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Zeng X, Wang R, Tang S, Dong X, Liao L, Chen S, Kong J, Chen L, Li Y, Shao G, Zhang X, Wong YH, Xie Q. Exosomal circ_CCDC7/gga-miR-6568-3p/Pax7 axis accelerates the differentiation of chicken embryonic stem cells infected with subgroup J avian leukosis virus. Poult Sci 2024; 103:103898. [PMID: 38936216 PMCID: PMC11259737 DOI: 10.1016/j.psj.2024.103898] [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: 02/29/2024] [Revised: 05/20/2024] [Accepted: 05/20/2024] [Indexed: 06/29/2024] Open
Abstract
Exosome-mediated horizontal and vertical transmission of subgroup J avian leukosis virus (ALV-J) in poultry flocks can lead to growth inhibition and severe immunosuppression. However, there are few reports on the early infection of chicken embryonic stem cells (cESCs) with ALV-J. In this study, we confirmed that early infection with ALV-J can accelerate the differentiation of cESCs and promote the secretion of exosomes. To investigate the modulation strategy of ALV-J in cESCs, circRNA sequencing was performed for further analysis. A total of 305 differentially expressed circRNAs (DECs) were obtained, including 71 upregulated DECs. Circ-CCDC7 was found to be the most upregulated DEC and was assessed by qRT-PCR, with the result consistent with the result of circRNA-seq. Based on qRT-PCR, gga-miR-6568-3p was found to be the target of the top 3 DECs, including circ-CCDC7, and the stem cell marker gene Pax7 was identified as the target gene of gga-miR-6568-3p. This study demonstrated that exosomal circ-CCDC7/gga-miR-6568-3p/Pax7 accelerates the differentiation of cESCs after early infection with ALV-J.
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Affiliation(s)
- Xiaona Zeng
- State Key Laboratory of Swine and Poultry Breeding Industry & Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Henry Fok School of Biology and Agriculture, Shaoguan University, Shaoguan, 512005, China; Guangdong Provincial Key Lab of AgroAnimal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, 510642, China
| | - Ruonan Wang
- State Key Laboratory of Swine and Poultry Breeding Industry & Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Lab of AgroAnimal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, 510642, China
| | - Shengqiu Tang
- Henry Fok School of Biology and Agriculture, Shaoguan University, Shaoguan, 512005, China
| | - Xiaoying Dong
- Henry Fok School of Biology and Agriculture, Shaoguan University, Shaoguan, 512005, China
| | - Liqin Liao
- State Key Laboratory of Swine and Poultry Breeding Industry & Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Lab of AgroAnimal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, 510642, China
| | - Sheng Chen
- State Key Laboratory of Swine and Poultry Breeding Industry & Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Lab of AgroAnimal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, 510642, China
| | - Jie Kong
- State Key Laboratory of Swine and Poultry Breeding Industry & Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Lab of AgroAnimal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, 510642, China
| | - Liyi Chen
- State Key Laboratory of Swine and Poultry Breeding Industry & Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Lab of AgroAnimal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, 510642, China
| | - Yajuan Li
- State Key Laboratory of Swine and Poultry Breeding Industry & Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Lab of AgroAnimal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, 510642, China
| | - Guanming Shao
- State Key Laboratory of Swine and Poultry Breeding Industry & Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Lab of AgroAnimal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, 510642, China
| | - Xinheng Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry & Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Lab of AgroAnimal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, 510642, China
| | - Yung Hou Wong
- Division of Life Sciences and the Biotechnology Research Institute, Hong Kong University of Science and Technology, Hong Kong, China
| | - Qingmei Xie
- State Key Laboratory of Swine and Poultry Breeding Industry & Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Lab of AgroAnimal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, 510642, China.
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2
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Linneberg-Agerholm M, Sell AC, Redó-Riveiro A, Perera M, Proks M, Knudsen TE, Barral A, Manzanares M, Brickman JM. The primitive endoderm supports lineage plasticity to enable regulative development. Cell 2024; 187:4010-4029.e16. [PMID: 38917790 PMCID: PMC11290322 DOI: 10.1016/j.cell.2024.05.051] [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: 05/19/2023] [Revised: 02/27/2024] [Accepted: 05/28/2024] [Indexed: 06/27/2024]
Abstract
Mammalian blastocyst formation involves the specification of the trophectoderm followed by the differentiation of the inner cell mass into embryonic epiblast and extra-embryonic primitive endoderm (PrE). During this time, the embryo maintains a window of plasticity and can redirect its cellular fate when challenged experimentally. In this context, we found that the PrE alone was sufficient to regenerate a complete blastocyst and continue post-implantation development. We identify an in vitro population similar to the early PrE in vivo that exhibits the same embryonic and extra-embryonic potency and can form complete stem cell-based embryo models, termed blastoids. Commitment in the PrE is suppressed by JAK/STAT signaling, collaborating with OCT4 and the sustained expression of a subset of pluripotency-related transcription factors that safeguard an enhancer landscape permissive for multi-lineage differentiation. Our observations support the notion that transcription factor persistence underlies plasticity in regulative development and highlight the importance of the PrE in perturbed development.
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Affiliation(s)
- Madeleine Linneberg-Agerholm
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Annika Charlotte Sell
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Alba Redó-Riveiro
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Marta Perera
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Martin Proks
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Teresa E Knudsen
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Antonio Barral
- Centro de Biología Molecular Severo Ochoa (CBM), CSIC-UAM, 28049 Madrid, Spain
| | - Miguel Manzanares
- Centro de Biología Molecular Severo Ochoa (CBM), CSIC-UAM, 28049 Madrid, Spain
| | - Joshua M Brickman
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 2200 Copenhagen N, Denmark.
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3
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Gui L, Zhong Q, Yang J, Sun J, Lu J, Picton HM, Li C. Acquisition of 2C-like totipotency through defined maternal-effect factors. Stem Cells 2024; 42:581-592. [PMID: 38655883 DOI: 10.1093/stmcls/sxae029] [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: 08/16/2023] [Accepted: 03/25/2024] [Indexed: 04/26/2024]
Abstract
Fully grown oocytes have the natural ability to transform 2 terminally differentiated gametes into a totipotent zygote representing the acquisition of totipotency. This process wholly depends on maternal-effect factors (MFs). MFs stored in the eggs are therefore likely to be able to induce cellular reprogramming to a totipotency state. Here we report the generation of totipotent-like stem cells from mESCs using 4MFs Hsf1, Zar1, Padi6, and Npm2, designated as MFiTLSCs. MFiTLSCs exhibited a unique and inherent capability to differentiate into embryonic and extraembryonic derivatives. Transcriptomic analysis revealed that MFiTLSCs are enriched with 2-cell-specific genes that appear to synergistically induce a transcriptional repressive state, in that parental genomes are remodeled to a poised transcriptional repression state while totipotency is established following fertilization. This method to derive MFiTLSCs could help advance the understanding of fate determinations of totipotent stem cells in a physiological context and establish a foundation for the development of oocyte biology-based reprogramming technology.
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Affiliation(s)
- Liming Gui
- Institute of Obstetrics and Gynaecology, Shenzhen Peking University-Hong Kong University of Science and Technology Medical Center, Shenzhen, Guangdong Province 518036, People's Republic of China
- Department of Obstetrics and Gynaecology, Peking University Shenzhen Hospital, Shenzhen, Guangdong Province 518036, People's Republic of China
- Centre for Tissue Engineering and Stem Cell Research, Guizhou Medical University, Guiyang, Guizhou Province 550004, People's Republic of China
| | - Qin Zhong
- Centre for Tissue Engineering and Stem Cell Research, Guizhou Medical University, Guiyang, Guizhou Province 550004, People's Republic of China
| | - Jue Yang
- Centre for Tissue Engineering and Stem Cell Research, Guizhou Medical University, Guiyang, Guizhou Province 550004, People's Republic of China
| | - Jiajia Sun
- Institute of Obstetrics and Gynaecology, Shenzhen Peking University-Hong Kong University of Science and Technology Medical Center, Shenzhen, Guangdong Province 518036, People's Republic of China
| | - Jianping Lu
- Reproduction and Early Development Research Group, Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, United Kingdom
| | - Helen M Picton
- Reproduction and Early Development Research Group, Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, United Kingdom
| | - Changzhong Li
- Institute of Obstetrics and Gynaecology, Shenzhen Peking University-Hong Kong University of Science and Technology Medical Center, Shenzhen, Guangdong Province 518036, People's Republic of China
- Department of Obstetrics and Gynaecology, Peking University Shenzhen Hospital, Shenzhen, Guangdong Province 518036, People's Republic of China
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4
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Gao C, Gao X, Gao F, Du X, Wu S. A CRISPR/Cas9 screen in embryonic stem cells reveals that Mdm2 regulates totipotency exit. Commun Biol 2024; 7:809. [PMID: 38961268 PMCID: PMC11222520 DOI: 10.1038/s42003-024-06507-9] [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: 11/10/2023] [Accepted: 06/25/2024] [Indexed: 07/05/2024] Open
Abstract
During early embryonic development, the transition from totipotency to pluripotency is a fundamental and critical process for proper development. However, the regulatory mechanisms governing this transition remain elusive. Here, we conducted a comprehensive genome-wide CRISPR/Cas9 screen to investigate the 2-cell-like cells (2CLCs) phenotype in mouse embryonic stem cells (mESCs). This effort led to the identification of ten regulators that play a pivotal role in determining cell fate during this transition. Notably, our study revealed Mdm2 as a significant negative regulator of 2CLCs, as perturbation of Mdm2 resulted in a higher proportion of 2CLCs. Mdm2 appears to influence cell fate through its impact on cell cycle progression and H3K27me3 epigenetic modifications. In summary, the results of our CRISPR/Cas9 screen have uncovered several genes with distinct functions in regulating totipotency and pluripotency at various levels, offering a valuable resource for potential targets in future molecular studies.
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Affiliation(s)
- Chen Gao
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xin Gao
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Sanya, 572025, China
| | - Fei Gao
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Sanya, 572025, China
| | - Xuguang Du
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
- Sanya Institute of China Agricultural University, Sanya, 572025, China.
| | - Sen Wu
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
- Sanya Institute of China Agricultural University, Sanya, 572025, China.
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5
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Li X, Bie L, Wang Y, Hong Y, Zhou Z, Fan Y, Yan X, Tao Y, Huang C, Zhang Y, Sun X, Li JXH, Zhang J, Chang Z, Xi Q, Meng A, Shen X, Xie W, Liu N. LINE-1 transcription activates long-range gene expression. Nat Genet 2024; 56:1494-1502. [PMID: 38849613 DOI: 10.1038/s41588-024-01789-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 05/06/2024] [Indexed: 06/09/2024]
Abstract
Long interspersed nuclear element-1 (LINE-1 or L1) is a retrotransposon group that constitutes 17% of the human genome and shows variable expression across cell types. However, the control of L1 expression and its function in gene regulation are incompletely understood. Here we show that L1 transcription activates long-range gene expression. Genome-wide CRISPR-Cas9 screening using a reporter driven by the L1 5' UTR in human cells identifies functionally diverse genes affecting L1 expression. Unexpectedly, altering L1 expression by knockout of regulatory genes impacts distant gene expression. L1s can physically contact their distal target genes, with these interactions becoming stronger upon L1 activation and weaker when L1 is silenced. Remarkably, L1s contact and activate genes essential for zygotic genome activation (ZGA), and L1 knockdown impairs ZGA, leading to developmental arrest in mouse embryos. These results characterize the regulation and function of L1 in long-range gene activation and reveal its importance in mammalian ZGA.
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Affiliation(s)
- Xiufeng Li
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Luyao Bie
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yang Wang
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yaqiang Hong
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Ziqiang Zhou
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yiming Fan
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xiaohan Yan
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yibing Tao
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing, China
| | - Chunyi Huang
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yongyan Zhang
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xueyan Sun
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - John Xiao He Li
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jing Zhang
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Zai Chang
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Qiaoran Xi
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Anming Meng
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xiaohua Shen
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing, China
| | - Wei Xie
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Nian Liu
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.
