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Zhang W, Chen X, Wang Z, Wang Q, Feng J, Wang D, Wang Z, Tang J, Qing S, Zhang Y. Identification of HIST1H2BH as the hub gene associated with multiple myeloma using integrated bioinformatics analysis. Hematology 2024; 29:2335421. [PMID: 38568025 DOI: 10.1080/16078454.2024.2335421] [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: 11/14/2023] [Accepted: 03/21/2024] [Indexed: 04/05/2024] Open
Abstract
OBJECTIVES Identifying the specific biomarkers and molecular signatures of MM might provide novel evidence for MM prognosis and targeted therapy. METHODS Bioinformatic analyses were performed through GEO and TCGA datasets. The differential expression of HIST1H2BH in MM sample was validated by the qRT-PCR. And the CCK-8 assay was performed to detect the proliferation activity of HIST1H2BH on MM cell lines. RESULTS A total of 793 DEGs were identified between bone marrow plasma cells from newly diagnosed myeloma and normal donors in GSE6477. Among them, four vital genes (HIST1H2AC, HIST1H2BH, CCND1 and TCF7L2) modeling were constructed. The increased HIST1H2BH expression was correlated with worse survival of MM based on TCGA datasets. The transcriptional expression of HIST1H2BH was significantly up-regulated in primary MM patients. And knockdown HIST1H2BH decreased the proliferation of MM cell lines. CONCLUSIONS We have identified up-regulated HIST1H2BH in MM patients associated with poor prognosis using integrated bioinformatical methods.
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Affiliation(s)
- Wenxue Zhang
- Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao, People's Republic of China
| | - Xian Chen
- Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao, People's Republic of China
| | - Zhe Wang
- Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao, People's Republic of China
| | - Qing Wang
- Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao, People's Republic of China
| | - Jiao Feng
- Department of Pathology, The Affiliated Hospital of Qingdao University, Qingdao, People's Republic of China
| | - Dexin Wang
- Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao, People's Republic of China
- Department of Clinical Laboratory, Municipal Hospital of Zibo, Zibo, People's Republic of China
| | - Zhichao Wang
- Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao, People's Republic of China
| | - Jiaxin Tang
- Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao, People's Republic of China
| | - Shiyu Qing
- Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao, People's Republic of China
| | - Yunyuan Zhang
- Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao, People's Republic of China
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2
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Liu X, Li J, Zhu L, Huang J, Zhang Q, Wang J, Xie J, Dong Q, Zou Z, Huang G, Gu Q, Wang J, Li J. Mechanistic insights into zinc oxide nanoparticles induced embryotoxicity via H3K9me3 modulation. Biomaterials 2024; 311:122679. [PMID: 38943823 DOI: 10.1016/j.biomaterials.2024.122679] [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: 02/08/2024] [Revised: 06/05/2024] [Accepted: 06/23/2024] [Indexed: 07/01/2024]
Abstract
The widespread application of nanoparticles (NPs) in various fields has raised health concerns, especially in reproductive health. Our research has shown zinc oxide nanoparticles (ZnONPs) exhibit the most significant toxicity to pre-implantation embryos in mice compared to other common NPs. In patients undergoing assisted reproduction technology (ART), a significant negative correlation was observed between Zn concentration and clinical outcomes. Therefore, this study explores the impact of ZnONPs exposure on pre-implantation embryonic development and its underlying mechanisms. We revealed that both in vivo and in vitro exposure to ZnONPs impairs pre-implantation embryonic development. Moreover, ZnONPs were found to reduce the pluripotency of mouse embryonic stem cells (mESCs), as evidenced by teratoma and diploid chimera assays. Employing multi-omics approaches, including RNA-Seq, CUT&Tag, and ATAC-seq, the embryotoxicity mechanisms of ZnONPs were elucidated. The findings indicate that ZnONPs elevate H3K9me3 levels, leading to increased heterochromatin and consequent inhibition of gene expression related to development and pluripotency. Notably, Chaetocin, a H3K9me3 inhibitor, sucessfully reversed the embryotoxicity effects induced by ZnONPs. Additionally, the direct interaction between ZnONPs and H3K9me3 was verified through pull-down and immunoprecipitation assays. Collectively, these findings offer new insights into the epigenetic mechanisms of ZnONPs toxicity, enhancing our understanding of their impact on human reproductive health.
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Affiliation(s)
- Xuemei Liu
- Chongqing Key Laboratory of Human Embryo Engineering and Precision Medicine, Center for Reproductive Medicine, Women and Children's Hospital of Chongqing Medical University, Chongqing, China; Chongqing Clinical Research Center for Reproductive Medicine, Chongqing Health Center for Women and Children, Chongqing, China
| | - Jie Li
- Molecular Biology Laboratory of Respiratory Disease, Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Ling Zhu
- Chongqing Key Laboratory of Human Embryo Engineering and Precision Medicine, Center for Reproductive Medicine, Women and Children's Hospital of Chongqing Medical University, Chongqing, China; Chongqing Clinical Research Center for Reproductive Medicine, Chongqing Health Center for Women and Children, Chongqing, China
| | - Jiayu Huang
- Reproductive Medicine Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Qi Zhang
- Chongqing Key Laboratory of Human Embryo Engineering and Precision Medicine, Center for Reproductive Medicine, Women and Children's Hospital of Chongqing Medical University, Chongqing, China; Chongqing Clinical Research Center for Reproductive Medicine, Chongqing Health Center for Women and Children, Chongqing, China
| | - Jianwu Wang
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Juan Xie
- Chongqing Key Laboratory of Human Embryo Engineering and Precision Medicine, Center for Reproductive Medicine, Women and Children's Hospital of Chongqing Medical University, Chongqing, China; Chongqing Clinical Research Center for Reproductive Medicine, Chongqing Health Center for Women and Children, Chongqing, China
| | - Qiang Dong
- Chongqing Key Laboratory of Human Embryo Engineering and Precision Medicine, Center for Reproductive Medicine, Women and Children's Hospital of Chongqing Medical University, Chongqing, China; Chongqing Clinical Research Center for Reproductive Medicine, Chongqing Health Center for Women and Children, Chongqing, China
| | - Zhen Zou
- Molecular Biology Laboratory of Respiratory Disease, Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Guoning Huang
- Chongqing Key Laboratory of Human Embryo Engineering and Precision Medicine, Center for Reproductive Medicine, Women and Children's Hospital of Chongqing Medical University, Chongqing, China; Chongqing Clinical Research Center for Reproductive Medicine, Chongqing Health Center for Women and Children, Chongqing, China.
| | - Qi Gu
- State Key Laboratory of Membrane Biology and the State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
| | - Jianyu Wang
- Molecular Biology Laboratory of Respiratory Disease, Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, China.
| | - Jingyu Li
- Chongqing Key Laboratory of Human Embryo Engineering and Precision Medicine, Center for Reproductive Medicine, Women and Children's Hospital of Chongqing Medical University, Chongqing, China; Chongqing Clinical Research Center for Reproductive Medicine, Chongqing Health Center for Women and Children, Chongqing, China.
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3
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Fukushima HS, Ikeda T, Ikeda S, Takeda H. Cell cycle length governs heterochromatin reprogramming during early development in non-mammalian vertebrates. EMBO Rep 2024; 25:3300-3323. [PMID: 38943003 PMCID: PMC11315934 DOI: 10.1038/s44319-024-00188-5] [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: 01/28/2024] [Revised: 06/06/2024] [Accepted: 06/12/2024] [Indexed: 06/30/2024] Open
Abstract
Heterochromatin marks such as H3K9me3 undergo global erasure and re-establishment after fertilization, and the proper reprogramming of H3K9me3 is essential for early development. Despite the widely conserved dynamics of heterochromatin reprogramming in invertebrates and non-mammalian vertebrates, previous studies have shown that the underlying mechanisms may differ between species. Here, we investigate the molecular mechanism of H3K9me3 dynamics in medaka (Japanese killifish, Oryzias latipes) as a non-mammalian vertebrate model, and show that rapid cell cycle during cleavage stages causes DNA replication-dependent passive erasure of H3K9me3. We also find that cell cycle slowing, toward the mid-blastula transition, permits increasing nuclear accumulation of H3K9me3 histone methyltransferase Setdb1, leading to the onset of H3K9me3 re-accumulation. We further demonstrate that cell cycle length in early development also governs H3K9me3 reprogramming in zebrafish and Xenopus laevis. Together with the previous studies in invertebrates, we propose that a cell cycle length-dependent mechanism for both global erasure and re-accumulation of H3K9me3 is conserved among rapid-cleavage species of non-mammalian vertebrates and invertebrates such as Drosophila, C. elegans, Xenopus and teleost fish.
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Affiliation(s)
- Hiroto S Fukushima
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.
- Center for Integrative Medical Sciences, RIKEN, Yokohama, 230-0045, Japan.
| | - Takafumi Ikeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
- Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto, 603-8555, Japan
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, 603-8555, Japan
| | - Shinra Ikeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, 603-8555, Japan.
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4
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Gao D, Li C, Liu SY, Xu TT, Lin XT, Tan YP, Gao FM, Yi LT, Zhang JV, Ma JY, Meng TG, Yeung WSB, Liu K, Ou XH, Su RB, Sun QY. P300 regulates histone crotonylation and preimplantation embryo development. Nat Commun 2024; 15:6418. [PMID: 39080296 PMCID: PMC11289097 DOI: 10.1038/s41467-024-50731-0] [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: 08/30/2023] [Accepted: 07/19/2024] [Indexed: 08/02/2024] Open
Abstract
Histone lysine crotonylation, an evolutionarily conserved modification differing from acetylation, exerts pivotal control over diverse biological processes. Among these are gene transcriptional regulation, spermatogenesis, and cell cycle processes. However, the dynamic changes and functions of histone crotonylation in preimplantation embryonic development in mammals remain unclear. Here, we show that the transcription coactivator P300 functions as a writer of histone crotonylation during embryonic development. Depletion of P300 results in significant developmental defects and dysregulation of the transcriptome of embryos. Importantly, we demonstrate that P300 catalyzes the crotonylation of histone, directly stimulating transcription and regulating gene expression, thereby ensuring successful progression of embryo development up to the blastocyst stage. Moreover, the modification of histone H3 lysine 18 crotonylation (H3K18cr) is primarily localized to active promoter regions. This modification serves as a distinctive epigenetic indicator of crucial transcriptional regulators, facilitating the activation of gene transcription. Together, our results propose a model wherein P300-mediated histone crotonylation plays a crucial role in regulating the fate of embryonic development.
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Affiliation(s)
- Di Gao
- Shenzhen Key Laboratory of Fertility Regulation, Center of Assisted Reproduction and Embryology, The University of Hong Kong Shenzhen Hospital, 518053, Shenzhen, China
- Center for Energy Metabolism and Reproduction, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
- Guangzhou Key Laboratory of Metabolic Diseases and Reproductive Health, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, 510317, Guangzhou, China
| | - Chao Li
- Guangzhou Key Laboratory of Metabolic Diseases and Reproductive Health, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, 510317, Guangzhou, China
| | - Shao-Yuan Liu
- Guangzhou Key Laboratory of Metabolic Diseases and Reproductive Health, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, 510317, Guangzhou, China
| | - Teng-Teng Xu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, China
| | - Xiao-Ting Lin
- Guangzhou Key Laboratory of Metabolic Diseases and Reproductive Health, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, 510317, Guangzhou, China
| | - Yong-Peng Tan
- Guangzhou Key Laboratory of Metabolic Diseases and Reproductive Health, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, 510317, Guangzhou, China
| | - Fu-Min Gao
- Guangzhou Key Laboratory of Metabolic Diseases and Reproductive Health, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, 510317, Guangzhou, China
| | - Li-Tao Yi
- Guangzhou Key Laboratory of Metabolic Diseases and Reproductive Health, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, 510317, Guangzhou, China
| | - Jian V Zhang
- Center for Energy Metabolism and Reproduction, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
| | - Jun-Yu Ma
- Guangzhou Key Laboratory of Metabolic Diseases and Reproductive Health, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, 510317, Guangzhou, China
| | - Tie-Gang Meng
- Guangzhou Key Laboratory of Metabolic Diseases and Reproductive Health, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, 510317, Guangzhou, China
| | - William S B Yeung
- Shenzhen Key Laboratory of Fertility Regulation, Center of Assisted Reproduction and Embryology, The University of Hong Kong Shenzhen Hospital, 518053, Shenzhen, China
| | - Kui Liu
- Shenzhen Key Laboratory of Fertility Regulation, Center of Assisted Reproduction and Embryology, The University of Hong Kong Shenzhen Hospital, 518053, Shenzhen, China
| | - Xiang-Hong Ou
- Guangzhou Key Laboratory of Metabolic Diseases and Reproductive Health, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, 510317, Guangzhou, China.
| | - Rui-Bao Su
- Guangzhou Key Laboratory of Metabolic Diseases and Reproductive Health, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, 510317, Guangzhou, China.
| | - Qing-Yuan Sun
- Guangzhou Key Laboratory of Metabolic Diseases and Reproductive Health, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, 510317, Guangzhou, China.
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5
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Chen H, Liu Y, Huang Y, Zhang P, Du D, Yu W, Wu C, Ruan H, Zhou P, Ding Z, Xiang H. Bisphenol M inhibits mouse oocyte maturation in vitro by disrupting cytoskeleton architecture and cell cycle processes. Reprod Toxicol 2024; 129:108667. [PMID: 39059776 DOI: 10.1016/j.reprotox.2024.108667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 07/12/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024]
Abstract
Bisphenol M (BPM), an alternative to bisphenol A (BPA), is commonly utilized in various industrial applications. However, BPM does not represent a safe substitute for BPA due to its detrimental effects on living beings. This research aimed to assess the influence of BPM exposure on the in vitro maturation of mouse oocytes. The findings revealed that BPM exposure had a notable impact on the germinal vesicle breakdown (GVBD) rate and polar body extrusion (PBE) rate throughout the meiotic progression of mouse oocytes, ultimately resulting in meiotic arrest. Investigations demonstrated that oocytes exposure to BPM led to continued activation of spindle assembly checkpoint. Further studies revealed that securin and cyclin B1 could not be degraded in BPM-exposed oocytes, and meiosis could not realize the transition from the MI to the AI stage. Mechanistically, BPM exposure resulted in abnormal spindle assembly and disrupted chromosome alignment of oocytes. Additionally, abnormal positioning of microtubule organizing center-associated proteins implied that MTOC may be dysfunctional. Furthermore, an elevation in the acetylation level of α-tubulin in oocytes was observed after BPM treatment, leading to decreased microtubule stability. In addition to its impact on microtubules, BPM exposure led to a reduction in the expression of the actin, signifying the disruption of actin assembly. Further research indicated a heightened incidence of DNA damage in oocytes following BPM exposure. Besides, BPM exposure induced alterations in histone modifications. The outcomes of this experiment demonstrate that BPM exposure impairs oocyte quality and inhibits meiotic maturation of mouse oocytes.
