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Firmin J, Ecker N, Rivet Danon D, Özgüç Ö, Barraud Lange V, Turlier H, Patrat C, Maître JL. Mechanics of human embryo compaction. Nature 2024; 629:646-651. [PMID: 38693259 DOI: 10.1038/s41586-024-07351-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/26/2024] [Indexed: 05/03/2024]
Abstract
The shaping of human embryos begins with compaction, during which cells come into close contact1,2. Assisted reproductive technology studies indicate that human embryos fail compaction primarily because of defective adhesion3,4. On the basis of our current understanding of animal morphogenesis5,6, other morphogenetic engines, such as cell contractility, could be involved in shaping human embryos. However, the molecular, cellular and physical mechanisms driving human embryo morphogenesis remain uncharacterized. Using micropipette aspiration on human embryos donated to research, we have mapped cell surface tensions during compaction. This shows a fourfold increase of tension at the cell-medium interface whereas cell-cell contacts keep a steady tension. Therefore, increased tension at the cell-medium interface drives human embryo compaction, which is qualitatively similar to compaction in mouse embryos7. Further comparison between human and mouse shows qualitatively similar but quantitively different mechanical strategies, with human embryos being mechanically least efficient. Inhibition of cell contractility and cell-cell adhesion in human embryos shows that, whereas both cellular processes are required for compaction, only contractility controls the surface tensions responsible for compaction. Cell contractility and cell-cell adhesion exhibit distinct mechanical signatures when faulty. Analysing the mechanical signature of naturally failing embryos, we find evidence that non-compacting or partially compacting embryos containing excluded cells have defective contractility. Together, our study shows that an evolutionarily conserved increase in cell contractility is required to generate the forces driving the first morphogenetic movement shaping the human body.
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Affiliation(s)
- Julie Firmin
- Institut Curie, Université PSL, CNRS UMR3215, INSERM U934, Paris, France
- Université de Paris, Paris, France
- Service de Biologie de la Reproduction - CECOS, Paris Centre Hospital, APHP centre, FHU Prema, Paris, France
| | - Nicolas Ecker
- Center for Interdisciplinary Research in Biology, Collège de France, CNRS, INSERM, Université PSL, FHU Prema, Paris, France
| | - Diane Rivet Danon
- Service de Biologie de la Reproduction - CECOS, Paris Centre Hospital, APHP centre, FHU Prema, Paris, France
| | - Özge Özgüç
- Institut Curie, Université PSL, CNRS UMR3215, INSERM U934, Paris, France
| | - Virginie Barraud Lange
- Service de Biologie de la Reproduction - CECOS, Paris Centre Hospital, APHP centre, FHU Prema, Paris, France
- Institut Cochin, Université de Paris, CNRS UMR1016, Paris, France
| | - Hervé Turlier
- Center for Interdisciplinary Research in Biology, Collège de France, CNRS, INSERM, Université PSL, FHU Prema, Paris, France
| | - Catherine Patrat
- Service de Biologie de la Reproduction - CECOS, Paris Centre Hospital, APHP centre, FHU Prema, Paris, France
- Institut Cochin, Université de Paris, CNRS UMR1016, Paris, France
| | - Jean-Léon Maître
- Institut Curie, Université PSL, CNRS UMR3215, INSERM U934, Paris, France.
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2
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Farzaneh M, Anbiyaee O, Azizidoost S, Nasrolahi A, Ghaedrahmati F, Kempisty B, Mozdziak P, Khoshnam SE, Najafi S. The Mechanisms of Long Non-coding RNA-XIST in Ischemic Stroke: Insights into Functional Roles and Therapeutic Potential. Mol Neurobiol 2024; 61:2745-2753. [PMID: 37932544 DOI: 10.1007/s12035-023-03740-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 10/18/2023] [Indexed: 11/08/2023]
Abstract
Ischemic stroke, which occurs due to the occlusion of cerebral arteries, is a common type of stroke. Recent research has highlighted the important role of long non-coding RNAs (lncRNAs) in the development of cerebrovascular diseases, specifically ischemic stroke. Understanding the functional roles of lncRNAs in ischemic stroke is crucial, given their potential contribution to the disease pathology. One noteworthy lncRNA is X-inactive specific transcript (XIST), which exhibits downregulation during the early stages of ischemic stroke and subsequent upregulation in later stages. XIST exert its influence on the development of ischemic stroke through interactions with multiple miRNAs and transcription factors. These interactions play a significant role in the pathogenesis of the condition. In this review, we have provided a comprehensive summary of the functional roles of XIST in ischemic stroke. By investigating the involvement of XIST in the disease process, we aim to enhance our understanding of the mechanisms underlying ischemic stroke and potentially identify novel therapeutic targets.
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Affiliation(s)
- Maryam Farzaneh
- Fertility, Infertility and Perinatology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Omid Anbiyaee
- Cardiovascular Research Center, Namazi Hospital, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Shirin Azizidoost
- Atherosclerosis Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Ava Nasrolahi
- Infectious Ophthalmologic Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Farhoodeh Ghaedrahmati
- Department of Immunology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Bartosz Kempisty
- Department of Human Morphology and Embryology, Division of Anatomy, Wroclaw Medical University, Wrocław, Poland
- Institute of Veterinary Medicine, Department of Veterinary Surgery, Nicolaus Copernicus University, Torun, Poland
- North Carolina State University College of Agriculture and Life Sciences, Raleigh, NC, 27695, USA
| | - Paul Mozdziak
- North Carolina State University College of Agriculture and Life Sciences, Raleigh, NC, 27695, USA
| | - Seyed Esmaeil Khoshnam
- Persian Gulf Physiology Research Center, Medical Basic Sciences Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
| | - Sajad Najafi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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3
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Saha D, Animireddy S, Bartholomew B. The SWI/SNF ATP-dependent chromatin remodeling complex in cell lineage priming and early development. Biochem Soc Trans 2024; 52:603-616. [PMID: 38572912 PMCID: PMC11088921 DOI: 10.1042/bst20230416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/22/2024] [Accepted: 03/26/2024] [Indexed: 04/05/2024]
Abstract
ATP dependent chromatin remodelers have pivotal roles in transcription, DNA replication and repair, and maintaining genome integrity. SWI/SNF remodelers were first discovered in yeast genetic screens for factors involved in mating type switching or for using alternative energy sources therefore termed SWI/SNF complex (short for SWItch/Sucrose NonFermentable). The SWI/SNF complexes utilize energy from ATP hydrolysis to disrupt histone-DNA interactions and shift, eject, or reposition nucleosomes making the underlying DNA more accessible to specific transcription factors and other regulatory proteins. In development, SWI/SNF orchestrates the precise activation and repression of genes at different stages, safe guards the formation of specific cell lineages and tissues. Dysregulation of SWI/SNF have been implicated in diseases such as cancer, where they can drive uncontrolled cell proliferation and tumor metastasis. Additionally, SWI/SNF defects are associated with neurodevelopmental disorders, leading to disruption of neural development and function. This review offers insights into recent developments regarding the roles of the SWI/SNF complex in pluripotency and cell lineage primining and the approaches that have helped delineate its importance. Understanding these molecular mechanisms is crucial for unraveling the intricate processes governing embryonic stem cell biology and developmental transitions and may potentially apply to human diseases linked to mutations in the SWI/SNF complex.
