1
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Pal S, Dhar R. Living in a noisy world-origins of gene expression noise and its impact on cellular decision-making. FEBS Lett 2024; 598:1673-1691. [PMID: 38724715 DOI: 10.1002/1873-3468.14898] [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: 12/21/2023] [Revised: 03/23/2024] [Accepted: 03/27/2024] [Indexed: 07/23/2024]
Abstract
The expression level of a gene can vary between genetically identical cells under the same environmental condition-a phenomenon referred to as gene expression noise. Several studies have now elucidated a central role of transcription factors in the generation of expression noise. Transcription factors, as the key components of gene regulatory networks, drive many important cellular decisions in response to cellular and environmental signals. Therefore, a very relevant question is how expression noise impacts gene regulation and influences cellular decision-making. In this Review, we summarize the current understanding of the molecular origins of expression noise, highlighting the role of transcription factors in this process, and discuss the ways in which noise can influence cellular decision-making. As advances in single-cell technologies open new avenues for studying expression noise as well as gene regulatory circuits, a better understanding of the influence of noise on cellular decisions will have important implications for many biological processes.
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Affiliation(s)
- Sampriti Pal
- Department of Bioscience and Biotechnology, IIT Kharagpur, India
| | - Riddhiman Dhar
- Department of Bioscience and Biotechnology, IIT Kharagpur, India
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2
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New insights into the epitranscriptomic control of pluripotent stem cell fate. Exp Mol Med 2022; 54:1643-1651. [PMID: 36266446 PMCID: PMC9636187 DOI: 10.1038/s12276-022-00824-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/26/2022] [Accepted: 06/01/2022] [Indexed: 12/29/2022] Open
Abstract
Each cell in the human body has a distinguishable fate. Pluripotent stem cells are challenged with a myriad of lineage differentiation options. Defects are more likely to be fatal to stem cells than to somatic cells due to the broad impact of the former on early development. Hence, a detailed understanding of the mechanisms that determine the fate of stem cells is needed. The mechanisms by which human pluripotent stem cells, although not fully equipped with complex chromatin structures or epigenetic regulatory mechanisms, accurately control gene expression and are important to the stem cell field. In this review, we examine the events driving pluripotent stem cell fate and the underlying changes in gene expression during early development. In addition, we highlight the role played by the epitranscriptome in the regulation of gene expression that is necessary for each fate-related event.
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3
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Allègre N, Chauveau S, Dennis C, Renaud Y, Meistermann D, Estrella LV, Pouchin P, Cohen-Tannoudji M, David L, Chazaud C. NANOG initiates epiblast fate through the coordination of pluripotency genes expression. Nat Commun 2022; 13:3550. [PMID: 35729116 PMCID: PMC9213552 DOI: 10.1038/s41467-022-30858-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 05/24/2022] [Indexed: 12/20/2022] Open
Abstract
The epiblast is the source of all mammalian embryonic tissues and of pluripotent embryonic stem cells. It differentiates alongside the primitive endoderm in a “salt and pepper” pattern from inner cell mass (ICM) progenitors during the preimplantation stages through the activity of NANOG, GATA6 and the FGF pathway. When and how epiblast lineage specification is initiated is still unclear. Here, we show that the coordinated expression of pluripotency markers defines epiblast identity. Conversely, ICM progenitor cells display random cell-to-cell variability in expression of various pluripotency markers, remarkably dissimilar from the epiblast signature and independently from NANOG, GATA6 and FGF activities. Coordination of pluripotency markers expression fails in Nanog and Gata6 double KO (DKO) embryos. Collectively, our data suggest that NANOG triggers epiblast specification by ensuring the coordinated expression of pluripotency markers in a subset of cells, implying a stochastic mechanism. These features are likely conserved, as suggested by analysis of human embryos. Pluripotent epiblast cells segregate from primitive endoderm in the blastocyst inner cell mass (ICM). Here the authors show that mosaic epiblast differentiation during mouse and human preimplantation development initiates stochastically in ICM progenitors, independently of the FGF pathway, and requires NANOG activity
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Affiliation(s)
- Nicolas Allègre
- Université Clermont Auvergne, CNRS, INSERM, GReD Institute, Faculté de Médecine, F-63000, Clermont-Ferrand, France
| | - Sabine Chauveau
- Université Clermont Auvergne, CNRS, INSERM, GReD Institute, Faculté de Médecine, F-63000, Clermont-Ferrand, France
| | - Cynthia Dennis
- Université Clermont Auvergne, CNRS, INSERM, GReD Institute, Faculté de Médecine, F-63000, Clermont-Ferrand, France
| | - Yoan Renaud
- Université Clermont Auvergne, CNRS, INSERM, GReD Institute, Faculté de Médecine, F-63000, Clermont-Ferrand, France.,Byonet, 19 rue du courait, F-63200, Riom, France
| | - Dimitri Meistermann
- Université de Nantes, CHU Nantes, INSERM, CR2TI, UMR 1064, ITUN, F-44000, Nantes, France.,Université de Nantes, CNRS, LS2N, CNRS UMR 6004, F-44000, Nantes, France
| | - Lorena Valverde Estrella
- Université Clermont Auvergne, CNRS, INSERM, GReD Institute, Faculté de Médecine, F-63000, Clermont-Ferrand, France
| | - Pierre Pouchin
- Université Clermont Auvergne, CNRS, INSERM, GReD Institute, Faculté de Médecine, F-63000, Clermont-Ferrand, France
| | - Michel Cohen-Tannoudji
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells, Department of Developmental and Stem Cell Biology, F-75015, Paris, France
| | - Laurent David
- Université de Nantes, CHU Nantes, INSERM, CR2TI, UMR 1064, ITUN, F-44000, Nantes, France.,Université de Nantes, CHU Nantes, INSERM, CNRS, UMS Biocore, INSERM UMS 016, CNRS UMS 3556, F-44000, Nantes, France
| | - Claire Chazaud
- Université Clermont Auvergne, CNRS, INSERM, GReD Institute, Faculté de Médecine, F-63000, Clermont-Ferrand, France.
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4
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Krawczyk K, Kosyl E, Częścik-Łysyszyn K, Wyszomirski T, Maleszewski M. Developmental capacity is unevenly distributed among single blastomeres of 2-cell and 4-cell stage mouse embryos. Sci Rep 2021; 11:21422. [PMID: 34728646 PMCID: PMC8563712 DOI: 10.1038/s41598-021-00834-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 10/14/2021] [Indexed: 11/25/2022] Open
Abstract
During preimplantation development, mammalian embryo cells (blastomeres) cleave, gradually losing their potencies and differentiating into three primary cell lineages: epiblast (EPI), trophectoderm (TE), and primitive endoderm (PE). The exact moment at which cells begin to vary in their potency for multilineage differentiation still remains unknown. We sought to answer the question of whether single cells isolated from 2- and 4-cell embryos differ in their ability to generate the progenitors and cells of blastocyst lineages. We revealed that twins were often able to develop into blastocysts containing inner cell masses (ICMs) with PE and EPI cells. Despite their capacity to create a blastocyst, the twins differed in their ability to produce EPI, PE, and TE cell lineages. In contrast, quadruplets rarely formed normal blastocysts, but instead developed into blastocysts with ICMs composed of only one cell lineage or completely devoid of an ICM altogether. We also showed that quadruplets have unequal capacities to differentiate into TE, PE, and EPI lineages. These findings could explain the difficulty of creating monozygotic twins and quadruplets from 2- and 4-cell stage mouse embryos.
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Affiliation(s)
- Katarzyna Krawczyk
- Department of Embryology, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland.
| | - Ewa Kosyl
- Department of Embryology, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Karolina Częścik-Łysyszyn
- Department of Embryology, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Tomasz Wyszomirski
- Department of Ecology and Environmental Protection, Institute of Environmental Biology, Faculty of Biology, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Marek Maleszewski
- Department of Embryology, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland.
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5
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Wang Y, Zheng X, Cheng R, Han J, Ma X, Xu W, Gao L, Lei A, Liu J, Quan F, Zhang Y, Liu X. Asymmetric expression of maternal mRNA governs first cell-fate decision. FASEB J 2021; 35:e22006. [PMID: 34694646 DOI: 10.1096/fj.202101196r] [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: 07/27/2021] [Revised: 09/23/2021] [Accepted: 10/06/2021] [Indexed: 11/11/2022]
Abstract
The goal of preimplantation development is to establish the fates of the embryonic and extra-embryonic cells. However, when and how cell fates are determined during early mammalian embryonic development remains unclear. We report that the high mobility group (HMG) protein family member HMGA1 was distributed differentially in mouse two-cell blastomeres. Knockdown of Hmga1 expression in one of the two cells reduced the number of cells contributing to the inner cell mass (ICM), suggesting that differential distribution of HMGA1 in the blastomeres in two-cell mouse embryos affected the selection of embryonic cell lineages. Mechanistically, HMGA1 promotes the expression of the ICM-specific gene Sox2. The results of this study show that mouse embryos demonstrate heterogeneity as early as the two-cell stage, and that these differences are related to cell-fate differentiation in early mouse embryos.
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Affiliation(s)
- Yingmei Wang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, PR China
| | - Xiaoman Zheng
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, PR China
| | - Rui Cheng
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, PR China
| | - Jing Han
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, PR China
| | - Xing Ma
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, PR China
| | - Wenjun Xu
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, PR China
| | - Lu Gao
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, PR China
| | - Anmin Lei
- College of Veterinary Medicine, Shaanxi Stem Cell Engineering and Technology Center, Northwest A&F University, Yangling, PR China
| | - Jun Liu
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, PR China
| | - Fusheng Quan
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, PR China
| | - Yong Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, PR China
| | - Xu Liu
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, PR China
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6
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Totipotency of mouse zygotes extends to single blastomeres of embryos at the four-cell stage. Sci Rep 2021; 11:11167. [PMID: 34045607 PMCID: PMC8160171 DOI: 10.1038/s41598-021-90653-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 05/12/2021] [Indexed: 02/06/2023] Open
Abstract
In multicellular organisms, oocytes and sperm undergo fusion during fertilization and the resulting zygote gives rise to a new individual. The ability of zygotes to produce a fully formed individual from a single cell when placed in a supportive environment is known as totipotency. Given that totipotent cells are the source of all multicellular organisms, a better understanding of totipotency may have a wide-ranging impact on biology. The precise delineation of totipotent cells in mammals has remained elusive, however, although zygotes and single blastomeres of embryos at the two-cell stage have been thought to be the only totipotent cells in mice. We now show that a single blastomere of two- or four-cell mouse embryos can give rise to a fertile adult when placed in a uterus, even though blastomere isolation disturbs the transcriptome of derived embryos. Single blastomeres isolated from embryos at the eight-cell or morula stages and cultured in vitro manifested pronounced defects in the formation of epiblast and primitive endoderm by the inner cell mass and in the development of blastocysts, respectively. Our results thus indicate that totipotency of mouse zygotes extends to single blastomeres of embryos at the four-cell stage.