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Affiliation(s)
- Huilei Chen
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, No.218 Jixi Road, Hefei 230022, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, No.81 Meishan Road, Hefei 230032, China; Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, No.81 Meishan Road, Hefei 230032, China; Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Bengbu Medical University, No.287 Changhuai Road, Bengbu 233000, China
| | - Yang Liu
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, No.218 Jixi Road, Hefei 230022, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, No.81 Meishan Road, Hefei 230032, China; Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, No.81 Meishan Road, Hefei 230032, China
| | - Yue Huang
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, No.218 Jixi Road, Hefei 230022, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, No.81 Meishan Road, Hefei 230032, China; Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, No.81 Meishan Road, Hefei 230032, China
| | - Pin Zhang
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, No.218 Jixi Road, Hefei 230022, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, No.81 Meishan Road, Hefei 230032, China; Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, No.81 Meishan Road, Hefei 230032, China
| | - Danli Du
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Bengbu Medical University, No.287 Changhuai Road, Bengbu 233000, China
| | - Wenhua Yu
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Bengbu Medical University, No.287 Changhuai Road, Bengbu 233000, China
| | - Caiyun Wu
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, No.218 Jixi Road, Hefei 230022, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, No.81 Meishan Road, Hefei 230032, China; Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, No.81 Meishan Road, Hefei 230032, China
| | - Hongzhen Ruan
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, No.218 Jixi Road, Hefei 230022, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, No.81 Meishan Road, Hefei 230032, China; Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, No.81 Meishan Road, Hefei 230032, China
| | - Ping Zhou
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, No.218 Jixi Road, Hefei 230022, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, No.81 Meishan Road, Hefei 230032, China; Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, No.81 Meishan Road, Hefei 230032, China; Engineering Research Center of Biopreservation and Artificial Organs, Ministry of Education, No.81 Meishan Road, Hefei, Anhui 230032, China; Anhui Province Key Laboratory of Reproductive Health and Genetics, No.81 Meishan Road, Hefei 230032, China; Biopreservation and Artificial Organs, Anhui Provincial Engineering Research Center, Anhui Medical University, No.81 Meishan Road, Hefei 230032, China; Anhui Provincial Institute of Translational Medicine, No.81 Meishan Road, Hefei 230032, China.
| | - Zhiming Ding
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, No.218 Jixi Road, Hefei 230022, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, No.81 Meishan Road, Hefei 230032, China; Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, No.81 Meishan Road, Hefei 230032, China; Engineering Research Center of Biopreservation and Artificial Organs, Ministry of Education, No.81 Meishan Road, Hefei, Anhui 230032, China; Anhui Province Key Laboratory of Reproductive Health and Genetics, No.81 Meishan Road, Hefei 230032, China; Biopreservation and Artificial Organs, Anhui Provincial Engineering Research Center, Anhui Medical University, No.81 Meishan Road, Hefei 230032, China; Anhui Provincial Institute of Translational Medicine, No.81 Meishan Road, Hefei 230032, China.
| | - Huifen Xiang
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, No.218 Jixi Road, Hefei 230022, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, No.81 Meishan Road, Hefei 230032, China; Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, No.81 Meishan Road, Hefei 230032, China; Engineering Research Center of Biopreservation and Artificial Organs, Ministry of Education, No.81 Meishan Road, Hefei, Anhui 230032, China; Anhui Province Key Laboratory of Reproductive Health and Genetics, No.81 Meishan Road, Hefei 230032, China; Biopreservation and Artificial Organs, Anhui Provincial Engineering Research Center, Anhui Medical University, No.81 Meishan Road, Hefei 230032, China; Anhui Provincial Institute of Translational Medicine, No.81 Meishan Road, Hefei 230032, China.
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6
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Li F, Karimi N, Wang S, Pan T, Dong J, Wang X, Ma S, Shan Q, Liu C, Zhang Y, Li W, Feng G. mRNA isoform switches during mouse zygotic genome activation. Cell Prolif 2024; 57:e13655. [PMID: 38764347 PMCID: PMC11216927 DOI: 10.1111/cpr.13655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/29/2024] [Accepted: 05/03/2024] [Indexed: 05/21/2024] Open
Affiliation(s)
- Fan Li
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Key Laboratory of Organ Regeneration and ReconstructionChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Najmeh Karimi
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Key Laboratory of Organ Regeneration and ReconstructionChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Siqi Wang
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Key Laboratory of Organ Regeneration and ReconstructionChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
| | - Tianshi Pan
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Key Laboratory of Organ Regeneration and ReconstructionChinese Academy of SciencesBeijingChina
- College of Life SciencesNortheast Agricultural UniversityHarbinChina
| | - Jingxi Dong
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Key Laboratory of Organ Regeneration and ReconstructionChinese Academy of SciencesBeijingChina
| | - Xin Wang
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Key Laboratory of Organ Regeneration and ReconstructionChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
- Medical SchoolUniversity of Chinese Academy of SciencesBeijingChina
| | - Sinan Ma
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Key Laboratory of Organ Regeneration and ReconstructionChinese Academy of SciencesBeijingChina
- College of Life SciencesNortheast Agricultural UniversityHarbinChina
| | - Qingtong Shan
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Key Laboratory of Organ Regeneration and ReconstructionChinese Academy of SciencesBeijingChina
- College of Life SciencesNortheast Agricultural UniversityHarbinChina
| | - Chao Liu
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Key Laboratory of Organ Regeneration and ReconstructionChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
| | - Ying Zhang
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Key Laboratory of Organ Regeneration and ReconstructionChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Key Laboratory of Organ Regeneration and ReconstructionChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
| | - Guihai Feng
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Key Laboratory of Organ Regeneration and ReconstructionChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
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7
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Su Z, Dong Y, Sun J, Wu Y, Wei Q, Liang Y, Lin Z, Li Y, Shen L, Xi C, Wu L, Xu Y, Liu Y, Yin J, Wang H, Shi K, Le R, Gao S, Xu X. RNA m 6A modification regulates cell fate transition between pluripotent stem cells and 2-cell-like cells. Cell Prolif 2024:e13696. [PMID: 38952035 DOI: 10.1111/cpr.13696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 05/28/2024] [Accepted: 06/06/2024] [Indexed: 07/03/2024] Open
Abstract
N6-methyladenosine (m6A) exerts essential roles in early embryos, especially in the maternal-to-zygotic transition stage. However, the landscape and roles of RNA m6A modification during the transition between pluripotent stem cells and 2-cell-like (2C-like) cells remain elusive. Here, we utilised ultralow-input RNA m6A immunoprecipitation to depict the dynamic picture of transcriptome-wide m6A modifications during 2C-like transitions. We found that RNA m6A modification was preferentially enriched in zygotic genome activation (ZGA) transcripts and MERVL with high expression levels in 2C-like cells. During the exit of the 2C-like state, m6A facilitated the silencing of ZGA genes and MERVL. Notably, inhibition of m6A methyltransferase METTL3 and m6A reader protein IGF2BP2 is capable of significantly delaying 2C-like state exit and expanding 2C-like cells population. Together, our study reveals the critical roles of RNA m6A modification in the transition between 2C-like and pluripotent states, facilitating the study of totipotency and cell fate decision in the future.
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Affiliation(s)
- Zhongqu Su
- College of Animal Science and Technology, Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, Shandong Agricultural University, Tai'an, Shandong, China
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yu Dong
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Jiatong Sun
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - You Wu
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Qingqing Wei
- College of Animal Science and Technology, Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, Shandong Agricultural University, Tai'an, Shandong, China
| | - Yuwei Liang
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Zhiyi Lin
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yujun Li
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Lu Shen
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Chenxiang Xi
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Li Wu
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yiliang Xu
- College of Animal Science and Technology, Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, Shandong Agricultural University, Tai'an, Shandong, China
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yingdong Liu
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Jiqing Yin
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Hong Wang
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Kerong Shi
- College of Animal Science and Technology, Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, Shandong Agricultural University, Tai'an, Shandong, China
| | - Rongrong Le
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Shaorong Gao
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Xiaocui Xu
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, China
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8
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Huang W, Chen ACH, Wei X, Fong SW, Yeung WSB, Lee YL. Uncovering the role of TET2-mediated ENPEP activation in trophoblast cell fate determination. Cell Mol Life Sci 2024; 81:270. [PMID: 38886218 DOI: 10.1007/s00018-024-05306-z] [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: 02/23/2024] [Revised: 05/24/2024] [Accepted: 06/04/2024] [Indexed: 06/20/2024]
Abstract
Early trophoblast differentiation is crucial for embryo implantation, placentation and fetal development. Dynamic changes in DNA methylation occur during preimplantation development and are critical for cell fate determination. However, the underlying regulatory mechanism remains unclear. Recently, we derived morula-like expanded potential stem cells from human preimplantation embryos (hEPSC-em), providing a valuable tool for studying early trophoblast differentiation. Data analysis on published datasets showed differential expressions of DNA methylation enzymes during early trophoblast differentiation in human embryos and hEPSC-em derived trophoblastic spheroids. We demonstrated downregulation of DNA methyltransferase 3 members (DNMT3s) and upregulation of ten-eleven translocation methylcytosine dioxygenases (TETs) during trophoblast differentiation. While DNMT inhibitor promoted trophoblast differentiation, TET inhibitor hindered the process and reduced implantation potential of trophoblastic spheroids. Further integrative analysis identified that glutamyl aminopeptidase (ENPEP), a trophectoderm progenitor marker, was hypomethylated and highly expressed in trophoblast lineages. Concordantly, progressive loss of DNA methylation in ENPEP promoter and increased ENPEP expression were detected in trophoblast differentiation. Knockout of ENPEP in hEPSC-em compromised trophoblast differentiation potency, reduced adhesion and invasion of trophoblastic spheroids, and impeded trophoblastic stem cell (TSC) derivation. Importantly, TET2 was involved in the loss of DNA methylation and activation of ENPEP expression during trophoblast differentiation. TET2-null hEPSC-em failed to produce TSC properly. Collectively, our results illustrated the crucial roles of ENPEP and TET2 in trophoblast fate commitments and the unprecedented TET2-mediated loss of DNA methylation in ENPEP promoter.
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Affiliation(s)
- Wen Huang
- Department of Obstetrics and Gynaecology, Li Ka Shing Faculty of Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, Special Administrative Region, China
- Centre for Translational Stem Cell Biology, Science Park, Sha Tin , Hong Kong, Special Administrative Region, China
| | - Andy Chun Hang Chen
- Department of Obstetrics and Gynaecology, Li Ka Shing Faculty of Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, Special Administrative Region, China
- Centre for Translational Stem Cell Biology, Science Park, Sha Tin , Hong Kong, Special Administrative Region, China
- Shenzhen Key Laboratory of Fertility Regulation, Reproductive Medicine Center, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Xujin Wei
- Department of Obstetrics and Gynaecology, Li Ka Shing Faculty of Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, Special Administrative Region, China
| | - Sze Wan Fong
- Department of Obstetrics and Gynaecology, Li Ka Shing Faculty of Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, Special Administrative Region, China
| | - William Shu Biu Yeung
- Department of Obstetrics and Gynaecology, Li Ka Shing Faculty of Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, Special Administrative Region, China.
- Centre for Translational Stem Cell Biology, Science Park, Sha Tin , Hong Kong, Special Administrative Region, China.
- Shenzhen Key Laboratory of Fertility Regulation, Reproductive Medicine Center, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China.
| | - Yin Lau Lee
- Department of Obstetrics and Gynaecology, Li Ka Shing Faculty of Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, Special Administrative Region, China.
- Centre for Translational Stem Cell Biology, Science Park, Sha Tin , Hong Kong, Special Administrative Region, China.
- Shenzhen Key Laboratory of Fertility Regulation, Reproductive Medicine Center, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China.
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9
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Yao F, Chu M, Xi G, Dai J, Wang Z, Hao J, Yang Q, Wang W, Tang Y, Zhang J, Yue Y, Wang Y, Xu Y, Zhao W, Ma L, Liu J, Zhang Z, Tian J, An L. Single-embryo transcriptomic atlas of oxygen response reveals the critical role of HIF-1α in prompting embryonic zygotic genome activation. Redox Biol 2024; 72:103147. [PMID: 38593632 PMCID: PMC11016760 DOI: 10.1016/j.redox.2024.103147] [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: 02/28/2024] [Revised: 03/28/2024] [Accepted: 04/01/2024] [Indexed: 04/11/2024] Open
Abstract
Adaptive response to physiological oxygen levels (physO2; 5% O2) enables embryonic survival in a low-oxygen developmental environment. However, the mechanism underlying the role of physO2 in supporting preimplantation development, remains elusive. Here, we systematically studied oxygen responses of hallmark events in preimplantation development. Focusing on impeded transcriptional upregulation under atmospheric oxygen levels (atmosO2; 20% O2) during the 2-cell stage, we functionally identified a novel role of HIF-1α in promoting major zygotic genome activation by serving as an oxygen-sensitive transcription factor. Moreover, during blastocyst formation, atmosO2 impeded H3K4me3 and H3K27me3 deposition by deregulating histone-lysine methyltransferases, thus impairing X-chromosome inactivation in blastocysts. In addition, we found atmosO2 impedes metabolic shift to glycolysis before blastocyst formation, thus resulting a low-level histone lactylation deposition. Notably, we also reported an increased sex-dimorphic oxygen response of embryos upon preimplantation development. Together, focusing on genetic and epigenetic events that are essential for embryonic survival and development, the present study advances current knowledge of embryonic adaptive responses to physO2, and provides novel insight into mechanism underlying irreversibly impaired developmental potential due to a short-term atmosO2 exposure.