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Affiliation(s)
- Dhurjhoti Saha
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77054, U.S.A
| | - Srinivas Animireddy
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77054, U.S.A
| | - Blaine Bartholomew
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77054, U.S.A
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4
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Aksit MA, Yu B, Roelen BAJ, Migeon BR. Silencing XIST on the future active X: Searching human and bovine preimplantation embryos for the repressor. Eur J Hum Genet 2024; 32:399-406. [PMID: 35585273 PMCID: PMC10999447 DOI: 10.1038/s41431-022-01115-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 03/28/2022] [Accepted: 04/26/2022] [Indexed: 11/09/2022] Open
Abstract
X inactivation is the means of equalizing the dosage of X chromosomal genes in male and female eutherian mammals, so that only one X is active in each cell. The XIST locus (in cis) on each additional X chromosome initiates the transcriptional silence of that chromosome, making it an inactive X. How the active X in both males and females is protected from inactivation by its own XIST locus is not well understood in any mammal. Previous studies of autosomal duplications suggest that gene(s) on the short arm of human chromosome 19 repress XIST on the active X. Here, we examine the time of transcription of some candidate genes in preimplantation embryos using single-cell RNA sequencing data from human embryos and qRT-PCR from bovine embryos. The candidate genes assayed are those transcribed from 19p13.3-13.2, which are widely expressed and can remodel chromatin. Our results confirm that XIST is expressed at low levels from the future active X in embryos of both sexes; they also show that the XIST locus is repressed in both sexes when pluripotency factors are being upregulated, during the 4-8 cell and morula stages in human and bovine embryos - well before the early blastocyst (E5) when XIST on the inactive X in females starts to be upregulated. Our data suggest a role for DNMT1, UHRF1, SAFB and SAFB2 in XIST repression; they also exclude XACT and other 19p candidate genes and provide the transcriptional timing for some genes not previously assayed in human or bovine preimplantation embryos.
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Affiliation(s)
- Melis A Aksit
- McKusick Nathans Department of Genetic Medicine and Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Bo Yu
- Farm Animal Health, Department of Population Health Sciences, and Utrecht University, 3584CM, Utrecht, The Netherlands
| | - Bernard A J Roelen
- Embryology, Anatomy and Physiology, Department of Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584CM, Utrecht, The Netherlands
| | - Barbara R Migeon
- McKusick Nathans Department of Genetic Medicine and Johns Hopkins University, School of Medicine, Baltimore, MD, USA.
- The Department of Pediatrics, Johns Hopkins University, School of Medicine, Baltimore, MD, USA.
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5
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Liang M, Zhang L, Lai L, Li Z. Unraveling the role of Xist in X chromosome inactivation: insights from rabbit model and deletion analysis of exons and repeat A. Cell Mol Life Sci 2024; 81:156. [PMID: 38551746 PMCID: PMC10980640 DOI: 10.1007/s00018-024-05151-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 04/01/2024]
Abstract
X chromosome inactivation (XCI) is a process that equalizes the expression of X-linked genes between males and females. It relies on Xist, continuously expressed in somatic cells during XCI maintenance. However, how Xist impacts XCI maintenance and its functional motifs remain unclear. In this study, we conducted a comprehensive analysis of Xist, using rabbits as an ideal non-primate model. Homozygous knockout of exon 1, exon 6, and repeat A in female rabbits resulted in embryonic lethality. However, X∆ReAX females, with intact X chromosome expressing Xist, showed no abnormalities. Interestingly, there were no significant differences between females with homozygous knockout of exons 2-5 and wild-type rabbits, suggesting that exons 2, 3, 4, and 5 are less important for XCI. These findings provide evolutionary insights into Xist function.
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Affiliation(s)
- Mingming Liang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Lichao Zhang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Liangxue Lai
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, 130062, China.
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
- Institute of Stem Cells and Regeneration, Chinese Academy of Sciences, Beijing, 100039, China.
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences, Guangzhou, 510530, China.
| | - Zhanjun Li
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, 130062, China.
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6
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Hamze JG, Peris-Frau P, Galiano-Cogolludo B, Tomás-Almenar C, Santiago-Moreno J, Bermejo-Álvarez P. Efficient and repeatable in vitro fertilization in rabbits. Theriogenology 2024; 217:64-71. [PMID: 38252980 DOI: 10.1016/j.theriogenology.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 12/22/2023] [Accepted: 01/08/2024] [Indexed: 01/24/2024]
Abstract
Rabbits constitute an interesting model to understand gamete interaction and test novel Artificial Reproductive Techniques, but in vitro fertilization (IVF) is particularly problematic in this species. We have conducted a series of experiments to develop a consistent IVF technique. Initially, we checked viability, acrosome integrity, capacitation and motility in ejaculated sperm purified by a density gradient and incubated at different times in three different media: Tyrode's Albumin Lactate Pyruvate (TALP), human tubal fluid (HTF), and Brackett and Oliphant (BO). Total and progressive motility at 10-24 h and linearity from 3 h onwards was significantly higher in BO medium compared to TALP and HTF. Subsequently, cumulus-oocyte complexes (COCs) collected 10 h after induction of ovulation were incubated with sperm in TALP, HTF or BO for 18 h with or without performing sperm pre-incubation for 6 h. Pronuclear formation rate at 18 h was significantly higher in BO compared to other media (∼84 % vs. 17-22 %) and was not improved by pre-incubation. As COCs recovery rate was low at 10 h after induction of ovulation, COCs were collected at 12 h and co-incubated with sperm in BO. Pronuclear formation rate was similar than those obtained in COCs collected at 10 h (∼85 %), and when embryos were allowed to develop in vitro, the protocol yielded high cleavage and blastocyst rates (91 and 59 %, respectively). In conclusion, ejaculated rabbit sperm purified in a density gradient fertilize efficiently COCs collected at 12 h in BO medium.
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Affiliation(s)
- J G Hamze
- Animal Reproduction Department, INIA, CSIC, Spain; Department of Cell Biology and Histology, Universidad de Murcia, International Excellence Campus for Higher Education and Research (Campus Mare Nostrum), Murcia, Spain
| | - P Peris-Frau
- Animal Reproduction Department, INIA, CSIC, Spain
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7
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Du P, Wu J. Hallmarks of totipotent and pluripotent stem cell states. Cell Stem Cell 2024; 31:312-333. [PMID: 38382531 PMCID: PMC10939785 DOI: 10.1016/j.stem.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/18/2024] [Accepted: 01/26/2024] [Indexed: 02/23/2024]
Abstract
Though totipotency and pluripotency are transient during early embryogenesis, they establish the foundation for the development of all mammals. Studying these in vivo has been challenging due to limited access and ethical constraints, particularly in humans. Recent progress has led to diverse culture adaptations of epiblast cells in vitro in the form of totipotent and pluripotent stem cells, which not only deepen our understanding of embryonic development but also serve as invaluable resources for animal reproduction and regenerative medicine. This review delves into the hallmarks of totipotent and pluripotent stem cells, shedding light on their key molecular and functional features.
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Affiliation(s)
- Peng Du
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China.
| | - Jun Wu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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8
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Dror I, Chitiashvili T, Tan SYX, Cano CT, Sahakyan A, Markaki Y, Chronis C, Collier AJ, Deng W, Liang G, Sun Y, Afasizheva A, Miller J, Xiao W, Black DL, Ding F, Plath K. XIST directly regulates X-linked and autosomal genes in naive human pluripotent cells. Cell 2024; 187:110-129.e31. [PMID: 38181737 PMCID: PMC10783549 DOI: 10.1016/j.cell.2023.11.033] [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: 12/21/2020] [Revised: 04/01/2023] [Accepted: 11/28/2023] [Indexed: 01/07/2024]
Abstract
X chromosome inactivation (XCI) serves as a paradigm for RNA-mediated regulation of gene expression, wherein the long non-coding RNA XIST spreads across the X chromosome in cis to mediate gene silencing chromosome-wide. In female naive human pluripotent stem cells (hPSCs), XIST is in a dispersed configuration, and XCI does not occur, raising questions about XIST's function. We found that XIST spreads across the X chromosome and induces dampening of X-linked gene expression in naive hPSCs. Surprisingly, XIST also targets specific autosomal regions, where it induces repressive chromatin changes and gene expression dampening. Thereby, XIST equalizes X-linked gene dosage between male and female cells while inducing differences in autosomes. The dispersed Xist configuration and autosomal localization also occur transiently during XCI initiation in mouse PSCs. Together, our study identifies XIST as the regulator of X chromosome dampening, uncovers an evolutionarily conserved trans-acting role of XIST/Xist, and reveals a correlation between XIST/Xist dispersal and autosomal targeting.