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7
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Suresh S, Huard S, Dubois T. CARM1/PRMT4: Making Its Mark beyond Its Function as a Transcriptional Coactivator. Trends Cell Biol 2021; 31:402-417. [PMID: 33485722 DOI: 10.1016/j.tcb.2020.12.010] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 12/14/2020] [Accepted: 12/18/2020] [Indexed: 12/16/2022]
Abstract
Coactivator-associated arginine methyltransferase 1 (CARM1), identified 20 years ago as a coregulator of transcription, is an enzyme that catalyzes arginine methylation of proteins. Beyond its well-established involvement in the regulation of transcription, the physiological functions of CARM1 are still poorly understood. However, recent studies have revealed novel roles of CARM1 in autophagy, metabolism, paraspeckles, and early development. In addition, CARM1 is emerging as an attractive therapeutic target and a drug response biomarker for certain types of cancer. Here, we provide a comprehensive overview of the structure of CARM1 and its post-translational modifications, its various functions, apart from transcriptional coactivation, and its involvement in cancer.
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Affiliation(s)
- Samyuktha Suresh
- Institut Curie - PSL Research University, Translational Research Department, Breast Cancer Biology Group, 75005 Paris, France
| | - Solène Huard
- Institut Curie - PSL Research University, Translational Research Department, Breast Cancer Biology Group, 75005 Paris, France
| | - Thierry Dubois
- Institut Curie - PSL Research University, Translational Research Department, Breast Cancer Biology Group, 75005 Paris, France.
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8
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Prasad MS, Charney RM, Patel LJ, García-Castro MI. Distinct molecular profile and restricted stem cell potential defines the prospective human cranial neural crest from embryonic stem cell state. Stem Cell Res 2020; 49:102086. [PMID: 33370869 PMCID: PMC7932500 DOI: 10.1016/j.scr.2020.102086] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 06/14/2020] [Accepted: 11/04/2020] [Indexed: 12/18/2022] Open
Abstract
Neural crest cells are an embryonic multipotent stem cell population. Recent studies in model organisms have suggested that neural crest cells are specified earlier than previously thought, at blastula stages. However, the molecular dynamics of early neural crest specification, and functional changes from pluripotent precursors to early specified NC, remain to be elucidated. In this report, we utilized a robust human model of cranial neural crest formation to address the distinct molecular character of the earliest stages of neural crest specification and assess the functional differences from its embryonic stem cell precursor. Our human neural crest model reveals a rapid change in the epigenetic state of neural crest and pluripotency genes, accompanied by changes in gene expression upon Wnt-based induction from embryonic stem cells. These changes in gene expression are directly regulated by the transcriptional activity of β-catenin. Furthermore, prospective cranial neural crest cells are characterized by restricted stem cell potential compared to embryonic stem cells. Our results suggest that human neural crest induced by Wnt/β-catenin signaling from human embryonic stem cells rapidly acquire a prospective neural crest cell state defined by a unique molecular signature and endowed with limited potential compared to pluripotent stem cells.
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Affiliation(s)
- Maneeshi S Prasad
- School of Medicine Division of Biomedical Sciences, University of California, Riverside, USA.
| | - Rebekah M Charney
- School of Medicine Division of Biomedical Sciences, University of California, Riverside, USA
| | - Lipsa J Patel
- School of Medicine Division of Biomedical Sciences, University of California, Riverside, USA
| | - Martín I García-Castro
- School of Medicine Division of Biomedical Sciences, University of California, Riverside, USA.
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9
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Fiorentino J, Torres-Padilla ME, Scialdone A. Measuring and Modeling Single-Cell Heterogeneity and Fate Decision in Mouse Embryos. Annu Rev Genet 2020; 54:167-187. [PMID: 32867543 DOI: 10.1146/annurev-genet-021920-110200] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cellular heterogeneity is a property of any living system; however, its relationship with cellular fate decision remains an open question. Recent technological advances have enabled valuable insights, especially in complex systems such as the mouse embryo. In this review, we discuss recent studies that characterize cellular heterogeneity at different levels during mouse development, from the two-cell stage up to gastrulation. In addition to key experimental findings, we review mathematical modeling approaches that help researchers interpret these findings. Disentangling the role of heterogeneity in cell fate decision will likely rely on the refined integration of experiments, large-scale omics data, and mathematical modeling, complemented by the use of synthetic embryos and gastruloids as promising in vitro models.
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Affiliation(s)
- Jonathan Fiorentino
- Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München, D-81377 München, Germany; .,Institute of Functional Epigenetics (IFE) and Institute of Computational Biology (ICB), Helmholtz Zentrum München, D-85764 Neuherberg, Germany
| | - Maria-Elena Torres-Padilla
- Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München, D-81377 München, Germany; .,Faculty of Biology, Ludwig-Maximilians Universität, D-82152 Planegg-Martinsried, Germany
| | - Antonio Scialdone
- Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München, D-81377 München, Germany; .,Institute of Functional Epigenetics (IFE) and Institute of Computational Biology (ICB), Helmholtz Zentrum München, D-85764 Neuherberg, Germany
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10
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Zhao C, Zhang N, Zhang Y, Tuersunjiang N, Gao S, Liu W, Zhang Y. A DNA methylation state transition model reveals the programmed epigenetic heterogeneity in human pre-implantation embryos. Genome Biol 2020; 21:277. [PMID: 33198783 PMCID: PMC7667739 DOI: 10.1186/s13059-020-02189-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 10/27/2020] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND During mammalian early embryogenesis, expression and epigenetic heterogeneity emerge before the first cell fate determination, but the programs causing such determinate heterogeneity are largely unexplored. RESULTS Here, we present MethylTransition, a novel DNA methylation state transition model, for characterizing methylation changes during one or a few cell cycles at single-cell resolution. MethylTransition involves the creation of a transition matrix comprising three parameters that represent the probabilities of DNA methylation-modifying activities in order to link the methylation states before and after a cell cycle. We apply MethylTransition to single-cell DNA methylome data from human pre-implantation embryogenesis and elucidate that the DNA methylation heterogeneity that emerges at promoters during this process is largely an intrinsic output of a program with unique probabilities of DNA methylation-modifying activities. Moreover, we experimentally validate the effect of the initial DNA methylation on expression heterogeneity in pre-implantation mouse embryos. CONCLUSIONS Our study reveals the programmed DNA methylation heterogeneity during human pre-implantation embryogenesis through a novel mathematical model and provides valuable clues for identifying the driving factors of the first cell fate determination during this process.
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Affiliation(s)
- Chengchen Zhao
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Science and Technology, Tongji University, Shanghai, 200092 China
| | - Naiqian Zhang
- School of Mathematics and Statistics, Shandong University at Weihai, Weihai, 264209 China
| | - Yalin Zhang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Science and Technology, Tongji University, Shanghai, 200092 China
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Tongji University, Shanghai, 200092 China
| | - Nuermaimaiti Tuersunjiang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Science and Technology, Tongji University, Shanghai, 200092 China
| | - Shaorong Gao
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Science and Technology, Tongji University, Shanghai, 200092 China
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Tongji University, Shanghai, 200092 China
| | - Wenqiang Liu
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Science and Technology, Tongji University, Shanghai, 200092 China
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Tongji University, Shanghai, 200092 China
| | - Yong Zhang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Science and Technology, Tongji University, Shanghai, 200092 China
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11
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Oh JN, Lee M, Choe GC, Lee DK, Choi KH, Kim SH, Jeong J, Lee CK. Identification of the Lineage Markers and Inhibition of DAB2 in In Vitro Fertilized Porcine Embryos. Int J Mol Sci 2020; 21:ijms21197275. [PMID: 33019677 PMCID: PMC7582820 DOI: 10.3390/ijms21197275] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/28/2020] [Accepted: 09/29/2020] [Indexed: 12/18/2022] Open
Abstract
Specification of embryonic lineages is an important question in the field of early development. Numerous studies analyzed the expression patterns of the candidate transcripts and proteins in humans and mice and clearly determined the markers of each lineage. To overcome the limitations of human and mouse embryos, the expression of the marker transcripts in each cell has been investigated using in vivo embryos in pigs. In vitro produced embryos are more accessible, can be rapidly processed with low cost. Therefore, we analyzed the characteristics of lineage markers and the effects of the DAB2 gene (trophectoderm marker) in in vitro fertilized porcine embryos. We investigated the expression levels of the marker genes during embryonic stages and distribution of the marker proteins was assayed in day 7 blastocysts. Then, the shRNA vectors were injected into the fertilized embryos and the differences in the marker transcripts were analyzed. Marker transcripts showed diverse patterns of expression, and each embryonic lineage could be identified with localization of marker proteins. In DAB2-shRNA vectors injected embryos, HNF4A and PDGFRA were upregulated. DAB2 protein level was lower in shRNA-injected embryos without significant differences. Our results will contribute to understanding of the mechanisms of embryonic lineage specification in pigs.