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6
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Soszyńska A, Krawczyk K, Szpila M, Winek E, Szpakowska A, Suwińska A. Exposure of chimaeric embryos to exogenous FGF4 leads to the production of pure ESC-derived mice. Theriogenology 2024; 222:10-21. [PMID: 38603966 DOI: 10.1016/j.theriogenology.2024.03.017] [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: 10/31/2023] [Revised: 03/28/2024] [Accepted: 03/31/2024] [Indexed: 04/13/2024]
Abstract
Producing chimaeras constitutes the most reliable method of verifying the pluripotency of newly established cells. Moreover, forming chimaeras by injecting genetically modified embryonic stem cells (ESCs) or induced pluripotent stem cells (iPSCs) into the embryo is part of the procedure for generating transgenic mice, which are used for understanding gene function. Conventional methods for generating transgenic mice, including the breeding of chimaeras and tetraploid complementation, are time-consuming and cost-inefficient, with significant limitations that hinder their effectiveness and widespread applications. In the present study, we modified the traditional method of chimaera generation to significantly speed up this process by generating mice exclusively derived from ESCs. This study aimed to assess whether fully ESC-derived mice could be obtained by modulating fibroblast growth factor 4 (FGF4) levels in the culture medium and changing the direction of cell differentiation in the chimaeric embryo. We found that exogenous FGF4 directs all host blastomeres to the primitive endoderm fate, but does not affect the localisation of ESCs in the epiblast of the chimaeric embryos. Consequently, all FGF4-treated chimaeric embryos contained an epiblast composed exclusively of ESCs, and following transfer into recipient mice, these embryos developed into fully ESC-derived newborns. Collectively, this simple approach could accelerate the generation of ESC-derived animals and thus optimise ESC-mediated transgenesis and the verification of cell pluripotency. Compared to traditional methods, it could speed up functional studies by several weeks and significantly reduce costs related to maintaining and breeding chimaeras. Moreover, since the effect of stimulating the FGF signalling pathway is universal across different animal species, our approach can be applied not only to rodents but also to other animals, offering its utility beyond laboratory settings.
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Affiliation(s)
- Anna Soszyńska
- Department of Embryology, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Warsaw, Poland.
| | - Katarzyna Krawczyk
- Department of Embryology, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Warsaw, Poland.
| | - Marcin Szpila
- Department of Embryology, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Warsaw, Poland.
| | - Eliza Winek
- Department of Embryology, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Warsaw, Poland.
| | - Anna Szpakowska
- Department of Embryology, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Warsaw, Poland.
| | - Aneta Suwińska
- Department of Embryology, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Warsaw, Poland.
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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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Deaville LA, Berrens RV. Technology to the rescue: how to uncover the role of transposable elements in preimplantation development. Biochem Soc Trans 2024; 52:1349-1362. [PMID: 38752836 DOI: 10.1042/bst20231262] [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: 02/14/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 06/27/2024]
Abstract
Transposable elements (TEs) are highly expressed in preimplantation development. Preimplantation development is the phase when the cells of the early embryo undergo the first cell fate choice and change from being totipotent to pluripotent. A range of studies have advanced our understanding of TEs in preimplantation, as well as their epigenetic regulation and functional roles. However, many questions remain about the implications of TE expression during early development. Challenges originate first due to the abundance of TEs in the genome, and second because of the limited cell numbers in preimplantation. Here we review the most recent technological advancements promising to shed light onto the role of TEs in preimplantation development. We explore novel avenues to identify genomic TE insertions and improve our understanding of the regulatory mechanisms and roles of TEs and their RNA and protein products during early development.
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Affiliation(s)
- Lauryn A Deaville
- Institute for Developmental and Regenerative Medicine, Oxford University, IMS-Tetsuya Nakamura Building, Old Road Campus, Roosevelt Dr, Oxford OX3 7TY, U.K
- Department of Paediatrics, Oxford University, Level 2, Children's Hospital, John Radcliffe Headington, Oxford OX3 9DU, U.K
- MRC Weatherall Institute of Molecular Medicine, Oxford University, John Radcliffe Hospital, Oxford OX3 9DS, U.K
| | - Rebecca V Berrens
- Institute for Developmental and Regenerative Medicine, Oxford University, IMS-Tetsuya Nakamura Building, Old Road Campus, Roosevelt Dr, Oxford OX3 7TY, U.K
- Department of Paediatrics, Oxford University, Level 2, Children's Hospital, John Radcliffe Headington, Oxford OX3 9DU, U.K
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9
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Guo Y, Kitano T, Inoue K, Murano K, Hirose M, Li TD, Sakashita A, Ishizu H, Ogonuki N, Matoba S, Sato M, Ogura A, Siomi H. Obox4 promotes zygotic genome activation upon loss of Dux. eLife 2024; 13:e95856. [PMID: 38856708 PMCID: PMC11196112 DOI: 10.7554/elife.95856] [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: 01/07/2024] [Accepted: 06/07/2024] [Indexed: 06/11/2024] Open
Abstract
Once fertilized, mouse zygotes rapidly proceed to zygotic genome activation (ZGA), during which long terminal repeats (LTRs) of murine endogenous retroviruses with leucine tRNA primer (MERVL) are activated by a conserved homeodomain-containing transcription factor, DUX. However, Dux-knockout embryos produce fertile mice, suggesting that ZGA is redundantly driven by an unknown factor(s). Here, we present multiple lines of evidence that the multicopy homeobox gene, Obox4, encodes a transcription factor that is highly expressed in mouse two-cell embryos and redundantly drives ZGA. Genome-wide profiling revealed that OBOX4 specifically binds and activates MERVL LTRs as well as a subset of murine endogenous retroviruses with lysine tRNA primer (MERVK) LTRs. Depletion of Obox4 is tolerated by embryogenesis, whereas concomitant Obox4/Dux depletion markedly compromises embryonic development. Our study identified OBOX4 as a transcription factor that provides genetic redundancy to preimplantation development.
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Grants
- Grant-in-Aid for Scientific Research in Innovative Areas,19H05753 Ministry of Education, Culture, Sports, Science and Technology
- Project to Elucidate and Control Mechanisms of Aging and Longevity Japan Agency for Medical Research and Development
- Grant-in-Aid for Scientific Research in Innovative Areas,19H05758 Ministry of Education, Culture, Sports, Science and Technology
- Grant-in-Aid for Scientific Research KAKENHI,20K21507 Japan Society for the Promotion of Science
- Grant-in-Aid for Scientific Research KAKENHI,22H02534 Japan Society for the Promotion of Science
- Student Grant-in-Aid Program Keio University
- Doctoral Program Student Support Fellowship Japan Science and Technology Agency
- Grant-in-Aid for Scientific Research in Innovative Areas 19H05753 Ministry of Education, Culture, Sports, Science and Technology
- Grant-in-Aid for Scientific Research in Innovative Areas 19H05758 Ministry of Education, Culture, Sports, Science and Technology
- Grant-in-Aid for Scientific Research KAKENHI 20K21507 Japan Society for the Promotion of Science
- Grant-in-Aid for Scientific Research KAKENHI 22H02534 Japan Society for the Promotion of Science
- Mochida Memorial Foundation for Medical and Pharmaceutical Research
- Sumitomo Foundation
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Affiliation(s)
- Youjia Guo
- Department of Molecular Biology, Keio University School of MedicineTokyoJapan
| | - Tomohiro Kitano
- Department of Molecular Biology, Keio University School of MedicineTokyoJapan
| | - Kimiko Inoue
- Bioresource Engineering Division, Bioresource Center, RIKENTsukubaJapan
- Graduate School of Life and Environmental Sciences, University of TsukubaTsukubaJapan
| | - Kensaku Murano
- Department of Molecular Biology, Keio University School of MedicineTokyoJapan
| | - Michiko Hirose
- Human Biology Microbiome Quantum Research Center (WPI-Bio2Q), Keio UniversityTokyoJapan
| | - Ten D Li
- Department of Molecular Biology, Keio University School of MedicineTokyoJapan
| | - Akihiko Sakashita
- Department of Molecular Biology, Keio University School of MedicineTokyoJapan
- Graduate School of Life and Environmental Sciences, University of TsukubaTsukubaJapan
| | - Hirotsugu Ishizu
- Department of Molecular Biology, Keio University School of MedicineTokyoJapan
| | - Narumi Ogonuki
- Bioresource Engineering Division, Bioresource Center, RIKENTsukubaJapan
| | - Shogo Matoba
- Bioresource Engineering Division, Bioresource Center, RIKENTsukubaJapan
| | - Masayuki Sato
- Department of Molecular Biology, Keio University School of MedicineTokyoJapan
| | - Atsuo Ogura
- Bioresource Engineering Division, Bioresource Center, RIKENTsukubaJapan
- Graduate School of Life and Environmental Sciences, University of TsukubaTsukubaJapan
| | - Haruhiko Siomi
- Department of Molecular Biology, Keio University School of MedicineTokyoJapan
- Human Biology Microbiome Quantum Research Center (WPI-Bio2Q), Keio UniversityTokyoJapan
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10
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Du Z, Lin M, Li Q, Guo D, Xue Y, Liu W, Shi H, Chen T, Dan J. The totipotent 2C-like state safeguards genomic stability of mouse embryonic stem cells. J Cell Physiol 2024. [PMID: 38860420 DOI: 10.1002/jcp.31337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 05/17/2024] [Accepted: 05/28/2024] [Indexed: 06/12/2024]
Abstract
Mouse embryonic stem cells (mESCs) sporadically transition to a transient totipotent state that resembles blastomeres of the two-cell (2C) embryo stage, which has been proposed to contribute to exceptional genomic stability, one of the key features of mESCs. However, the biological significance of the rare population of 2C-like cells (2CLCs) in ESC cultures remains to be tested. Here we generated an inducible reporter cell system for specific elimination of 2CLCs from the ESC cultures to disrupt the equilibrium between ESCs and 2CLCs. We show that removing 2CLCs from the ESC cultures leads to dramatic accumulation of DNA damage, genomic mutations, and rearrangements, indicating impaired genomic instability. Furthermore, 2CLCs removal results in increased apoptosis and reduced proliferation of mESCs in both serum/LIF and 2i/LIF culture conditions. Unexpectedly, p53 deficiency results in defective response to DNA damage, leading to early accumulation of DNA damage, micronuclei, indicative of genomic instability, cell apoptosis, and reduced self-renewal capacity of ESCs when devoid of 2CLCs in cultures. Together, our data reveal that transition to the privileged 2C-like state is a major component of the intrinsic mechanisms that maintain the exceptional genomic stability of mESCs for long-term self-renewal.
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Affiliation(s)
- Zeling Du
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, China
- Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, China
| | - Meiqi Lin
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, China
- Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, China
| | - Qiaohua Li
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, China
- Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, China
| | - Dan Guo
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, China
- Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, China
| | - Yanna Xue
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, China
- Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, China
| | - Wei Liu
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, China
- Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, China
| | - Hong Shi
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, China
- Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, China
| | - Taiping Chen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Programs in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas, USA
| | - Jiameng Dan
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, China
- Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, China
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11
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Hu X, Huang X, Yang Y, Sun Y, Zhao Y, Zhang Z, Qiu D, Wu Y, Wu G, Lei L. Dux activates metabolism-lactylation-MET network during early iPSC reprogramming with Brg1 as the histone lactylation reader. Nucleic Acids Res 2024; 52:5529-5548. [PMID: 38512058 PMCID: PMC11162783 DOI: 10.1093/nar/gkae183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 02/24/2024] [Accepted: 03/15/2024] [Indexed: 03/22/2024] Open
Abstract
The process of induced pluripotent stem cells (iPSCs) reprogramming involves several crucial events, including the mesenchymal-epithelial transition (MET), activation of pluripotent genes, metabolic reprogramming, and epigenetic rewiring. Although these events intricately interact and influence each other, the specific element that regulates the reprogramming network remains unclear. Dux, a factor known to promote totipotency during the transition from embryonic stem cells (ESC) to 2C-like ESC (2CLC), has not been extensively studied in the context of iPSC reprogramming. In this study, we demonstrate that the modification of H3K18la induced by Dux overexpression controls the metabolism-H3K18la-MET network, enhancing the efficiency of iPSC reprogramming through a metabolic switch and the recruitment of p300 via its C-terminal domain. Furthermore, our proteomic analysis of H3K18la immunoprecipitation experiment uncovers the specific recruitment of Brg1 during reprogramming, with both H3K18la and Brg1 being enriched on the promoters of genes associated with pluripotency and epithelial junction. In summary, our study has demonstrated the significant role of Dux-induced H3K18la in the early reprogramming process, highlighting its function as a potent trigger. Additionally, our research has revealed, for the first time, the binding of Brg1 to H3K18la, indicating its role as a reader of histone lactylation.