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Affiliation(s)
- Fusheng Yao
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, No.2 Yuanmingyuan West Road, Beijing, 100193, PR China
| | - Meiqiang Chu
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, No.2 Yuanmingyuan West Road, Beijing, 100193, PR China
| | - Guangyin Xi
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, No.2 Yuanmingyuan West Road, Beijing, 100193, PR China
| | - Jiage Dai
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, No.2 Yuanmingyuan West Road, Beijing, 100193, PR China
| | - Zhaochen Wang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, No.2 Yuanmingyuan West Road, Beijing, 100193, PR China
| | - Jia Hao
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, No.2 Yuanmingyuan West Road, Beijing, 100193, PR China
| | - Qianying Yang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, No.2 Yuanmingyuan West Road, Beijing, 100193, PR China
| | - Wenjing Wang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, No.2 Yuanmingyuan West Road, Beijing, 100193, PR China
| | - Yawen Tang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, No.2 Yuanmingyuan West Road, Beijing, 100193, PR China
| | - Jingyu Zhang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, No.2 Yuanmingyuan West Road, Beijing, 100193, PR China
| | - Yuan Yue
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, No.2 Yuanmingyuan West Road, Beijing, 100193, PR China
| | - Yue Wang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, No.2 Yuanmingyuan West Road, Beijing, 100193, PR China
| | - Yefen Xu
- Animal Science Department, Tibet Agricultural and Animal Husbandry College, 100 Yucai Road, Bayi District, Tibet, 860000, Nyingchi, PR China
| | - Wei Zhao
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, No.2 Yuanmingyuan West Road, Beijing, 100193, PR China
| | - Lizhu Ma
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, No.2 Yuanmingyuan West Road, Beijing, 100193, PR China
| | - Juan Liu
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, No.2 Yuanmingyuan West Road, Beijing, 100193, PR China
| | - Zhenni Zhang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, No.2 Yuanmingyuan West Road, Beijing, 100193, PR China
| | - Jianhui Tian
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, No.2 Yuanmingyuan West Road, Beijing, 100193, PR China.
| | - Lei An
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, No.2 Yuanmingyuan West Road, Beijing, 100193, PR China.
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10
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Sciorio R, Tramontano L, Campos G, Greco PF, Mondrone G, Surbone A, Greco E, Talevi R, Pluchino N, Fleming S. Vitrification of human blastocysts for couples undergoing assisted reproduction: an updated review. Front Cell Dev Biol 2024; 12:1398049. [PMID: 38827525 PMCID: PMC11140474 DOI: 10.3389/fcell.2024.1398049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 04/25/2024] [Indexed: 06/04/2024] Open
Abstract
Over the past 40 years there has been a worldwide critical change in the field of assisted reproduction technology (ART), leading to the increased application of single blastocyst transfer, which is extremely important to avoid the risks of multiple pregnancy and associated complications for both mother and babies. Indeed, advancements in ART over the last few decades have been obtained thanks to several improvements, including ovarian stimulation, embryo culture conditions and, of course, progress in cryopreservation methods, especially with the application of vitrification. The ability to cryopreserve human embryos has improved significantly with vitrification compared to the initially adopted slow-freezing procedures. Since the introduction of vitrification, it has become the gold standard method to effectively cryopreserve human blastocysts. However, some new protocols are now being explored, such as the short warming procedure and even shorter exposure to the equilibration solution before vitrification, which seem to provide optimal results. Therefore, the main aim of the current narrative review, will be to illustrate the benefit of vitrification as an effective method to cryopreserve the human blastocyst and to illustrate new protocols and variations which in future may increase the performance of vitrification protocols.
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Affiliation(s)
- Romualdo Sciorio
- Fertility Medicine and Gynaecological Endocrinology Unit, Department Woman Mother Child, Lausanne University Hospital, Lausanne, Switzerland
| | - Luca Tramontano
- Département de Gynécologie-Obstétrique, Réseau Hospitalier Neuchâtelois, Neuchâtel, Switzerland
| | - Gerard Campos
- Fertility Geisinger Medical Center, Women’s Health Fertility Clinic, Danville, PA, United States
- GIREXX Fertility Clinics, Girona-Barcelona, Spain
| | | | | | - Anna Surbone
- Fertility Medicine and Gynaecological Endocrinology Unit, Department Woman Mother Child, Lausanne University Hospital, Lausanne, Switzerland
| | - Ermanno Greco
- Villa Mafalda, Centre for Reproductive Medicine, Rome, Italy
- Department of Obstetrics and Gynecology, UniCamillus, International Medical University, Rome, Italy
| | - Riccardo Talevi
- Dipartimento di Biologia Strutturale e Funzionale, Universita’ di Napoli ‘Federico II’, Complesso Universitario di Monte S, Napoli, Italy
| | - Nicola Pluchino
- Fertility Medicine and Gynaecological Endocrinology Unit, Department Woman Mother Child, Lausanne University Hospital, Lausanne, Switzerland
| | - Steven Fleming
- Discipline of Anatomy and Histology, School of Medical Sciences, University of Sydney, Sydney, NSW, Australia
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11
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Gong X, He W, Jin W, Ma H, Wang G, Li J, Xiao Y, Zhao Y, Chen Q, Guo H, Yang J, Qi Y, Dong W, Fu M, Li X, Liu J, Liu X, Yin A, Zhang Y, Wei Y. Disruption of maternal vascular remodeling by a fetal endoretrovirus-derived gene in preeclampsia. Genome Biol 2024; 25:117. [PMID: 38715110 PMCID: PMC11075363 DOI: 10.1186/s13059-024-03265-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 04/30/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Preeclampsia, one of the most lethal pregnancy-related diseases, is associated with the disruption of uterine spiral artery remodeling during placentation. However, the early molecular events leading to preeclampsia remain unknown. RESULTS By analyzing placentas from preeclampsia, non-preeclampsia, and twin pregnancies with selective intrauterine growth restriction, we show that the pathogenesis of preeclampsia is attributed to immature trophoblast and maldeveloped endothelial cells. Delayed epigenetic reprogramming during early extraembryonic tissue development leads to generation of excessive immature trophoblast cells. We find reduction of de novo DNA methylation in these trophoblast cells results in selective overexpression of maternally imprinted genes, including the endoretrovirus-derived gene PEG10 (paternally expressed gene 10). PEG10 forms virus-like particles, which are transferred from the trophoblast to the closely proximate endothelial cells. In normal pregnancy, only a low amount of PEG10 is transferred to maternal cells; however, in preeclampsia, excessive PEG10 disrupts maternal vascular development by inhibiting TGF-beta signaling. CONCLUSIONS Our study reveals the intricate epigenetic mechanisms that regulate trans-generational genetic conflict and ultimately ensure proper maternal-fetal interface formation.
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Affiliation(s)
- Xiaoli Gong
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Wei He
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Wan Jin
- Euler Technology, Beijing, China
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hongwei Ma
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, China
- Department Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Gang Wang
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
- Human Genetic Resources Preservation Center of Hubei Province, Wuhan, China
- Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jiaxin Li
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Yu Xiao
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
- Human Genetic Resources Preservation Center of Hubei Province, Wuhan, China
- Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yangyu Zhao
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | | | | | - Jiexia Yang
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Yiming Qi
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Wei Dong
- Maternity Ward, Haidian Maternal and Child Health Hospital, Beijing, China
| | - Meng Fu
- Department of Obstetrics and Gynecology, Haidian Maternal and Child Health Hospital, Beijing, China
| | - Xiaojuan Li
- Euler Technology, Beijing, China
- Present Address: International Max Planck Research School for Genome Science, and University of Göttingen, Göttingen Center for Molecular Biosciences, Göttingen, Germany
| | | | - Xinghui Liu
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, China.
- Department Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China.
| | - Aihua Yin
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China.
| | - Yi Zhang
- Euler Technology, Beijing, China.
| | - Yuan Wei
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.
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12
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Sotomayor-Lugo F, Iglesias-Barrameda N, Castillo-Aleman YM, Casado-Hernandez I, Villegas-Valverde CA, Bencomo-Hernandez AA, Ventura-Carmenate Y, Rivero-Jimenez RA. The Dynamics of Histone Modifications during Mammalian Zygotic Genome Activation. Int J Mol Sci 2024; 25:1459. [PMID: 38338738 PMCID: PMC10855761 DOI: 10.3390/ijms25031459] [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: 12/29/2023] [Revised: 01/22/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
Mammalian fertilization initiates the reprogramming of oocytes and sperm, forming a totipotent zygote. During this intricate process, the zygotic genome undergoes a maternal-to-zygotic transition (MZT) and subsequent zygotic genome activation (ZGA), marking the initiation of transcriptional control and gene expression post-fertilization. Histone modifications are pivotal in shaping cellular identity and gene expression in many mammals. Recent advances in chromatin analysis have enabled detailed explorations of histone modifications during ZGA. This review delves into conserved and unique regulatory strategies, providing essential insights into the dynamic changes in histone modifications and their variants during ZGA in mammals. The objective is to explore recent advancements in leading mechanisms related to histone modifications governing this embryonic development phase in depth. These considerations will be useful for informing future therapeutic approaches that target epigenetic regulation in diverse biological contexts. It will also contribute to the extensive areas of evolutionary and developmental biology and possibly lay the foundation for future research and discussion on this seminal topic.
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Affiliation(s)
| | | | | | | | | | | | | | - Rene Antonio Rivero-Jimenez
- Abu Dhabi Stem Cells Center, Abu Dhabi P.O. Box 4600, United Arab Emirates; (F.S.-L.); (N.I.-B.); (Y.M.C.-A.); (I.C.-H.); (C.A.V.-V.); (A.A.B.-H.); (Y.V.-C.)
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13
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Yu T, Zhang C, Song W, Zhao X, Cheng Y, Liu J, Su J. Single-cell RNA-seq and single-cell bisulfite-sequencing reveal insights into yak preimplantation embryogenesis. J Biol Chem 2024; 300:105562. [PMID: 38097189 PMCID: PMC10821408 DOI: 10.1016/j.jbc.2023.105562] [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: 03/24/2023] [Revised: 11/17/2023] [Accepted: 12/03/2023] [Indexed: 01/13/2024] Open
Abstract
Extensive epigenetic reprogramming occurs during preimplantation embryonic development. However, the impact of DNA methylation in plateau yak preimplantation embryos and how epigenetic reprogramming contributes to transcriptional regulatory networks are unclear. In this study, we quantified gene expression and DNA methylation in oocytes and a series of yak embryos at different developmental stages and at single-cell resolution using single-cell bisulfite-sequencing and RNA-seq. We characterized embryonic genome activation and maternal transcript degradation and mapped epigenetic reprogramming events critical for embryonic development. Through cross-species transcriptome analysis, we identified 31 conserved maternal hub genes and 39 conserved zygotic hub genes, including SIN3A, PRC1, HDAC1/2, and HSPD1. Notably, by combining single-cell DNA methylation and transcriptome analysis, we identified 43 candidate methylation driver genes, such as AURKA, NUSAP1, CENPF, and PLK1, that may be associated with embryonic development. Finally, using functional approaches, we further determined that the epigenetic modifications associated with the histone deacetylases HDAC1/2 are essential for embryonic development and that the deubiquitinating enzyme USP7 may affect embryonic development by regulating DNA methylation. Our data represent an extensive resource on the transcriptional dynamics of yak embryonic development and DNA methylation remodeling, and provide new insights into strategies for the conservation of germplasm resources, as well as a better understanding of mammalian early embryonic development that can be applied to investigate the causes of early developmental disorders.
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Affiliation(s)
- Tong Yu
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Chengtu Zhang
- Academician Zhang Yong Innovation Center, Xining Animal Disease Control Center, Xining, Qinghai, China
| | - Weijia Song
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Xinyi Zhao
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Yuyao Cheng
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Jun Liu
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.
| | - Jianmin Su
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.
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14
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Kretschmer M, Fischer V, Gapp K. When Dad's Stress Gets under Kid's Skin-Impacts of Stress on Germline Cargo and Embryonic Development. Biomolecules 2023; 13:1750. [PMID: 38136621 PMCID: PMC10742275 DOI: 10.3390/biom13121750] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 11/24/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
Multiple lines of evidence suggest that paternal psychological stress contributes to an increased prevalence of neuropsychiatric and metabolic diseases in the progeny. While altered paternal care certainly plays a role in such transmitted disease risk, molecular factors in the germline might additionally be at play in humans. This is supported by findings on changes to the molecular make up of germ cells and suggests an epigenetic component in transmission. Several rodent studies demonstrate the correlation between paternal stress induced changes in epigenetic modifications and offspring phenotypic alterations, yet some intriguing cases also start to show mechanistic links in between sperm and the early embryo. In this review, we summarise efforts to understand the mechanism of intergenerational transmission from sperm to the early embryo. In particular, we highlight how stress alters epigenetic modifications in sperm and discuss the potential for these modifications to propagate modified molecular trajectories in the early embryo to give rise to aberrant phenotypes in adult offspring.
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Affiliation(s)
- Miriam Kretschmer
- Laboratory of Epigenetics and Neuroendocrinology, Department of Health Sciences and Technology, Institute for Neuroscience, ETH Zürich, 8057 Zürich, Switzerland; (M.K.); (V.F.)
- Neuroscience Center Zurich, ETH Zürich and University of Zürich, 8057 Zürich, Switzerland
| | - Vincent Fischer
- Laboratory of Epigenetics and Neuroendocrinology, Department of Health Sciences and Technology, Institute for Neuroscience, ETH Zürich, 8057 Zürich, Switzerland; (M.K.); (V.F.)
- Neuroscience Center Zurich, ETH Zürich and University of Zürich, 8057 Zürich, Switzerland
| | - Katharina Gapp
- Laboratory of Epigenetics and Neuroendocrinology, Department of Health Sciences and Technology, Institute for Neuroscience, ETH Zürich, 8057 Zürich, Switzerland; (M.K.); (V.F.)
- Neuroscience Center Zurich, ETH Zürich and University of Zürich, 8057 Zürich, Switzerland
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15
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Sciorio R, Pluchino N, Fuller BJ. Review of human oocyte cryopreservation in ART programs: Current challenges and opportunities. Cryobiology 2023; 113:104590. [PMID: 37804949 DOI: 10.1016/j.cryobiol.2023.104590] [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: 05/16/2023] [Revised: 09/29/2023] [Accepted: 10/02/2023] [Indexed: 10/09/2023]
Abstract
Oocyte cryopreservation has notably increased in recent times, to become an essential part of clinical infertility treatment. Since the 1980s, many improvements in oocyte cryopreservation (OC) have been adopted, including the great advance with the application of vitrification. The commonly used vitrification protocol applies different cryoprotectants (Ethylene glycol and/or DMSO and/or PROH and sucrose and/or Trehalose) and two different steps: firstly, exposure in equilibration solution for 5-15 min, followed by a vitrification solution for 60-90 s at room temperature. The warming method includes a first step for 1 min at 37 °C and 3 subsequent steps at room temperature to remove the cryoprotectant for a total of 9-12 min. In addition, biosafety is a critical aspect to mention, and it is related to devices used during the vitrification, mainly in terms of whether the biological vitrified material comes in direct contact with liquid nitrogen (open vitrification) or not (closed vitrification), where LN2 may contain potentially contaminating viruses or pathogens. Furthermore, during early development major waves of epigenetic reprogramming take place. Recent literature suggests that epigenetic and transcriptomic profiles are sensitive to the stress induced by vitrification, including osmotic shock, temperature, rapid changes of pH and toxicity of cryoprotectants. It is, therefore, important to better understand the potential perturbations of epigenetic modifications that may be associated with the globally used vitrification methods. Therefore, we here discuss the benefits and efficiency of human oocyte vitrification; we also review the evidence surrounding oocyte cryopreservation-related epigenetic modifications and potential epigenetic dysregulations, together with long-term consequences for offspring health.