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Affiliation(s)
- Jong-Nam Oh
- Department of Agricultural Biotechnology, Animal Biotechnology Major and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea; (J.-N.O.); (M.L.); (G.C.C.); (D.-K.L.); (K.-H.C.); (S.-H.K.); (J.J.)
| | - Mingyun Lee
- Department of Agricultural Biotechnology, Animal Biotechnology Major and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea; (J.-N.O.); (M.L.); (G.C.C.); (D.-K.L.); (K.-H.C.); (S.-H.K.); (J.J.)
| | - Gyung Cheol Choe
- Department of Agricultural Biotechnology, Animal Biotechnology Major and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea; (J.-N.O.); (M.L.); (G.C.C.); (D.-K.L.); (K.-H.C.); (S.-H.K.); (J.J.)
| | - Dong-Kyung Lee
- Department of Agricultural Biotechnology, Animal Biotechnology Major and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea; (J.-N.O.); (M.L.); (G.C.C.); (D.-K.L.); (K.-H.C.); (S.-H.K.); (J.J.)
| | - Kwang-Hwan Choi
- Department of Agricultural Biotechnology, Animal Biotechnology Major and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea; (J.-N.O.); (M.L.); (G.C.C.); (D.-K.L.); (K.-H.C.); (S.-H.K.); (J.J.)
| | - Seung-Hun Kim
- Department of Agricultural Biotechnology, Animal Biotechnology Major and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea; (J.-N.O.); (M.L.); (G.C.C.); (D.-K.L.); (K.-H.C.); (S.-H.K.); (J.J.)
| | - Jinsol Jeong
- Department of Agricultural Biotechnology, Animal Biotechnology Major and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea; (J.-N.O.); (M.L.); (G.C.C.); (D.-K.L.); (K.-H.C.); (S.-H.K.); (J.J.)
| | - Chang-Kyu Lee
- Department of Agricultural Biotechnology, Animal Biotechnology Major and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea; (J.-N.O.); (M.L.); (G.C.C.); (D.-K.L.); (K.-H.C.); (S.-H.K.); (J.J.)
- Institute of Green Bio Science and Technology, Seoul National University, Pyeongchang 25354, Korea
- Correspondence:
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12
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Lim HYG, Alvarez YD, Gasnier M, Wang Y, Tetlak P, Bissiere S, Wang H, Biro M, Plachta N. Keratins are asymmetrically inherited fate determinants in the mammalian embryo. Nature 2020; 585:404-409. [PMID: 32848249 DOI: 10.1038/s41586-020-2647-4] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 07/30/2020] [Indexed: 11/08/2022]
Abstract
To implant in the uterus, the mammalian embryo first specifies two cell lineages: the pluripotent inner cell mass that forms the fetus, and the outer trophectoderm layer that forms the placenta1. In many organisms, asymmetrically inherited fate determinants drive lineage specification2, but this is not thought to be the case during early mammalian development. Here we show that intermediate filaments assembled by keratins function as asymmetrically inherited fate determinants in the mammalian embryo. Unlike F-actin or microtubules, keratins are the first major components of the cytoskeleton that display prominent cell-to-cell variability, triggered by heterogeneities in the BAF chromatin-remodelling complex. Live-embryo imaging shows that keratins become asymmetrically inherited by outer daughter cells during cell division, where they stabilize the cortex to promote apical polarization and YAP-dependent expression of CDX2, thereby specifying the first trophectoderm cells of the embryo. Together, our data reveal a mechanism by which cell-to-cell heterogeneities that appear before the segregation of the trophectoderm and the inner cell mass influence lineage fate, via differential keratin regulation, and identify an early function for intermediate filaments in development.
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Affiliation(s)
- Hui Yi Grace Lim
- Institute of Molecular and Cell Biology, ASTAR, Singapore, Singapore
| | - Yanina D Alvarez
- Institute of Molecular and Cell Biology, ASTAR, Singapore, Singapore
| | - Maxime Gasnier
- Institute of Molecular and Cell Biology, ASTAR, Singapore, Singapore
| | - Yiming Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Science, Beijing, China
| | - Piotr Tetlak
- Institute of Molecular and Cell Biology, ASTAR, Singapore, Singapore
| | | | - Hongmei Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Science, Beijing, China
| | - Maté Biro
- EMBL Australia, Single Molecule Science Node, School of Medical Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Nicolas Plachta
- Institute of Molecular and Cell Biology, ASTAR, Singapore, Singapore.
- Department of Cell and Developmental Biology and Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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13
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Vergaro P, Tiscornia G, Zambelli F, Rodríguez A, Santaló J, Vassena R. Trophoblast attachment to the endometrial epithelium elicits compartment-specific transcriptional waves in an in-vitro model. Reprod Biomed Online 2020; 42:26-38. [PMID: 33051136 DOI: 10.1016/j.rbmo.2020.08.037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 08/14/2020] [Accepted: 08/23/2020] [Indexed: 01/02/2023]
Abstract
RESEARCH QUESTION Which are the early compartment-specific transcriptional responses of the trophoblast and the endometrial epithelium throughout early attachment during implantation? DESIGN An endometrial epithelium proxy (cell line Ishikawa) was co-cultured with spheroids of a green fluorescent protein (GFP) expressing trophoblast cell line (JEG-3). After 0, 8 and 24 h of co-culture, the compartments were sorted by fluorescence-activated cell sorting; GFP+ (trophoblast), GFP- (epithelium) and non-co-cultured control populations were analysed (in triplicate) by RNA-seq and gene set enrichment analysis (GSEA). RESULTS Trophoblast challenge induced a wave of transcriptional changes in the epithelium that resulted in 295 differentially regulated genes involving epithelial to mesenchymal transition (EMT), cell movement, apoptosis, hypoxia, inflammation, allograft rejection, myogenesis and cell signalling at 8 h. Interestingly, many of the enriched pathways were subsequently de-enriched by 24 h (i.e. EMT, cell movement, allograft rejection, myogenesis and cell signalling). In the trophoblast, the co-culture induced more transcriptional changes and regulation of a variety of pathways. A total of 1247 and 481 genes were differentially expressed after 8 h and from 8 to 24 h, respectively. Angiogenesis and hypoxia were over-represented at both stages, while EMT and cell signalling only were at 8 h; from 8 to 24 h, inflammation and oestrogen response were enriched, while proliferation was under-represented. CONCLUSIONS Successful attachment produced a series of dynamic changes in gene expression, characterized by an overall early and transient transcriptional up-regulation in the receptive epithelium, in contrast to a more dynamic transcriptional response in the trophoblast.
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Affiliation(s)
- Paula Vergaro
- Clínica EUGIN Barcelona, Spain; Facultat de Biociències, Unitat de Biologia Cel•lular, Universitat Autònoma de Barcelona, Spain
| | - Gustavo Tiscornia
- Clínica EUGIN Barcelona, Spain; Centro de Investigação em Biomedicina (CBMR), Universidade do Algarve, Portugal
| | | | | | - Josep Santaló
- Facultat de Biociències, Unitat de Biologia Cel•lular, Universitat Autònoma de Barcelona, Spain
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14
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Płusa B, Piliszek A. Common principles of early mammalian embryo self-organisation. Development 2020; 147:147/14/dev183079. [PMID: 32699138 DOI: 10.1242/dev.183079] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Pre-implantation mammalian development unites extreme plasticity with a robust outcome: the formation of a blastocyst, an organised multi-layered structure ready for implantation. The process of blastocyst formation is one of the best-known examples of self-organisation. The first three cell lineages in mammalian development specify and arrange themselves during the morphogenic process based on cell-cell interactions. Despite decades of research, the unifying principles driving early mammalian development are still not fully defined. Here, we discuss the role of physical forces, and molecular and cellular mechanisms, in driving self-organisation and lineage formation that are shared between eutherian mammals.
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Affiliation(s)
- Berenika Płusa
- Faculty of Biology, Medicine and Health (FBMH), Division of Developmental Biology & Medicine, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Anna Piliszek
- Department of Experimental Embryology, Institute of Genetics and Animal Biotechnology, Polish Academy of Sciences, Jastrzebiec, Postepu 36A, 05-552 Magdalenka, Poland
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15
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Abstract
Mammalian fertilization begins with the fusion of two specialized gametes, followed by major epigenetic remodeling leading to the formation of a totipotent embryo. During the development of the pre-implantation embryo, precise reprogramming progress is a prerequisite for avoiding developmental defects or embryonic lethality, but the underlying molecular mechanisms remain elusive. For the past few years, unprecedented breakthroughs have been made in mapping the regulatory network of dynamic epigenomes during mammalian early embryo development, taking advantage of multiple advances and innovations in low-input genome-wide chromatin analysis technologies. The aim of this review is to highlight the most recent progress in understanding the mechanisms of epigenetic remodeling during early embryogenesis in mammals, including DNA methylation, histone modifications, chromatin accessibility and 3D chromatin organization.
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16
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White MD, Plachta N. Specification of the First Mammalian Cell Lineages In Vivo and In Vitro. Cold Spring Harb Perspect Biol 2020; 12:cshperspect.a035634. [PMID: 31615786 DOI: 10.1101/cshperspect.a035634] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Our understanding of how the first mammalian cell lineages arise has been shaped largely by studies of the preimplantation mouse embryo. Painstaking work over many decades has begun to reveal how a single totipotent cell is transformed into a multilayered structure representing the foundations of the body plan. Here, we review how the first lineage decision is initiated by epigenetic regulation but consolidated by the integration of morphological features and transcription factor activity. The establishment of pluripotent and multipotent stem cell lines has enabled deeper analysis of molecular and epigenetic regulation of cell fate decisions. The capability to assemble these stem cells into artificial embryos is an exciting new avenue of research that offers a long-awaited window into cell fate specification in the human embryo. Together, these approaches are poised to profoundly increase our understanding of how the first lineage decisions are made during mammalian embryonic development.
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Affiliation(s)
- Melanie D White
- Institute of Molecular and Cell Biology, A*STAR, Singapore 138673
| | - Nicolas Plachta
- Institute of Molecular and Cell Biology, A*STAR, Singapore 138673
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17
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Le R, Huang Y, Zhao A, Gao S. Lessons from expanded potential of embryonic stem cells: Moving toward totipotency. J Genet Genomics 2020; 47:123-130. [PMID: 32305172 DOI: 10.1016/j.jgg.2020.02.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 01/20/2020] [Accepted: 02/10/2020] [Indexed: 02/06/2023]
Abstract
Embryonic stem cells possess fascinating capacity of self-renewal and developmental potential, leading to significant progress in understanding the molecular basis of pluripotency, disease modeling, and reprogramming technology. Recently, 2-cell-like embryonic stem cells (ESCs) and expanded potential stem cells or extended pluripotent stem cells (EPSCs) generated from early-cleavage embryos display some features of totipotent embryos. These cell lines provide valuable in vitro models to study underlying principles of totipotency, cell plasticity, and lineage segregation. In this review, we summarize the current progress in this filed and highlight the application potentials of these cells in the future.