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Affiliation(s)
- Iris Dror
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Tsotne Chitiashvili
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Shawn Y X Tan
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Clara T Cano
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Anna Sahakyan
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yolanda Markaki
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Institute for Structural and Chemical Biology & Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Constantinos Chronis
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Amanda J Collier
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Weixian Deng
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Guohao Liang
- Department of Biomedical Engineering, University of California Irvine, Irvine, CA 92697, USA
| | - Yu Sun
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Anna Afasizheva
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jarrett Miller
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Wen Xiao
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Douglas L Black
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Fangyuan Ding
- Department of Biomedical Engineering, University of California Irvine, Irvine, CA 92697, USA; Department of Developmental and Cell Biology, Department of Pharmaceutical Sciences, University of California Irvine, Irvine, CA 92697, USA
| | - Kathrin Plath
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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9
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Wilkinson AL, Zorzan I, Rugg-Gunn PJ. Epigenetic regulation of early human embryo development. Cell Stem Cell 2023; 30:1569-1584. [PMID: 37858333 DOI: 10.1016/j.stem.2023.09.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/18/2023] [Accepted: 09/25/2023] [Indexed: 10/21/2023]
Abstract
Studies of mammalian development have advanced our understanding of the genetic, epigenetic, and cellular processes that orchestrate embryogenesis and have uncovered new insights into the unique aspects of human embryogenesis. Recent studies have now produced the first epigenetic maps of early human embryogenesis, stimulating new ideas about epigenetic reprogramming, cell fate control, and the potential mechanisms underpinning developmental plasticity in human embryos. In this review, we discuss these new insights into the epigenetic regulation of early human development and the importance of these processes for safeguarding development. We also highlight unanswered questions and key challenges that remain to be addressed.
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Affiliation(s)
| | - Irene Zorzan
- Epigenetics Programme, Babraham Institute, Cambridge, UK
| | - Peter J Rugg-Gunn
- Epigenetics Programme, Babraham Institute, Cambridge, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge, UK; Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK.
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10
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Kaufmann C, Wutz A. IndiSPENsable for X Chromosome Inactivation and Gene Silencing. EPIGENOMES 2023; 7:28. [PMID: 37987303 PMCID: PMC10660550 DOI: 10.3390/epigenomes7040028] [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: 09/27/2023] [Revised: 10/23/2023] [Accepted: 10/30/2023] [Indexed: 11/22/2023] Open
Abstract
For about 30 years, SPEN has been the subject of research in many different fields due to its variety of functions and its conservation throughout a wide spectrum of species, like worms, arthropods, and vertebrates. To date, 216 orthologues have been documented. SPEN had been studied for its role in gene regulation in the context of cell signaling, including the NOTCH or nuclear hormone receptor signaling pathways. More recently, SPEN has been identified as a major regulator of initiation of chromosome-wide gene silencing during X chromosome inactivation (XCI) in mammals, where its function remains to be fully understood. Dependent on the biological context, SPEN functions via mechanisms which include different domains. While some domains of SPEN are highly conserved in sequence and secondary structure, species-to-species differences exist that might lead to mechanistic differences. Initiation of XCI appears to be different between humans and mice, which raises additional questions about the extent of generalization of SPEN's function in XCI. In this review, we dissect the mechanism of SPEN in XCI. We discuss its subregions and domains, focusing on its role as a major regulator. We further highlight species-related research, specifically of mouse and human SPEN, with the aim to reveal and clarify potential species-to-species differences in SPEN's function.
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Affiliation(s)
| | - Anton Wutz
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology ETH Hönggerberg, 8093 Zurich, Switzerland;
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11
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Ravid Lustig L, Sampath Kumar A, Schwämmle T, Dunkel I, Noviello G, Limberg E, Weigert R, Pacini G, Buschow R, Ghauri A, Stötzel M, Wittler L, Meissner A, Schulz EG. GATA transcription factors drive initial Xist upregulation after fertilization through direct activation of long-range enhancers. Nat Cell Biol 2023; 25:1704-1715. [PMID: 37932452 PMCID: PMC10635832 DOI: 10.1038/s41556-023-01266-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/22/2023] [Indexed: 11/08/2023]
Abstract
X-chromosome inactivation (XCI) balances gene expression between the sexes in female mammals. Shortly after fertilization, upregulation of Xist RNA from one X chromosome initiates XCI, leading to chromosome-wide gene silencing. XCI is maintained in all cell types, except the germ line and the pluripotent state where XCI is reversed. The mechanisms triggering Xist upregulation have remained elusive. Here we identify GATA transcription factors as potent activators of Xist. Through a pooled CRISPR activation screen in murine embryonic stem cells, we demonstrate that GATA1, as well as other GATA transcription factors can drive ectopic Xist expression. Moreover, we describe GATA-responsive regulatory elements in the Xist locus bound by different GATA factors. Finally, we show that GATA factors are essential for XCI induction in mouse preimplantation embryos. Deletion of GATA1/4/6 or GATA-responsive Xist enhancers in mouse zygotes effectively prevents Xist upregulation. We propose that the activity or complete absence of various GATA family members controls initial Xist upregulation, XCI maintenance in extra-embryonic lineages and XCI reversal in the epiblast.
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Affiliation(s)
- Liat Ravid Lustig
- Systems Epigenetics, Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Abhishek Sampath Kumar
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Till Schwämmle
- Systems Epigenetics, Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Ilona Dunkel
- Systems Epigenetics, Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Gemma Noviello
- Systems Epigenetics, Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Elodie Limberg
- Systems Epigenetics, Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Raha Weigert
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Guido Pacini
- Systems Epigenetics, Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - René Buschow
- Microscopy and Cryo-Electron Microscopy, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Afrah Ghauri
- Systems Epigenetics, Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Maximilian Stötzel
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Lars Wittler
- Transgenic Unit, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Alexander Meissner
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Edda G Schulz
- Systems Epigenetics, Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, Germany.
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12
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Werner JM, Hover J, Gillis J. Population variability in X-chromosome inactivation across 9 mammalian species. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.17.562732. [PMID: 37904929 PMCID: PMC10614859 DOI: 10.1101/2023.10.17.562732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
One of the two X chromosomes in female mammals is epigenetically silenced in embryonic stem cells by X chromosome inactivation (XCI). This creates a mosaic of cells expressing either the maternal or the paternal X allele. The XCI ratio, the proportion of inactivated parental alleles, varies widely among individuals, representing the largest instance of epigenetic variability within mammalian populations. While various contributing factors to XCI variability are recognized, namely stochastic and/or genetic effects, their relative contributions are poorly understood. This is due in part to limited cross-species analysis, making it difficult to distinguish between generalizable or species-specific mechanisms for XCI ratio variability. To address this gap, we measured XCI ratios in nine mammalian species (9,143 individual samples), ranging from rodents to primates, and compared the strength of stochastic models or genetic factors for explaining XCI variability. Our results demonstrate the embryonic stochasticity of XCI is a general explanatory model for population XCI variability in mammals, while genetic factors play a minor role.
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Affiliation(s)
- Jonathan M Werner
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - John Hover
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Jesse Gillis
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
- Physiology Department and Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
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13
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Khan SA, Theunissen TW. Modeling X-chromosome inactivation and reactivation during human development. Curr Opin Genet Dev 2023; 82:102096. [PMID: 37597506 PMCID: PMC10588740 DOI: 10.1016/j.gde.2023.102096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 06/27/2023] [Accepted: 07/16/2023] [Indexed: 08/21/2023]
Abstract
Stem-cell-based embryo models generate much excitement as they offer a window into an early phase of human development that has remained largely inaccessible to scientific investigation. An important epigenetic phenomenon during early embryogenesis is the epigenetic silencing of one of the two X chromosomes in female embryos, which ensures an equal output of X-linked gene expression between the sexes. X-chromosome inactivation (XCI) is thought to be established within the first three weeks of human development, although the inactive X-chromosome is reactivated in primordial germ cells (PGCs) that migrate to the embryonic gonads. Here, we summarize our current understanding of X-chromosome dynamics during human development and comment on the potential of recently established stem-cell-based models to reveal the underlying mechanisms.
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Affiliation(s)
- Shafqat A Khan
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA. https://twitter.com/@sakhan2019
| | - Thorold W Theunissen
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.