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Affiliation(s)
- Romualdo Sciorio
- Fertility Medicine and Gynaecological Endocrinology Unit, Department Woman-Mother-Child, CHUV-Lausanne University Hospital, 1011, Lausanne, Switzerland.
| | - Nicola Pluchino
- Fertility Medicine and Gynaecological Endocrinology Unit, Department Woman-Mother-Child, CHUV-Lausanne University Hospital, 1011, Lausanne, Switzerland
| | - Barry J Fuller
- Division of Surgery & Interventional Science, University College London Medical School, London, UK
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16
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Zhang YR, Yin TL, Zhou LQ. CRISPR/Cas9 technology: applications in oocytes and early embryos. J Transl Med 2023; 21:746. [PMID: 37875936 PMCID: PMC10594749 DOI: 10.1186/s12967-023-04610-9] [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: 07/12/2023] [Accepted: 10/09/2023] [Indexed: 10/26/2023] Open
Abstract
CRISPR/Cas9, a highly versatile genome-editing tool, has garnered significant attention in recent years. Despite the unique characteristics of oocytes and early embryos compared to other cell types, this technology has been increasing used in mammalian reproduction. In this comprehensive review, we elucidate the fundamental principles of CRISPR/Cas9-related methodologies and explore their wide-ranging applications in deciphering molecular intricacies during oocyte and early embryo development as well as in addressing associated diseases. However, it is imperative to acknowledge the limitations inherent to these technologies, including the potential for off-target effects, as well as the ethical concerns surrounding the manipulation of human embryos. Thus, a judicious and thoughtful approach is warranted. Regardless of these challenges, CRISPR/Cas9 technology undeniably represents a formidable tool for genome and epigenome manipulation within oocytes and early embryos. Continuous refinements in this field are poised to fortify its future prospects and applications.
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Affiliation(s)
- Yi-Ran Zhang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Tai-Lang Yin
- Reproductive Medical Center, Renmin Hospital of Wuhan University & Hubei Clinic Research Center for Assisted Reproductive Technology and Embryonic Development, Wuhan, China.
| | - Li-Quan Zhou
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
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17
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Wang J, Liu T, Wang J, Chen T, Jiang Y. Genome-Wide Profiling of Transcriptome and DNA Methylome in Human Embryonic Stem Cells Exposed to Extractable Organic Matter from PM2.5. TOXICS 2023; 11:840. [PMID: 37888691 PMCID: PMC10611369 DOI: 10.3390/toxics11100840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023]
Abstract
Increasing evidence indicates that PM2.5 exposure disrupts early embryonic development, but the mechanisms remain unclear. We hypothesized that PM2.5 cause abnormal embryonic development by interfering with DNA methylation and mRNA expression. In this study, we observed that human embryonic stem cells (hESCs) treated with extractable organic matters (EOM) from PM2.5 concentrations above 100 μg/mL exhibited reduced viability. While EOM within non-cytotoxicity concentrations did not affect the expression levels of pluripotency genes, it did enhance cellular proliferation, as indicated by increased Edu incorporation and the upregulation of cell cycle genes (Cdk2, Mdm2). Additionally, EOM significantly influenced the transcriptome patterns in hESCs. Notably, the differentially expressed genes were found to be significantly enriched in processes such as extracellular matrix organization, cell-cell junction organization, chromatin organization, and DNA methylation. Furthermore, we observed whole genomic-wide DNA methylation changes. Through a cross-analysis of changes in DNA methylation and mRNA expression, we identified an enrichment of terms related to the VEGFR signaling pathway and extracellular matrix. The gene signal transduction networks revealed that crucial hubs were implicated in cell growth and division. In conclusion, our findings demonstrate that PM2.5 induce significant alterations in transcriptome and DNA methylome in hESCs, leading to aberrant cell proliferation. This research provides novel insights into the molecular mechanisms underlying the developmental toxicity of PM2.5.
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Affiliation(s)
- Jianming Wang
- Suzhou Medical College, Soochow University, Suzhou 215123, China
| | - Tiantian Liu
- Suzhou Medical College, Soochow University, Suzhou 215123, China
| | - Jin Wang
- Suzhou Medical College, Soochow University, Suzhou 215123, China
| | - Tao Chen
- Suzhou Medical College, Soochow University, Suzhou 215123, China
- Education Key Laboratory of Geriatric Diseases and Immunology, Suzhou 215123, China
| | - Yan Jiang
- Suzhou Medical College, Soochow University, Suzhou 215123, China
- Education Key Laboratory of Geriatric Diseases and Immunology, Suzhou 215123, China
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18
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Sciorio R, Campos G, Tramontano L, Bulletti FM, Baldini GM, Vinciguerra M. Exploring the effect of cryopreservation in assisted reproductive technology and potential epigenetic risk. ZYGOTE 2023; 31:420-432. [PMID: 37409505 DOI: 10.1017/s0967199423000345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023]
Abstract
Since the birth of the first baby by in vitro fertilization in 1978, more than 9 million children have been born worldwide using medically assisted reproductive treatments. Fertilization naturally takes place in the maternal oviduct where unique physiological conditions enable the early healthy development of the embryo. During this dynamic period of early development major waves of epigenetic reprogramming, crucial for the normal fate of the embryo, take place. Increasingly, over the past 20 years concerns relating to the increased incidence of epigenetic anomalies in general, and genomic-imprinting disorders in particular, have been raised following assisted reproduction technology (ART) treatments. Epigenetic reprogramming is particularly susceptible to environmental conditions during the periconceptional period and non-physiological conditions such as ovarian stimulation, in vitro fertilization and embryo culture, as well as cryopreservation procedure, might have the potential to independently or collectively contribute to epigenetic dysregulation. Therefore, this narrative review offers a critical reappraisal of the evidence relating to the association between embryo cryopreservation and potential epigenetic regulation and the consequences on gene expression together with long-term consequences for offspring health and wellbeing. Current literature suggests that epigenetic and transcriptomic profiles are sensitive to the stress induced by vitrification, in terms of osmotic shock, temperature and pH changes, and toxicity of cryoprotectants, it is therefore, critical to have a more comprehensive understanding and recognition of potential unanticipated iatrogenic-induced perturbations of epigenetic modifications that may or may not be a consequence of vitrification.
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Affiliation(s)
- Romualdo Sciorio
- Edinburgh Assisted Conception Programme, EFREC, Royal Infirmary of Edinburgh, UK
| | | | - Luca Tramontano
- Department of Women, Infants and Adolescents, Division of Obstetrics, Geneve University Hospitals, Boulevard de la Cluse 30, Geneve 14, Switzerland
| | - Francesco M Bulletti
- Department Obstetrics and Gynecology, University Hospital of Vaud, Lausanne, Switzerland
| | | | - Marina Vinciguerra
- Department of Biomedical Sciences and Human Oncology, Obstetrics and Gynaecology Section, University of Bari, Italy
- Clinic of Obstetrics and Gynecology 'Santa Caterina Novella', Galatina Hospital, Italy
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19
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Das A, Boese KG, Tachibana K, Baek SH, Lampson MA, Black BE. Centromere-specifying nucleosomes persist in aging mouse oocytes in the absence of nascent assembly. Curr Biol 2023; 33:3759-3765.e3. [PMID: 37582374 PMCID: PMC10528140 DOI: 10.1016/j.cub.2023.07.032] [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: 04/21/2023] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 08/17/2023]
Abstract
Centromeres direct genetic inheritance but are not themselves genetically encoded. Instead, centromeres are defined epigenetically by the presence of a histone H3 variant, CENP-A.1 In cultured somatic cells, an established paradigm of cell-cycle-coupled propagation maintains centromere identity: CENP-A is partitioned between sisters during replication and replenished by new assembly, which is restricted to G1. The mammalian female germ line challenges this model because of the cell-cycle arrest between pre-meiotic S phase and the subsequent G1, which can last for the entire reproductive lifespan (months to decades). New CENP-A chromatin assembly maintains centromeres during prophase I in worm and starfish oocytes,2,3 suggesting that a similar process may be required for centromere inheritance in mammals. To test this hypothesis, we developed an oocyte-specific conditional knockout (cKO) mouse for Mis18α, an essential component of the assembly machinery. We find that embryos derived from Mis18α knockout oocytes fail to assemble CENP-A nucleosomes prior to zygotic genome activation (ZGA), validating the knockout model. We show that deletion of Mis18α in the female germ line at the time of birth has no impact on centromeric CENP-A nucleosome abundance, even after 6-8 months of aging. In addition, there is no detectable detriment to fertility. Thus, centromere chromatin is maintained long-term, independent of new assembly during the extended prophase I arrest in mouse oocytes.
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Affiliation(s)
- Arunika Das
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Katelyn G Boese
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kikue Tachibana
- Department of Totipotency, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Sung Hee Baek
- Creative Research Initiatives Center for Epigenetic Code and Diseases, Seoul National University, Seoul 08826, Republic of Korea
| | - Michael A Lampson
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Center for Genome Integrity, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Ben E Black
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Center for Genome Integrity, University of Pennsylvania, Philadelphia, PA 19104, USA.
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20
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Li D, Quan Z, Ni J, Li H, Qing H. The many faces of the zinc finger protein 335 in brain development and immune system. Biomed Pharmacother 2023; 165:115257. [PMID: 37541176 DOI: 10.1016/j.biopha.2023.115257] [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: 06/02/2023] [Revised: 07/25/2023] [Accepted: 07/28/2023] [Indexed: 08/06/2023] Open
Abstract
Zinc finger protein 335 (ZNF335) plays a crucial role in the methylation and, consequently, regulates the expression of a specific set of genes. Variants of the ZNF335 gene have been identified as risk factors for microcephaly in a variety of populations worldwide. Meanwhile, ZNF335 has also been identified as an essential regulator of T-cell development. However, an in-depth understanding of the role of ZNF335 in brain development and T cell maturation is still lacking. In this review, we summarize current knowledge of the molecular mechanisms underlying the involvement of ZNF335 in neuronal and T cell development across a wide range of pre-clinical, post-mortem, ex vivo, in vivo, and clinical studies. We also review the current limitations regarding the study of the pathophysiological functions of ZNF335. Finally, we hypothesize a potential role for ZNF335 in brain disorders and discuss the rationale of targeting ZNF335 as a therapeutic strategy for preventing brain disorders.
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Affiliation(s)
- Danyang Li
- Key Laboratory of Molecular Medicine and Biotherapy, Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing 100081, China.
| | - Zhenzhen Quan
- Key Laboratory of Molecular Medicine and Biotherapy, Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing 100081, China.
| | - Junjun Ni
- Key Laboratory of Molecular Medicine and Biotherapy, Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing 100081, China.
| | - Hui Li
- Key Laboratory of Molecular Medicine and Biotherapy, Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing 100081, China.
| | - Hong Qing
- Key Laboratory of Molecular Medicine and Biotherapy, Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing 100081, China.
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21
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Ma C, Yang Z, Zhang S, Zhang X, Wang S, Cheng H, Liu Y, Ruan H, Xu Z, Liang C, Liang D, Ding Z, Liu Y, Cao Y. Carbendazim exposure inhibits mouse oocytes meiotic maturation in vitro by destroying spindle assembly. Food Chem Toxicol 2023; 179:113966. [PMID: 37506866 DOI: 10.1016/j.fct.2023.113966] [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: 06/01/2023] [Revised: 07/13/2023] [Accepted: 07/24/2023] [Indexed: 07/30/2023]
Abstract
Successful fertilization and early embryonic development heavily depend on the quality of the oocytes. Carbendazim (CBZ), a broad-spectrum fungicide, is widely available in the environment and has adverse effects on organisms. The present study focused on exploring the potential reproductive toxicity of CBZ exposure by investigating its effects on the maturation of mouse oocytes. The results demonstrated that although no disruptions were observed in the G2/M stage transition for meiosis resumption, CBZ did hinder the polar body extrusion (PBE) occurring during oocyte maturation. Cell cycle distribution analysis revealed that CBZ exposure interfered with the meiotic process, causing oocytes to be arrested at the metaphase I (MI) stage. The subsequent investigation highlighted that CBZ exposure impeded the spindle assembly and chromosomal alignment, which was linked to a decline in the level of p-MAPK. Additionally, CBZ exposure adversely affected the kinetochore-microtubule (K-MT) attachment, leading to the persistent activation of the spindle-assembly checkpoint (SAC). The study further noticed a substantial rise in the acetylation of α-tubulin and a reduction in spindle microtubule stability in CBZ-treated oocytes. In addition, the distribution pattern of estrogen receptor alpha (ERα) was altered in oocytes treated with CBZ, with abnormal aggregation on the spindles. CBZ exposure also resulted in altered histone modifications. A notable finding from this research was that the meiotic maturation of some oocytes remained unaffected even after CBZ treatment. However, during the ensuing metaphase II (MII) stage, these oocytes displayed anomalies in their spindle morphology and chromosome arrangement and diminished ability to bind to the sperm. The observations made in this study underscore the potential for CBZ to disrupt the meiotic maturation of oocytes, leading to a decline in the overall quality of oocytes.