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Affiliation(s)
- Xinglin Hu
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, 194 Xuefu Rd, Nangang District, Harbin, Heilongjiang Province 150081, China
| | - Xingwei Huang
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, 194 Xuefu Rd, Nangang District, Harbin, Heilongjiang Province 150081, China
- Guangzhou Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005 Guangdong Province, China
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510320, China
| | - Yue Yang
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, 194 Xuefu Rd, Nangang District, Harbin, Heilongjiang Province 150081, China
| | - Yuchen Sun
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, 194 Xuefu Rd, Nangang District, Harbin, Heilongjiang Province 150081, China
| | - Yanhua Zhao
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, 194 Xuefu Rd, Nangang District, Harbin, Heilongjiang Province 150081, China
| | - Zhijing Zhang
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, 194 Xuefu Rd, Nangang District, Harbin, Heilongjiang Province 150081, China
| | - Dan Qiu
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, 194 Xuefu Rd, Nangang District, Harbin, Heilongjiang Province 150081, China
| | - Yanshuang Wu
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, 194 Xuefu Rd, Nangang District, Harbin, Heilongjiang Province 150081, China
| | - Guangming Wu
- Guangzhou Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005 Guangdong Province, China
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510320, China
| | - Lei Lei
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, 194 Xuefu Rd, Nangang District, Harbin, Heilongjiang Province 150081, China
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12
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Herbert A. The ancient Z-DNA and Z-RNA specific Zα fold has evolved modern roles in immunity and transcription through the natural selection of flipons. ROYAL SOCIETY OPEN SCIENCE 2024; 11:240080. [PMID: 39092141 PMCID: PMC11293857 DOI: 10.1098/rsos.240080] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/29/2024] [Accepted: 05/08/2024] [Indexed: 08/04/2024]
Abstract
The Zα fold specifically binds to both Z-DNA and Z-RNA, left-handed nucleic acid structures that form under physiological conditions and are encoded by flipons. I trace the Zα fold back to unicellular organisms representing all three domains of life and to the realm of giant nucleocytoplasmic DNA viruses (NCVs). The canonical Zα fold is present in the earliest known holozoan unicellular symbiont Capsaspora owczarzaki and persists in vertebrates and some invertebrates, but not in plants or fungi. In metazoans, starting with porifera, Zα is incorporated into the double-stranded RNA editing enzyme ADAR and reflects an early symbiont relationship with NCV. In vertebrates, Zα is also present in ZBP1 and PKZ proteins that recognize host-derived Z-RNAs to defend against modern-day viruses. A related Zα fold, also likely to bind Z-DNA, is present in proteins thought to modulate gene expression, including a subset of prokaryote arsR proteins and the p15 (PC4) family present in algae. Other Zα variants that probably play a more general role in the reinitiation of transcription include the archaeal and human transcription factor E and the human RNA polymerase 3 subunit C proteins. The roles in immunity and transcription underlie the natural selection of flipons.
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Affiliation(s)
- Alan Herbert
- Discovery, InsideOutBio, 42 8th Street, Charlestown, MA02129, USA
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13
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Ooga M. Chromatin structure in totipotent mouse early preimplantation embryos. J Reprod Dev 2024; 70:152-159. [PMID: 38462486 PMCID: PMC11153117 DOI: 10.1262/jrd.2023-106] [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: 12/22/2023] [Accepted: 02/12/2024] [Indexed: 03/12/2024] Open
Abstract
Totipotency refers to the ability of a single cell to give rise to all the different cell types in the body. Terminally differentiated germ cells (sperm and oocytes) undergo reprogramming, which results in the acquisition of totipotency in zygotes. Since the 1990s, numerous studies have focused on the mechanisms of totipotency. With the emergence of the concept of epigenetic reprogramming, which is important for the undifferentiated and differentiated states of cells, the epigenomes of germ cells and fertilized oocytes have been thoroughly analyzed. However, in early immunostaining studies, detailed epigenomic information was difficult to obtain. In recent years, the explosive development of next-generation sequencing has made it possible to acquire genome-wide information and the rise of genome editing has facilitated the analysis of knockout mice, which was previously difficult. In addition, live imaging can effectively analyze zygotes and 2-cell embryos, for which the number of samples is limited, and provides biological insights that cannot be obtained by other methods. In this review, the progress of our research using these advanced techniques is traced back from the present to its earliest years.
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Affiliation(s)
- Masatoshi Ooga
- Department of Animal Science and Biotechnology, School of Veterinary Medicine, Azabu University, Kanagawa 252-5201, Japan
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14
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Huang B, Peng X, Zhai X, Hu J, Chen J, Yang S, Huang Q, Deng E, Li H, Barakat TS, Chen J, Pei D, Fan X, Chambers I, Zhang M. Inhibition of HDAC activity directly reprograms murine embryonic stem cells to trophoblast stem cells. Dev Cell 2024:S1534-5807(24)00326-5. [PMID: 38823394 DOI: 10.1016/j.devcel.2024.05.009] [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: 07/11/2023] [Revised: 01/23/2024] [Accepted: 05/09/2024] [Indexed: 06/03/2024]
Abstract
Embryonic stem cells (ESCs) can differentiate into all cell types of the embryonic germ layers. ESCs can also generate totipotent 2C-like cells and trophectodermal cells. However, these latter transitions occur at low frequency due to epigenetic barriers, the nature of which is not fully understood. Here, we show that treating mouse ESCs with sodium butyrate (NaB) increases the population of 2C-like cells and enables direct reprogramming of ESCs into trophoblast stem cells (TSCs) without a transition through a 2C-like state. Mechanistically, NaB inhibits histone deacetylase activities in the LSD1-HDAC1/2 corepressor complex. This increases acetylation levels in the regulatory regions of both 2C- and TSC-specific genes, promoting their expression. In addition, NaB-treated cells acquire the capacity to generate blastocyst-like structures that can develop beyond the implantation stage in vitro and form deciduae in vivo. These results identify how epigenetics restrict the totipotent and trophectoderm fate in mouse ESCs.
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Affiliation(s)
- Boyan Huang
- GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou 510005, China; Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou, China
| | - Xing Peng
- GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou 510005, China
| | - Xuzhao Zhai
- GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou 510005, China; Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou, China; Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Jie Hu
- GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou 510005, China; Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou, China
| | - Junyu Chen
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou, China; School of Life Science, South China Normal University, Guangzhou 510005, China
| | - Suming Yang
- GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou 510005, China; Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou, China
| | - Qingpei Huang
- GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou 510005, China
| | - Enze Deng
- GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou 510005, China
| | - Huanhuan Li
- GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou 510005, China; Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou, China
| | - Tahsin Stefan Barakat
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Jiekai Chen
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510525, China; Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou, China
| | - Duanqing Pei
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510525, China
| | - Xiaoying Fan
- GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou 510005, China.
| | - Ian Chambers
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH16 4UU, Scotland.
| | - Man Zhang
- GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou 510005, China; Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou, China.
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15
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Fang Y, Barrows D, Dabas Y, Carroll T, Singer S, Tap W, Nacev B. ATRX guards against aberrant differentiation in mesenchymal progenitor cells. Nucleic Acids Res 2024; 52:4950-4968. [PMID: 38477352 PMCID: PMC11109985 DOI: 10.1093/nar/gkae160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 01/19/2024] [Accepted: 03/05/2024] [Indexed: 03/14/2024] Open
Abstract
Alterations in the tumor suppressor ATRX are recurrently observed in mesenchymal neoplasms. ATRX has multiple epigenetic functions including heterochromatin formation and maintenance and regulation of transcription through modulation of chromatin accessibility. Here, we show in murine mesenchymal progenitor cells (MPCs) that Atrx deficiency aberrantly activated mesenchymal differentiation programs. This includes adipogenic pathways where ATRX loss induced expression of adipogenic transcription factors and enhanced adipogenic differentiation in response to differentiation stimuli. These changes are linked to loss of heterochromatin near mesenchymal lineage genes together with increased chromatin accessibility and gains of active chromatin marks. We additionally observed depletion of H3K9me3 at transposable elements, which are derepressed including near mesenchymal genes where they could serve as regulatory elements. Finally, we demonstrated that loss of ATRX in a mesenchymal malignancy, undifferentiated pleomorphic sarcoma, results in similar epigenetic disruption and de-repression of transposable elements. Together, our results reveal a role for ATRX in maintaining epigenetic states and transcriptional repression in mesenchymal progenitors and tumor cells and in preventing aberrant differentiation in the progenitor context.
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Affiliation(s)
- Yan Fang
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY10065, USA
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY 10065, USA
| | - Douglas Barrows
- Bioinformatics Resource Center, The Rockefeller University, New York, NY10065, USA
| | - Yakshi Dabas
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY 10065, USA
| | - Thomas S Carroll
- Bioinformatics Resource Center, The Rockefeller University, New York, NY10065, USA
| | - Sam Singer
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY10065, USA
| | - William D Tap
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY10065, USA
| | - Benjamin A Nacev
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA 15213, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
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16
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Liuzzi G, Artimagnella O, Frisari S, Mallamaci A. Foxg1 bimodally tunes L1-mRNA and -DNA dynamics in the developing murine neocortex. Development 2024; 151:dev202292. [PMID: 38655654 PMCID: PMC11190451 DOI: 10.1242/dev.202292] [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: 08/23/2023] [Accepted: 04/16/2024] [Indexed: 04/26/2024]
Abstract
Foxg1 masters telencephalic development via a pleiotropic control over its progression. Expressed within the central nervous system (CNS), L1 retrotransposons are implicated in progression of its histogenesis and tuning of its genomic plasticity. Foxg1 represses gene transcription, and L1 elements share putative Foxg1-binding motifs, suggesting the former might limit telencephalic expression (and activity) of the latter. We tested such a prediction, in vivo as well as in engineered primary neural cultures, using loss- and gain-of-function approaches. We found that Foxg1-dependent, transcriptional L1 repression specifically occurs in neopallial neuronogenic progenitors and post-mitotic neurons, where it is supported by specific changes in the L1 epigenetic landscape. Unexpectedly, we discovered that Foxg1 physically interacts with L1-mRNA and positively regulates neonatal neopallium L1-DNA content, antagonizing the retrotranscription-suppressing activity exerted by Mov10 and Ddx39a helicases. To the best of our knowledge, Foxg1 represents the first CNS patterning gene acting as a bimodal retrotransposon modulator, limiting transcription of L1 elements and promoting their amplification, within a specific domain of the developing mouse brain.
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Affiliation(s)
- Gabriele Liuzzi
- Laboratory of Cerebral Cortex Development, SISSA, Trieste 34136, Italy
| | | | - Simone Frisari
- Laboratory of Cerebral Cortex Development, SISSA, Trieste 34136, Italy
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17
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Chen K, Liu W, Zhu J, Kou X, Zhao Y, Wang H, Jiang C, Gao S, Kang L. Pivotal role for long noncoding RNAs in zygotic genome activation in mice. SCIENCE CHINA. LIFE SCIENCES 2024; 67:958-969. [PMID: 38305985 DOI: 10.1007/s11427-023-2502-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 11/22/2023] [Indexed: 02/03/2024]
Abstract
Vertebrate life begins with fertilization, and then the zygote genome is activated after transient silencing, a process termed zygotic genome activation (ZGA). Despite its fundamental role in totipotency and the initiation of life, the precise mechanism underlying ZGA initiation remains unclear. The existence of minor ZGA implies the possible critical role of noncoding RNAs in the initiation of ZGA. Here, we delineate the expression profile of long noncoding RNAs (lncRNAs) in early mouse embryonic development and elucidate their critical role in minor ZGA. Compared with protein-coding genes (PCGs), lncRNAs exhibit a stronger correlation with minor ZGA. Distinct H3K9me3 profiles can be observed between lncRNA genes and PCGs, and the enrichment of H3K9me3 before ZGA might explain the suspended expression of major ZGA-related PCGs despite possessing PolII pre-configuration. Furthermore, we identified the presence of PolII-enriched MuERV-L around the transcriptional start site of minor ZGA-related lncRNAs, and these repeats are responsible for the activation of minor ZGA-related lncRNAs and subsequent embryo development. Our study suggests that MuERV-L mediates minor ZGA lncRNA activation as a critical driver between epigenetic reprogramming triggered by fertilization and the embryo developmental program, thus providing clues for understanding the regulatory mechanism of totipotency and establishing bona fide totipotent stem cells.