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Affiliation(s)
- Rongrong Le
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Yixin Huang
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Anqi Zhao
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Shaorong Gao
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
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18
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Prasad MS, Uribe-Querol E, Marquez J, Vadasz S, Yardley N, Shelar PB, Charney RM, García-Castro MI. Blastula stage specification of avian neural crest. Dev Biol 2020; 458:64-74. [PMID: 31610145 PMCID: PMC7050198 DOI: 10.1016/j.ydbio.2019.10.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 10/09/2019] [Accepted: 10/09/2019] [Indexed: 11/21/2022]
Abstract
Cell fate specification defines the earliest steps towards a distinct cell lineage. Neural crest, a multipotent stem cell population, is thought to be specified from the ectoderm, but its varied contributions defy canons of segregation potential and challenges its embryonic origin. Aiming to resolve this conflict, we have assayed the earliest specification of neural crest using blastula stage chick embryos. Specification assays on isolated chick epiblast explants identify an intermediate region specified towards the neural crest cell fate. Furthermore, low density culture suggests that the specification of intermediate cells towards the neural crest lineage is independent of contact mediated induction and Wnt-ligand induced signaling, but is, however, dependent on transcriptional activity of β-catenin. Finally, we have validated the regional identity of the intermediate region towards the neural crest cell fate using fate map studies. Our results suggest a model of neural crest specification within a restricted epiblast region in blastula stage chick embryos.
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Affiliation(s)
- Maneeshi S Prasad
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, USA
| | | | | | | | | | - Patrick B Shelar
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, USA
| | - Rebekah M Charney
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, USA
| | - Martín I García-Castro
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, USA.
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19
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Yu JR, Feng TJ, Zheng XD, Chen DH, Tao Y. Transitions in the cell-fate induction induced by colored noise associated with the inductive stimulus. J Theor Biol 2020; 484:110018. [PMID: 31550442 DOI: 10.1016/j.jtbi.2019.110018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 09/17/2019] [Accepted: 09/20/2019] [Indexed: 11/15/2022]
Abstract
The cell-fate induction based on the saddle-node bifurcation is undoubtedly a very important concept in developmental biology, which provides a possible mechanism to explain the intrinsic irreversibility in the developmental process. In this paper, the effect of a colored noise, which is associated with the inductive stimulus, on the saddle-node landscape of cell-fate induction is investigated, especially, the effect of the change of correlation time of colored noise on cell-fate induction. The main results show clearly that the change of correlation time of colored noise could induce the transitions of the system. This implies that the colored noise associated with inductive stimulus may have a profound effect on the saddle-node bifurcation landscape of cell-fate induction. This will also help us to understand more deeply the role of cell-fate induction in developmental biology.
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Affiliation(s)
- Jie-Ru Yu
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou 730070, China; Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Tian-Jiao Feng
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; School of Systems Science, Beijing Normal University, Beijing 100875, China
| | - Xiu-Deng Zheng
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Da-Hua Chen
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Tao
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
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20
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Lv B, Liu C, Chen Y, Qi L, Wang L, Ji Y, Xue Z. Light-induced injury in mouse embryos revealed by single-cell RNA sequencing. Biol Res 2019; 52:48. [PMID: 31466525 PMCID: PMC6716870 DOI: 10.1186/s40659-019-0256-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 08/21/2019] [Indexed: 11/18/2022] Open
Abstract
Background Light exposure is a common stress factor in in vitro manipulation of embryos in the reproductive center. Many studies have shown the deleterious effects of high-intensity light exposure in different animal embryos. However, no transcriptomic studies have explored the light-induced injury and response in preimplantation embryos. Results Here, we adopt different time-courses and illumination intensities to treat mouse embryos at the 2-cell stage and evaluate their effects on blastulation. Meanwhile, single-cell transcriptomes from the 2-cell to blastocyst stage were analyzed after high-intensity light exposure. These data show that cells at each embryonic stage can be categorized into different light conditions. Further analyses of differentially expressed genes and GO terms revealed the light-induced injury as well as the potential repair response after high-intensity lighting. Maternal-to-zygote transition is also affected by the failure to remove maternal RNAs and deactivate zygotic genome expression. Conclusion Our work revealed an integrated response to high-intensity lighting, involving morphological changes, long-lasting injury effects, and intracellular damage repair mechanisms.
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Affiliation(s)
- Bo Lv
- Department of Regenerative Medicine, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Chaojie Liu
- Department of Regenerative Medicine, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Yu Chen
- School of Life Sciences and Environment, Avans University of Applied Sciences, Breda, 4818 AJ, The Netherlands
| | - Lingbin Qi
- Department of Regenerative Medicine, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Lu Wang
- Department of Regenerative Medicine, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Yazhong Ji
- Reproductive Medicine Center, Tongji Hospital, Tongji University, Shanghai, 200065, China.
| | - Zhigang Xue
- Department of Regenerative Medicine, School of Medicine, Tongji University, Shanghai, 200092, China. .,Reproductive Medicine Center, Tongji Hospital, Tongji University, Shanghai, 200065, China.
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21
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Hupalowska A, Jedrusik A, Zhu M, Bedford MT, Glover DM, Zernicka-Goetz M. CARM1 and Paraspeckles Regulate Pre-implantation Mouse Embryo Development. Cell 2019; 175:1902-1916.e13. [PMID: 30550788 PMCID: PMC6292842 DOI: 10.1016/j.cell.2018.11.027] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 07/29/2018] [Accepted: 11/16/2018] [Indexed: 01/20/2023]
Abstract
Nuclear architecture has never been carefully examined during early mammalian development at the stages leading to establishment of the embryonic and extra-embryonic lineages. Heterogeneous activity of the methyltransferase CARM1 during these stages results in differential methylation of histone H3R26 to modulate establishment of these two lineages. Here we show that CARM1 accumulates in nuclear granules at the 2- to 4-cell stage transition in the mouse embryo, with the majority corresponding to paraspeckles. The paraspeckle component Neat1 and its partner p54nrb are required for CARM1's association with paraspeckles and for H3R26 methylation. Conversely, CARM1 also influences paraspeckle organization. Depletion of Neat1 or p54nrb results in arrest at the 16- to 32-cell stage, with elevated expression of transcription factor Cdx2, promoting differentiation into the extra-embryonic lineage. This developmental arrest occurs at an earlier stage than following CARM1 depletion, indicating that paraspeckles act upstream of CARM1 but also have additional earlier roles in fate choice.
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Affiliation(s)
- Anna Hupalowska
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK
| | - Agnieszka Jedrusik
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK
| | - Meng Zhu
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK
| | - Mark T Bedford
- Department of Epigenetics and Molecular Carcinogenesis, MD Anderson Cancer Center, The University of Texas, 1808 Park Road 1C, Smithville, TX 78957, USA
| | - David M Glover
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK
| | - Magdalena Zernicka-Goetz
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK.
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22
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Zhang Y, Shi J, Rassoulzadegan M, Tuorto F, Chen Q. Sperm RNA code programmes the metabolic health of offspring. Nat Rev Endocrinol 2019; 15:489-498. [PMID: 31235802 PMCID: PMC6626572 DOI: 10.1038/s41574-019-0226-2] [Citation(s) in RCA: 138] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/29/2019] [Indexed: 12/31/2022]
Abstract
Mammalian sperm RNA is increasingly recognized as an additional source of paternal hereditary information beyond DNA. Environmental inputs, including an unhealthy diet, mental stresses and toxin exposure, can reshape the sperm RNA signature and induce offspring phenotypes that relate to paternal environmental stressors. Our understanding of the categories of sperm RNAs (such as tRNA-derived small RNAs, microRNAs, ribosomal RNA-derived small RNAs and long non-coding RNAs) and associated RNA modifications is expanding and has begun to reveal the functional diversity and information capacity of these molecules. However, the coding mechanism endowed by sperm RNA structures and by RNA interactions with DNA and other epigenetic factors remains unknown. How sperm RNA-encoded information is decoded in early embryos to control offspring phenotypes also remains unclear. Complete deciphering of the 'sperm RNA code' with regard to metabolic control could move the field towards translational applications and precision medicine, and this may lead to prevention of intergenerational transmission of obesity and type 2 diabetes mellitus susceptibility.
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Affiliation(s)
- Yunfang Zhang
- Medical Center of Hematology, The Xinqiao Hospital of Army Medical University, Chongqing, China
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA
| | - Junchao Shi
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA, USA
| | | | - Francesca Tuorto
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Qi Chen
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA.
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA, USA.