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14
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Calderari S, Archilla C, Jouneau L, Daniel N, Peynot N, Dahirel M, Richard C, Mourier E, Schmaltz-Panneau B, Vitorino Carvalho A, Rousseau-Ralliard D, Lager F, Marchiol C, Renault G, Gatien J, Nadal-Desbarats L, Couturier-Tarrade A, Duranthon V, Chavatte-Palmer P. Alteration of the embryonic microenvironment and sex-specific responses of the preimplantation embryo related to a maternal high-fat diet in the rabbit model. J Dev Orig Health Dis 2023; 14:602-613. [PMID: 37822211 DOI: 10.1017/s2040174423000260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
The maternal metabolic environment can be detrimental to the health of the offspring. In a previous work, we showed that maternal high-fat (HH) feeding in rabbit induced sex-dependent metabolic adaptation in the fetus and led to metabolic syndrome in adult offspring. As early development representing a critical window of susceptibility, in the present work we aimed to explore the effects of the HH diet on the oocyte, preimplantation embryo and its microenvironment. In oocytes from females on HH diet, transcriptomic analysis revealed a weak modification in the content of transcripts mainly involved in meiosis and translational control. The effect of maternal HH diet on the embryonic microenvironment was investigated by identifying the metabolite composition of uterine and embryonic fluids collected in vivo by biomicroscopy. Metabolomic analysis revealed differences in the HH uterine fluid surrounding the embryo, with increased pyruvate concentration. Within the blastocoelic fluid, metabolomic profiles showed decreased glucose and alanine concentrations. In addition, the blastocyst transcriptome showed under-expression of genes and pathways involved in lipid, glucose and amino acid transport and metabolism, most pronounced in female embryos. This work demonstrates that the maternal HH diet disrupts the in vivo composition of the embryonic microenvironment, where the presence of nutrients is increased. In contrast to this nutrient-rich environment, the embryo presents a decrease in nutrient sensing and metabolism suggesting a potential protective process. In addition, this work identifies a very early sex-specific response to the maternal HH diet, from the blastocyst stage.
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Affiliation(s)
- Sophie Calderari
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas78350, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort94700, France
| | - Catherine Archilla
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas78350, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort94700, France
| | - Luc Jouneau
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas78350, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort94700, France
| | - Nathalie Daniel
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas78350, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort94700, France
| | - Nathalie Peynot
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas78350, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort94700, France
| | - Michele Dahirel
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas78350, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort94700, France
| | - Christophe Richard
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas78350, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort94700, France
- Plateforme MIMA2-CIMA, Jouy en Josas, France
| | - Eve Mourier
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas78350, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort94700, France
- Plateforme MIMA2-CIMA, Jouy en Josas, France
| | - Barbara Schmaltz-Panneau
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas78350, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort94700, France
| | - Anaïs Vitorino Carvalho
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas78350, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort94700, France
| | - Delphine Rousseau-Ralliard
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas78350, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort94700, France
| | - Franck Lager
- Université Paris Cité, Institut Cochin, Inserm, CNRS, ParisF-75014, France
| | - Carmen Marchiol
- Université Paris Cité, Institut Cochin, Inserm, CNRS, ParisF-75014, France
| | - Gilles Renault
- Université Paris Cité, Institut Cochin, Inserm, CNRS, ParisF-75014, France
| | - Julie Gatien
- Research and Development Department, Eliance, Nouzilly, France
| | - Lydie Nadal-Desbarats
- UMR 1253, iBrain, University of Tours, Inserm, Tours, France
- PST-ASB, University of Tours, Tours, France
| | - Anne Couturier-Tarrade
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas78350, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort94700, France
| | - Véronique Duranthon
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas78350, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort94700, France
| | - Pascale Chavatte-Palmer
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas78350, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort94700, France
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15
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Agostinho de Sousa J, Wong CW, Dunkel I, Owens T, Voigt P, Hodgson A, Baker D, Schulz EG, Reik W, Smith A, Rostovskaya M, von Meyenn F. Epigenetic dynamics during capacitation of naïve human pluripotent stem cells. SCIENCE ADVANCES 2023; 9:eadg1936. [PMID: 37774033 PMCID: PMC10541016 DOI: 10.1126/sciadv.adg1936] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 08/30/2023] [Indexed: 10/01/2023]
Abstract
Human pluripotent stem cells (hPSCs) are of fundamental relevance in regenerative medicine. Naïve hPSCs hold promise to overcome some of the limitations of conventional (primed) hPSCs, including recurrent epigenetic anomalies. Naïve-to-primed transition (capacitation) follows transcriptional dynamics of human embryonic epiblast and is necessary for somatic differentiation from naïve hPSCs. We found that capacitated hPSCs are transcriptionally closer to postimplantation epiblast than conventional hPSCs. This prompted us to comprehensively study epigenetic and related transcriptional changes during capacitation. Our results show that CpG islands, gene regulatory elements, and retrotransposons are hotspots of epigenetic dynamics during capacitation and indicate possible distinct roles of specific epigenetic modifications in gene expression control between naïve and primed hPSCs. Unexpectedly, PRC2 activity appeared to be dispensable for the capacitation. We find that capacitated hPSCs acquire an epigenetic state similar to conventional hPSCs. Significantly, however, the X chromosome erosion frequently observed in conventional female hPSCs is reversed by resetting and subsequent capacitation.
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Affiliation(s)
- João Agostinho de Sousa
- Laboratory of Nutrition and Metabolic Epigenetics, Department of Health Sciences and Technology, ETH Zurich, 8603 Schwerzenbach, Switzerland
| | - Chee-Wai Wong
- Laboratory of Nutrition and Metabolic Epigenetics, Department of Health Sciences and Technology, ETH Zurich, 8603 Schwerzenbach, Switzerland
| | - Ilona Dunkel
- Systems Epigenetics, Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Thomas Owens
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Philipp Voigt
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Adam Hodgson
- School of Biosciences, The Julia Garnham Centre, University of Sheffield, S10 2TN Sheffield, UK
| | - Duncan Baker
- Sheffield Diagnostic Genetics Services, Sheffield Children’s NHS Foundation Trust, S5 7AU Sheffield, UK
| | - Edda G. Schulz
- Systems Epigenetics, Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Wolf Reik
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1QR, UK
- Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK
- Altos Labs Cambridge Institute of Science, Cambridge CB21 6GP, UK
| | - Austin Smith
- Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
- Living Systems Institute, University of Exeter, EX4 4QD Exeter, UK
| | - Maria Rostovskaya
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Ferdinand von Meyenn
- Laboratory of Nutrition and Metabolic Epigenetics, Department of Health Sciences and Technology, ETH Zurich, 8603 Schwerzenbach, Switzerland
- Department of Medical and Molecular Genetics, King’s College London, Guy’s Hospital, SE1 9RT London, UK
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16
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Patterson B, Yang B, Tanaka Y, Kim KY, Cakir B, Xiang Y, Kim J, Wang S, Park IH. Female naïve human pluripotent stem cells carry X chromosomes with Xa-like and Xi-like folding conformations. SCIENCE ADVANCES 2023; 9:eadf2245. [PMID: 37540754 PMCID: PMC10403202 DOI: 10.1126/sciadv.adf2245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 07/06/2023] [Indexed: 08/06/2023]
Abstract
Three-dimensional (3D) genomics shows immense promise for studying X chromosome inactivation (XCI) by interrogating changes to the X chromosomes' 3D states. Here, we sought to characterize the 3D state of the X chromosome in naïve and primed human pluripotent stem cells (hPSCs). Using chromatin tracing, we analyzed X chromosome folding conformations in these cells with megabase genomic resolution. X chromosomes in female naïve hPSCs exhibit folding conformations similar to the active X chromosome (Xa) and the inactive X chromosome (Xi) in somatic cells. However, naïve X chromosomes do not exhibit the chromatin compaction typically associated with these somatic X chromosome states. In H7 naïve human embryonic stem cells, XIST accumulation observed on damaged X chromosomes demonstrates the potential for naïve hPSCs to activate XCI-related mechanisms. Overall, our findings provide insight into the X chromosome status of naïve hPSCs with a single-chromosome resolution and are critical in understanding the unique epigenetic regulation in early embryonic cells.