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Affiliation(s)
- 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, Shanghai, 200120, China
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenju Liu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - 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, Shanghai, 200120, China
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, 200092, China
| | - Xiaochen Kou
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, 200092, China
| | - Yanhong Zhao
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, 200092, China
| | - Hong Wang
- Clinical and Translation Research Center of Shanghai First Maternity & Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Cizhong Jiang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease 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, School of Life Sciences and Technology, Tongji University, Shanghai, 200120, China.
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, 200092, China.
- Clinical and Translation Research Center of Shanghai First Maternity & Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, 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, Shanghai, 200120, China.
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, 200092, China.
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18
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Fu B, Ma H, Liu D. Essential roles of the nucleolus during early embryonic development: a regulatory hub for chromatin organization. Open Biol 2024; 14:230358. [PMID: 38689555 PMCID: PMC11065130 DOI: 10.1098/rsob.230358] [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: 10/02/2023] [Revised: 12/26/2023] [Accepted: 03/15/2024] [Indexed: 05/02/2024] Open
Abstract
The nucleolus is the most prominent liquid droplet-like membrane-less organelle in mammalian cells. Unlike the nucleolus in terminally differentiated somatic cells, those in totipotent cells, such as murine zygotes or two-cell embryos, have a unique nucleolar structure known as nucleolus precursor bodies (NPBs). Previously, it was widely accepted that NPBs in zygotes are simply passive repositories of materials that will be gradually used to construct a fully functional nucleolus after zygotic genome activation (ZGA). However, recent research studies have challenged this simplistic view and demonstrated that functions of the NPBs go beyond ribosome biogenesis. In this review, we provide a snapshot of the functions of NPBs in zygotes and early two-cell embryos in mice. We propose that these membrane-less organelles function as a regulatory hub for chromatin organization. On the one hand, NPBs provide the structural platform for centric and pericentric chromatin remodelling. On the other hand, the dynamic changes in nucleolar structure control the release of the pioneer factors (i.e. double homeobox (Dux)). It appears that during transition from totipotency to pluripotency, decline of totipotency and initiation of fully functional nucleolus formation are not independent events but are interconnected. Consequently, it is reasonable to hypothesize that dissecting more unknown functions of NPBs may shed more light on the enigmas of early embryonic development and may ultimately provide novel approaches to improve reprogramming efficiency.
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Affiliation(s)
- Bo Fu
- Institute of Animal Husbandry, HeiLongJiang Academy of
Agricultural Sciences, Harbin150086, People's Republic of China
- Key Laboratory of Combining Farming and Animal Husbandry,
Ministry of Agriculture and Rural Affairs, Harbin150086, People's Republic of China
| | - Hong Ma
- Institute of Animal Husbandry, HeiLongJiang Academy of
Agricultural Sciences, Harbin150086, People's Republic of China
- Key Laboratory of Combining Farming and Animal Husbandry,
Ministry of Agriculture and Rural Affairs, Harbin150086, People's Republic of China
| | - Di Liu
- Institute of Animal Husbandry, HeiLongJiang Academy of
Agricultural Sciences, Harbin150086, People's Republic of China
- Key Laboratory of Combining Farming and Animal Husbandry,
Ministry of Agriculture and Rural Affairs, Harbin150086, People's Republic of China
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19
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Han Q, Ma R, Liu N. Epigenetic reprogramming in the transition from pluripotency to totipotency. J Cell Physiol 2024; 239:e31222. [PMID: 38375873 DOI: 10.1002/jcp.31222] [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: 10/17/2023] [Revised: 01/08/2024] [Accepted: 02/05/2024] [Indexed: 02/21/2024]
Abstract
Mammalian development commences with the zygote, which can differentiate into both embryonic and extraembryonic tissues, a capability known as totipotency. Only the zygote and embryos around zygotic genome activation (ZGA) (two-cell embryo stage in mice and eight-cell embryo in humans) are totipotent cells. Epigenetic modifications undergo extremely extensive changes during the acquisition of totipotency and subsequent development of differentiation. However, the underlying molecular mechanisms remain elusive. Recently, the discovery of mouse two-cell embryo-like cells, human eight-cell embryo-like cells, extended pluripotent stem cells and totipotent-like stem cells with extra-embryonic developmental potential has greatly expanded our understanding of totipotency. Experiments with these in vitro models have led to insights into epigenetic changes in the reprogramming of pluri-to-totipotency, which have informed the exploration of preimplantation development. In this review, we highlight the recent findings in understanding the mechanisms of epigenetic remodeling during totipotency capture, including RNA splicing, DNA methylation, chromatin configuration, histone modifications, and nuclear organization.
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Affiliation(s)
- Qingsheng Han
- School of Medicine, Nankai University, Tianjin, China
| | - Ru Ma
- School of Medicine, Nankai University, Tianjin, China
| | - Na Liu
- School of Medicine, Nankai University, Tianjin, China
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20
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Tian Q, Chung H, Wen D. The role of lipids in genome integrity and pluripotency. Biochem Soc Trans 2024; 52:639-650. [PMID: 38506536 PMCID: PMC11088914 DOI: 10.1042/bst20230479] [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: 10/10/2023] [Revised: 03/05/2024] [Accepted: 03/11/2024] [Indexed: 03/21/2024]
Abstract
Pluripotent stem cells (PSCs), comprising embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs), offer immense potential for regenerative medicine due to their ability to differentiate into all cell types of the adult body. A critical aspect of harnessing this potential is understanding their metabolic requirements during derivation, maintenance, and differentiation in vitro. Traditional culture methods using fetal bovine serum often lead to issues such as heterogeneous cell populations and diminished pluripotency. Although the chemically-defined 2i/LIF medium has provided solutions to some of these challenges, prolonged culturing of these cells, especially female ESCs, raises concerns related to genome integrity. This review discusses the pivotal role of lipids in genome stability and pluripotency of stem cells. Notably, the introduction of lipid-rich albumin, AlbuMAX, into the 2i/LIF culture medium offers a promising avenue for enhancing the genomic stability and pluripotency of cultured ESCs. We further explore the unique characteristics of lipid-induced pluripotent stem cells (LIP-ESCs), emphasizing their potential in regenerative medicine and pluripotency research.
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Affiliation(s)
- Qiyu Tian
- Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY 10065, U.S.A
| | - Hoyoung Chung
- Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY 10065, U.S.A
| | - Duancheng Wen
- Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY 10065, U.S.A
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21
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Yu H, Zhao J, Shen Y, Qiao L, Liu Y, Xie G, Chang S, Ge T, Li N, Chen M, Li H, Zhang J, Wang X. The dynamic landscape of enhancer-derived RNA during mouse early embryo development. Cell Rep 2024; 43:114077. [PMID: 38592974 DOI: 10.1016/j.celrep.2024.114077] [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: 10/03/2023] [Revised: 01/10/2024] [Accepted: 03/22/2024] [Indexed: 04/11/2024] Open
Abstract
Enhancer-derived RNAs (eRNAs) play critical roles in diverse biological processes by facilitating their target gene expression. However, the abundance and function of eRNAs in early embryos are not clear. Here, we present a comprehensive eRNA atlas by systematically integrating publicly available datasets of mouse early embryos. We characterize the transcriptional and regulatory network of eRNAs and show that different embryo developmental stages have distinct eRNA expression and regulatory profiles. Paternal eRNAs are activated asymmetrically during zygotic genome activation (ZGA). Moreover, we identify an eRNA, MZGAe1, which plays an important function in regulating mouse ZGA and early embryo development. MZGAe1 knockdown leads to a developmental block from 2-cell embryo to blastocyst. We create an online data portal, M2ED2, to query and visualize eRNA expression and regulation. Our study thus provides a systematic landscape of eRNA and reveals the important role of eRNAs in regulating mouse early embryo development.
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Affiliation(s)
- Hua Yu
- Westlake Genomics and Bioinformatics Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China; School of Life Sciences, Westlake University, Hangzhou 310024, China; Westlake Institute for Advanced Study, Hangzhou 310024, China; School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330006, China; The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China; Institute of Life Sciences, Nanchang University, Nanchang 330031, China.
| | - Jing Zhao
- Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China
| | - Yuxuan Shen
- Center of Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Lu Qiao
- Westlake Genomics and Bioinformatics Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China; School of Life Sciences, Westlake University, Hangzhou 310024, China; Westlake Institute for Advanced Study, Hangzhou 310024, China
| | - Yuheng Liu
- HPC Center, Westlake University, Hangzhou 310024, China
| | - Guanglei Xie
- Westlake Genomics and Bioinformatics Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China; School of Life Sciences, Westlake University, Hangzhou 310024, China; Westlake Institute for Advanced Study, Hangzhou 310024, China
| | - Shuhui Chang
- School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Tingying Ge
- School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Nan Li
- HPC Center, Westlake University, Hangzhou 310024, China
| | - Ming Chen
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hu Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55904, USA
| | - Jin Zhang
- Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China; Center of Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China.
| | - Xi Wang
- Westlake Genomics and Bioinformatics Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China; School of Life Sciences, Westlake University, Hangzhou 310024, China; Westlake Institute for Advanced Study, Hangzhou 310024, China.
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22
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Azagury M, Buganim Y. Unlocking trophectoderm mysteries: In vivo and in vitro perspectives on human and mouse trophoblast fate induction. Dev Cell 2024; 59:941-960. [PMID: 38653193 DOI: 10.1016/j.devcel.2024.03.029] [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: 09/07/2023] [Revised: 11/10/2023] [Accepted: 03/18/2024] [Indexed: 04/25/2024]
Abstract
In recent years, the pursuit of inducing the trophoblast stem cell (TSC) state has gained prominence as a compelling research objective, illuminating the establishment of the trophoblast lineage and unlocking insights into early embryogenesis. In this review, we examine how advancements in diverse technologies, including in vivo time course transcriptomics, cellular reprogramming to TSC state, chemical induction of totipotent stem-cell-like state, and stem-cell-based embryo-like structures, have enriched our insights into the intricate molecular mechanisms and signaling pathways that define the mouse and human trophectoderm/TSC states. We delve into disparities between mouse and human trophectoderm/TSC fate establishment, with a special emphasis on the intriguing role of pluripotency in this context. Additionally, we re-evaluate recent findings concerning the potential of totipotent-stem-like cells and embryo-like structures to fully manifest the trophectoderm/trophoblast lineage's capabilities. Lastly, we briefly discuss the potential applications of induced TSCs in pregnancy-related disease modeling.
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Affiliation(s)
- Meir Azagury
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Yosef Buganim
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel.
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23
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Lin Y, Yu L, Xu Q, Qiu P, Zhang Y, Dong X, Yan G, Sun H, Cao G. GATAD2B is required for pre-implantation embryonic development by regulating zygotic genome activation. Cell Prolif 2024:e13647. [PMID: 38605678 DOI: 10.1111/cpr.13647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 03/20/2024] [Accepted: 04/03/2024] [Indexed: 04/13/2024] Open
Abstract
Major zygotic genome activation (ZGA) occurs at the late 2-cell stage and involves the activation of thousands of genes, supporting early embryonic development. The reasons underlying the regulation of ZGA are not clear. Acetylation modifications of histone tails promote transcriptional activation, and the maternal deletion of H4K16ac leads to failure in ZGA. GATAD2B is one of the core subunits of the nucleosome remodelling and histone deacetylation (NuRD) complex. Our research has shown that GATAD2B exhibits specific nucleus localization and high protein expression from the late 2-cell stage to the 8-cell stage. This intriguing phenomenon prompted us to investigate the relationship between GATAD2B and the ZGA. We discovered a distinctive pattern of GATAD2B, starting from the late 2-cell stage with nuclear localization. GATAD2B depletion resulted in defective embryonic development, including increased DNA damage at morula, decreased blastocyst formation rate, and abnormal differentiation of ICM/TE lineages. Consistent with the delay during the cleavage stage, the transcriptome analysis of the 2-cell embryo revealed inhibition of the cell cycle G2/M phase transition pathway. Furthermore, the GATAD2B proteomic data provided clear evidence of a certain association between GATAD2B and molecules involved in the cell cycle pathway. As hypothesized, GATAD2B-deficient 2-cell embryos exhibited abnormalities in ZGA during the maternal-to-embryonic transition, with lower expression of the major ZGA marker MERVL. Overall, our results demonstrate that GATAD2B is essential for early embryonic development, in part through facilitating ZGA.