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23
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Casser E, Israel S, Schlatt S, Nordhoff V, Boiani M. Retrospective analysis: reproducibility of interblastomere differences of mRNA expression in 2-cell stage mouse embryos is remarkably poor due to combinatorial mechanisms of blastomere diversification. Mol Hum Reprod 2019; 24:388-400. [PMID: 29746690 DOI: 10.1093/molehr/gay021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 05/05/2018] [Indexed: 01/13/2023] Open
Abstract
STUDY QUESTION What is the prevalence, reproducibility and biological significance of transcriptomic differences between sister blastomeres of the mouse 2-cell embryo? SUMMARY ANSWER Sister 2-cell stage blastomeres are distinguishable from each other by mRNA analysis, attesting to the fact that differentiation starts mostly early in the mouse embryo; however, the interblastomere differences are poorly reproducible and invoke the combinatorial effects of known and new mechanisms of blastomere diversification. WHAT IS KNOWN ALREADY Transcriptomic datasets for single blastomeres in mice have been available for years but have never been systematically analysed together, although such an analysis may shed light onto some unclarified topics of early mammalian development. Two unknowns that remain are at which stage embryonic blastomeres start to diversify from each other and what is the molecular origin of that difference. At the earliest postzygotic stage, the 2-cell stage, opinions differ regarding the answer to these questions; one group claims that the first zygotic division yields two equal blastomeres capable of forming a full organism (totipotency) and another group claims evidence for interblastomere differences reminiscent of the prepatterning found in embryos of lower taxa. Regarding the molecular origin of interblastomere differences, there are four prevalent models which invoke (1) oocyte anisotropy, (2) sperm entry point, (3) partition errors of the transcript pool and (4) asynchronous embryonic genome activation in the two blastomeres. STUDY DESIGN, SIZE, DURATION Seven transcriptomic studies published between 2011 and 2017 were eligible for retrospective analysis, since both blastomeres of the mouse 2-cell embryo had been analysed individually regarding the original pair associations and since the datasets were made available in public repositories. Five of these studies, encompassing a total of 43 pairs of sister blastomeres, were selected for further analyses based on high interblastomere correlations of mRNA levels. A double cut-off was used to select mRNAs that had robust interblastomere differences both within and between embryos (hits). The hits of each study were compared and contrasted with the hits of the other studies using Venn diagrams. The hits shared by at least four of five studies were analysed further by bioinformatics. PARTICIPANTS/MATERIALS, SETTING, METHODS PubMed was systematically examined for mRNA expression profiles of single 2-cell stage blastomeres in addition to publicly available microarray datasets (GEO, ArrayExpress). Based on the original normalizations, data from seven studies were screened for pairwise sample correlation at the gene level (Spearman), and the top five datasets with the highest correlation were subjected to hierarchical cluster analysis. Interblastomere differences of gene expression were expressed as a ratio of the higher to the lower mRNA level for each pair of blastomeres. A double cut-off was used to make the call of interblastomere difference, accepting genes with mRNA ratios above 2 when observed in at least 50% of the pairs, and discarding the other genes. The proportion of interblastomere differences common to at least four of the five datasets was calculated. Finally, the corresponding gene, pathway and enrichment analyses were performed utilizing PANTHER and GORILLA platforms. MAIN RESULTS AND THE ROLE OF CHANCE An average of 17% of genes within the datasets are differently expressed between sister blastomeres, a proportion which falls to 1% when considering the differences that are common to at least four of the five studies. Housekeeping mRNAs were not included in the 17% and 1% gene lists, suggesting that the interblastomere differences do not occur simply by chance. The 1% of shared interblastomere differences comprise 100 genes, of which 35 are consistent with at least one of the four prevalent models of sister blastomere diversification. Bioinformatics analysis of the remaining 65 genes that are not consistent with the four models suggests that at least one more mechanism is at play, potentially related to the endomembrane system. Although there are many dimensions to the issue of reproducibility (biological, experimental, analytical), we consider that the sister blastomeres are poised to escape high interblastomere correlations of mRNA levels, because at least five sources of diversity superimpose on each other, accounting for at least 25 = 32 different states. As a result, interblastomere mRNA differences of a given 2-cell embryo are necessarily difficult to reproduce in another 2-cell embryo. LARGE SCALE DATA Data were as provided by the original studies (GSE21688, GSE22182, GSE27396, GSE45719, GSE57249, E-MTAB-3321, GSE94050). LIMITATIONS, REASONS FOR CAUTION The original studies present similarities (e.g. fertilization in vivo after ovarian stimulation) as well as differences (e.g. mouse strains, method and timing of blastomere separation). We identified robust mRNA differences between the sister blastomeres, but these differences are underestimated because our double cut-off method works with thresholds and affords more protection against false positives than false negatives. Regarding the false negatives, transcriptome analysis may have captured only part of the interblastomere differences due to: (1) the 2-fold cut-off not being sensitive enough to detect the remaining part of the interblastomere differences, (2) the detection limit of the transcriptomic methods not being sufficient, or (3) interblastomere differences being oblivious to transcriptomic identification because transcriptional changes are oscillatory or because differences are mediated non-transcriptionally or post-transcriptionally. Regarding the false positives, it seems unlikely that a difference was found just by chance for the same group of transcripts due to the same technical error, given that different laboratories produced the data. WIDER IMPLICATIONS OF THE FINDINGS It is clear that the sister blastomeres are distinguishable from each other by mRNA analysis even at the 2-cell stage; however, efforts to identify large stable patterns may be in vain. This elicits thoughts about the wisdom of adding new transcriptomic datasets to the ones that already exist; if all transcriptomic datasets produced so far show a reproducibility of 1%, then any future study would probably face the same issue again. Possibly, a solid identification of the 'large stable pattern that should be there but was not found' requires an even larger dataset than the sum of the seven datasets considered here. Conversely, small stable patterns may be easier to identify, but their biological relevance is less obvious. Alternatively, interblastomere differences may not be mediated by nucleic acids but by other cellular components. STUDY FUNDING/COMPETING INTEREST(S) This study was supported by the Deutsche Forschungsgemeinschaft (grant DFG BO 2540-4-3 to M.B. and grant NO 413/3-3 to V.N.). The authors declare that they have no competing financial interests.
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Affiliation(s)
- E Casser
- Max Planck Institute for Molecular Biomedicine, Roentgenstrasse 20, Muenster, Germany
| | - S Israel
- Max Planck Institute for Molecular Biomedicine, Roentgenstrasse 20, Muenster, Germany
| | - S Schlatt
- University Hospital Muenster, Centre of Reproductive Medicine and Andrology (CeRA), Albert Schweitzer-Campus 1, Building D11, Muenster, Germany
| | - V Nordhoff
- University Hospital Muenster, Centre of Reproductive Medicine and Andrology (CeRA), Albert Schweitzer-Campus 1, Building D11, Muenster, Germany
| | - M Boiani
- Max Planck Institute for Molecular Biomedicine, Roentgenstrasse 20, Muenster, Germany
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24
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Asymmetric Inheritance of Cell Fate Determinants: Focus on RNA. Noncoding RNA 2019; 5:ncrna5020038. [PMID: 31075989 PMCID: PMC6630313 DOI: 10.3390/ncrna5020038] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 04/30/2019] [Accepted: 05/06/2019] [Indexed: 12/20/2022] Open
Abstract
During the last decade, and mainly primed by major developments in high-throughput sequencing technologies, the catalogue of RNA molecules harbouring regulatory functions has increased at a steady pace. Current evidence indicates that hundreds of mammalian RNAs have regulatory roles at several levels, including transcription, translation/post-translation, chromatin structure, and nuclear architecture, thus suggesting that RNA molecules are indeed mighty controllers in the flow of biological information. Therefore, it is logical to suggest that there must exist a series of molecular systems that safeguard the faithful inheritance of RNA content throughout cell division and that those mechanisms must be tightly controlled to ensure the successful segregation of key molecules to the progeny. Interestingly, whilst a handful of integral components of mammalian cells seem to follow a general pattern of asymmetric inheritance throughout division, the fate of RNA molecules largely remains a mystery. Herein, we will discuss current concepts of asymmetric inheritance in a wide range of systems, including prions, proteins, and finally RNA molecules, to assess overall the biological impact of RNA inheritance in cellular plasticity and evolutionary fitness.
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25
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Zhang Y, Duan E. LncRNAs and paraspeckles predict cell fate in early mouse embryo†. Biol Reprod 2019; 100:1129-1131. [PMID: 30721989 DOI: 10.1093/biolre/ioz021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 02/02/2019] [Indexed: 11/15/2022] Open
Affiliation(s)
- Ying Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Enkui Duan
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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Smith HL, Stevens A, Minogue B, Sneddon S, Shaw L, Wood L, Adeniyi T, Xiao H, Lio P, Kimber SJ, Brison DR. Systems based analysis of human embryos and gene networks involved in cell lineage allocation. BMC Genomics 2019; 20:171. [PMID: 30836937 PMCID: PMC6399968 DOI: 10.1186/s12864-019-5558-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 02/22/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Little is understood of the molecular mechanisms involved in the earliest cell fate decision in human development, leading to the establishment of the trophectoderm (TE) and inner cell mass (ICM) stem cell population. Notably, there is a lack of understanding of how transcriptional networks arise during reorganisation of the embryonic genome post-fertilisation. RESULTS We identified a hierarchical structure of preimplantation gene network modules around the time of embryonic genome activation (EGA). Using network models along with eukaryotic initiation factor (EIF) and epigenetic-associated gene expression we defined two sets of blastomeres that exhibited diverging tendencies towards ICM or TE. Analysis of the developmental networks demonstrated stage specific EIF expression and revealed that histone modifications may be an important epigenetic regulatory mechanism in preimplantation human embryos. Comparison to published RNAseq data confirmed that during EGA the individual 8-cell blastomeres are transcriptionally primed for the first lineage decision in development towards ICM or TE. CONCLUSIONS Using multiple systems biology approaches to compare developmental stages in the early human embryo with single cell transcript data from blastomeres, we have shown that blastomeres considered to be totipotent are not transcriptionally equivalent. Furthermore we have linked the developmental interactome to individual blastomeres and to later cell lineage. This has clinical implications for understanding the impact of fertility treatments and developmental programming of long term health.
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Affiliation(s)
- H. L. Smith
- Maternal and Fetal Health Research Centre, University of Manchester, Manchester Academic Health Sciences Centre, Oxford Road, Manchester, M13 9WL UK
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, Oxford Road, Manchester, M13 9WL UK
| | - A. Stevens
- Division of Developmental Biology & Medicine, School of Medical Sciences, University of Manchester, Manchester Academic Health Sciences Centre, 5th Floor Research, Royal Manchester Children’s Hospital, Oxford Road, Manchester, M13 9WL UK
| | - B. Minogue
- Maternal and Fetal Health Research Centre, University of Manchester, Manchester Academic Health Sciences Centre, Oxford Road, Manchester, M13 9WL UK
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, Oxford Road, Manchester, M13 9WL UK
| | - S. Sneddon
- Maternal and Fetal Health Research Centre, University of Manchester, Manchester Academic Health Sciences Centre, Oxford Road, Manchester, M13 9WL UK
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, Oxford Road, Manchester, M13 9WL UK
| | - L. Shaw
- Maternal and Fetal Health Research Centre, University of Manchester, Manchester Academic Health Sciences Centre, Oxford Road, Manchester, M13 9WL UK
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, Oxford Road, Manchester, M13 9WL UK
| | - L. Wood
- Department of Reproductive Medicine, Saint Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Sciences Centre, Oxford Road, Manchester, M13 9WL UK
| | - T. Adeniyi
- Department of Reproductive Medicine, Saint Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Sciences Centre, Oxford Road, Manchester, M13 9WL UK
| | - H. Xiao
- Computer Laboratory, William Gates Building, University of Cambridge, Cambridge, UK
| | - P. Lio
- Computer Laboratory, William Gates Building, University of Cambridge, Cambridge, UK
| | - S. J. Kimber
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, Oxford Road, Manchester, M13 9WL UK
| | - D. R. Brison
- Maternal and Fetal Health Research Centre, University of Manchester, Manchester Academic Health Sciences Centre, Oxford Road, Manchester, M13 9WL UK
- Department of Reproductive Medicine, Saint Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Sciences Centre, Oxford Road, Manchester, M13 9WL UK
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Liu K, Xu K, Song Y. Faster, higher, stronger: timely and robust cell fate/identity commitment in stem cell lineages. Open Biol 2019; 9:180243. [PMID: 30958098 PMCID: PMC6395883 DOI: 10.1098/rsob.180243] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Precise specification of cell fate or identity within stem cell lineages is critical for ensuring correct stem cell lineage progression and tissue homeostasis. Failure to specify cell fate or identity in a timely and robust manner can result in developmental abnormalities and diseases such as cancer. However, the molecular basis of timely cell fate/identity specification is only beginning to be understood. In this review, we discuss key regulatory strategies employed in cell fate specification and highlight recent results revealing how timely and robust cell fate/identity commitment is achieved through transcriptional control.