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Affiliation(s)
- Benjamin Patterson
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Bing Yang
- Department of Genetics, and Department of Cell Biology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Yoshiaki Tanaka
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Kun-Yong Kim
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Bilal Cakir
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Yangfei Xiang
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Jonghun Kim
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Siyuan Wang
- Department of Genetics, and Department of Cell Biology, Yale School of Medicine, New Haven, CT 06520, USA
| | - In-Hyun Park
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
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17
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Schwämmle T, Schulz EG. Regulatory principles and mechanisms governing the onset of random X-chromosome inactivation. Curr Opin Genet Dev 2023; 81:102063. [PMID: 37356341 PMCID: PMC10465972 DOI: 10.1016/j.gde.2023.102063] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/27/2023]
Abstract
X-chromosome inactivation (XCI) has evolved in mammals to compensate for the difference in X-chromosomal dosage between the sexes. In placental mammals, XCI is initiated during early embryonic development through upregulation of the long noncoding RNA Xist from one randomly chosen X chromosome in each female cell. The Xist locus must thus integrate both X-linked and developmental trans-regulatory factors in a dosage-dependent manner. Furthermore, the two alleles must coordinate to ensure inactivation of exactly one X chromosome per cell. In this review, we summarize the regulatory principles that govern the onset of XCI. We go on to provide an overview over the factors that have been implicated in Xist regulation and discuss recent advances in our understanding of how Xist's cis-regulatory landscape integrates information in a precise fashion.
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Affiliation(s)
- Till Schwämmle
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, Germany. https://twitter.com/@TSchwammle
| | - Edda G Schulz
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, Germany.
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18
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Valledor M, Byron M, Dumas B, Carone DM, Hall LL, Lawrence JB. Early chromosome condensation by XIST builds A-repeat RNA density that facilitates gene silencing. Cell Rep 2023; 42:112686. [PMID: 37384527 PMCID: PMC10461597 DOI: 10.1016/j.celrep.2023.112686] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 10/31/2022] [Accepted: 06/08/2023] [Indexed: 07/01/2023] Open
Abstract
XIST RNA triggers chromosome-wide gene silencing and condenses an active chromosome into a Barr body. Here, we use inducible human XIST to examine early steps in the process, showing that XIST modifies cytoarchitecture before widespread gene silencing. In just 2-4 h, barely visible transcripts populate the large "sparse zone" surrounding the smaller "dense zone"; importantly, density zones exhibit different chromatin impacts. Sparse transcripts immediately trigger immunofluorescence for H2AK119ub and CIZ1, a matrix protein. H3K27me3 appears hours later in the dense zone, which enlarges with chromosome condensation. Genes examined are silenced after compaction of the RNA/DNA territory. Insights into this come from the findings that the A-repeat alone can silence genes and rapidly, but only where dense RNA supports sustained histone deacetylation. We propose that sparse XIST RNA quickly impacts architectural elements to condense the largely non-coding chromosome, coalescing RNA density that facilitates an unstable, A-repeat-dependent step required for gene silencing.
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Affiliation(s)
- Melvys Valledor
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Meg Byron
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Brett Dumas
- Department of Medicine, Boston University Medical Center, Boston, MA 02118, USA
| | - Dawn M Carone
- Department of Biology, Swarthmore College, Swarthmore, PA 19081, USA
| | - Lisa L Hall
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.
| | - Jeanne B Lawrence
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA; Department of Pediatrics, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.
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19
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Stenhouse C, Bazer FW, Ashworth CJ. Sexual dimorphism in placental development and function: Comparative physiology with an emphasis on the pig. Mol Reprod Dev 2023; 90:684-696. [PMID: 35466463 DOI: 10.1002/mrd.23573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/31/2022] [Accepted: 04/07/2022] [Indexed: 11/10/2022]
Abstract
Across mammalian species, it has been demonstrated that sex influences birth weight, with males being heavier than females; a characteristic that can be observed from early gestation. Male piglets are more likely to be stillborn and have greater preweaning mortality than their female littermates, despite the additional maternal investment into male fetal growth. Given the conserved nature of the genome between the sexes, it is hypothesized that these developmental differences between males and females are most likely orchestrated by differential placental adaptation. This review summarizes the current understanding of fetal sex-specific differences in placental and endometrial structure and function, with an emphasis on pathways found to be differentially regulated in the pig including angiogenesis, apoptosis, and proliferation. Given the importance of piglet sex in agricultural enterprises, and the potential for skewed litter sex ratios, it is imperative to improve understanding of the relationship between fetal sex and molecular signaling in both the placenta and endometria across gestation.
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Affiliation(s)
- Claire Stenhouse
- Department of Animal Science, Texas A&M University, College Station, Texas, USA
- Functional Genetics and Development Division, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, UK
| | - Fuller W Bazer
- Department of Animal Science, Texas A&M University, College Station, Texas, USA
| | - Cheryl J Ashworth
- Functional Genetics and Development Division, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, UK
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20
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Gong Y, Bai B, Sun N, Ci B, Shao H, Zhang T, Yao H, Zhang Y, Niu Y, Liu L, Zhao H, Wu H, Zhang L, Wang T, Li S, Wei Y, Yu Y, Ribeiro Orsi AE, Liu B, Ji W, Wu J, Chen Y, Tan T. Ex utero monkey embryogenesis from blastocyst to early organogenesis. Cell 2023; 186:2092-2110.e23. [PMID: 37172563 DOI: 10.1016/j.cell.2023.04.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 01/18/2023] [Accepted: 04/12/2023] [Indexed: 05/15/2023]
Abstract
The third and fourth weeks of gestation in primates are marked by several developmental milestones, including gastrulation and the formation of organ primordia. However, our understanding of this period is limited due to restricted access to in vivo embryos. To address this gap, we developed an embedded 3D culture system that allows for the extended ex utero culture of cynomolgus monkey embryos for up to 25 days post-fertilization. Morphological, histological, and single-cell RNA-sequencing analyses demonstrate that ex utero cultured monkey embryos largely recapitulated key events of in vivo development. With this platform, we were able to delineate lineage trajectories and genetic programs involved in neural induction, lateral plate mesoderm differentiation, yolk sac hematopoiesis, primitive gut, and primordial germ-cell-like cell development in monkeys. Our embedded 3D culture system provides a robust and reproducible platform for growing monkey embryos from blastocysts to early organogenesis and studying primate embryogenesis ex utero.
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Affiliation(s)
- Yandong Gong
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China; State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Senior Department of Hematology, Fifth Medical Center, Medical Innovation Research Department, Chinese PLA General Hospital, Beijing 100071, China
| | - Bing Bai
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China
| | - Nianqin Sun
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China
| | - Baiquan Ci
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China
| | - Honglian Shao
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China
| | - Ting Zhang
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China
| | - Hui Yao
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China
| | - Youyue Zhang
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China
| | - Yuyu Niu
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China
| | - Lizhong Liu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hu Zhao
- Chinese Institute for Brain Research, Beijing 102206, China
| | - Hao Wu
- School of Information Science and Engineering, Yunnan University, Kunming, Yunnan 650504, China
| | - Lei Zhang
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China
| | - Tianxiang Wang
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China
| | - Shangang Li
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China
| | - Yulei Wei
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yang Yu
- Reproductive Medical Center and Clinical Stem Cell Research Center, Peking University Third Hospital, Beijing 100191, China
| | - Ana Elisa Ribeiro Orsi
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP 05508-090, Brazil
| | - Bing Liu
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Senior Department of Hematology, Fifth Medical Center, Medical Innovation Research Department, Chinese PLA General Hospital, Beijing 100071, China.
| | - Weizhi Ji
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China.
| | - Jun Wu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Yongchang Chen
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China.
| | - Tao Tan
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China.
