiliation(s)
- Atsuya Nishiyama
- Division of Cancer Cell Biology, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.
| | - Makoto Nakanishi
- Division of Cancer Cell Biology, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.
| |
Collapse
|
48
|
Making it or breaking it: DNA methylation and genome integrity. Essays Biochem 2021; 64:687-703. [PMID: 32808652 DOI: 10.1042/ebc20200009] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/22/2020] [Accepted: 07/29/2020] [Indexed: 12/11/2022]
Abstract
Cells encounter a multitude of external and internal stress-causing agents that can ultimately lead to DNA damage, mutations and disease. A cascade of signaling events counters these challenges to DNA, which is termed as the DNA damage response (DDR). The DDR preserves genome integrity by engaging appropriate repair pathways, while also coordinating cell cycle and/or apoptotic responses. Although many of the protein components in the DDR are identified, how chemical modifications to DNA impact the DDR is poorly understood. This review focuses on our current understanding of DNA methylation in maintaining genome integrity in mammalian cells. DNA methylation is a reversible epigenetic mark, which has been implicated in DNA damage signaling, repair and replication. Sites of DNA methylation can trigger mutations, which are drivers of human diseases including cancer. Indeed, alterations in DNA methylation are associated with increased susceptibility to tumorigenesis but whether this occurs through effects on the DDR, transcriptional responses or both is not entirely clear. Here, we also highlight epigenetic drugs currently in use as therapeutics that target DNA methylation pathways and discuss their effects in the context of the DDR. Finally, we pose unanswered questions regarding the interplay between DNA methylation, transcription and the DDR, positing the potential coordinated efforts of these pathways in genome integrity. While the impact of DNA methylation on gene regulation is widely understood, how this modification contributes to genome instability and mutations, either directly or indirectly, and the potential therapeutic opportunities in targeting DNA methylation pathways in cancer remain active areas of investigation.
Collapse
|
49
|
Alberio R, Kobayashi T, Surani MA. Conserved features of non-primate bilaminar disc embryos and the germline. Stem Cell Reports 2021; 16:1078-1092. [PMID: 33979595 PMCID: PMC8185373 DOI: 10.1016/j.stemcr.2021.03.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 03/11/2021] [Accepted: 03/12/2021] [Indexed: 12/12/2022] Open
Abstract
Post-implantation embryo development commences with a bilaminar disc in most mammals, including humans. Whereas access to early human embryos is limited and subject to greater ethical scrutiny, studies on non-primate embryos developing as bilaminar discs offer exceptional opportunities for advances in gastrulation, the germline, and the basis for evolutionary divergence applicable to human development. Here, we discuss the advantages of investigations in the pig embryo as an exemplar of development of a bilaminar disc embryo with relevance to early human development. Besides, the pig has the potential for the creation of humanized organs for xenotransplantation. Precise genetic engineering approaches, imaging, and single-cell analysis are cost effective and efficient, enabling research into some outstanding questions on human development and for developing authentic models of early human development with stem cells.
Collapse
Affiliation(s)
- Ramiro Alberio
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK.
| | - Toshihiro Kobayashi
- Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, Okazaki, Aichi 444-8787, Japan; The Graduate University of Advanced Studies, Okazaki, Aichi 444-8787, Japan
| | - M Azim Surani
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK; Wellcome Trust/Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK.
| |
Collapse
|
50
|
Vaginal Aging-What We Know and What We Do Not Know. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18094935. [PMID: 34066357 PMCID: PMC8125346 DOI: 10.3390/ijerph18094935] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/02/2021] [Accepted: 05/04/2021] [Indexed: 12/20/2022]
Abstract
The aging of the organism is a complex and multifactorial process. It can be viewed in the context of the whole organism, but also of individual tissues and organs. The problem of vaginal aging and the related genitourinary syndrome of menopause significantly reduces the quality of women’s lives. The aging process of the vagina includes estrogen deficiencies, changes in the microbiome, and changes at the genetic level associated with DNA methylation. During the menopause, the number of Lactobacillus colonies decreases, and the number of pathological bacteria colonies increases. The decrease in estrogen levels results in a decrease in vaginal epithelial permeability, perfusion, and elastin levels, resulting in vaginal dryness and atrophy. Changes at the molecular level are the least clear. It can also be assumed that, similarly to the tissues studied so far, there are changes in cytosine methylation and TET (ten-eleven translocation) expression. The interrelationships between DNA methylation, hormonal changes, and the vaginal microbiome have not yet been fully elucidated.
Collapse
|