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Affiliation(s)
- Kun Liu
- 1 Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences , Beijing 100871 , People's Republic of China.,2 Peking-Tsinghua Center for Life Sciences, Peking University , Beijing 100871 , People's Republic of China
| | - Ke Xu
- 1 Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences , Beijing 100871 , People's Republic of China
| | - Yan Song
- 1 Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences , Beijing 100871 , People's Republic of China.,2 Peking-Tsinghua Center for Life Sciences, Peking University , Beijing 100871 , People's Republic of China
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28
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Transcriptome profiling of human oocytes experiencing recurrent total fertilization failure. Sci Rep 2018; 8:17890. [PMID: 30559372 PMCID: PMC6297154 DOI: 10.1038/s41598-018-36275-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 11/16/2018] [Indexed: 11/24/2022] Open
Abstract
There exist some patients who face recurrent total fertilization failure during assisted reproduction treatment, but the pathological mechanism underlying is elusive. Here, by using sc-RNA-seq method, the transcriptome profiles of ten abnormally fertilized zygotes were assessed, including five zygotes from one patient with recurrent Poly-PN zygotes, and five zygotes from a patient with pronuclear fusion failure. Four zygotes with three pronuclear (Tri-PN) were collected from four different patients as controls. After that, we identified 951 and 1697 significantly differentially expressed genes (SDEGs) in Poly-PN and PN arrest zygotes, respectively as compared with the control group. KEGG analyses indicated down regulated genes in the Poly-PN group included oocyte meiosis related genes, such as PPP2R1B, YWHAZ, MAD2L1, SPDYC, SKP1 and CDC27, together with genes associated with RNA processing, such as SF3B1, LOC645691, MAGOHB, PHF5A, PRPF18, DDX5, THOC1 and BAT1. In contrast, down regulated genes in the PN arrest group, included cell cycle genes, such as E2F4, DBF4, YWHAB, SKP2, CDC23, SMC3, CDC25A, CCND3, BUB1B, MDM2, CCNA2 and CDC7, together with homologous recombination related genes, such as NBN, XRCC3, SHFM1, RAD54B and RAD51. Thus, our work provides a better understanding of transcriptome profiles underlying RTFF, although it based on a limited number of patients.
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29
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Asymmetric Expression of LincGET Biases Cell Fate in Two-Cell Mouse Embryos. Cell 2018; 175:1887-1901.e18. [DOI: 10.1016/j.cell.2018.11.039] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 07/01/2018] [Accepted: 11/22/2018] [Indexed: 11/21/2022]
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30
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Chen F, Fu Q, Pu L, Zhang P, Huang Y, Hou Z, Xu Z, Chen D, Huang F, Deng T, Liang X, Lu Y, Zhang M. Integrated Analysis of Quantitative Proteome and Transcriptional Profiles Reveals the Dynamic Function of Maternally Expressed Proteins After Parthenogenetic Activation of Buffalo Oocyte. Mol Cell Proteomics 2018; 17:1875-1891. [PMID: 30002204 PMCID: PMC6166679 DOI: 10.1074/mcp.ra118.000556] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 05/16/2018] [Indexed: 01/09/2023] Open
Abstract
Maternal-effect genes are especially critical for early embryonic development after fertilization and until massive activation of the embryonic genome occurs. By applying a tandem mass tag (TMT)-labeled quantitative proteomics combined with RNA sequencing approach, the proteome of the buffalo was quantitatively analyzed during parthenogenesis of mature oocytes and the two-cell stage embryo. Of 1908 quantified proteins, 123 differed significantly. The transcriptome was analyzed eight stages (GV, MII, 2-cell, 4-cell, 8-cell, 16-cell, morula, blastocyst) of Buffalo using the RNA sequencing approach, and a total of 3567 unique genes were identified to be differently expressed between all consecutive stages of pre-implantation development. Validation of proteomics results (TUBB3, CTNNA1, CDH3, MAP2K1), which are involved in tight junction and gap junction, revealing that the maternal expression of the proteins possibly plays a role in the formation of cellular junctions firstly after parthenogenetic activation. Correlation and hierarchical analyses of transcriptional profiles and the expression of NPM2 and NLRP5 mRNA of buffalo in vitro developed oocytes and parthenogenetic embryos indicated that the "maternal-to-zygotic transition" (MZT) process might exist in the model of parthenogenesis, which is similar to a normally fertilized embryo, and may occur between the 8-cell to 16-cell stage. These data provide a rich resource for further studies on maternal proteins and genes and are conducive to improving nuclear transfer technology.
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Affiliation(s)
- Fumei Chen
- From the ‡State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi 530004, China
| | - Qiang Fu
- From the ‡State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi 530004, China
| | - Liping Pu
- From the ‡State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi 530004, China
| | - Pengfei Zhang
- From the ‡State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi 530004, China
| | - Yulin Huang
- From the ‡State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi 530004, China
| | - Zhen Hou
- From the ‡State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi 530004, China
| | - Zhuangzhuang Xu
- From the ‡State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi 530004, China
| | - Dongrong Chen
- From the ‡State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi 530004, China
| | - Fengling Huang
- From the ‡State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi 530004, China
| | - Tingxian Deng
- §Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Ministry of Agriculture and Buffalo Research Institute, Chinese Academy of Agricultural Science, Nanning, Guangxi 530001, China
| | - Xianwei Liang
- §Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Ministry of Agriculture and Buffalo Research Institute, Chinese Academy of Agricultural Science, Nanning, Guangxi 530001, China
| | - Yangqing Lu
- From the ‡State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi 530004, China;
| | - Ming Zhang
- From the ‡State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi 530004, China;
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31
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Biase FH, Wu Q, Calandrelli R, Rivas-Astroza M, Zhou S, Chen Z, Zhong S. Rainbow-Seq: Combining Cell Lineage Tracing with Single-Cell RNA Sequencing in Preimplantation Embryos. iScience 2018; 7:16-29. [PMID: 30267678 PMCID: PMC6135740 DOI: 10.1016/j.isci.2018.08.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 08/01/2018] [Accepted: 08/10/2018] [Indexed: 02/06/2023] Open
Abstract
We developed the Rainbow-seq technology to trace cell division history and reveal single-cell transcriptomes. With distinct fluorescent protein genes as lineage markers, Rainbow-seq enables each single-cell RNA sequencing (RNA-seq) experiment to simultaneously decode the lineage marker genes and read single-cell transcriptomes. We triggered lineage tracking in each blastomere at the 2-cell stage, observed microscopically inequivalent contributions of the progeny to the two embryonic poles at the blastocyst stage, and analyzed every single cell at either 4- or 8-cell stage with deep paired-end sequencing of full-length transcripts. Although lineage difference was not marked unequivocally at a single-gene level, it became clear when the transcriptome was analyzed as a whole. Moreover, several groups of novel transcript isoforms with embedded repeat sequences exhibited lineage difference, suggesting a possible link between DNA demethylation and cell fate decision. Rainbow-seq bridged a critical gap between division history and single-cell RNA-seq assays.
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Affiliation(s)
- Fernando H Biase
- Department of Bioengineering, University of California San Diego, San Diego, CA 92130, USA
| | - Qiuyang Wu
- Department of Bioengineering, University of California San Diego, San Diego, CA 92130, USA; Department of Computer Science and Technology, Tongji University, Shanghai 201804, China
| | - Riccardo Calandrelli
- Department of Bioengineering, University of California San Diego, San Diego, CA 92130, USA
| | - Marcelo Rivas-Astroza
- Department of Bioengineering, University of California San Diego, San Diego, CA 92130, USA
| | - Shuigeng Zhou
- School of Computer Science, Fudan University, Shanghai 200433, China
| | - Zhen Chen
- Department of Diabetes Complications and Metabolism, City of Hope, Duarte, CA 91010, USA
| | - Sheng Zhong
- Department of Bioengineering, University of California San Diego, San Diego, CA 92130, USA.
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32
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Shahbazi MN, Zernicka-Goetz M. Deconstructing and reconstructing the mouse and human early embryo. Nat Cell Biol 2018; 20:878-887. [PMID: 30038253 DOI: 10.1038/s41556-018-0144-x] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 06/15/2018] [Indexed: 02/07/2023]
Abstract
The emergence of form and function during mammalian embryogenesis is a complex process that involves multiple regulatory levels. The foundations of the body plan are laid throughout the first days of post-implantation development as embryonic stem cells undergo symmetry breaking and initiate lineage specification, in a process that coincides with a global morphological reorganization of the embryo. Here, we review experimental models and how they have shaped our current understanding of the post-implantation mammalian embryo.
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Affiliation(s)
- Marta N Shahbazi
- Department of Physiology, Development and Neuroscience, Mammalian Embryo and Stem Cell Group, University of Cambridge, Cambridge, UK.
| | - Magdalena Zernicka-Goetz
- Department of Physiology, Development and Neuroscience, Mammalian Embryo and Stem Cell Group, University of Cambridge, Cambridge, UK.