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21
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El Fouikar S, Duranthon V, Helies V, Jammes H, Couturier-Tarrade A, Gayrard V, Van Acker N, Frenois FX, Archilla C, Rousseau-Ralliard D, Gatimel N, Léandri R. Multigenerational Effects of a Complex Human-Relevant Exposure during Folliculogenesis and Preimplantation Embryo Development: The FEDEXPO Study. TOXICS 2023; 11:toxics11050425. [PMID: 37235240 DOI: 10.3390/toxics11050425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023]
Abstract
Animal toxicological studies often fail to mimic the complexity of the human exposome, associating low doses, combined molecules and long-term exposure. Since the reproductive potential of a woman begins in the fetal ovary, the literature regarding the disruption of its reproductive health by environmental toxicants remains limited. Studies draw attention to follicle development, a major determinant for the quality of the oocyte, and the preimplantation embryo, as both of them are targets for epigenetic reprogramming. The "Folliculogenesis and Embryo Development EXPOsure to a mixture of toxicants: evaluation in the rabbit model" (FEDEXPO) project emerged from consideration of these limitations and aims to evaluate in the rabbit model the impacts of an exposure to a mixture of known and suspected endocrine disrupting chemicals (EDCs) during two specific windows, including folliculogenesis and preimplantation embryo development. The mixture combines eight environmental toxicants, namely perfluorooctanesulfonic acid (PFOS), perfluorooctanoic acid (PFOA), dichlorodiphenyldichloroethylene (DDE), hexachlorobenzene (HCB), β-hexachlorocyclohexane (β-HCH), 2,2'4,4'-tetrabromodiphenyl ether (BDE-47), di(2-ethylhexyl) phthalate (DEHP) and bisphenol S (BPS), at relevant exposure levels for reproductive-aged women based on biomonitoring data. The project will be organized in order to assess the consequences of this exposure on the ovarian function of the directly exposed F0 females and monitor the development and health of the F1 offspring from the preimplantation stage. Emphasis will be made on the reproductive health of the offspring. Lastly, this multigenerational study will also tackle potential mechanisms for the inheritance of health disruption via the oocyte or the preimplantation embryo.
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Affiliation(s)
- Sara El Fouikar
- ToxAlim (Research Center in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, 31062 Toulouse, France
| | | | - Virginie Helies
- GenPhySE (Génétique Physiologie et Système d'Elevage), Université de Toulouse, INRAE, ENVT, INPT, 31326 Castanet-Tolosan, France
| | - Hélène Jammes
- BREED INRAE, UVSQ, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | | | - Véronique Gayrard
- ToxAlim (Research Center in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, 31062 Toulouse, France
| | - Nathalie Van Acker
- Plateforme Imag'IN, Service d'Anatomie Pathologie, Institut Universitaire du Cancer-Oncopole de Toulouse, Centre Hospitalier Universitaire de Toulouse, 31059 Toulouse, France
| | - François-Xavier Frenois
- Plateforme Imag'IN, Service d'Anatomie Pathologie, Institut Universitaire du Cancer-Oncopole de Toulouse, Centre Hospitalier Universitaire de Toulouse, 31059 Toulouse, France
| | | | | | - Nicolas Gatimel
- DEFE (Développement Embryonnaire, Fertilité et Environnement), UMR 1203 Inserm, Universités Toulouse et Montpellier, Toulouse Teaching Hospital Group, 31059 Toulouse, France
- Médecine de la Reproduction, Hôpital Paule de Viguier, Centre Hospitalier Universitaire de Toulouse, 31059 Toulouse, France
| | - Roger Léandri
- ToxAlim (Research Center in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, 31062 Toulouse, France
- Médecine de la Reproduction, Hôpital Paule de Viguier, Centre Hospitalier Universitaire de Toulouse, 31059 Toulouse, France
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22
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Gyobu‐Motani S, Yabuta Y, Mizuta K, Katou Y, Okamoto I, Kawasaki M, Kitamura A, Tsukiyama T, Iwatani C, Tsuchiya H, Tsujimura T, Yamamoto T, Nakamura T, Saitou M. Induction of fetal meiotic oocytes from embryonic stem cells in cynomolgus monkeys. EMBO J 2023; 42:e112962. [PMID: 36929479 PMCID: PMC10152148 DOI: 10.15252/embj.2022112962] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 03/18/2023] Open
Abstract
Human in vitro oogenesis provides a framework for clarifying the mechanism of human oogenesis. To create its benchmark, it is vital to promote in vitro oogenesis using a model physiologically close to humans. Here, we establish a foundation for in vitro oogenesis in cynomolgus (cy) monkeys (Macaca fascicularis): cy female embryonic stem cells harboring one active and one inactive X chromosome (Xa and Xi, respectively) differentiate robustly into primordial germ cell-like cells, which in xenogeneic reconstituted ovaries develop efficiently into oogonia and, remarkably, further into meiotic oocytes at the zygotene stage. This differentiation entails comprehensive epigenetic reprogramming, including Xi reprogramming, yet Xa and Xi remain epigenetically asymmetric with, as partly observed in vivo, incomplete Xi reactivation. In humans and monkeys, the Xi epigenome in pluripotent stem cells functions as an Xi-reprogramming determinant. We further show that developmental pathway over-activations with suboptimal up-regulation of relevant meiotic genes impede in vitro meiotic progression. Cy in vitro oogenesis exhibits critical homology with the human system, including with respect to bottlenecks, providing a salient model for advancing human in vitro oogenesis.
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Affiliation(s)
- Sayuri Gyobu‐Motani
- Institute for the Advanced Study of Human Biology (WPI‐ASHBi)Kyoto UniversityKyotoJapan
- Department of Anatomy and Cell Biology, Graduate School of MedicineKyoto UniversityKyotoJapan
| | - Yukihiro Yabuta
- Institute for the Advanced Study of Human Biology (WPI‐ASHBi)Kyoto UniversityKyotoJapan
- Department of Anatomy and Cell Biology, Graduate School of MedicineKyoto UniversityKyotoJapan
| | - Ken Mizuta
- Institute for the Advanced Study of Human Biology (WPI‐ASHBi)Kyoto UniversityKyotoJapan
- Department of Anatomy and Cell Biology, Graduate School of MedicineKyoto UniversityKyotoJapan
| | - Yoshitaka Katou
- Institute for the Advanced Study of Human Biology (WPI‐ASHBi)Kyoto UniversityKyotoJapan
- Department of Anatomy and Cell Biology, Graduate School of MedicineKyoto UniversityKyotoJapan
| | - Ikuhiro Okamoto
- Institute for the Advanced Study of Human Biology (WPI‐ASHBi)Kyoto UniversityKyotoJapan
- Department of Anatomy and Cell Biology, Graduate School of MedicineKyoto UniversityKyotoJapan
| | - Masanori Kawasaki
- Institute for the Advanced Study of Human Biology (WPI‐ASHBi)Kyoto UniversityKyotoJapan
- Department of Anatomy and Cell Biology, Graduate School of MedicineKyoto UniversityKyotoJapan
| | - Ayaka Kitamura
- Institute for the Advanced Study of Human Biology (WPI‐ASHBi)Kyoto UniversityKyotoJapan
- Department of Anatomy and Cell Biology, Graduate School of MedicineKyoto UniversityKyotoJapan
| | - Tomoyuki Tsukiyama
- Institute for the Advanced Study of Human Biology (WPI‐ASHBi)Kyoto UniversityKyotoJapan
- Research Center for Animal Life ScienceShiga University of Medical ScienceOtsuJapan
| | - Chizuru Iwatani
- Research Center for Animal Life ScienceShiga University of Medical ScienceOtsuJapan
| | - Hideaki Tsuchiya
- Research Center for Animal Life ScienceShiga University of Medical ScienceOtsuJapan
| | - Taro Tsujimura
- Institute for the Advanced Study of Human Biology (WPI‐ASHBi)Kyoto UniversityKyotoJapan
| | - Takuya Yamamoto
- Institute for the Advanced Study of Human Biology (WPI‐ASHBi)Kyoto UniversityKyotoJapan
- Center for iPS Cell Research and Application (CiRA)Kyoto UniversityKyotoJapan
- Center for Advanced Intelligence Project, RIKENTokyoJapan
| | - Tomonori Nakamura
- Institute for the Advanced Study of Human Biology (WPI‐ASHBi)Kyoto UniversityKyotoJapan
- Department of Anatomy and Cell Biology, Graduate School of MedicineKyoto UniversityKyotoJapan
- The Hakubi Center for Advanced ResearchKyoto UniversityKyotoJapan
| | - Mitinori Saitou
- Institute for the Advanced Study of Human Biology (WPI‐ASHBi)Kyoto UniversityKyotoJapan
- Department of Anatomy and Cell Biology, Graduate School of MedicineKyoto UniversityKyotoJapan
- Center for iPS Cell Research and Application (CiRA)Kyoto UniversityKyotoJapan
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23
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Mattimoe T, Payer B. The compleX balancing act of controlling X-chromosome dosage and how it impacts mammalian germline development. Biochem J 2023; 480:521-537. [PMID: 37096944 DOI: 10.1042/bcj20220450] [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: 08/24/2022] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 04/26/2023]
Abstract
In female mammals, the two X chromosomes are subject to epigenetic gene regulation in order to balance X-linked gene dosage with autosomes and in relation to males, which have one X and one Y chromosome. This is achieved by an intricate interplay of several processes; X-chromosome inactivation and reactivation elicit global epigenetic regulation of expression from one X chromosome in a stage-specific manner, whilst the process of X-chromosome upregulation responds to this by fine-tuning transcription levels of the second X. The germline is unique in its function of transmitting both the genetic and epigenetic information from one generation to the next, and remodelling of the X chromosome is one of the key steps in setting the stage for successful development. Here, we provide an overview of the complex dynamics of X-chromosome dosage control during embryonic and germ cell development, and aim to decipher its potential role for normal germline competency.