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Affiliation(s)
- Cong Ma
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, No.218 Jixi Road, Hefei, 230022, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, No.81 Meishan Road, Hefei, 230032, China; Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, No.81 Meishan Road, Hefei, 230032, China
| | - Zhuonan Yang
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, No.218 Jixi Road, Hefei, 230022, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, No.81 Meishan Road, Hefei, 230032, China; Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, No.81 Meishan Road, Hefei, 230032, China
| | - Shouxin Zhang
- Biochip Laboratory, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000, China
| | - Xueke Zhang
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, No.218 Jixi Road, Hefei, 230022, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, No.81 Meishan Road, Hefei, 230032, China; Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, No.81 Meishan Road, Hefei, 230032, China
| | - Siyuan Wang
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, No.81 Meishan Road, Hefei, 230032, China; Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, No.81 Meishan Road, Hefei, 230032, China; Anhui Province Key Laboratory of Reproductive Health and Genetics, No.81 Meishan Road, Hefei, 230032, China
| | - Huiru Cheng
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, No.81 Meishan Road, Hefei, 230032, China; Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, No.81 Meishan Road, Hefei, 230032, China; Anhui Province Key Laboratory of Reproductive Health and Genetics, No.81 Meishan Road, Hefei, 230032, China
| | - Yang Liu
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, No.81 Meishan Road, Hefei, 230032, China; Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, No.81 Meishan Road, Hefei, 230032, China; Anhui Province Key Laboratory of Reproductive Health and Genetics, No.81 Meishan Road, Hefei, 230032, China
| | - Hongzhen Ruan
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, No.218 Jixi Road, Hefei, 230022, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, No.81 Meishan Road, Hefei, 230032, China; Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, No.81 Meishan Road, Hefei, 230032, China
| | - Zuying Xu
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, No.218 Jixi Road, Hefei, 230022, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, No.81 Meishan Road, Hefei, 230032, China; Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, No.81 Meishan Road, Hefei, 230032, China
| | - Chunmei Liang
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, No.81 Meishan Road, Hefei, 230032, China; Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, No.81 Meishan Road, Hefei, 230032, China; Anhui Province Key Laboratory of Reproductive Health and Genetics, No.81 Meishan Road, Hefei, 230032, China
| | - Dan Liang
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, No.218 Jixi Road, Hefei, 230022, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, No.81 Meishan Road, Hefei, 230032, China; Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, No.81 Meishan Road, Hefei, 230032, China; Anhui Province Key Laboratory of Reproductive Health and Genetics, No.81 Meishan Road, Hefei, 230032, China; Biopreservation and Artificial Organs, Anhui Provincial Engineering Research Center, Anhui Medical University, No.81 Meishan Road, Hefei, 230032, China; Anhui Provincial Institute of Translational Medicine, No.81 Meishan Road, Hefei, 230032, China
| | - Zhiming Ding
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, No.218 Jixi Road, Hefei, 230022, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, No.81 Meishan Road, Hefei, 230032, China; Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, No.81 Meishan Road, Hefei, 230032, China; Anhui Province Key Laboratory of Reproductive Health and Genetics, No.81 Meishan Road, Hefei, 230032, China; Biopreservation and Artificial Organs, Anhui Provincial Engineering Research Center, Anhui Medical University, No.81 Meishan Road, Hefei, 230032, China; Anhui Provincial Institute of Translational Medicine, No.81 Meishan Road, Hefei, 230032, China.
| | - Yajing Liu
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, No.218 Jixi Road, Hefei, 230022, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, No.81 Meishan Road, Hefei, 230032, China; Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, No.81 Meishan Road, Hefei, 230032, China; Anhui Province Key Laboratory of Reproductive Health and Genetics, No.81 Meishan Road, Hefei, 230032, China; Biopreservation and Artificial Organs, Anhui Provincial Engineering Research Center, Anhui Medical University, No.81 Meishan Road, Hefei, 230032, China; Anhui Provincial Institute of Translational Medicine, No.81 Meishan Road, Hefei, 230032, China.
| | - Yunxia Cao
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, No.218 Jixi Road, Hefei, 230022, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, No.81 Meishan Road, Hefei, 230032, China; Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, No.81 Meishan Road, Hefei, 230032, China; Anhui Province Key Laboratory of Reproductive Health and Genetics, No.81 Meishan Road, Hefei, 230032, China; Biopreservation and Artificial Organs, Anhui Provincial Engineering Research Center, Anhui Medical University, No.81 Meishan Road, Hefei, 230032, China; Anhui Provincial Institute of Translational Medicine, No.81 Meishan Road, Hefei, 230032, China.
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22
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Chen Y, Wang L, Guo F, Dai X, Zhang X. Epigenetic reprogramming during the maternal-to-zygotic transition. MedComm (Beijing) 2023; 4:e331. [PMID: 37547174 PMCID: PMC10397483 DOI: 10.1002/mco2.331] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 08/08/2023] Open
Abstract
After fertilization, sperm and oocyte fused and gave rise to a zygote which is the beginning of a new life. Then the embryonic development is monitored and regulated precisely from the transition of oocyte to the embryo at the early stage of embryogenesis, and this process is termed maternal-to-zygotic transition (MZT). MZT involves two major events that are maternal components degradation and zygotic genome activation. The epigenetic reprogramming plays crucial roles in regulating the process of MZT and supervising the normal development of early development of embryos. In recent years, benefited from the rapid development of low-input epigenome profiling technologies, new epigenetic modifications are found to be reprogrammed dramatically and may play different roles during MZT whose dysregulation will cause an abnormal development of embryos even abortion at various stages. In this review, we summarized and discussed the important novel findings on epigenetic reprogramming and the underlying molecular mechanisms regulating MZT in mammalian embryos. Our work provided comprehensive and detailed references for the in deep understanding of epigenetic regulatory network in this key biological process and also shed light on the critical roles for epigenetic reprogramming on embryonic failure during artificial reproductive technology and nature fertilization.
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Affiliation(s)
- Yurong Chen
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education First Hospital of Jilin University Changchun China
- National-Local Joint Engineering Laboratory of Animal Models for Human Disease First Hospital of Jilin University Changchun China
| | - Luyao Wang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education First Hospital of Jilin University Changchun China
- National-Local Joint Engineering Laboratory of Animal Models for Human Disease First Hospital of Jilin University Changchun China
| | - Fucheng Guo
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education First Hospital of Jilin University Changchun China
- National-Local Joint Engineering Laboratory of Animal Models for Human Disease First Hospital of Jilin University Changchun China
| | - Xiangpeng Dai
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education First Hospital of Jilin University Changchun China
- National-Local Joint Engineering Laboratory of Animal Models for Human Disease First Hospital of Jilin University Changchun China
| | - Xiaoling Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education First Hospital of Jilin University Changchun China
- National-Local Joint Engineering Laboratory of Animal Models for Human Disease First Hospital of Jilin University Changchun China
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23
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Yu W, Zhou R, Li N, Lei ZC, Guo D, Peng F, Li Y, Bai X, Feng S, Wang Y, He J, Yin S, Zeng X, He L, Gao Y, Li M, Guo YR, Liu K, Wang Y. Histone tyrosine sulfation by SULT1B1 regulates H4R3me2a and gene transcription. Nat Chem Biol 2023; 19:855-864. [PMID: 36805701 DOI: 10.1038/s41589-023-01267-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 01/16/2023] [Indexed: 02/22/2023]
Abstract
Tyrosine sulfation is a common posttranslational modification in mammals. To date, it has been thought to be limited to secreted and transmembrane proteins, but little is known about tyrosine sulfation on nuclear proteins. Here we report that SULT1B1 is a histone sulfotransferase that can sulfate the tyrosine 99 residue of nascent histone H3 in cytosol. The sulfated histone H3 can be transported into the nucleus and majorly deposited in the promoter regions of genes in chromatin. While the H3Y99 residue is buried inside octameric nucleosome, dynamically regulated subnucleosomal structures provide chromatin-H3Y99sulf the opportunity of being recognized and bound by PRMT1, which deposits H4R3me2a in chromatin. Disruption of H3Y99sulf reduces PRMT1 binding to chromatin, H4R3me2a level and gene transcription. These findings reveal the mechanisms underlying H3Y99 sulfation and its cross-talk with H4R3me2a to regulate gene transcription. This study extends the spectrum of tyrosine sulfation on nuclear proteins and the repertoire of histone modifications regulating chromatin functions.
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Affiliation(s)
- Weixing Yu
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Runxin Zhou
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Nan Li
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhi-Chao Lei
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dingyuan Guo
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fei Peng
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yan Li
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xue Bai
- Mass Spectrometry & Metabolomics Core Facility, The Biomedical Research Core Facility, Center for Research Equipment and Facilities, Westlake University, Hangzhou, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Shan Feng
- Mass Spectrometry & Metabolomics Core Facility, The Biomedical Research Core Facility, Center for Research Equipment and Facilities, Westlake University, Hangzhou, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Yu Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jie He
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Sibi Yin
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiao Zeng
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Leya He
- Department of Gastrointestinal Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuan Gao
- Institute of Precision Medicine, Jining Medical University, Jining, China
| | - Mingchang Li
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yusong R Guo
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ke Liu
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China.
| | - Yugang Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- Cell Architecture Research Center, Huazhong University of Science and Technology, Wuhan, China.
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24
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Pandupuspitasari NS, Khan FA, Huang C, Ali A, Yousaf MR, Shakeel F, Putri EM, Negara W, Muktiani A, Prasetiyono BWHE, Kustiawan L, Wahyuni DS. Recent advances in chromosome capture techniques unraveling 3D genome architecture in germ cells, health, and disease. Funct Integr Genomics 2023; 23:214. [PMID: 37386239 DOI: 10.1007/s10142-023-01146-5] [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: 04/08/2023] [Revised: 06/16/2023] [Accepted: 06/20/2023] [Indexed: 07/01/2023]
Abstract
In eukaryotes, the genome does not emerge in a specific shape but rather as a hierarchial bundle within the nucleus. This multifaceted genome organization consists of multiresolution cellular structures, such as chromosome territories, compartments, and topologically associating domains, which are frequently defined by architecture, design proteins including CTCF and cohesin, and chromatin loops. This review briefly discusses the advances in understanding the basic rules of control, chromatin folding, and functional areas in early embryogenesis. With the use of chromosome capture techniques, the latest advancements in technologies for visualizing chromatin interactions come close to revealing 3D genome formation frameworks with incredible detail throughout all genomic levels, including at single-cell resolution. The possibility of detecting variations in chromatin architecture might open up new opportunities for disease diagnosis and prevention, infertility treatments, therapeutic approaches, desired exploration, and many other application scenarios.
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Affiliation(s)
- Nuruliarizki Shinta Pandupuspitasari
- Laboratory of Animal Nutrition and Feed Science, Animal Science Department, Faculty of Animal and Agricultural Sciences, Universitas Diponegoro, Semarang, Indonesia.
| | - Faheem Ahmed Khan
- Research Center for Animal Husbandry, National Research and Innovation Agency, Bogor, Indonesia
| | - Chunjie Huang
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong, 226001, China
| | - Azhar Ali
- Laboratory of Molecular Biology and Genomics, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Muhammad Rizwan Yousaf
- Laboratory of Molecular Biology and Genomics, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Farwa Shakeel
- Laboratory of Molecular Biology and Genomics, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Ezi Masdia Putri
- Research Center for Animal Husbandry, National Research and Innovation Agency, Bogor, Indonesia
| | - Windu Negara
- Research Center for Animal Husbandry, National Research and Innovation Agency, Bogor, Indonesia
| | - Anis Muktiani
- Laboratory of Animal Nutrition and Feed Science, Animal Science Department, Faculty of Animal and Agricultural Sciences, Universitas Diponegoro, Semarang, Indonesia
| | - Bambang Waluyo Hadi Eko Prasetiyono
- Laboratory of Feed Technology, Animal Science Department, Faculty of Animal and Agricultural Sciences Universitas Diponegoro, Semarang, Indonesia
| | - Limbang Kustiawan
- Laboratory of Animal Nutrition and Feed Science, Animal Science Department, Faculty of Animal and Agricultural Sciences, Universitas Diponegoro, Semarang, Indonesia
| | - Dimar Sari Wahyuni
- Research Center for Animal Husbandry, National Research and Innovation Agency, Bogor, Indonesia
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25
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Das A, Boese KG, Tachibana K, Baek SH, Lampson MA, Black BE. Centromere-specifying nucleosomes persist in aging mouse oocytes in the absence of nascent assembly. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.18.541332. [PMID: 37292821 PMCID: PMC10245701 DOI: 10.1101/2023.05.18.541332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Centromeres direct genetic inheritance but are not themselves genetically encoded. Instead, centromeres are defined epigenetically by the presence of a histone H3 variant, CENP-A 1 . In cultured somatic cells, an established paradigm of cell cycle-coupled propagation maintains centromere identity: CENP-A is partitioned between sisters during replication and replenished by new assembly, which is restricted to G1. The mammalian female germline challenges this model because of the cell cycle arrest between pre-meiotic S-phase and the subsequent G1, which can last for the entire reproductive lifespan (months to decades). New CENP-A chromatin assembly maintains centromeres during prophase I in worm and starfish oocyte 2,3 , suggesting that a similar process may be required for centromere inheritance in mammals. However, we show that centromere chromatin is maintained long-term independent of new assembly during the extended prophase I arrest in mouse oocytes. Conditional knockout of Mis18α, an essential component of the assembly machinery, in the female germline at the time of birth has almost no impact on centromeric CENP-A nucleosome abundance nor any detectable detriment to fertility.
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Affiliation(s)
- Arunika Das
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Katelyn G. Boese
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kikue Tachibana
- Department of Totipotency, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Sung Hee Baek
- Creative Research Initiatives Center for Epigenetic Code and Diseases, Seoul National University, Seoul 08826
| | - Michael A. Lampson
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Center for Genome Integrity, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ben E. Black
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Epigenetics Institute; University of Pennsylvania, Philadelphia PA 19104, USA
- Penn Center for Genome Integrity, University of Pennsylvania, Philadelphia, PA 19104, USA
- Lead Contact
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26
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Zhao Y, Zhai Y, Fu C, Shi L, Kong X, Li Q, Yu H, An X, Zhang S, Li Z. Transcription factor ELK1 regulates the expression of histone 3 lysine 9 to affect developmental potential of porcine preimplantation embryos. Theriogenology 2023; 206:170-180. [PMID: 37224706 DOI: 10.1016/j.theriogenology.2023.05.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/07/2023] [Accepted: 05/17/2023] [Indexed: 05/26/2023]
Abstract
A series of changes occur in the early embryo that are critical for subsequent development, and the pig is an excellent animal model of human disease, so understanding the regulatory mechanisms of early embryonic development in the pig is of very importance. To find key transcription factors regulating pig early embryonic development, we first profiled the transcriptome of pig early embryos, and confirmed that zygotic gene activation (ZGA) in porcine embryos starts from 4 cell stage. Subsequent enrichment analysis of up-regulated gene motifs during ZGA revealed that the transcription factor ELK1 ranked first. The expression pattern of ELK1 in porcine early embryos was analyzed by immunofluorescence staining and qPCR, and the results showed that the transcript level of ELK1 reached the highest at the 8 cell stage, while the protein level reached the highest at 4 cell stage. To further investigate the effect of ELK1 on early embryo development in pigs, we silenced ELK1 in zygotes and showed that ELK1 silencing significantly reduced cleavage rate, blastocyst rate as well as blastocyst quality. A significant decrease in the expression of the pluripotency gene Oct4 was also observed in blastocysts from the ELK1 silenced group by immunofluorescence staining. Silencing of ELK1 also resulted in decreased H3K9Ac modification and increased H3K9me3 modification at 4 cell stage. To investigate the effect of ELK1 on ZGA, we analyzed transcriptome changes in 4 cell embryos after ELK1 silencing by RNA seq, which revealed that ELK1 silencing resulted in significant differences in the expression of a total of 1953 genes at the 4 cell stage compared with their normal counterparts, including 1106 genes that were significantly upregulated and 847 genes that were significantly downregulated. Through GO and KEGG enrichment, we found that the functions and pathways of down-regulated genes were concentrated in protein synthesis, processing, cell cycle regulation, etc., while the functions of up-regulated genes were focused on aerobic respiration process. In conclusion, this study demonstrates that the transcription factor ELK1 plays an important role in regulation of preimplantation embryo development of pigs and deficiency of ELK1 leads to abnormal epigenetic reprogramming as well as zygotic genome activation, thus adversely affecting embryonic development. This study will provide important reference for the regulation of transcription factors in porcine embryo development.