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33
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Pfeffer PL. Building Principles for Constructing a Mammalian Blastocyst Embryo. BIOLOGY 2018; 7:biology7030041. [PMID: 30041494 PMCID: PMC6164496 DOI: 10.3390/biology7030041] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 07/19/2018] [Accepted: 07/20/2018] [Indexed: 12/16/2022]
Abstract
The self-organisation of a fertilised egg to form a blastocyst structure, which consists of three distinct cell lineages (trophoblast, epiblast and hypoblast) arranged around an off-centre cavity, is unique to mammals. While the starting point (the zygote) and endpoint (the blastocyst) are similar in all mammals, the intervening events have diverged. This review examines and compares the descriptive and functional data surrounding embryonic gene activation, symmetry-breaking, first and second lineage establishment, and fate commitment in a wide range of mammalian orders. The exquisite detail known from mouse embryogenesis, embryonic stem cell studies and the wealth of recent single cell transcriptomic experiments are used to highlight the building principles underlying early mammalian embryonic development.
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Affiliation(s)
- Peter L Pfeffer
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand.
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34
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White MD, Zenker J, Bissiere S, Plachta N. Instructions for Assembling the Early Mammalian Embryo. Dev Cell 2018; 45:667-679. [DOI: 10.1016/j.devcel.2018.05.013] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 01/23/2018] [Accepted: 05/10/2018] [Indexed: 12/15/2022]
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35
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Chen Q, Shi J, Tao Y, Zernicka-Goetz M. Tracing the origin of heterogeneity and symmetry breaking in the early mammalian embryo. Nat Commun 2018; 9:1819. [PMID: 29739935 PMCID: PMC5940674 DOI: 10.1038/s41467-018-04155-2] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 04/06/2018] [Indexed: 01/02/2023] Open
Abstract
A fundamental question in developmental and stem cell biology concerns the origin and nature of signals that initiate asymmetry leading to pattern formation and self-organization. Instead of having prominent pre-patterning determinants as present in model organisms (worms, sea urchin, frog), we propose that the mammalian embryo takes advantage of more subtle cues such as compartmentalized intracellular reactions that generate micro-scale inhomogeneity, which is gradually amplified over several cellular generations to drive pattern formation while keeping developmental plasticity. It is therefore possible that by making use of compartmentalized information followed by its amplification, mammalian embryos would follow general principle of development found in other organisms in which the spatial cue is more robustly presented.
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Affiliation(s)
- Qi Chen
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, 89557, USA
| | - Junchao Shi
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, 89557, USA
| | - Yi Tao
- Center for Computational and Evolutionary Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Magdalena Zernicka-Goetz
- Mammalian Development and Stem Cell Group, Department of Physiology, Development & Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3EG, UK.
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36
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Simon CS, Hadjantonakis AK, Schröter C. Making lineage decisions with biological noise: Lessons from the early mouse embryo. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2018; 7:e319. [PMID: 29709110 DOI: 10.1002/wdev.319] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 02/09/2018] [Accepted: 03/13/2018] [Indexed: 12/18/2022]
Abstract
Understanding how individual cells make fate decisions that lead to the faithful formation and homeostatic maintenance of tissues is a fundamental goal of contemporary developmental and stem cell biology. Seemingly uniform populations of stem cells and multipotent progenitors display a surprising degree of heterogeneity, primarily originating from the inherent stochastic nature of molecular processes underlying gene expression. Despite this heterogeneity, lineage decisions result in tissues of a defined size and with consistent proportions of differentiated cell types. Using the early mouse embryo as a model we review recent developments that have allowed the quantification of molecular intercellular heterogeneity during cell differentiation. We first discuss the relationship between these heterogeneities and developmental cellular potential. We then review recent theoretical approaches that formalize the mechanisms underlying fate decisions in the inner cell mass of the blastocyst stage embryo. These models build on our extensive knowledge of the genetic control of fate decisions in this system and will become essential tools for a rigorous understanding of the connection between noisy molecular processes and reproducible outcomes at the multicellular level. We conclude by suggesting that cell-to-cell communication provides a mechanism to exploit and buffer intercellular variability in a self-organized process that culminates in the reproducible formation of the mature mammalian blastocyst stage embryo that is ready for implantation into the maternal uterus. This article is categorized under: Gene Expression and Transcriptional Hierarchies > Cellular Differentiation Establishment of Spatial and Temporal Patterns > Regulation of Size, Proportion, and Timing Gene Expression and Transcriptional Hierarchies > Gene Networks and Genomics Gene Expression and Transcriptional Hierarchies > Quantitative Methods and Models.
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Affiliation(s)
- Claire S Simon
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Anna-Katerina Hadjantonakis
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Christian Schröter
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
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37
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Zhong L, Mu H, Wen B, Zhang W, Wei Q, Gao G, Han J, Cao S. Long non-coding RNAs involved in the regulatory network during porcine pre-implantation embryonic development and iPSC induction. Sci Rep 2018; 8:6649. [PMID: 29703926 PMCID: PMC5923264 DOI: 10.1038/s41598-018-24863-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 04/05/2018] [Indexed: 12/16/2022] Open
Abstract
Long non-coding RNAs (lncRNA) play a key role in the orchestration of transcriptional regulation during development and many other cellular processes. The importance of the regulatory co-expression network was highlighted in the identification of the mechanism of these processes in humans and mice. However, elucidation of the properties of porcine lncRNAs involved in the regulatory network during pre-implantation embryonic development and fibroblast reprogramming to induced pluripotent stem cell (iPSC) has been limited to date. Using a weighted gene co-expression network analysis, we constructed the regulatory network and determined that the novel lncRNAs were functionally involved in key events of embryonic development during the pre-implantation period; moreover, reprogramming could be delineated by a small number of potentially functional modules of co-expressed genes. These findings indicate that lncRNAs may be involved in the transcriptional regulation of zygotic genome activation, first lineage segregation and somatic reprogramming to pluripotency. Furthermore, we performed a conservation and synteny analysis with the significant lncRNAs involved in these vital events and validated the results via experimental assays. In summary, the current findings provide a valuable resource to dissect the protein coding gene and lncRNA regulatory networks that underlie the progressive development of embryos and somatic reprogramming.
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Affiliation(s)
- Liang Zhong
- The Animal Science and Technology College, Beijing University of Agriculture, Beijing, China.,State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Haiyuan Mu
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Bingqiang Wen
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Wei Zhang
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Qingqing Wei
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Ge Gao
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Peking University, Beijing, China
| | - Jianyong Han
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China.
| | - Suying Cao
- The Animal Science and Technology College, Beijing University of Agriculture, Beijing, China. .,Beijing Key Laboratory of Traditional Chinese Veterinary Medicine, Beijing University of Agriculture, Beijing, China.
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38
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Pijuan-Sala B, Guibentif C, Göttgens B. Single-cell transcriptional profiling: a window into embryonic cell-type specification. Nat Rev Mol Cell Biol 2018; 19:399-412. [DOI: 10.1038/s41580-018-0002-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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39
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Griffiths JA, Scialdone A, Marioni JC. Using single-cell genomics to understand developmental processes and cell fate decisions. Mol Syst Biol 2018; 14:e8046. [PMID: 29661792 PMCID: PMC5900446 DOI: 10.15252/msb.20178046] [Citation(s) in RCA: 142] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 12/20/2017] [Accepted: 01/19/2018] [Indexed: 12/20/2022] Open
Abstract
High-throughput -omics techniques have revolutionised biology, allowing for thorough and unbiased characterisation of the molecular states of biological systems. However, cellular decision-making is inherently a unicellular process to which "bulk" -omics techniques are poorly suited, as they capture ensemble averages of cell states. Recently developed single-cell methods bridge this gap, allowing high-throughput molecular surveys of individual cells. In this review, we cover core concepts of analysis of single-cell gene expression data and highlight areas of developmental biology where single-cell techniques have made important contributions. These include understanding of cell-to-cell heterogeneity, the tracing of differentiation pathways, quantification of gene expression from specific alleles, and the future directions of cell lineage tracing and spatial gene expression analysis.
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Affiliation(s)
| | - Antonio Scialdone
- EMBL-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, München, Germany
- Institute of Functional Epigenetics, Helmholtz Zentrum München, München, Germany
- Institute of Computational Biology, Helmholtz Zentrum München, München, Germany
| | - John C Marioni
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- EMBL-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
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40
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Klimczewska K, Kasperczuk A, Suwińska A. The Regulative Nature of Mammalian Embryos. Curr Top Dev Biol 2018; 128:105-149. [DOI: 10.1016/bs.ctdb.2017.10.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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41
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Transcriptional Regulation and Genes Involved in First Lineage Specification During Preimplantation Development. ADVANCES IN ANATOMY, EMBRYOLOGY, AND CELL BIOLOGY 2018; 229:31-46. [PMID: 29177763 DOI: 10.1007/978-3-319-63187-5_4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The successful development from a single-cell zygote into a complex multicellular organism requires precise coordination of multiple cell-fate decisions. The very first of these is lineage specification into the inner cell mass (ICM) and trophectoderm (TE) during mammalian preimplantation development. In mouse embryos, transcription factors (TFs) such as Oct4, Sox2, and Nanog are enriched in cells of ICM, which gives rise to the fetus and yolk sac. Conversely, TFs such as Cdx2 and Eomes become highly upregulated in TE, which contribute to the placenta. Here, we review the current understanding of key transcriptional control mechanisms and genes responsible for these distinct differences during the first cell lineage specification. In particular, we highlight recent insights gained through advances in genome manipulation, live imaging, single-cell transcriptomics, and loss-of-function studies.
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Bissiere S, Gasnier M, Alvarez YD, Plachta N. Cell Fate Decisions During Preimplantation Mammalian Development. Curr Top Dev Biol 2017; 128:37-58. [PMID: 29477170 DOI: 10.1016/bs.ctdb.2017.11.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The early mouse embryo offers a phenomenal system to dissect how changes in the mechanisms controlling cell fate are integrated with morphogenetic events at the single-cell level. New technologies based on live imaging have enabled the discovery of dynamic changes in the regulation of single genes, transcription factors, and epigenetic mechanisms directing early cell fate decision in the early embryo. Here, we review recent progress in linking molecular dynamic events occurring at the level of the single cell in vivo, to some of the key morphogenetic changes regulating early mouse development.