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Affiliation(s)
- Yuling Lin
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, China
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, China
| | - Lina Yu
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, China
| | - Qian Xu
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Panpan Qiu
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, China
| | - Yang Zhang
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, China
| | - Xiaohan Dong
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, China
| | - Guijun Yan
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, China
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, China
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Haixiang Sun
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, China
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, China
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Guangyi Cao
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, China
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, China
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
- Key Laboratory of Reproductive Medicine of Guangdong Province, Guangzhou, China
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24
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Honda S, Hatamura M, Kunimoto Y, Ikeda S, Minami N. Chimeric PRMT6 protein produced by an endogenous retrovirus promoter regulates cell fate decision in mouse preimplantation embryos†. Biol Reprod 2024; 110:698-710. [PMID: 38196172 DOI: 10.1093/biolre/ioae002] [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: 05/29/2023] [Revised: 10/11/2023] [Accepted: 01/07/2023] [Indexed: 01/11/2024] Open
Abstract
Murine endogenous retrovirus with leucine tRNA primer, also known as MERVL, is expressed during zygotic genome activation in mammalian embryos. Here we show that protein arginine N-methyltransferase 6 (Prmt6) forms a chimeric transcript with MT2B2, one of the long terminal repeat sequences of murine endogenous retrovirus with leucine tRNA primer, and is translated into an elongated chimeric protein (PRMT6MT2B2) whose function differs from that of the canonical PRMT6 protein (PRMT6CAN) in mouse preimplantation embryos. Overexpression of PRMT6CAN in fibroblast cells increased asymmetric dimethylation of the third arginine residue of both histone H2A (H2AR3me2a) and histone H4 (H4R3me2a), while overexpression of PRMT6MT2B2 increased only H2AR3me2a. In addition, overexpression of PRMT6MT2B2 in one blastomere of mouse two-cell embryos promoted cell proliferation and differentiation of the blastomere into epiblast cells at the blastocyst stage, while overexpression of PRMT6CAN repressed cell proliferation. This is the first report of the translation of a chimeric protein (PRMT6MT2B2) in mouse preimplantation embryos. Our results suggest that analyzing chimeric transcripts with murine endogenous retrovirus with leucine tRNA primer will provide insight into the relationship between zygotic genome activation and subsequent intra- and extra-cellular lineage determination.
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Affiliation(s)
- Shinnosuke Honda
- Laboratory of Reproductive Biology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Maho Hatamura
- Laboratory of Reproductive Biology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Yuri Kunimoto
- Laboratory of Reproductive Biology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Shuntaro Ikeda
- Laboratory of Reproductive Biology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Naojiro Minami
- Laboratory of Reproductive Biology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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25
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da Silva AL, Guedes BLM, Santos SN, Correa GF, Nardy A, Nali LHDS, Bachi ALL, Romano CM. Beyond pathogens: the intriguing genetic legacy of endogenous retroviruses in host physiology. Front Cell Infect Microbiol 2024; 14:1379962. [PMID: 38655281 PMCID: PMC11035796 DOI: 10.3389/fcimb.2024.1379962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 03/22/2024] [Indexed: 04/26/2024] Open
Abstract
The notion that viruses played a crucial role in the evolution of life is not a new concept. However, more recent insights suggest that this perception might be even more expansive, highlighting the ongoing impact of viruses on host evolution. Endogenous retroviruses (ERVs) are considered genomic remnants of ancient viral infections acquired throughout vertebrate evolution. Their exogenous counterparts once infected the host's germline cells, eventually leading to the permanent endogenization of their respective proviruses. The success of ERV colonization is evident so that it constitutes 8% of the human genome. Emerging genomic studies indicate that endogenous retroviruses are not merely remnants of past infections but rather play a corollary role, despite not fully understood, in host genetic regulation. This review presents some evidence supporting the crucial role of endogenous retroviruses in regulating host genetics. We explore the involvement of human ERVs (HERVs) in key physiological processes, from their precise and orchestrated activities during cellular differentiation and pluripotency to their contributions to aging and cellular senescence. Additionally, we discuss the costs associated with hosting a substantial amount of preserved viral genetic material.
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Affiliation(s)
- Amanda Lopes da Silva
- Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Bruno Luiz Miranda Guedes
- Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Samuel Nascimento Santos
- UNISA Research Center, Universidade Santo Amaro, Post-Graduation in Health Sciences, São Paulo, Brazil
| | - Giovanna Francisco Correa
- Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Ariane Nardy
- UNISA Research Center, Universidade Santo Amaro, Post-Graduation in Health Sciences, São Paulo, Brazil
| | | | - Andre Luis Lacerda Bachi
- UNISA Research Center, Universidade Santo Amaro, Post-Graduation in Health Sciences, São Paulo, Brazil
| | - Camila Malta Romano
- Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil
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26
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Oomen ME, Torres-Padilla ME. Jump-starting life: balancing transposable element co-option and genome integrity in the developing mammalian embryo. EMBO Rep 2024; 25:1721-1733. [PMID: 38528171 PMCID: PMC11015026 DOI: 10.1038/s44319-024-00118-5] [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: 12/07/2023] [Revised: 02/23/2024] [Accepted: 03/05/2024] [Indexed: 03/27/2024] Open
Abstract
Remnants of transposable elements (TEs) are widely expressed throughout mammalian embryo development. Originally infesting our genomes as selfish elements and acting as a source of genome instability, several of these elements have been co-opted as part of a complex system of genome regulation. Many TEs have lost transposition ability and their transcriptional potential has been tampered as a result of interactions with the host throughout evolutionary time. It has been proposed that TEs have been ultimately repurposed to function as gene regulatory hubs scattered throughout our genomes. In the early embryo in particular, TEs find a perfect environment of naïve chromatin to escape transcriptional repression by the host. As a consequence, it is thought that hosts found ways to co-opt TE sequences to regulate large-scale changes in chromatin and transcription state of their genomes. In this review, we discuss several examples of TEs expressed during embryo development, their potential for co-option in genome regulation and the evolutionary pressures on TEs and on our genomes.
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Affiliation(s)
- Marlies E Oomen
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, München, Germany
| | - Maria-Elena Torres-Padilla
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, München, Germany.
- Faculty of Biology, Ludwig-Maximilians Universität, München, Germany.
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27
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Exit from totipotency is controlled by DUXBL in mice. Nat Genet 2024; 56:563-564. [PMID: 38528243 DOI: 10.1038/s41588-024-01690-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
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28
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Wang J, Lu X, Zhang W, Liu GH. Endogenous retroviruses in development and health. Trends Microbiol 2024; 32:342-354. [PMID: 37802660 DOI: 10.1016/j.tim.2023.09.006] [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: 07/14/2023] [Revised: 09/12/2023] [Accepted: 09/13/2023] [Indexed: 10/08/2023]
Abstract
Endogenous retroviruses (ERVs) are evolutionary remnants of retroviral infections in which the viral genome became embedded as a dormant regulatory element within the host germline. When ERVs become activated, they comprehensively rewire genomic regulatory networks of the host and facilitate critical developmental events, such as preimplantation development and placentation, in a manner specific to species, developmental stage, and tissues. However, accumulating evidence suggests that aberrant ERV transcription compromises genome stability and has been implicated in cellular senescence and various pathogenic processes, underscoring the significance of host genomic surveillance mechanisms. Here, we revisit the prominent functions of ERVs in early development and highlight their emerging roles in mammalian post-implantation development and organogenesis. We also discuss their implications for aging and pathological processes such as microbial infection, immune response. Furthermore, we discuss recent advances in stem-cell-based models, single-cell omics, and genome editing technologies, which serve as beacons illuminating the versatile nature of ERVs in mammalian development and health.
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Affiliation(s)
- Jichang Wang
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China.
| | - Xinyi Lu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, China.
| | - Weiqi Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics and China National Center for Bioinformation, Chinese Academy of Sciences, Beijing 100101, China.
| | - Guang-Hui Liu
- State Key Laboratory of Membrane 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; Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China.
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29
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Vega-Sendino M, Lüttmann FF, Olbrich T, Chen Y, Kuenne C, Stein P, Tillo D, Carey GI, Zhong J, Savy V, Radonova L, Lu T, Saykali B, Kim KP, Domingo CN, Schüler L, Günther S, Bentsen M, Bosnakovski D, Schöler H, Kyba M, Maity TK, Jenkins LM, Looso M, Williams CJ, Kim J, Ruiz S. The homeobox transcription factor DUXBL controls exit from totipotency. Nat Genet 2024; 56:697-709. [PMID: 38509386 PMCID: PMC11149696 DOI: 10.1038/s41588-024-01692-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: 11/18/2022] [Accepted: 02/16/2024] [Indexed: 03/22/2024]
Abstract
In mice, exit from the totipotent two-cell (2C) stage embryo requires silencing of the 2C-associated transcriptional program. However, the molecular mechanisms involved in this process remain poorly understood. Here we demonstrate that the 2C-specific transcription factor double homeobox protein (DUX) mediates an essential negative feedback loop by inducing the expression of DUXBL to promote this silencing. We show that DUXBL gains accessibility to DUX-bound regions specifically upon DUX expression. Furthermore, we determine that DUXBL interacts with TRIM24 and TRIM33, members of the TRIM superfamily involved in gene silencing, and colocalizes with them in nuclear foci upon DUX expression. Importantly, DUXBL overexpression impairs 2C-associated transcription, whereas Duxbl inactivation in mouse embryonic stem cells increases DUX-dependent induction of the 2C-transcriptional program. Consequently, DUXBL deficiency in embryos results in sustained expression of 2C-associated transcripts leading to early developmental arrest. Our study identifies DUXBL as an essential regulator of totipotency exit enabling the first divergence of cell fates.
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Affiliation(s)
| | - Felipe F Lüttmann
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
- Cardio-Pulmonary Institute, Frankfurt, Germany
| | - Teresa Olbrich
- Laboratory of Genome Integrity, CCR, NCI, NIH, Bethesda, MD, USA
| | - Yanpu Chen
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
- Cardio-Pulmonary Institute, Frankfurt, Germany
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Department of Cardiology, Guangzhou Institute of Cardiovascular Disease, Guangdong Key Laboratory of Vascular Diseases, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Carsten Kuenne
- Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Paula Stein
- Reproductive and Developmental Biology Laboratory, NIEHS, NIH, Research Triangle Park, NC, USA
| | | | - Grace I Carey
- Laboratory of Genome Integrity, CCR, NCI, NIH, Bethesda, MD, USA
| | - Jiasheng Zhong
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
- German Cancer Research Center, Heidelberg, Germany
| | - Virginia Savy
- Reproductive and Developmental Biology Laboratory, NIEHS, NIH, Research Triangle Park, NC, USA
| | - Lenka Radonova
- Reproductive and Developmental Biology Laboratory, NIEHS, NIH, Research Triangle Park, NC, USA
| | - Tianlin Lu
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
- Cardio-Pulmonary Institute, Frankfurt, Germany
| | - Bechara Saykali
- Laboratory of Genome Integrity, CCR, NCI, NIH, Bethesda, MD, USA
| | - Kee-Pyo Kim
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
- Department of Medical Life Sciences, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | | | - Leah Schüler
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Stefan Günther
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Rhein/Main, Germany
| | - Mette Bentsen
- Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Darko Bosnakovski
- Lillehei Heart Institute, Department of Pediatrics, University of Minnesota, Minneapolis, USA
| | - Hans Schöler
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Michael Kyba
- Lillehei Heart Institute, Department of Pediatrics, University of Minnesota, Minneapolis, USA
| | - Tapan K Maity
- Laboratory of Cell Biology, CCR, NCI, NIH, Bethesda, MD, USA
| | - Lisa M Jenkins
- Laboratory of Cell Biology, CCR, NCI, NIH, Bethesda, MD, USA
| | - Mario Looso
- Cardio-Pulmonary Institute, Frankfurt, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Rhein/Main, Germany
| | - Carmen J Williams
- Reproductive and Developmental Biology Laboratory, NIEHS, NIH, Research Triangle Park, NC, USA
| | - Johnny Kim
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany.