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Affiliation(s)
- Tom Mattimoe
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Carrer Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Bernhard Payer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Carrer Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
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24
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Zhou J, Hu J, Wang Y, Gao S. Induction and application of human naive pluripotency. Cell Rep 2023; 42:112379. [PMID: 37043354 DOI: 10.1016/j.celrep.2023.112379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 12/18/2022] [Accepted: 03/26/2023] [Indexed: 04/13/2023] Open
Abstract
Over the past few decades, many attempts have been made to capture different states of pluripotency in vitro. Naive and primed pluripotent stem cells, corresponding to the pluripotency states of pre- and post-implantation epiblasts, respectively, have been well characterized in mice and can be interconverted in vitro. Here, we summarize the recently reported strategies to generate human naive pluripotent stem cells in vitro. We discuss their applications in studies of regulatory mechanisms involved in early developmental processes, including identification of molecular features, X chromosome inactivation modeling, transposable elements regulation, metabolic characteristics, and cell fate regulation, as well as potential for extraembryonic differentiation and blastoid construction for embryogenesis modeling. We further discuss the naive pluripotency-related research, including 8C-like cell establishment and disease modeling. We also highlight limitations of current naive pluripotency studies, such as imperfect culture conditions and inadequate responsiveness to differentiation signals.
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Affiliation(s)
- Jianfeng Zhou
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Jindian Hu
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Yixuan Wang
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China.
| | - Shaorong Gao
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China.
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25
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Sakata Y, Zhang H, Sugiyama A, Motosugi N, Kimura H, Okamura Y, Fukuda A. Nanosheet coating improves stability of human pluripotent stem cell culture on glass substrates. Biochem Biophys Res Commun 2023; 650:55-61. [PMID: 36773340 DOI: 10.1016/j.bbrc.2023.01.077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 01/17/2023] [Accepted: 01/23/2023] [Indexed: 02/03/2023]
Abstract
High-resolution imaging analysis using various types of cells is an essential tool for dissecting cell functions. Generally, obtaining such images requires the cells to be cultured on glass substrates; however, it often results in the unstable status of cells. In this study, we report that coating the glass substrate using nanosheet composed of hydrophobic polystyrene, with Matrigel, significantly improves the viability of human pluripotent stem cells (hPSCs). Moreover, the nanosheet coating does not affect the transcriptome status of hPSC and enables researchers to perform the high-resolution imaging assay. These results indicate that the nanosheet coating is beneficial to the cells vulnerable to glass substrate culture. Using the nanosheet coating, we revealed that the spreading status of lnc RNA XIST, essential for X-chromosome inactivation (XCI) in female cells, in the nuclei significantly differs in each hPSC line. Taken together, our study provides a novel method to investigate biological questions using high-resolution imaging techniques.
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Affiliation(s)
- Yuka Sakata
- Department of Molecular Life Sciences, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Hong Zhang
- Micro/Nano Technology Center, Tokai University, Hiratsuka, Kanagawa, Japan; School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Akiko Sugiyama
- Department of Molecular Life Sciences, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Nami Motosugi
- Department of Molecular Life Sciences, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Hiroshi Kimura
- Micro/Nano Technology Center, Tokai University, Hiratsuka, Kanagawa, Japan; Department of Bioengineering, School of Engineering, Tokai University, Hiratsuka, Kanagawa, Japan
| | - Yosuke Okamura
- Micro/Nano Technology Center, Tokai University, Hiratsuka, Kanagawa, Japan; Department of Applied Chemistry, School of Engineering, Tokai University, Hiratsuka, Kanagawa, Japan.
| | - Atsushi Fukuda
- Department of Molecular Life Sciences, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Kanagawa, Japan; The Institute of Medical Sciences, Tokai University, Isehara, Japan; Micro/Nano Technology Center, Tokai University, Hiratsuka, Kanagawa, Japan; Center for Regenerative Medicine, National Center for Child Health and Development, Tokyo, Japan.
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26
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Jali I, Vanamamalai VK, Garg P, Navarrete P, Gutiérrez-Adán A, Sharma S. Identification and differential expression of long non-coding RNAs and their association with XIST gene during early embryonic developmental stages of Bos taurus. Int J Biol Macromol 2023; 229:896-908. [PMID: 36572076 DOI: 10.1016/j.ijbiomac.2022.12.221] [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: 07/25/2022] [Revised: 10/07/2022] [Accepted: 12/20/2022] [Indexed: 12/26/2022]
Abstract
X-chromosomes inactivation (XCI) is a phenomenon that aims to equalize the dosage of X-linked gene products between XY males and XX females in mammals. XIST gene is the master regulator of X chromosome inactivation during early embryonic developmental stages of Bos taurus. Biological molecule such as lncRNA plays significant role in the control of XCI, by RNA-based regulatory mechanisms and are non-coding regions of the genome. In our study, using in-silico transcriptome data analysis approach, we analysed RNA-seq data of E35, E39 and E43 samples from bovine genital ridges of early embryonic stages, and identified lncRNA transcripts. More than 7 lakh lncRNA transcripts were identified. Further, our study identified DE-lncRNAs and genes between male and female and studied their co-expression. More than four thousand differentially expressed lncRNAs identified. The co-expression and RT-PCR study in the result showed that there exists an association between the XIST and DE-lncRNAs in early embryonic gonads of bovine at E35. In this study, the association between DE-lncRNAs and XIST gene indicates, the potentially important role of DE-lncRNAs during embryo development in bovine. In conclusion, this study shows there exist an interplay between genes and lncRNAs at transcriptome level of bovine during early embryonic days.
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Affiliation(s)
- Itishree Jali
- National Institute of Animal Biotechnology (NIAB), Opp. Journalist Colony, Near Gowlidoddi, Extended Q City Road, Gachibowli, Hyderabad 500 032, Telangana, India; DBT-Regional Centre for Biotechnology (RCB), Faridabad 121001, Haryana, India
| | - Venkata Krishna Vanamamalai
- National Institute of Animal Biotechnology (NIAB), Opp. Journalist Colony, Near Gowlidoddi, Extended Q City Road, Gachibowli, Hyderabad 500 032, Telangana, India; DBT-Regional Centre for Biotechnology (RCB), Faridabad 121001, Haryana, India
| | - Priyanka Garg
- National Institute of Animal Biotechnology (NIAB), Opp. Journalist Colony, Near Gowlidoddi, Extended Q City Road, Gachibowli, Hyderabad 500 032, Telangana, India
| | - Paula Navarrete
- INIA-CSIC Centro Nacional Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)-Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Alfonso Gutiérrez-Adán
- INIA-CSIC Centro Nacional Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)-Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Shailesh Sharma
- National Institute of Animal Biotechnology (NIAB), Opp. Journalist Colony, Near Gowlidoddi, Extended Q City Road, Gachibowli, Hyderabad 500 032, Telangana, India; DBT-Regional Centre for Biotechnology (RCB), Faridabad 121001, Haryana, India.