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Affiliation(s)
- Yuanshen Zhao
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Yanhui Zhai
- Shenzhen Key Laboratory of Fertility Regulation, Center of Assisted Reproduction and Embryology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, 518053, China
| | - Cong Fu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Lijing Shi
- College of Animal Science, Jilin University, Changchun, Jilin, 130062, China
| | - Xiangjie Kong
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Qi Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Hao Yu
- College of Animal Science, Jilin University, Changchun, Jilin, 130062, China
| | - Xinglan An
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Sheng Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Ziyi Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital of Jilin University, Changchun, Jilin, 130021, China.
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27
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Ouyang W, Zhang X, Guo M, Wang J, Wang X, Gao R, Ma M, Xiang X, Luan S, Xing F, Cao Z, Yan J, Li G, Li X. Haplotype mapping of H3K27me3-associated chromatin interactions defines topological regulation of gene silencing in rice. Cell Rep 2023; 42:112350. [PMID: 37071534 DOI: 10.1016/j.celrep.2023.112350] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 02/06/2023] [Accepted: 03/20/2023] [Indexed: 04/19/2023] Open
Abstract
Histone modification H3K27me3 is an important chromatin mark that plays vital roles in repressing expression of developmental genes. Here, we construct high-resolution 3D genome maps using long-read chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) and characterize H3K27me3-associated chromatin interactions in an elite rice hybrid, Shanyou 63. We find that many H3K27me3-marked regions may function as silencer-like regulatory elements. The silencer-like elements can come into proximity with distal target genes via forming chromatin loops in 3D space of the nuclei, regulating gene silencing and plant traits. Natural and induced deletion of silencers upregulate expression of distal connected genes. Furthermore, we identify extensive allele-specific chromatin loops. We find that genetic variations alter allelic chromatin topology, thus modulating allelic gene imprinting in rice hybrids. In conclusion, the characterization of silencer-like regulatory elements and haplotype-resolved chromatin interaction maps provide insights into the understanding of molecular mechanisms underlying allelic gene silencing and plant trait controlling.
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Affiliation(s)
- Weizhi Ouyang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiwen Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Minrong Guo
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Jing Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaoting Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Runxin Gao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Meng Ma
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Xu Xiang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Shiping Luan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Feng Xing
- College of Life Science, Xinyang Normal University, Xinyang 464000, China
| | - Zhilin Cao
- Department of Resources and Environment, Henan University of Engineering, Zhengzhou 451191, China
| | - Jiapei Yan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
| | - Xingwang Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
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28
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Zhu W, Ding Y, Meng J, Gu L, Liu W, Li L, Chen H, Wang Y, Li Z, Li C, Sun Y, Liu Z. Reading and writing of mRNA m 6A modification orchestrate maternal-to-zygotic transition in mice. Genome Biol 2023; 24:67. [PMID: 37024923 PMCID: PMC10080794 DOI: 10.1186/s13059-023-02918-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 03/31/2023] [Indexed: 04/08/2023] Open
Abstract
N6-methyladenosine (m6A) modification has been shown to regulate RNA metabolism. Here, we investigate m6A dynamics during maternal-to-zygotic transition (MZT) in mice through multi-omic analysis. Our results show that m6A can be maternally inherited or de novo gained after fertilization. Interestingly, m6A modification on maternal mRNAs not only correlates with mRNA degradation, but also maintains the stability of a small group of mRNAs thereby promoting their translation after fertilization. We identify Ythdc1 and Ythdf2 as key m6A readers for mouse preimplantation development. Our study reveals a key role of m6A mediated RNA metabolism during MZT in mammals.
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Affiliation(s)
- Wencheng Zhu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, China
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China
| | - Yufeng Ding
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, China
| | - Juan Meng
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lei Gu
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenjun Liu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Li Li
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, China
| | - Hongyu Chen
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, China
| | - Yining Wang
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, China
| | - Ziyi Li
- Shanghai Applied Protein Technology Co., Ltd., Shanghai, China
| | - Chen Li
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Yidi Sun
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, China.
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China.
| | - Zhen Liu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, China.
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China.
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29
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Zhu D, Wen Y, Yao W, Zheng H, Zhou S, Zhang Q, Qu LJ, Chen X, Wu Z. Distinct chromatin signatures in the Arabidopsis male gametophyte. Nat Genet 2023; 55:706-720. [PMID: 36864100 DOI: 10.1038/s41588-023-01329-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 01/30/2023] [Indexed: 03/04/2023]
Abstract
Epigenetic reprogramming in the germline contributes to the erasure of epigenetic inheritance across generations in mammals but remains poorly characterized in plants. Here we profiled histone modifications throughout Arabidopsis male germline development. We find that the sperm cell has widespread apparent chromatin bivalency, which is established by the acquisition of H3K27me3 or H3K4me3 at pre-existing H3K4me3 or H3K27me3 regions, respectively. These bivalent domains are associated with a distinct transcriptional status. Somatic H3K27me3 is generally reduced in sperm, while dramatic loss of H3K27me3 is observed at only ~700 developmental genes. The incorporation of the histone variant H3.10 facilitates the establishment of sperm chromatin identity without a strong impact on resetting of somatic H3K27me3. Vegetative nuclei harbor thousands of specific H3K27me3 domains at repressed genes, while pollination-related genes are highly expressed and marked by gene body H3K4me3. Our work highlights putative chromatin bivalency and restricted resetting of H3K27me3 at developmental regulators as key features in plant pluripotent sperm.
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Affiliation(s)
- Danling Zhu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yi Wen
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Wanyue Yao
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Haiyan Zheng
- Center for Advanced Biotechnology and Medicine, Biological Mass Spectrometry Facility, Rutgers University, Piscataway, NJ, USA
| | - Sixian Zhou
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Qiqi Zhang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Li-Jia Qu
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing, China
| | - Xi Chen
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.
| | - Zhe Wu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.
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30
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Spadafora C. The epigenetic basis of evolution. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2023; 178:57-69. [PMID: 36720315 DOI: 10.1016/j.pbiomolbio.2023.01.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/17/2022] [Accepted: 01/26/2023] [Indexed: 01/31/2023]
Abstract
An increasing body of data are revealing key roles of epigenetics in evolutionary processes. The scope of this manuscript is to assemble in a coherent frame experimental evidence supporting a role of epigenetic factors and networks, active during embryogenesis, in orchestrating variation-inducing phenomena underlying evolution, seen as a global process. This process unfolds over two crucial levels: i) a flow of RNA-based information - predominantly small regulatory RNAs released from somatic cells exposed to environmental stimuli - taken up by spermatozoa and delivered to oocytes at fertilization and ii) the highly permissive and variation-prone environments offered by zygotes and totipotent early embryos. Totipotent embryos provide a variety of biological tools favouring the emergence of evolutionarily significant phenotypic novelties driven by RNA information. Under this light, neither random genomic mutations, nor the sieving role of natural selection are required, as the sperm-delivered RNA cargo conveys specific information and acts as "phenotypic-inducer" of defined environmentally acquired traits.
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Affiliation(s)
- Corrado Spadafora
- Institute of Translational Pharmacology, National Research Council (CNR), Rome, Italy.
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31
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Zhu J, Chen K, Sun YH, Ye W, Liu J, Zhang D, Su N, Wu L, Kou X, Zhao Y, Wang H, Gao S, Kang L. LSM1-mediated Major Satellite RNA decay is required for nonequilibrium histone H3.3 incorporation into parental pronuclei. Nat Commun 2023; 14:957. [PMID: 36810573 PMCID: PMC9944933 DOI: 10.1038/s41467-023-36584-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 02/06/2023] [Indexed: 02/24/2023] Open
Abstract
Epigenetic reprogramming of the parental genome is essential for zygotic genome activation and subsequent embryo development in mammals. Asymmetric incorporation of histone H3 variants into the parental genome has been observed previously, but the underlying mechanism remains elusive. In this study, we discover that RNA-binding protein LSM1-mediated major satellite RNA decay plays a central role in the preferential incorporation of histone variant H3.3 into the male pronucleus. Knockdown of Lsm1 disrupts nonequilibrium pronucleus histone incorporation and asymmetric H3K9me3 modification. Subsequently, we find that LSM1 mainly targets major satellite repeat RNA (MajSat RNA) for decay and that accumulated MajSat RNA in Lsm1-depleted oocytes leads to abnormal incorporation of H3.1 into the male pronucleus. Knockdown of MajSat RNA reverses the anomalous histone incorporation and modifications in Lsm1-knockdown zygotes. Our study therefore reveals that accurate histone variant incorporation and incidental modifications in parental pronuclei are specified by LSM1-dependent pericentromeric RNA decay.
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Affiliation(s)
- Jiang Zhu
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, 200120, Shanghai, China.,Frontier Science Center for Stem Cell Research, Tongji University, 200092, Shanghai, China
| | - Kang Chen
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, 200120, Shanghai, China.,Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yu H Sun
- Departments of Biology, University of Rochester, 14642, Rochester, NY, USA
| | - Wen Ye
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, 200120, Shanghai, China
| | - Juntao Liu
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, 200120, Shanghai, China
| | - Dandan Zhang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, 200120, Shanghai, China
| | - Nan Su
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, 200120, Shanghai, China
| | - Li Wu
- Clinical and Translation Research Center of Shanghai First Maternity & Infant Hospital, School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China
| | - Xiaochen Kou
- Frontier Science Center for Stem Cell Research, Tongji University, 200092, Shanghai, China
| | - Yanhong Zhao
- Frontier Science Center for Stem Cell Research, Tongji University, 200092, Shanghai, China
| | - Hong Wang
- Clinical and Translation Research Center of Shanghai First Maternity & Infant Hospital, School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China
| | - Shaorong Gao
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, 200120, Shanghai, China. .,Frontier Science Center for Stem Cell Research, Tongji University, 200092, Shanghai, China. .,Clinical and Translation Research Center of Shanghai First Maternity & Infant Hospital, School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China.
| | - Lan Kang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, 200120, Shanghai, China. .,Frontier Science Center for Stem Cell Research, Tongji University, 200092, Shanghai, China.
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32
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Zhao L, Yang Y, Chen J, Lin X, Zhang H, Wang H, Wang H, Bie X, Jiang J, Feng X, Fu X, Zhang X, Du Z, Xiao J. Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat. Genome Biol 2023; 24:7. [PMID: 36639687 PMCID: PMC9837924 DOI: 10.1186/s13059-022-02844-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 12/31/2022] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Plant and animal embryogenesis have conserved and distinct features. Cell fate transitions occur during embryogenesis in both plants and animals. The epigenomic processes regulating plant embryogenesis remain largely elusive. RESULTS Here, we elucidate chromatin and transcriptomic dynamics during embryogenesis of the most cultivated crop, hexaploid wheat. Time-series analysis reveals stage-specific and proximal-distal distinct chromatin accessibility and dynamics concordant with transcriptome changes. Following fertilization, the remodeling kinetics of H3K4me3, H3K27ac, and H3K27me3 differ from that in mammals, highlighting considerable species-specific epigenomic dynamics during zygotic genome activation. Polycomb repressive complex 2 (PRC2)-mediated H3K27me3 deposition is important for embryo establishment. Later H3K27ac, H3K27me3, and chromatin accessibility undergo dramatic remodeling to establish a permissive chromatin environment facilitating the access of transcription factors to cis-elements for fate patterning. Embryonic maturation is characterized by increasing H3K27me3 and decreasing chromatin accessibility, which likely participates in restricting totipotency while preventing extensive organogenesis. Finally, epigenomic signatures are correlated with biased expression among homeolog triads and divergent expression after polyploidization, revealing an epigenomic contributor to subgenome diversification in an allohexaploid genome. CONCLUSIONS Collectively, we present an invaluable resource for comparative and mechanistic analysis of the epigenomic regulation of crop embryogenesis.
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Affiliation(s)
- Long Zhao
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Yiman Yang
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.,Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Jinchao Chen
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuelei Lin
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hao Zhang
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hao Wang
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hongzhe Wang
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaomin Bie
- Shandong Agricultural University, Tai'an, Shandong, China
| | - Jiafu Jiang
- Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Xiaoqi Feng
- John Innes Centre, Colney Lane, Norwich, NR4 7UH, UK
| | - Xiangdong Fu
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | | | - Zhuo Du
- University of Chinese Academy of Sciences, Beijing, 100049, China.,State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jun Xiao
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
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33
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Roles of Polycomb Complexes in the Reconstruction of 3D Genome Architecture during Preimplantation Embryonic Development. Genes (Basel) 2022; 13:genes13122382. [PMID: 36553649 PMCID: PMC9778514 DOI: 10.3390/genes13122382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 11/29/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
The appropriate deployment of developmental programs depends on complex genetic information encoded by genomic DNA sequences and their positioning and contacts in the three-dimensional (3D) space within the nucleus. Current studies using novel techniques including, but not limited to, Hi-C, ChIA-PET, and Hi-ChIP reveal that regulatory elements (Res), such as enhancers and promoters, may participate in the precise regulation of expression of tissue-specific genes important for both embryogenesis and organogenesis by recruiting Polycomb Group (PcG) complexes. PcG complexes usually poise the transcription of developmental genes by forming Polycomb bodies to compact poised enhancers and promoters marked by H3K27me3 in the 3D space. Additionally, recent studies have also uncovered their roles in transcriptional activation. To better understand the full complexities in the mechanisms of how PcG complexes regulate transcription and long-range 3D contacts of enhancers and promoters during developmental programs, we outline novel insights regarding PcG-associated dramatic changes in the 3D chromatin conformation in developmental programs of early embryos and naïve-ground-state transitions of pluripotent embryonic stem cells (ESCs), and highlight the distinct roles of unique and common subunits of canonical and non-canonical PcG complexes in shaping genome architectures and transcriptional programs.