- Cardio-Pulmonary Institute, Frankfurt, Germany.
- German Center for Cardiovascular Research (DZHK), Partner Site Rhein/Main, Germany.
- German Center for Lung Research (DZL), Partner Site Rhein/Main, Germany.
- Institute of Lung Health (ILH), Justus-Liebig-University Giessen, Giessen, Germany.
- The Center for Cardiovascular Regeneration and Immunology at TRON-Translational Oncology at the University Medical Center of the Johannes Gutenberg-University Mainz gGmbH, Mainz, Germany.
| | - Sergio Ruiz
- Laboratory of Genome Integrity, CCR, NCI, NIH, Bethesda, MD, USA.
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Yang J, Cook L, Chen Z. Systematic evaluation of retroviral LTRs as cis-regulatory elements in mouse embryos. Cell Rep 2024; 43:113775. [PMID: 38381606 PMCID: PMC11024894 DOI: 10.1016/j.celrep.2024.113775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/27/2023] [Accepted: 01/24/2024] [Indexed: 02/23/2024] Open
Abstract
In mammals, many retrotransposons are de-repressed during zygotic genome activation (ZGA). However, their functions in early development remain elusive largely due to the challenge to simultaneously manipulate thousands of retrotransposon insertions in embryos. Here, we applied CRISPR interference (CRISPRi) to perturb the long terminal repeat (LTR) MT2_Mm, a well-known ZGA and totipotency marker that exists in ∼2,667 insertions throughout the mouse genome. CRISPRi robustly perturbed 2,485 (∼93%) MT2_Mm insertions and 1,090 (∼55%) insertions of the closely related MT2C_Mm in 2-cell embryos. Remarkably, such perturbation caused downregulation of hundreds of ZGA genes and embryonic arrest mostly at the morula stage. Mechanistically, MT2 LTRs are globally enriched for open chromatin and H3K27ac and function as promoters/enhancers downstream of OBOX/DUX proteins. Thus, we not only provide direct evidence to support the functional importance of MT2 activation in development but also systematically define cis-regulatory function of MT2 in embryos by integrating functional perturbation and multi-omic analyses.
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Affiliation(s)
- Jian Yang
- Reproductive Sciences Center, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Lauryn Cook
- Reproductive Sciences Center, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Zhiyuan Chen
- Reproductive Sciences Center, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA.
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31
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Hu Y, Wang Y, He Y, Ye M, Yuan J, Ren C, Wang X, Wang S, Guo Y, Cao Q, Zhou S, Wang B, He A, Hu J, Guo X, Shu W, Huo R. Maternal KLF17 controls zygotic genome activation by acting as a messenger for RNA Pol II recruitment in mouse embryos. Dev Cell 2024; 59:613-626.e6. [PMID: 38325372 DOI: 10.1016/j.devcel.2024.01.013] [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: 10/13/2022] [Revised: 09/01/2023] [Accepted: 01/17/2024] [Indexed: 02/09/2024]
Abstract
Initiation of timely and sufficient zygotic genome activation (ZGA) is crucial for the beginning of life, yet our knowledge of transcription factors (TFs) contributing to ZGA remains limited. Here, we screened the proteome of early mouse embryos after cycloheximide (CHX) treatment and identified maternally derived KLF17 as a potential TF for ZGA genes. Using a conditional knockout (cKO) mouse model, we further investigated the role of maternal KLF17 and found that it promotes embryonic development and full fertility. Mechanistically, KLF17 preferentially binds to promoters and recruits RNA polymerase II (RNA Pol II) in early 2-cell embryos, facilitating the expression of major ZGA genes. Maternal Klf17 knockout resulted in a downregulation of 9% of ZGA genes and aberrant RNA Pol II pre-configuration, which could be partially rescued by introducing exogenous KLF17. Overall, our study provides a strategy for screening essential ZGA factors and identifies KLF17 as a crucial TF in this process.
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Affiliation(s)
- Yue Hu
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Histology and Embryology, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China
| | | | - Yuanlin He
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Histology and Embryology, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China
| | - Maosheng Ye
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Histology and Embryology, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China
| | - Jie Yuan
- Bioinformatics Center of AMMS, Beijing, China
| | - Chao Ren
- Bioinformatics Center of AMMS, Beijing, China
| | - Xia Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Histology and Embryology, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China
| | - Siqi Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Histology and Embryology, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China
| | - Yueshuai Guo
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Histology and Embryology, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China
| | - Qiqi Cao
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Histology and Embryology, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China
| | - Shuai Zhou
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Histology and Embryology, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China
| | - Bing Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Histology and Embryology, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China
| | - Anlan He
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Histology and Embryology, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China
| | | | - Xuejiang Guo
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Histology and Embryology, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China
| | - Wenjie Shu
- Bioinformatics Center of AMMS, Beijing, China.
| | - Ran Huo
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Histology and Embryology, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China; Innovation Center of Suzhou Nanjing Medical University, Suzhou, China.
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32
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Du P, Wu J. Hallmarks of totipotent and pluripotent stem cell states. Cell Stem Cell 2024; 31:312-333. [PMID: 38382531 PMCID: PMC10939785 DOI: 10.1016/j.stem.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/18/2024] [Accepted: 01/26/2024] [Indexed: 02/23/2024]
Abstract
Though totipotency and pluripotency are transient during early embryogenesis, they establish the foundation for the development of all mammals. Studying these in vivo has been challenging due to limited access and ethical constraints, particularly in humans. Recent progress has led to diverse culture adaptations of epiblast cells in vitro in the form of totipotent and pluripotent stem cells, which not only deepen our understanding of embryonic development but also serve as invaluable resources for animal reproduction and regenerative medicine. This review delves into the hallmarks of totipotent and pluripotent stem cells, shedding light on their key molecular and functional features.
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Affiliation(s)
- Peng Du
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China.
| | - Jun Wu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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33
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Vega-Sendino M, Ruiz S. Transition from totipotency to pluripotency in mice: insights into molecular mechanisms. Biochem Soc Trans 2024; 52:231-239. [PMID: 38288760 DOI: 10.1042/bst20230442] [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: 11/02/2023] [Revised: 12/26/2023] [Accepted: 01/08/2024] [Indexed: 02/29/2024]
Abstract
Totipotency is the ability of a single cell to develop into a full organism and, in mammals, is strictly associated with the early stages of development following fertilization. This unlimited developmental potential becomes quickly restricted as embryonic cells transition into a pluripotent state. The loss of totipotency seems a consequence of the zygotic genome activation (ZGA), a process that determines the switch from maternal to embryonic transcription, which in mice takes place following the first cleavage. ZGA confers to the totipotent cell a transient transcriptional profile characterized by the expression of stage-specific genes and a set of transposable elements that prepares the embryo for subsequent development. The timely silencing of this transcriptional program during the exit from totipotency is required to ensure proper development. Importantly, the molecular mechanisms regulating the transition from totipotency to pluripotency have remained elusive due to the scarcity of embryonic material. However, the development of new in vitro totipotent-like models together with advances in low-input genome-wide technologies, are providing a better mechanistic understanding of how this important transition is achieved. This review summarizes the current knowledge on the molecular determinants that regulate the exit from totipotency.
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Affiliation(s)
- Maria Vega-Sendino
- Laboratory of Genome Integrity, CCR, NCI, NIH, Bethesda, MD 20814, U.S.A
| | - Sergio Ruiz
- Laboratory of Genome Integrity, CCR, NCI, NIH, Bethesda, MD 20814, U.S.A
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34
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Khoa LTP, Yang W, Shan M, Zhang L, Mao F, Zhou B, Li Q, Malcore R, Harris C, Zhao L, Rao RC, Iwase S, Kalantry S, Bielas SL, Lyssiotis CA, Dou Y. Quiescence enables unrestricted cell fate in naive embryonic stem cells. Nat Commun 2024; 15:1721. [PMID: 38409226 PMCID: PMC10897426 DOI: 10.1038/s41467-024-46121-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 02/14/2024] [Indexed: 02/28/2024] Open
Abstract
Quiescence in stem cells is traditionally considered as a state of inactive dormancy or with poised potential. Naive mouse embryonic stem cells (ESCs) can enter quiescence spontaneously or upon inhibition of MYC or fatty acid oxidation, mimicking embryonic diapause in vivo. The molecular underpinning and developmental potential of quiescent ESCs (qESCs) are relatively unexplored. Here we show that qESCs possess an expanded or unrestricted cell fate, capable of generating both embryonic and extraembryonic cell types (e.g., trophoblast stem cells). These cells have a divergent metabolic landscape comparing to the cycling ESCs, with a notable decrease of the one-carbon metabolite S-adenosylmethionine. The metabolic changes are accompanied by a global reduction of H3K27me3, an increase of chromatin accessibility, as well as the de-repression of endogenous retrovirus MERVL and trophoblast master regulators. Depletion of methionine adenosyltransferase Mat2a or deletion of Eed in the polycomb repressive complex 2 results in removal of the developmental constraints towards the extraembryonic lineages. Our findings suggest that quiescent ESCs are not dormant but rather undergo an active transition towards an unrestricted cell fate.
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Affiliation(s)
- Le Tran Phuc Khoa
- Department of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90033, USA
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Wentao Yang
- Department of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90033, USA
| | - Mengrou Shan
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Li Zhang
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Fengbiao Mao
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China
| | - Bo Zhou
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Qiang Li
- Department of Ophthalmology & Visual Sciences, W.K. Kellogg Eye Center, University of Michigan, 1000 Wall St., Ann Arbor, MI, 48105, USA
| | - Rebecca Malcore
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Clair Harris
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Lili Zhao
- Beaumont Hospital, Wayne, 33155 Annapolis St., Wayne, MI, 48184, USA
| | - Rajesh C Rao
- Department of Ophthalmology & Visual Sciences, W.K. Kellogg Eye Center, University of Michigan, 1000 Wall St., Ann Arbor, MI, 48105, USA
| | - Shigeki Iwase
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Sundeep Kalantry
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Stephanie L Bielas
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Costas A Lyssiotis
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Yali Dou
- Department of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90033, USA.
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Kawase M, Ichiyanagi K. Mouse retrotransposons: sequence structure, evolutionary age, genomic distribution and function. Genes Genet Syst 2024; 98:337-351. [PMID: 37989301 DOI: 10.1266/ggs.23-00221] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023] Open
Abstract
Retrotransposons are transposable elements that are transposed via transcription and reverse transcription. Their copies have accumulated in the genome of mammals, occupying approximately 40% of mammalian genomic mass. These copies are often involved in numerous phenomena, such as chromatin spatial organization, gene expression, development and disease, and have been recognized as a driving force in evolution. Different organisms have gained specific retrotransposon subfamilies and retrotransposed copies, such as hundreds of Mus-specific subfamilies with diverse sequences and genomic locations. Despite this complexity, basic information is still necessary for present-day genomic and epigenomic studies. Herein, we describe the characteristics of each subfamily of Mus-specific retrotransposons in terms of sequence structure, phylogenetic relationships, evolutionary age, and preference for A or B compartments of chromatin.
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Affiliation(s)
- Masaki Kawase
- Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University
| | - Kenji Ichiyanagi
- Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University
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36
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Mehta P, Singh R. Small RNAs: an ideal choice as sperm quality biomarkers. FRONTIERS IN REPRODUCTIVE HEALTH 2024; 6:1329760. [PMID: 38406667 PMCID: PMC10884189 DOI: 10.3389/frph.2024.1329760] [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: 10/29/2023] [Accepted: 01/17/2024] [Indexed: 02/27/2024] Open
Abstract
Spermatozoa were classically known as vehicles for the delivery of the paternal genome to the oocyte. However, in 1962, spermatozoa were discovered to carry significant amounts of RNA in them, which raised questions about the significance of these molecules in such a highly specialized cell. Scientific research in the last six decades has investigated the biological significance of sperm RNAs by various means. Irrespective of what sperm RNAs do, their presence in spermatozoa has attracted attention for their exploitation as biomarkers of fertility. Research in this direction started in the year 2000 and is still underway. A major hurdle in this research is the definition of the standard human sperm RNAome. Only a few normozoospermic samples have been analyzed to define the normal sperm RNAome. In this article, we provide a perspective on the suitability of sperm RNAs as biomarkers of fertility and the importance of defining the normal sperm RNAome before we can succeed in identifying RNA-based biomarkers of sperm quality and fertility. The identification of sperm RNA biomarkers of fertility can be exploited for quality screening of donor sperm samples, explain infertility in idiopathic cases, and RNA therapeutics for the treatment of male infertility.