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Affiliation(s)
| | - Maxime Gasnier
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore
| | - Yanina D Alvarez
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore; Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Conicet, Buenos Aires, Argentina
| | - Nicolas Plachta
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore; National University of Singapore, Singapore, Singapore.
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43
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Kumar P, Tan Y, Cahan P. Understanding development and stem cells using single cell-based analyses of gene expression. Development 2017; 144:17-32. [PMID: 28049689 DOI: 10.1242/dev.133058] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In recent years, genome-wide profiling approaches have begun to uncover the molecular programs that drive developmental processes. In particular, technical advances that enable genome-wide profiling of thousands of individual cells have provided the tantalizing prospect of cataloging cell type diversity and developmental dynamics in a quantitative and comprehensive manner. Here, we review how single-cell RNA sequencing has provided key insights into mammalian developmental and stem cell biology, emphasizing the analytical approaches that are specific to studying gene expression in single cells.
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Affiliation(s)
- Pavithra Kumar
- Department of Biomedical Engineering, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Yuqi Tan
- Department of Biomedical Engineering, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Patrick Cahan
- Department of Biomedical Engineering, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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44
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Totipotency segregates between the sister blastomeres of two-cell stage mouse embryos. Sci Rep 2017; 7:8299. [PMID: 28811525 PMCID: PMC5557898 DOI: 10.1038/s41598-017-08266-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 07/06/2017] [Indexed: 11/09/2022] Open
Abstract
Following fertilization in mammals, it is generally accepted that totipotent cells are exclusive to the zygote and to each of the two blastomeres originating from the first mitotic division. This model of totipotency was inferred from a minority of cases in which blastomeres produced monozygotic twins in mice. Was this due to experimental limitation or biological constraint? Here we removed experimental obstacles and achieved reliable quantification of the prevalence of dual totipotency among mouse two-cell stage blastomeres. We separated the blastomeres of 1,252 two-cell embryos, preserving 1,210 of the pairs. Two classes of monozygotic twins became apparent at the blastocyst stage: 27% formed a functional epiblast in both members (concordant), and 73% did so in only one member of the pair (discordant) - a partition that proved insensitive to oocyte quality, sperm-entry point, culture environment and pattern of cleavage. In intact two-cell embryos, the ability of sister blastomeres to generate epiblast was also skewed. Class discovery clustering of the individual blastomeres' and blastocysts' transcriptomes points to an innate origin of concordance and discordance rather than developmental acquisition. Our data place constraints on the commonly accepted idea that totipotency is allocated equally between the two-cell stage blastomeres in mice.
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45
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Mohammed H, Hernando-Herraez I, Savino A, Scialdone A, Macaulay I, Mulas C, Chandra T, Voet T, Dean W, Nichols J, Marioni JC, Reik W. Single-Cell Landscape of Transcriptional Heterogeneity and Cell Fate Decisions during Mouse Early Gastrulation. Cell Rep 2017; 20:1215-1228. [PMID: 28768204 PMCID: PMC5554778 DOI: 10.1016/j.celrep.2017.07.009] [Citation(s) in RCA: 204] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 06/07/2017] [Accepted: 07/06/2017] [Indexed: 01/08/2023] Open
Abstract
The mouse inner cell mass (ICM) segregates into the epiblast and primitive endoderm (PrE) lineages coincident with implantation of the embryo. The epiblast subsequently undergoes considerable expansion of cell numbers prior to gastrulation. To investigate underlying regulatory principles, we performed systematic single-cell RNA sequencing (seq) of conceptuses from E3.5 to E6.5. The epiblast shows reactivation and subsequent inactivation of the X chromosome, with Zfp57 expression associated with reactivation and inactivation together with other candidate regulators. At E6.5, the transition from epiblast to primitive streak is linked with decreased expression of polycomb subunits, suggesting a key regulatory role. Notably, our analyses suggest elevated transcriptional noise at E3.5 and within the non-committed epiblast at E6.5, coinciding with exit from pluripotency. By contrast, E6.5 primitive streak cells became highly synchronized and exhibit a shortened G1 cell-cycle phase, consistent with accelerated proliferation. Our study systematically charts transcriptional noise and uncovers molecular processes associated with early lineage decisions.
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Affiliation(s)
- Hisham Mohammed
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | | | - Aurora Savino
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Antonio Scialdone
- EMBL-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK; Wellcome Trust Sanger Institute, Single-Cell Genomics Centre, Cambridge CB10 1SA, UK
| | - Iain Macaulay
- Wellcome Trust Sanger Institute, Single-Cell Genomics Centre, Cambridge CB10 1SA, UK
| | - Carla Mulas
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 3EG, UK
| | - Tamir Chandra
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Thierry Voet
- Wellcome Trust Sanger Institute, Single-Cell Genomics Centre, Cambridge CB10 1SA, UK; Department of Human Genetics, Human Genome Laboratory, KU Leuven, 3000 Leuven, Belgium
| | - Wendy Dean
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Jennifer Nichols
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 3EG, UK.
| | - John C Marioni
- EMBL-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK; Wellcome Trust Sanger Institute, Single-Cell Genomics Centre, Cambridge CB10 1SA, UK; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 ORE, UK.
| | - Wolf Reik
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK; Wellcome Trust Sanger Institute, Single-Cell Genomics Centre, Cambridge CB10 1SA, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK.
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46
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Otte J, Wruck W, Adjaye J. New insights into human primordial germ cells and early embryonic development from single-cell analysis. FEBS Lett 2017. [PMID: 28627120 DOI: 10.1002/1873-3468.12716] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Human preimplantation developmental studies are difficult to accomplish due to associated ethical and moral issues. Preimplantation cells are rare and exist only in transient cell states. From a single cell, it is very challenging to analyse the origination of the heterogeneity and complexity inherent to the human body. However, recent advances in single-cell technology and data analysis have provided new insights into the process of early human development and germ cell specification. In this Review, we examine the latest single-cell datasets of human preimplantation embryos and germ cell development, compare them to bulk cell analyses, and interpret their biological implications.
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Affiliation(s)
- Jörg Otte
- Institute for Stem Cell Research and Regenerative Medicine, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany
| | - Wasco Wruck
- Institute for Stem Cell Research and Regenerative Medicine, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany
| | - James Adjaye
- Institute for Stem Cell Research and Regenerative Medicine, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany
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47
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Zhang Y, Wang Q, Wang H, Duan E. Uterine Fluid in Pregnancy: A Biological and Clinical Outlook. Trends Mol Med 2017. [DOI: 10.1016/j.molmed.2017.05.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
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48
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Simunovic M, Brivanlou AH. Embryoids, organoids and gastruloids: new approaches to understanding embryogenesis. Development 2017; 144:976-985. [PMID: 28292844 PMCID: PMC5358114 DOI: 10.1242/dev.143529] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cells have an intrinsic ability to self-assemble and self-organize into complex and functional tissues and organs. By taking advantage of this ability, embryoids, organoids and gastruloids have recently been generated in vitro, providing a unique opportunity to explore complex embryological events in a detailed and highly quantitative manner. Here, we examine how such approaches are being used to answer fundamental questions in embryology, such as how cells self-organize and assemble, how the embryo breaks symmetry, and what controls timing and size in development. We also highlight how further improvements to these exciting technologies, based on the development of quantitative platforms to precisely follow and measure subcellular and molecular events, are paving the way for a more complete understanding of the complex events that help build the human embryo.
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Affiliation(s)
- Mijo Simunovic
- Center for Studies in Physics and Biology, The Rockefeller University, New York, NY 10065, USA
- Laboratory of Stem Cell Biology and Molecular Embryology, The Rockefeller University, New York, NY 10065, USA
| | - Ali H Brivanlou
- Laboratory of Stem Cell Biology and Molecular Embryology, The Rockefeller University, New York, NY 10065, USA
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49
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Destouni A, Vermeesch JR. How can zygotes segregate entire parental genomes into distinct blastomeres? The zygote metaphase revisited. Bioessays 2017; 39. [DOI: 10.1002/bies.201600226] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Aspasia Destouni
- Laboratory of Cytogenetics and Genome Research; Center of Human Genetics; KU Leuven; Leuven Belgium
| | - Joris R. Vermeesch
- Laboratory of Cytogenetics and Genome Research; Center of Human Genetics; KU Leuven; Leuven Belgium
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50
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Ge SX. Exploratory bioinformatics investigation reveals importance of "junk" DNA in early embryo development. BMC Genomics 2017; 18:200. [PMID: 28231763 PMCID: PMC5324221 DOI: 10.1186/s12864-017-3566-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 02/07/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Instead of testing predefined hypotheses, the goal of exploratory data analysis (EDA) is to find what data can tell us. Following this strategy, we re-analyzed a large body of genomic data to study the complex gene regulation in mouse pre-implantation development (PD). RESULTS Starting with a single-cell RNA-seq dataset consisting of 259 mouse embryonic cells derived from zygote to blastocyst stages, we reconstructed the temporal and spatial gene expression pattern during PD. The dynamics of gene expression can be partially explained by the enrichment of transposable elements in gene promoters and the similarity of expression profiles with those of corresponding transposons. Long Terminal Repeats (LTRs) are associated with transient, strong induction of many nearby genes at the 2-4 cell stages, probably by providing binding sites for Obox and other homeobox factors. B1 and B2 SINEs (Short Interspersed Nuclear Elements) are correlated with the upregulation of thousands of nearby genes during zygotic genome activation. Such enhancer-like effects are also found for human Alu and bovine tRNA SINEs. SINEs also seem to be predictive of gene expression in embryonic stem cells (ESCs), raising the possibility that they may also be involved in regulating pluripotency. We also identified many potential transcription factors underlying PD and discussed the evolutionary necessity of transposons in enhancing genetic diversity, especially for species with longer generation time. CONCLUSIONS Together with other recent studies, our results provide further evidence that many transposable elements may play a role in establishing the expression landscape in early embryos. It also demonstrates that exploratory bioinformatics investigation can pinpoint developmental pathways for further study, and serve as a strategy to generate novel insights from big genomic data.
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Affiliation(s)
- Steven Xijin Ge
- Department of Mathematics and Statistics, South Dakota State University, Box 2225, Brookings, SD, 57110, USA.
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