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34
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Deluao JC, Winstanley Y, Robker RL, Pacella-Ince L, Gonzalez MB, McPherson NO. OXIDATIVE STRESS AND REPRODUCTIVE FUNCTION: Reactive oxygen species in the mammalian pre-implantation embryo. Reproduction 2022; 164:F95-F108. [PMID: 36111646 DOI: 10.1530/rep-22-0121] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 09/15/2022] [Indexed: 11/08/2022]
Abstract
In brief Reactive oxygen species are generated throughout the pre-implantation period and are necessary for normal embryo formation. However, at pathological levels, they result in reduced embryo viability which can be mediated through factors delivered by sperm and eggs at conception or from the external environment. Abstract Reactive oxygen species (ROS) occur naturally in pre-implantation embryos as a by-product of ATP generation through oxidative phosphorylation and enzymes such as NADPH oxidase and xanthine oxidase. Biological concentrations of ROS are required for crucial embryonic events such as pronuclear formation, first cleavage and cell proliferation. However, high concentrations of ROS are detrimental to embryo development, resulting in embryo arrest, increased DNA damage and modification of gene expression leading to aberrant fetal growth and health. In vivo embryos are protected against oxidative stress by oxygen scavengers present in follicular and oviductal fluids, while in vitro, embryos rely on their own antioxidant defence mechanisms to protect against oxidative damage, including superoxide dismutase, catalase, glutathione and glutamylcysteine synthestase. Pre-implantation embryonic ROS originate from eggs, sperm and embryos themselves or from the external environment (i.e. in vitro culture system, obesity and ageing). This review examines the biological and pathological roles of ROS in the pre-implantation embryo, maternal and paternal origins of embryonic ROS, and from a clinical perspective, we comment on the growing interest in combating increased oxidative damage in the pre-implantation embryo through the addition of antioxidants.
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Affiliation(s)
- Joshua C Deluao
- Robinson Research Institute, The University of Adelaide, Adelaide, Australia.,Freemasons Centre for Male Health and Wellbeing, The University of Adelaide, Adelaide, Australia.,Adelaide Health and Medical School, School of Biomedicine, Discipline of Reproduction and Development, The University of Adelaide, Adelaide, Australia
| | - Yasmyn Winstanley
- Robinson Research Institute, The University of Adelaide, Adelaide, Australia.,Adelaide Health and Medical School, School of Biomedicine, Discipline of Reproduction and Development, The University of Adelaide, Adelaide, Australia
| | - Rebecca L Robker
- Robinson Research Institute, The University of Adelaide, Adelaide, Australia.,Adelaide Health and Medical School, School of Biomedicine, Discipline of Reproduction and Development, The University of Adelaide, Adelaide, Australia.,Department of Anatomy and Developmental Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Leanne Pacella-Ince
- Adelaide Health and Medical School, School of Biomedicine, Discipline of Reproduction and Development, The University of Adelaide, Adelaide, Australia.,Repromed, Dulwich, Australia
| | - Macarena B Gonzalez
- Robinson Research Institute, The University of Adelaide, Adelaide, Australia.,Adelaide Health and Medical School, School of Biomedicine, Discipline of Reproduction and Development, The University of Adelaide, Adelaide, Australia
| | - Nicole O McPherson
- Robinson Research Institute, The University of Adelaide, Adelaide, Australia.,Freemasons Centre for Male Health and Wellbeing, The University of Adelaide, Adelaide, Australia.,Adelaide Health and Medical School, School of Biomedicine, Discipline of Reproduction and Development, The University of Adelaide, Adelaide, Australia.,Repromed, Dulwich, Australia
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35
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Verdikt R, Armstrong AA, Allard P. Transgenerational inheritance and its modulation by environmental cues. Curr Top Dev Biol 2022; 152:31-76. [PMID: 36707214 PMCID: PMC9940302 DOI: 10.1016/bs.ctdb.2022.10.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The epigenome plays an important role in shaping phenotypes. However, whether the environment can alter an organism's phenotype across several generations through epigenetic remodeling in the germline is still a highly debated topic. In this chapter, we briefly review the mechanisms of epigenetic inheritance and their connection with germline development before highlighting specific developmental windows of susceptibility to environmental cues. We further discuss the evidence of transgenerational inheritance to a range of different environmental cues, both epidemiological in humans and experimental in rodent models. Doing so, we pinpoint the current challenges in demonstrating transgenerational inheritance to environmental cues and offer insight in how recent technological advances may help deciphering the epigenetic mechanisms at play. Together, we draw a detailed picture of how our environment can influence our epigenomes, ultimately reshaping our phenotypes, in an extended theory of inheritance.
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Affiliation(s)
- Roxane Verdikt
- Institute for Society and Genetics, University of California, Los Angeles, Los Angeles, CA, United States.
| | - Abigail A Armstrong
- Department of Obstetrics/Gynecology and Division of Reproductive Endocrinology and Infertility, University of California, Los Angeles, CA, United States
| | - Patrick Allard
- Institute for Society and Genetics, University of California, Los Angeles, Los Angeles, CA, United States; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, United States.
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36
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Jin J, Jiang J, Wu Z, Huang R, Sun M, Bao W. Transcriptomic and chromatin accessibility dynamics of porcine alveolar macrophages in exposure to fumonisin B1. Front Cell Dev Biol 2022; 10:876247. [PMID: 36330331 PMCID: PMC9623295 DOI: 10.3389/fcell.2022.876247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 09/29/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Jian Jin
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Jiayao Jiang
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Zhengchang Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Ruihua Huang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Mingan Sun
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Wenbin Bao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- *Correspondence: Wenbin Bao,
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37
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H3K27me3 at pericentromeric heterochromatin is a defining feature of the early mouse blastocyst. Sci Rep 2022; 12:13908. [PMID: 35974030 PMCID: PMC9381757 DOI: 10.1038/s41598-022-17730-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 07/29/2022] [Indexed: 11/09/2022] Open
Abstract
Early mouse development is characterized by structural and epigenetic changes while cells progress towards differentiation. At blastocyst stage, the segregation of the three primordial lineages is accompanied by establishment of differential patterns of DNA methylation and post-translational modifications of histones, such as H3K27me3. Here, we analysed the dynamics of H3K27me3 at pericentromeric heterochromatin (PCH) during early development. We also followed the localization of EZH2 and BEND3, previously shown in ESCs to drive PRC2 to hypomethylated PCH. We show that the location of H3K27me3 at PCH, in addition to H3K9me3, is a defining feature of embryonic cells in vivo. Moreover, it may play an important role in structuring PCH and preserving genomic integrity at a time of globally relaxed chromatin. At peri-implantation stages, while DNA methylation is still low, EZH2 and then H3K27me3, leave PCH in epiblast progenitors at the time of their spatial segregation from primitive endoderm cells, while BEND3 remains there up to implantation. The comparison with stem cells (ESCs and TSCs) reveals that the epigenetic marks (i.e. H3K9me3 and H3K27me3) of PCH are reset during in vitro derivation and only partially restored thereafter. This highlights possible divergences between in vitro and "in embryo" epigenetic regulation regarding constitutive heterochromatin.
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38
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Chen H, Wang Y, Su H, Zhang X, Chen H, Yu J. RNA N6-Methyladenine Modification, Cellular Reprogramming, and Cancer Stemness. Front Cell Dev Biol 2022; 10:935224. [PMID: 35859892 PMCID: PMC9289108 DOI: 10.3389/fcell.2022.935224] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 05/26/2022] [Indexed: 11/13/2022] Open
Abstract
N6-Methyladenosine (m6A) is the most abundant modification on eukaryote messenger RNA and plays a key role in posttranscriptional regulation of RNA metabolism including splicing, intracellular transport, degradation, and translation. m6A is dynamically regulated by methyltransferases (writers), RNA-binding proteins (readers), and demethylases (erasers). Recent studies demonstrate that perturbation of m6A regulators remarkably influences cell fate transitions through rewiring various biological processes, such as growth, differentiation, and survival. Moreover, aberrant m6A modification is implicated in a variety of diseases, in particular cancer. In this review, we describe the functional linkage of m6A modifications to cellular reprogramming and cancer stemness properties.
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Affiliation(s)
- Huarong Chen
- Department of Anaesthesia and Intensive Care and Peter Hung Pain Research Institute, The Chinese University of Hong Kong, Hong Kong, China
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
- *Correspondence: Huarong Chen, ; Jun Yu,
| | - Yifei Wang
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Oncology in South China, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Hao Su
- Department of Anaesthesia and Intensive Care and Peter Hung Pain Research Institute, The Chinese University of Hong Kong, Hong Kong, China
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Xiaoting Zhang
- Department of Anaesthesia and Intensive Care and Peter Hung Pain Research Institute, The Chinese University of Hong Kong, Hong Kong, China
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Hongyan Chen
- Department of Anaesthesia and Intensive Care and Peter Hung Pain Research Institute, The Chinese University of Hong Kong, Hong Kong, China
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Jun Yu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
- *Correspondence: Huarong Chen, ; Jun Yu,
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39
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Qu P, Cao W, Zhang Y, Qi J, Meng B, Liu S, Zhuang Y, Duan C, Liu E. Sperm-borne proteins improve rabbit cloning efficiency via regulating embryonic cleavage and epigenetics. Proteomics 2022; 22:e2200020. [PMID: 35779011 DOI: 10.1002/pmic.202200020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 05/25/2022] [Accepted: 06/24/2022] [Indexed: 11/12/2022]
Abstract
Somatic cell nuclear transfer (SCNT) shows great application value in the generation of transgenic animals, protection of endangered species, and therapeutic cloning. However, the cloning efficiency is still very low, which greatly restricts its application. Compared to fertilized embryos, cloned embryos lack the sperm proteins, which are considered to play an important role in embryonic development. Here we compared the sperm proteome, with that of donor fibroblasts and oocytes, and identified 342 proteins unique to sperm, with 42 being highly expressed. The 384 proteins were mainly enriched in the categories of post-translational modification and cytoskeletal arrangement. Extracts of soluble sperm or fibroblast proteins were injected into cloned embryos, and the result showed that injection of sperm protein significantly inhibited abnormal embryonic cleavage, significantly decreased the level of trimethylated histone H3Lys9 (H3K9me3) and the apoptotic index, and increased the inner cell mass (ICM)-to-trophectoderm (TE) ratio. More importantly, the sperm proteins also significantly enhanced the birthrate. The results of in vitro and in vivo experiments demonstrate that sperm-derived proteins improve embryo cloning efficiency. Our findings not only provide new insights into ways to overcome low cloning efficiency, but also add to the understanding of sperm protein function. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Pengxiang Qu
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Centre, Xi'an, Shaanxi, China.,Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China, Xi'an, Shaanxi, China
| | - Wenbin Cao
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Centre, Xi'an, Shaanxi, China.,Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China, Xi'an, Shaanxi, China
| | - Yanru Zhang
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Centre, Xi'an, Shaanxi, China.,Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China, Xi'an, Shaanxi, China
| | - Jia Qi
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Centre, Xi'an, Shaanxi, China.,Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China, Xi'an, Shaanxi, China
| | - Bin Meng
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Centre, Xi'an, Shaanxi, China.,The Assisted Reproduction Center, Northwest Women's and Children's Hospital, Xi'an, Shaanxi, China
| | - Shuangqing Liu
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Centre, Xi'an, Shaanxi, China
| | - Yanxin Zhuang
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Centre, Xi'an, Shaanxi, China
| | - Chenjin Duan
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Centre, Xi'an, Shaanxi, China
| | - Enqi Liu
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Centre, Xi'an, Shaanxi, China.,Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China, Xi'an, Shaanxi, China
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40
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Stage-specific H3K9me3 occupancy ensures retrotransposon silencing in human pre-implantation embryos. Cell Stem Cell 2022; 29:1051-1066.e8. [DOI: 10.1016/j.stem.2022.06.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 03/31/2022] [Accepted: 06/01/2022] [Indexed: 12/13/2022]
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41
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Abstract
Dramatic nuclear reorganization occurs during early development to convert terminally differentiated gametes to a totipotent zygote, which then gives rise to an embryo. Aberrant epigenome resetting severely impairs embryo development and even leads to lethality. How the epigenomes are inherited, reprogrammed, and reestablished in this critical developmental period has gradually been unveiled through the rapid development of technologies including ultrasensitive chromatin analysis methods. In this review, we summarize the latest findings on epigenetic reprogramming in gametogenesis and embryogenesis, and how it contributes to gamete maturation and parental-to-zygotic transition. Finally, we highlight the key questions that remain to be answered to fully understand chromatin regulation and nuclear reprogramming in early development.
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Affiliation(s)
- Zhenhai Du
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Ke Zhang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
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42
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Dang Y, Li S, Zhao P, Xiao L, Wang L, Shi Y, Luo L, Wang S, Wang H, Zhang K. The lysine deacetylase activity of histone deacetylases 1 and 2 is required to safeguard zygotic genome activation in mice and cattle. Development 2022; 149:275603. [PMID: 35575026 DOI: 10.1242/dev.200854] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 05/03/2022] [Indexed: 12/15/2022]
Abstract
The genome is transcriptionally inert at fertilization and must be activated through a remarkable developmental process called zygotic genome activation (ZGA). Epigenetic reprogramming contributes significantly to the dynamic gene expression during ZGA; however, the mechanism has yet to be resolved. Here, we find histone deacetylases 1 and 2 (HDAC1/2) can regulate ZGA through lysine deacetylase activity. Notably, in mouse embryos, overexpression of a HDAC1/2 dominant-negative mutant leads to developmental arrest at the two-cell stage. RNA-seq reveals that 64% of downregulated genes are ZGA genes and 49% of upregulated genes are developmental genes. Inhibition of the deacetylase activity of HDAC1/2 causes a failure of histone deacetylation at multiple sites, including H4K5, H4K16, H3K14, H3K18 and H3K27. ChIP-seq analysis exhibits an increase and decrease of H3K27ac enrichment at promoters of up- and downregulated genes, respectively. Moreover, HDAC1 mutants prohibit the removal of H3K4me3 by impeding expression of Kdm5 genes. Importantly, the developmental block can be greatly rescued by Kdm5b injection and by partially correcting the expression of the majority of dysregulated genes. Similar functional significance of HDAC1/2 is conserved in bovine embryos. Overall, we propose that HDAC1/2 are indispensable for ZGA by creating correct transcriptional repressive and active states in mouse and bovine embryos.