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Affiliation(s)
- Poonam Mehta
- Division of Endocrinology, Central Drug Research Institute, Lucknow, India
- Division of Endocrinology, Academy of Scientific and Industrial Research (AcSIR), Ghaziabad, India
| | - Rajender Singh
- Division of Endocrinology, Central Drug Research Institute, Lucknow, India
- Division of Endocrinology, Academy of Scientific and Industrial Research (AcSIR), Ghaziabad, India
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Wu B, Wang Y, Wei X, Zhang J, Wu J, Cao G, Zhang Y, Liu J, Li X, Bao S. NELFA and BCL2 induce the 2C-like state in mouse embryonic stem cells in a chemically defined medium. Cell Prolif 2024; 57:e13534. [PMID: 37592709 PMCID: PMC10849787 DOI: 10.1111/cpr.13534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/19/2023] [Accepted: 07/21/2023] [Indexed: 08/19/2023] Open
Abstract
A minority of mouse embryonic stem cells (ESCs) display totipotent features resembling 2-cell stage embryos and are known as 2-cell-like (2C-like) cells. However, how ESCs transit into this 2C-like state remains largely unknown. Here, we report that the overexpression of negative elongation factor A (Nelfa), a maternally provided factor, enhances the conversion of ESCs into 2C-like cells in chemically defined conditions, while the deletion of endogenous Nelfa does not block this transition. We also demonstrate that Nelfa overexpression significantly enhances somatic cell reprogramming efficiency. Interestingly, we found that the co-overexpression of Nelfa and Bcl2 robustly activates the 2C-like state in ESCs and endows the cells with dual cell fate potential. We further demonstrate that Bcl2 overexpression upregulates endogenous Nelfa expression and can induce the 2C-like state in ESCs even in the absence of Nelfa. Our findings highlight the importance of BCL2 in the regulation of the 2C-like state and provide insights into the mechanism underlying the roles of Nelfa and Bcl2 in the establishment and regulation of the totipotent state in mouse ESCs.
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Affiliation(s)
- Baojiang Wu
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland LivestockInner Mongolia UniversityHohhotChina
- Research Centre for Animal Genetic Resources of Mongolia Plateau, College of Life SciencesInner Mongolia UniversityHohhotChina
| | - Yanqiu Wang
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland LivestockInner Mongolia UniversityHohhotChina
- Research Centre for Animal Genetic Resources of Mongolia Plateau, College of Life SciencesInner Mongolia UniversityHohhotChina
| | - Xinhua Wei
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland LivestockInner Mongolia UniversityHohhotChina
- Research Centre for Animal Genetic Resources of Mongolia Plateau, College of Life SciencesInner Mongolia UniversityHohhotChina
| | - Jingcheng Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, College of Veterinary MedicineNorthwest A&F UniversityYanglingChina
| | - Jiahui Wu
- School of Veterinary MedicineInner Mongolia Agricultural UniversityHohhotChina
| | - Guifang Cao
- School of Veterinary MedicineInner Mongolia Agricultural UniversityHohhotChina
- Inner Mongolia Saikexing Institute of Breeding and Reproductive Biotechnology in Domestic AnimalHohhotChina
| | - Yong Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, College of Veterinary MedicineNorthwest A&F UniversityYanglingChina
| | - Jun Liu
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, College of Veterinary MedicineNorthwest A&F UniversityYanglingChina
| | - Xihe Li
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland LivestockInner Mongolia UniversityHohhotChina
- Research Centre for Animal Genetic Resources of Mongolia Plateau, College of Life SciencesInner Mongolia UniversityHohhotChina
- Inner Mongolia Saikexing Institute of Breeding and Reproductive Biotechnology in Domestic AnimalHohhotChina
| | - Siqin Bao
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland LivestockInner Mongolia UniversityHohhotChina
- Research Centre for Animal Genetic Resources of Mongolia Plateau, College of Life SciencesInner Mongolia UniversityHohhotChina
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38
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Fernandez-Rial C, Fidalgo M. Induction of Transient Morula-Like Cells in Mice Through STAT3 Activation. Cell Reprogram 2024; 26:8-9. [PMID: 38300527 DOI: 10.1089/cell.2023.0116] [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: 02/02/2024] Open
Abstract
Developing in vitro cell models that faithfully replicate the molecular and functional traits of cells from the earliest stages of mammalian development presents a significant challenge. The strategic induction of signal transducer and activator of transcription 3 (STAT3) phosphorylation, coupled with carefully defined culture conditions, facilitates the efficient reprogramming of mouse pluripotent cells into a transient morula-like cell (MLC) state. The resulting MLCs closely mirror their in vivo counterparts, exhibiting not only molecular resemblance but also the ability to differentiate into both embryonic and extraembryonic lineages. This reprogramming approach provides valuable insights into controlled cellular fate choice and opens new opportunities for studying early developmental processes in a dish.
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Affiliation(s)
- Celia Fernandez-Rial
- Stem Cells and Human Diseases Group, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Health Research Institute (IDIS), Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
| | - Miguel Fidalgo
- Stem Cells and Human Diseases Group, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Health Research Institute (IDIS), Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
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Akiyama T, Ishiguro KI, Chikazawa N, Ko SBH, Yukawa M, Ko MSH. ZSCAN4-binding motif-TGCACAC is conserved and enriched in CA/TG microsatellites in both mouse and human genomes. DNA Res 2024; 31:dsad029. [PMID: 38153767 PMCID: PMC10785592 DOI: 10.1093/dnares/dsad029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 12/18/2023] [Accepted: 12/26/2023] [Indexed: 12/29/2023] Open
Abstract
The Zinc finger and SCAN domain containing 4 (ZSCAN4) protein, expressed transiently in pluripotent stem cells, gametes, and early embryos, extends telomeres, enhances genome stability, and improves karyotypes in mouse embryonic stem (mES) cells. To gain insights into the mechanism of ZSCAN4 function, we identified genome-wide binding sites of endogenous ZSCAN4 protein using ChIP-seq technology in mouse and human ES cells, where the expression of endogenous ZSCAN4 was induced by treating cells with retinoic acids or by overexpressing DUX4. We revealed that both mouse and human ZSCAN4 bind to the TGCACAC motif located in CA/TG microsatellite repeats, which are known to form unstable left-handed duplexes called Z-DNA that can induce double-strand DNA breaks and mutations. These ZSCAN4 binding sites are mostly located in intergenic and intronic regions of the genomes. By generating ZSCAN4 knockout in human ES cells, we showed that ZSCAN4 does not seem to be involved in transcriptional regulation. We also found that ectopic expression of mouse ZSCAN4 enhances the suppression of chromatin at ZSCAN4-binding sites. These results together suggest that some of the ZSCAN4 functions are mediated by binding to the error-prone regions in mouse and human genomes.
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Affiliation(s)
- Tomohiko Akiyama
- Department of Systems Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
- Department of Molecular Biology, Yokohama City University, School of Medicine, Kanagawa 236-0027, Japan
| | - Kei-ichiro Ishiguro
- Department of Systems Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
- Department of Chromosome Biology, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Kumamoto 860-0811, Japan
| | - Nana Chikazawa
- Department of Systems Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Shigeru B H Ko
- Department of Systems Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Masashi Yukawa
- Integrated Medical and Agricultural School of Public Health, Ehime University, Ehime 791-0295, Japan
- Division of Allergy & Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229-3026, USA
| | - Minoru S H Ko
- Department of Systems Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
- Elixirgen Therapeutics, Inc., Baltimore, MD 21205, USA
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40
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Yakhou L, Azogui A, Therizols P, Defossez PA. [Using 2C-like cells to understand embryonic totipotency]. Med Sci (Paris) 2024; 40:147-153. [PMID: 38411422 DOI: 10.1051/medsci/2023217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024] Open
Abstract
Totipotency is the ability of a cell to generate a whole organism, a property that characterizes the first embryonic cells, such as the zygote and the blastomeres. This review provides a retrospective on the progress made in the last decade in the study of totipotency, especially with the discovery of mouse ES cells expressing markers of the 2-cell stage (2C-like cells). This model has greatly contributed to a better understanding of the molecular mechanisms involved in totipotency (pioneer factors, epigenetic regulation, splicing, nuclear maturation). 2C-like cells have also paved the way for the development of new cellular models of human totipotency.
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Affiliation(s)
- Lounis Yakhou
- Équipe dynamiquede la méthylation de l'ADN des génomes eucaryotes, Centre épigénétique et destin cellulaire, UMR7216 CNRS, université Paris-Cité, 35 rue Hélène Brion, 75205 Paris Cedex 13, France
| | - Anaelle Azogui
- Équipe dynamiquede la méthylation de l'ADN des génomes eucaryotes, Centre épigénétique et destin cellulaire, UMR7216 CNRS, université Paris-Cité, 35 rue Hélène Brion, 75205 Paris Cedex 13, France
| | - Pierre Therizols
- Équipe dynamiquede la méthylation de l'ADN des génomes eucaryotes, Centre épigénétique et destin cellulaire, UMR7216 CNRS, université Paris-Cité, 35 rue Hélène Brion, 75205 Paris Cedex 13, France
| | - Pierre-Antoine Defossez
- Équipe dynamiquede la méthylation de l'ADN des génomes eucaryotes, Centre épigénétique et destin cellulaire, UMR7216 CNRS, université Paris-Cité, 35 rue Hélène Brion, 75205 Paris Cedex 13, France
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41
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Liang Y, Qu X, Shah NM, Wang T. Towards targeting transposable elements for cancer therapy. Nat Rev Cancer 2024; 24:123-140. [PMID: 38228901 DOI: 10.1038/s41568-023-00653-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/04/2023] [Indexed: 01/18/2024]
Abstract
Transposable elements (TEs) represent almost half of the human genome. Historically deemed 'junk DNA', recent technological advancements have stimulated a wave of research into the functional impact of TEs on gene-regulatory networks in evolution and development, as well as in diseases including cancer. The genetic and epigenetic evolution of cancer involves the exploitation of TEs, whereby TEs contribute directly to cancer-specific gene activities. This Review provides a perspective on the role of TEs in cancer as being a 'double-edged sword', both promoting cancer evolution and representing a vulnerability that could be exploited in cancer therapy. We discuss how TEs affect transcriptome regulation and other cellular processes in cancer. We highlight the potential of TEs as therapeutic targets for cancer. We also summarize technical hurdles in the characterization of TEs with genomic assays. Last, we outline open questions and exciting future research avenues.
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Affiliation(s)
- Yonghao Liang
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Xuan Qu
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Nakul M Shah
- Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA.
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO, USA.
- McDonnell Genome Institute, Washington University School of Medicine, Saint Louis, MO, USA.
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42
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Handford CE, Junyent S, Jorgensen V, Zernicka-Goetz M. Topical section: embryonic models (2023) for Current Opinion in Genetics & Development. Curr Opin Genet Dev 2024; 84:102134. [PMID: 38052116 DOI: 10.1016/j.gde.2023.102134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 10/20/2023] [Accepted: 11/03/2023] [Indexed: 12/07/2023]
Abstract
Stem cell-based mammalian embryo models facilitate the discovery of developmental mechanisms because they are more amenable to genetic and epigenetic perturbations than natural embryos. Here, we highlight exciting recent advances that have yielded a plethora of models of embryonic development. Imperfections in these models highlight gaps in our current understanding and outline future research directions, ushering in an exciting new era for embryology.
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Affiliation(s)
- Charlotte E Handford
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA. https://twitter.com/@CEHandford
| | - Sergi Junyent
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA. https://twitter.com/@JunyentSergi
| | - Victoria Jorgensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Magdalena Zernicka-Goetz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK.