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Affiliation(s)
- Yanna Dang
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, and Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Shuang Li
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, and Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Panpan Zhao
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, and Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Lieying Xiao
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, and Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Lefeng Wang
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, and Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China.,Department of Veterinary Sciences, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yan Shi
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, and Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Lei Luo
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, and Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Shaohua Wang
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, and Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Huanan Wang
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, and Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China.,Department of Veterinary Sciences, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Kun Zhang
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, and Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
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43
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Human Sperm Morphology as a Marker of Its Nuclear Quality and Epigenetic Pattern. Cells 2022; 11:cells11111788. [PMID: 35681482 PMCID: PMC9180039 DOI: 10.3390/cells11111788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/22/2022] [Accepted: 05/26/2022] [Indexed: 11/30/2022] Open
Abstract
Background: Human sperm chromatin condensation is a sum of epigenetic events that allows for the near-complete replacement of histones with protamines. Under high-magnification microscopy, nuclear vacuoles have been described as thumbprints with poor chromatin condensation. The objective of this study is to examine whether vacuolated spermatozoa carry specific epigenetic marks, which may influence embryo development. Methods: The presence and three-dimensional distribution of ten epigenetic marks (protamine-P2, histone-H3, H3K4me1/me2/me3, H3K9me1/me2/me3, H3K27me3, H4k20me2) were evaluated and compared in morphometrically normal spermatozoa according to the presence or absence of a large vacuole occupying more than 15% of the head surface (n = 4193). Results: Vacuolated spermatozoa were significantly more frequently labelled with H3 and H3K4me3 than normal spermatozoa (88.1% ± 2.7 and 78.5% ± 5.2 vs. 74.8% ± 4.8 and 49.1% ± 7.4, respectively; p = 0.009 and p < 0.001) and significantly less marked by P2 and H3K27me3 (50.2% ± 6.2 and 63.9% ± 6.3 vs. 82.1% ± 4.4 and 73.6% ± 5.1, respectively; p < 0.001 and p = 0.028). In three dimensions, vacuoles are nuclear concavities filled with DNA carrying the H3K4me3 marker. Conclusion: High-magnification microscopy is a simple tool to estimate in real time the sperm epigenetic profile. The selection of normal spermatozoa without vacuoles and the deselection of spermatozoa with vacuoles appear to be epigenetically favorable to embryo development and safe offspring.
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44
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Qian J, Guo F. De novo programming: establishment of epigenome in mammalian oocytes. Biol Reprod 2022; 107:40-53. [PMID: 35552602 DOI: 10.1093/biolre/ioac091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/21/2022] [Accepted: 05/02/2022] [Indexed: 11/14/2022] Open
Abstract
Innovations in ultrasensitive and single-cell measurements enable us to study layers of genome regulation in the view of cellular and regulatory heterogeneity. Genome-scale mapping allows to evaluate epigenetic features and dynamics in different genomic contexts, including genebodies, CGIs, ICRs, promoters, PMDs, and repetitive elements. The epigenome of early embryos, fetal germ cells, and sperm has been extensively studied for the past decade, while oocytes remain less clear. Emerging evidence now supports the notion that transcription and chromatin accessibility precede de novo DNA methylation in both human and mouse oocytes. Recent studies also start to chart correlations among different histone modifications and DNA methylation. We discussed the potential mechanistic hierarchy by which shapes oocyte DNA methylome, also provided insights into the convergent and divergent features between human and mice.
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Affiliation(s)
- Jingjing Qian
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Fan Guo
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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45
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Das A, Iwata-Otsubo A, Destouni A, Dawicki-McKenna JM, Boese KG, Black BE, Lampson MA. Epigenetic, genetic and maternal effects enable stable centromere inheritance. Nat Cell Biol 2022; 24:748-756. [PMID: 35534577 PMCID: PMC9107508 DOI: 10.1038/s41556-022-00897-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 03/16/2022] [Indexed: 12/31/2022]
Abstract
Centromeres are defined epigenetically by the histone H3 variant, CENP-A. The propagation cycle by which preexisting CENP-A nucleosomes serve as templates for nascent assembly predicts epigenetic memory of weakened centromeres. Using a mouse model with reduced levels of CENP-A nucleosomes, we find that an embryonic plastic phase precedes epigenetic memory through development. During this phase, nascent CENP-A nucleosome assembly depends on the maternal Cenpa genotype rather than the preexisting template. Weakened centromeres are thus limited to a single generation, and parental epigenetic differences are eliminated by equal assembly on maternal and paternal centromeres. These differences persist, however, when the underlying DNA of parental centromeres differs in repeat abundance, as assembly during the plastic phase also depends on sufficient repetitive centromere DNA. With contributions of centromere DNA and Cenpa maternal effect, we propose that centromere inheritance naturally minimizes fitness costs associated with weakened centromeres or epigenetic differences between parents.
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Affiliation(s)
- Arunika Das
- Department of Biochemistry and Biophysics; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.,Penn Center for Genome Integrity, University of Pennsylvania, Philadelphia, PA, USA.,Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Aiko Iwata-Otsubo
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.,Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Aspasia Destouni
- Department of Biochemistry and Biophysics; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Laboratory of Cytogenetics and Molecular Genetics, Faculty of Medicine, University of Thessaly, Larissa, Greece
| | - Jennine M Dawicki-McKenna
- Department of Biochemistry and Biophysics; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Katelyn G Boese
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Ben E Black
- Department of Biochemistry and Biophysics; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. .,Penn Center for Genome Integrity, University of Pennsylvania, Philadelphia, PA, USA. .,Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA.
| | - Michael A Lampson
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA. .,Penn Center for Genome Integrity, University of Pennsylvania, Philadelphia, PA, USA.
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46
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Chen C, Gao Y, Liu W, Gao S. Epigenetic regulation of cell fate transition: learning from early embryo development and somatic cell reprogramming. Biol Reprod 2022; 107:183-195. [PMID: 35526125 PMCID: PMC9310515 DOI: 10.1093/biolre/ioac087] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 03/29/2022] [Accepted: 04/25/2022] [Indexed: 11/12/2022] Open
Abstract
Epigenetic regulations play a central role in governing the embryo development and somatic cell reprogramming. Taking advantage of recent advances in low-input sequencing techniques, researchers have uncovered a comprehensive view of the epigenetic landscape during rapid transcriptome transitions involved in the cell fate commitment. The well-organized epigenetic reprogramming also highlights the essential roles of specific epigenetic regulators to support efficient regulation of transcription activity and chromatin remodeling. This review briefly introduces the recent progress in the molecular dynamics and regulation mechanisms implicated in mouse early embryo development and somatic cell reprograming, as well as the multi-omics regulatory mechanisms of totipotency mediated by several key factors, which provide valuable resources for further investigations on the complicated regulatory network in essential biological events.
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Affiliation(s)
- Chuan Chen
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China
| | - Yawei Gao
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China
| | - Wenqiang Liu
- Clinical and Translation Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Shaorong Gao
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China.,Clinical and Translation Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
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47
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Cai J, Chen H, Xie S, Hu Z, Bai Y. Research Progress of Totipotent Stem Cells. Stem Cells Dev 2022; 31:335-345. [PMID: 35502477 DOI: 10.1089/scd.2022.0061] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Totipotent stem cells (TSCs), can develop into complete organisms, used in biological fields such as regenerative medicine, mammalian breeding, and conservation. However, cells from early-stage embryos cultured are hard to self-renew and maintain developmental totipotency, which becomes a key factor limiting the research of TSCs. Fortunately, a break-through in the study of induced pluripotent stem cells returning to their totipotent state has been made, resulting in the establishment of multiple TSCs and igniting a new wave of stem cell research. Furthermore, the blastocyst-like structures can be generated by the established TSCs, which lays a foundation for synthetic embryos in vitro. In this review, we summarize the totipotent stage of the early embryos, the establishment and cultivation of TSCs, and the developmental ability exploration of TSCs to promote further research of TSCs.
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Affiliation(s)
- Jianfeng Cai
- Foshan University School of Life Science and Engineering, 118208, Foshan, China, 528000;
| | - Huifang Chen
- Foshan University School of Life Science and Engineering, 118208, Foshan, China;
| | - Shiting Xie
- Foshan University School of Life Science and Engineering, 118208, Foshan, China;
| | - Zhichao Hu
- Foshan University School of Life Science and Engineering, 118208, Foshan, China;
| | - Yinshan Bai
- Foshan University School of Life Science and Engineering, 118208, Foshan, China;
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48
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Yang H, Bai D, Li Y, Yu Z, Wang C, Sheng Y, Liu W, Gao S, Zhang Y. Allele-specific H3K9me3 and DNA methylation co-marked CpG-rich regions serve as potential imprinting control regions in pre-implantation embryo. Nat Cell Biol 2022; 24:783-792. [PMID: 35484247 DOI: 10.1038/s41556-022-00900-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 03/16/2022] [Indexed: 12/13/2022]
Abstract
Parental DNA methylation and histone modifications undergo distinct global reprogramming in mammalian pre-implantation embryos, but the landscape of epigenetic crosstalk and its effects on embryogenesis are largely unknown. Here we comprehensively analyse the association between DNA methylation and H3K9me3 reprogramming in mouse pre-implantation embryos and reveal that CpG-rich genomic loci with high H3K9me3 signal and DNA methylation level (CHM) are hotspots of DNA methylation maintenance during pre-implantation embryogenesis. We further profile the allele-specific epigenetic map with unprecedented resolution in gynogenetic and androgenetic embryos, respectively, and identify 1,279 allele-specific CHMs, including 19 known imprinting control regions (ICRs). Our study suggests that 22 ICR-like regions (ICRLRs) may regulate allele-specific transcription similarly to known ICRs, and five of them are confirmed to be important for mouse embryo development. Taken together, our study reveals the widespread existence of allele-specific CHMs and largely extends the scope of allele-specific regulation in mammalian pre-implantation embryos.
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Affiliation(s)
- Hui Yang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China.,Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai, China
| | - Dandan Bai
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China.,Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai, China
| | - Yanhe Li
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China.,Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai, China
| | - Zhaowei Yu
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China.,Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai, China
| | - Chenfei Wang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yifan Sheng
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China.,Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai, China
| | - Wenqiang Liu
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China. .,Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai, China. .,Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China.
| | - Shaorong Gao
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China. .,Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai, China. .,Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China.
| | - Yong Zhang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China. .,Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai, China.
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49
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Quarato P, Singh M, Bourdon L, Cecere G. Inheritance and maintenance of small RNA-mediated epigenetic effects. Bioessays 2022; 44:e2100284. [PMID: 35338497 DOI: 10.1002/bies.202100284] [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: 12/06/2021] [Revised: 02/04/2022] [Accepted: 03/15/2022] [Indexed: 11/08/2022]
Abstract
Heritable traits are predominantly encoded within genomic DNA, but it is now appreciated that epigenetic information is also inherited through DNA methylation, histone modifications, and small RNAs. Several examples of transgenerational epigenetic inheritance of traits have been documented in plants and animals. These include even the inheritance of traits acquired through the soma during the life of an organism, implicating the transfer of epigenetic information via the germline to the next generation. Small RNAs appear to play a significant role in carrying epigenetic information across generations. This review focuses on how epigenetic information in the form of small RNAs is transmitted from the germline to the embryos through the gametes. We also consider how inherited epigenetic information is maintained across generations in a small RNA-dependent and independent manner. Finally, we discuss how epigenetic traits acquired from the soma can be inherited through small RNAs.
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Affiliation(s)
- Piergiuseppe Quarato
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université de Paris, CNRS UMR3738, Mechanisms of Epigenetic Inheritance, Paris, France
| | - Meetali Singh
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université de Paris, CNRS UMR3738, Mechanisms of Epigenetic Inheritance, Paris, France
| | - Loan Bourdon
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université de Paris, CNRS UMR3738, Mechanisms of Epigenetic Inheritance, Paris, France
| | - Germano Cecere
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université de Paris, CNRS UMR3738, Mechanisms of Epigenetic Inheritance, Paris, France
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50
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Dang Y, Luo L, Shi Y, Li S, Wang S, Zhang K. KDM5-mediated redistribution of H3K4me3 is required for oocyte-to-embryonic transition in cattle. Biol Reprod 2022; 106:1059-1071. [PMID: 35243485 DOI: 10.1093/biolre/ioac047] [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: 11/26/2021] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 11/12/2022] Open
Abstract
Reprogramming of histone modifications is critical to safeguard correct gene expression profile during preimplantation development. Of interest, trimethylation of lysine 4 on histone 3 (H3K4me3) exhibits a unique and dynamic landscape with a potential species-specific feature. Here, we address how it is reprogrammed and its functional significance during oocyte maturation and early embryonic development in cows. Notably, the overall signal of H3K4me3 decreased sharply during embryonic genome activation (EGA). By using low input ChIP-seq, we find widespread broad H3K4me3 domains in oocytes and early cleaved embryos. The broad domains are gradually removed after fertilization, which is obviously seen during EGA. Meanwhile, H3K4me3 become enriched at promoter regions after the removal of broad H3K4me3. Interestingly, the gene expression level displays a positive correlation with the relative H3K4me3 signal of their promoters when embryos reach 16-cell stage. Importantly, disruption of H3K4me3 demethylases KDM5 increases H3K4me3 level, decreases the embryonic developmental rate and results in dysregulation of over a thousand genes. Meanwhile, KDM5 deficiency causes a redistribution of H3K4me3 across genome. In particular, H3K4me3 in gene body or intergenic regions can't be removed and H3K4me3 in promoter regions is aberrantly reduced. Besides, the positive correlation between promoter H3K4me3 enrichment and gene expression level disappear. Overall, we describe the genomic reprogramming of H3K4me3 with a greater resolution during bovine preimplantation development and propose that KDM5-mediated redistribution of H3K4me3 plays an important role in modulating oocyte-to-embryonic transition.
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Affiliation(s)
- Yanna Dang
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Lei Luo
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yan Shi
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Shuang Li
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Shaohua Wang
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Kun Zhang
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
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