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43
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Guo Y, Xue Z, Gong M, Jin S, Wu X, Liu W. CRISPR-TE: a web-based tool to generate single guide RNAs targeting transposable elements. Mob DNA 2024; 15:3. [PMID: 38303094 PMCID: PMC10832116 DOI: 10.1186/s13100-024-00313-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 01/13/2024] [Indexed: 02/03/2024] Open
Abstract
BACKGROUND The CRISPR/Cas systems have emerged as powerful tools in genome engineering. Recent studies highlighting the crucial role of transposable elements (TEs) have stimulated research interest in manipulating these elements to understand their functions. However, designing single guide RNAs (sgRNAs) that are specific and efficient for TE manipulation is a significant challenge, given their sequence repetitiveness and high copy numbers. While various sgRNA design tools have been developed for gene editing, an optimized sgRNA designer for TE manipulation has yet to be established. RESULTS We present CRISPR-TE, a web-based application featuring an accessible graphical user interface, available at https://www.crisprte.cn/ , and currently tailored to the human and mouse genomes. CRISPR-TE identifies all potential sgRNAs for TEs and provides a comprehensive solution for efficient TE targeting at both the single copy and subfamily levels. Our analysis shows that sgRNAs targeting TEs can more effectively target evolutionarily young TEs with conserved sequences at the subfamily level. CONCLUSIONS CRISPR-TE offers a versatile framework for designing sgRNAs for TE targeting. CRISPR-TE is publicly accessible at https://www.crisprte.cn/ as an online web service and the source code of CRISPR-TE is available at https://github.com/WanluLiuLab/CRISPRTE/ .
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Affiliation(s)
- Yixin Guo
- Department of Orthopedic Surgery of the Second Affiliated Hospital, and Centre of Biomedical Systems and Informatics of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Zhejiang, Hangzhou, 310003, China
| | - Ziwei Xue
- Department of Orthopedic Surgery of the Second Affiliated Hospital, and Centre of Biomedical Systems and Informatics of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Zhejiang, Hangzhou, 310003, China
- Future Health Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314100, China
| | - Meiting Gong
- Department of Orthopedic Surgery of the Second Affiliated Hospital, and Centre of Biomedical Systems and Informatics of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Zhejiang, Hangzhou, 310003, China
| | - Siqian Jin
- Department of Orthopedic Surgery of the Second Affiliated Hospital, and Centre of Biomedical Systems and Informatics of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Zhejiang, Hangzhou, 310003, China
| | - Xindi Wu
- Department of Orthopedic Surgery of the Second Affiliated Hospital, and Centre of Biomedical Systems and Informatics of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Zhejiang, Hangzhou, 310003, China
| | - Wanlu Liu
- Department of Orthopedic Surgery of the Second Affiliated Hospital, and Centre of Biomedical Systems and Informatics of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Zhejiang, Hangzhou, 310003, China.
- Future Health Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314100, China.
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44
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de la Rosa S, del Mar Rigual M, Vargiu P, Ortega S, Djouder N. Endogenous retroviruses shape pluripotency specification in mouse embryos. SCIENCE ADVANCES 2024; 10:eadk9394. [PMID: 38266080 PMCID: PMC10807815 DOI: 10.1126/sciadv.adk9394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 12/22/2023] [Indexed: 01/26/2024]
Abstract
The smooth and precise transition from totipotency to pluripotency is a key process in embryonic development, generating pluripotent stem cells capable of forming all cell types. While endogenous retroviruses (ERVs) are essential for early development, their precise roles in this transition remains mysterious. Using cutting-edge genetic and biochemical techniques in mice, we identify MERVL-gag, a retroviral protein, as a crucial modulator of pluripotent factors OCT4 and SOX2 during lineage specification. MERVL-gag tightly operates with URI, a prefoldin protein that concurs with pluripotency bias in mouse blastomeres, and which is indeed required for totipotency-to-pluripotency transition. Accordingly, URI loss promotes a stable totipotent-like state and embryo arrest at 2C stage. Mechanistically, URI binds and shields OCT4 and SOX2 from proteasome degradation, while MERVL-gag displaces URI from pluripotent factor interaction, causing their degradation. Our findings reveal the symbiotic coevolution of ERVs with their host cells to ensure the smooth and timely progression of early embryo development.
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Affiliation(s)
- Sergio de la Rosa
- Growth Factors, Nutrients and Cancer Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - María del Mar Rigual
- Growth Factors, Nutrients and Cancer Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Pierfrancesco Vargiu
- Mouse Genome Editing Core Unit, Biotechnology Programme, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Sagrario Ortega
- Mouse Genome Editing Core Unit, Biotechnology Programme, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Nabil Djouder
- Growth Factors, Nutrients and Cancer Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
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45
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Lu X. Regulation of endogenous retroviruses in murine embryonic stem cells and early embryos. J Mol Cell Biol 2024; 15:mjad052. [PMID: 37604781 PMCID: PMC10794949 DOI: 10.1093/jmcb/mjad052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 11/24/2022] [Accepted: 08/19/2023] [Indexed: 08/23/2023] Open
Abstract
Endogenous retroviruses (ERVs) are important components of transposable elements that constitute ∼40% of the mouse genome. ERVs exhibit dynamic expression patterns during early embryonic development and are engaged in numerous biological processes. Therefore, ERV expression must be closely monitored in cells. Most studies have focused on the regulation of ERV expression in mouse embryonic stem cells (ESCs) and during early embryonic development. This review touches on the classification, expression, and functions of ERVs in mouse ESCs and early embryos and mainly discusses ERV modulation strategies from the perspectives of transcription, epigenetic modification, nucleosome/chromatin assembly, and post-transcriptional control.
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Affiliation(s)
- Xinyi Lu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, China
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46
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Stévant I, Gonen N, Poulat F. Transposable elements acquire time- and sex-specific transcriptional and epigenetic signatures along mouse fetal gonad development. Front Cell Dev Biol 2024; 11:1327410. [PMID: 38283992 PMCID: PMC10811072 DOI: 10.3389/fcell.2023.1327410] [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: 10/24/2023] [Accepted: 12/20/2023] [Indexed: 01/30/2024] Open
Abstract
Gonadal sex determination in mice is a complex and dynamic process, which is crucial for the development of functional reproductive organs. The expression of genes involved in this process is regulated by a variety of genetic and epigenetic mechanisms. Recently, there has been increasing evidence that transposable elements (TEs), which are a class of mobile genetic elements, play a significant role in regulating gene expression during embryogenesis and organ development. In this study, we aimed to investigate the involvement of TEs in the regulation of gene expression during mouse embryonic gonadal development. Through bioinformatics analysis, we aimed to identify and characterize specific TEs that operate as regulatory elements for sex-specific genes, as well as their potential mechanisms of regulation. We identified TE loci expressed in a time- and sex-specific manner along fetal gonad development that correlate positively and negatively with nearby gene expression, suggesting that their expression is integrated to the gonadal regulatory network. Moreover, chromatin accessibility and histone post-transcriptional modification analyses in differentiating supporting cells revealed that TEs are acquiring a sex-specific signature for promoter-, enhancer-, and silencer-like elements, with some of them being proximal to critical sex-determining genes. Altogether, our study introduces TEs as the new potential players in the gene regulatory network that controls gonadal development in mammals.
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Affiliation(s)
- Isabelle Stévant
- The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
- Institute of Human Genetics, CNRS UMR9002 University of Montpellier, Montpellier, France
| | - Nitzan Gonen
- The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Francis Poulat
- Institute of Human Genetics, CNRS UMR9002 University of Montpellier, Montpellier, France
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47
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Dopkins N, Singh B, Michael S, Zhang P, Marston JL, Fei T, Singh M, Feschotte C, Collins N, Bendall ML, Nixon DF. Ribosomal profiling of human endogenous retroviruses in healthy tissues. BMC Genomics 2024; 25:5. [PMID: 38166631 PMCID: PMC10759522 DOI: 10.1186/s12864-023-09909-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 12/14/2023] [Indexed: 01/05/2024] Open
Abstract
Human endogenous retroviruses (HERVs) are the germline embedded proviral fragments of ancient retroviral infections that make up roughly 8% of the human genome. Our understanding of HERVs in physiology primarily surrounds their non-coding functions, while their protein coding capacity remains virtually uncharacterized. Therefore, we applied the bioinformatic pipeline "hervQuant" to high-resolution ribosomal profiling of healthy tissues to provide a comprehensive overview of translationally active HERVs. We find that HERVs account for 0.1-0.4% of all translation in distinct tissue-specific profiles. Collectively, our study further supports claims that HERVs are actively translated throughout healthy tissues to provide sequences of retroviral origin to the human proteome.
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Affiliation(s)
- Nicholas Dopkins
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, 10021, USA.
| | - Bhavya Singh
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Stephanie Michael
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Panpan Zhang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA
| | - Jez L Marston
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Tongyi Fei
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Manvendra Singh
- Clinical Neuroscience, Max Planck Institute for Multidisciplinary Sciences, City Campus, Göttingen, Germany
| | - Cedric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA
| | - Nicholas Collins
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Matthew L Bendall
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Douglas F Nixon
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, 10021, USA
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48
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Guo Y, Li TD, Modzelewski AJ, Siomi H. Retrotransposon renaissance in early embryos. Trends Genet 2024; 40:39-51. [PMID: 37949723 DOI: 10.1016/j.tig.2023.10.010] [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: 07/22/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 11/12/2023]
Abstract
Despite being the predominant genetic elements in mammalian genomes, retrotransposons were often dismissed as genomic parasites with ambiguous biological significance. However, recent studies reveal their functional involvement in early embryogenesis, encompassing crucial processes such as zygotic genome activation (ZGA) and cell fate decision. This review underscores the paradigm shift in our understanding of retrotransposon roles during early preimplantation development, as well as their rich functional reservoir that is exploited by the host to provide cis-regulatory elements, noncoding RNAs, and functional proteins. The rapid advancement in long-read sequencing, low input multiomics profiling, advanced in vitro systems, and precise gene editing techniques encourages further dissection of retrotransposon functions that were once obscured by the intricacies of their genomic footprints.
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Affiliation(s)
- Youjia Guo
- Department of Molecular Biology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
| | - Ten D Li
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104-4539, USA
| | - Andrew J Modzelewski
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104-4539, USA.
| | - Haruhiko Siomi
- Department of Molecular Biology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan; Human Biology Microbiome Quantum Research Center (WPI-Bio2Q), Keio University, Tokyo 160-8582, Japan.
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49
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Martello G. The rules of the totipotency treasure hunt. Nat Cell Biol 2024; 26:19-21. [PMID: 38228827 DOI: 10.1038/s41556-023-01282-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
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50
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He T, Peng J, Yang S, Liu D, Gao S, Zhu Y, Chai Z, Lee BC, Wei R, Wang J, Liu Z, Jin JX. SINE-Associated LncRNA SAWPA Regulates Porcine Zygotic Genome Activation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307505. [PMID: 37984872 PMCID: PMC10787077 DOI: 10.1002/advs.202307505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 10/28/2023] [Indexed: 11/22/2023]
Abstract
In mice, retrotransposon-associated long noncoding RNAs (lncRNA) play important regulatory roles in pre-implantation development; however, it is largely unknown whether they function in the pre-implantation development in pigs. The current study aims to screen for retrotransposon-associated lncRNA in porcine early embryos and identifies a porcine 8-cell embryo-specific SINE-associated nuclear long noncoding RNA named SAWPA. SAWPA is essential for porcine embryonic development as depletion of SAWPA results in a developmental arrest at the 8-cell stage, accompanied by the inhibition of the JNK-MAPK signaling pathway. Mechanistically, SAWPA works in trans as a transcription factor for JNK through the formation of an RNA-protein complex with HNRNPA1 and MED8 binding the SINE elements upstream of JNK. Therefore, as the first functional SINE-associated long noncoding RNAs in pigs, SAWPA provides novel insights for the mechanism research on retrotransposons in mammalian pre-implantation development.
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Affiliation(s)
- Tianyao He
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, 150030, P. R. China
| | - Jinyu Peng
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, 150030, P. R. China
| | - Shu Yang
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, 150030, P. R. China
| | - Dongsong Liu
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, 150030, P. R. China
| | - Shuang Gao
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, 150030, P. R. China
| | - Yanlong Zhu
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, 150030, P. R. China
| | - Zhuang Chai
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, 150030, P. R. China
| | - Byeong Chun Lee
- Department of Theriogenology and Biotechnology, College of Veterinary Medicine, Seoul National University, Seoul, 08826, South Korea
| | - Renyue Wei
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, 150030, P. R. China
| | - Jiaqiang Wang
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, 150030, P. R. China
| | - Zhonghua Liu
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, 150030, P. R. China
| | - Jun-Xue Jin
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, 150030, P. R. China
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