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27
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Vargas LN, Silveira MM, Franco MM. Epigenetic Reprogramming and Somatic Cell Nuclear Transfer. Methods Mol Biol 2023; 2647:37-58. [PMID: 37041328 DOI: 10.1007/978-1-0716-3064-8_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Epigenetics is an area of genetics that studies the heritable modifications in gene expression and phenotype that are not controlled by the primary sequence of DNA. The main epigenetic mechanisms are DNA methylation, post-translational covalent modifications in histone tails, and non-coding RNAs. During mammalian development, there are two global waves of epigenetic reprogramming. The first one occurs during gametogenesis and the second one begins immediately after fertilization. Environmental factors such as exposure to pollutants, unbalanced nutrition, behavioral factors, stress, in vitro culture conditions can negatively affect epigenetic reprogramming events. In this review, we describe the main epigenetic mechanisms found during mammalian preimplantation development (e.g., genomic imprinting, X chromosome inactivation). Moreover, we discuss the detrimental effects of cloning by somatic cell nuclear transfer on the reprogramming of epigenetic patterns and some molecular alternatives to minimize these negative impacts.
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Affiliation(s)
- Luna N Vargas
- Laboratory of Animal Reproduction, Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil
- Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil
| | - Márcia M Silveira
- Laboratory of Animal Reproduction, Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil
- Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil
| | - Maurício M Franco
- Laboratory of Animal Reproduction, Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil.
- Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil.
- School of Veterinary Medicine, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil.
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28
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Goissis MD, Cibelli JB. Early Cell Specification in Mammalian Fertilized and Somatic Cell Nuclear Transfer Embryos. Methods Mol Biol 2023; 2647:59-81. [PMID: 37041329 DOI: 10.1007/978-1-0716-3064-8_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Early cell specification in mammalian preimplantation embryos is an intricate cellular process that leads to coordinated spatial and temporal expression of specific genes. Proper segregation into the first two cell lineages, the inner cell mass (ICM) and the trophectoderm (TE), is imperative for developing the embryo proper and the placenta, respectively. Somatic cell nuclear transfer (SCNT) allows the formation of a blastocyst containing both ICM and TE from a differentiated cell nucleus, which means that this differentiated genome must be reprogrammed to a totipotent state. Although blastocysts can be generated efficiently through SCNT, the full-term development of SCNT embryos is impaired mostly due to placental defects. In this review, we examine the early cell fate decisions in fertilized embryos and compare them to observations in SCNT-derived embryos, in order to understand if these processes are affected by SCNT and could be responsible for the low success of reproductive cloning.
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Affiliation(s)
- Marcelo D Goissis
- Department of Animal Reproduction, School of Veterinary Medicine and Animal Science, University of Sao Paulo, Sao Paulo, SP, Brazil.
| | - Jose B Cibelli
- Department of Animal Science, Michigan State University, East Lansing, MI, USA
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29
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Juchniewicz P, Kloska A, Portalska K, Jakóbkiewicz-Banecka J, Węgrzyn G, Liss J, Głodek P, Tukaj S, Piotrowska E. X-chromosome inactivation patterns depend on age and tissue but not conception method in humans. Chromosome Res 2023; 31:4. [PMID: 36695960 PMCID: PMC9877087 DOI: 10.1007/s10577-023-09717-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/27/2022] [Accepted: 12/06/2022] [Indexed: 01/26/2023]
Abstract
Female somatic X-chromosome inactivation (XCI) balances the X-linked transcriptional dosages between the sexes, randomly silencing the maternal or paternal X chromosome in each cell of 46,XX females. Skewed XCI toward one parental X has been observed in association with ageing and in some female carriers of X-linked diseases. To address the problem of non-random XCI, we quantified the XCI skew in different biological samples of naturally conceived females of different age groups and girls conceived after in vitro fertilization (IVF). Generally, XCI skew differed between saliva, blood, and buccal swabs, while saliva and blood had the most similar XCI patterns in individual females. XCI skew increased with age in saliva, but not in other tissues. We showed no significant differences in the XCI patterns in tissues of naturally conceived and IVF females. The gene expression profile of the placenta and umbilical cord blood was determined depending on the XCI pattern. The increased XCI skewing in the placental tissue was associated with the differential expression of several genes out of 40 considered herein. Notably, skewed XCI patterns (> 80:20) were identified with significantly increased expression levels of four genes: CD44, KDM6A, PHLDA2, and ZRSR2. The differences in gene expression patterns between samples with random and non-random XCI may shed new light on factors contributing to the XCI pattern outcome and indicate new paths in future research on the phenomenon of XCI skewing.
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Affiliation(s)
- Patrycja Juchniewicz
- Department of Medical Biology and Genetics, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - Anna Kloska
- Department of Medical Biology and Genetics, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - Karolina Portalska
- Department of Molecular Biology, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - Joanna Jakóbkiewicz-Banecka
- Department of Medical Biology and Genetics, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - Joanna Liss
- Department of Medical Biology and Genetics, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland ,Research and Development Center, INVICTA, Sopot, Poland
| | - Piotr Głodek
- Research and Development Center, INVICTA, Sopot, Poland
| | - Stefan Tukaj
- Department of Molecular Biology, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - Ewa Piotrowska
- Department of Molecular Biology, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland
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30
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Shevchenko AI, Rifel NA, Zakian SM, Zakharova IS. Constitutive heterochromatin propagation contributes to the X chromosome inactivation. Chromosome Res 2022; 30:289-307. [PMID: 35920963 DOI: 10.1007/s10577-022-09706-4] [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: 04/27/2022] [Revised: 07/08/2022] [Accepted: 07/15/2022] [Indexed: 01/25/2023]
Abstract
Imprinted X chromosome inactivation (iXCI) balances the expression of X-linked genes in preimplantation embryos and extraembryonic tissues in rodents. Long noncoding Xist RNA drives iXCI, silencing genes and recruiting Xist-dependent chromatin repressors. Some domains on the inactive X chromosome include repressive modifications specific to constitutive heterochromatin, which show no direct link to Xist RNA. We explored the relationship between Xist RNA and chromatin silencing during iXCI in vole Microtus levis. We performed locus-specific activation of Xist transcription on the only active X chromosome using the dCas9-SAM system in XO vole trophoblast stem cells (TSCs), which allow modeling iXCI events to some extent. The artificially activated endogenous vole Xist transcript is truncated and restricted ~ 6.6 kb of the exon 1. Ectopic Xist RNA accumulates on the X chromosome and recruits Xist-dependent modifications during TSC differentiation, yet is incapable by itself repressing X-linked genes. Transcriptional silencing occurs upon ectopic Xist upregulation only when repressive marks spread from the massive telomeric constitutive heterochromatin to the X chromosome region containing genes. We hypothesize that the Xist RNA-induced propagation of repressive marks from the constitutive heterochromatin could be a mechanism involved in X chromosome inactivation.
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Affiliation(s)
- Alexander I Shevchenko
- Federal Research Center, "Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences", Novosibirsk, 630090, Russia.,Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.,E.N. Meshalkin National Medical Research Center, Ministry of Health Care of Russian Federation, Novosibirsk, 630055, Russia
| | - Nikita A Rifel
- Federal Research Center, "Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences", Novosibirsk, 630090, Russia
| | - Suren M Zakian
- Federal Research Center, "Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences", Novosibirsk, 630090, Russia.,Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.,E.N. Meshalkin National Medical Research Center, Ministry of Health Care of Russian Federation, Novosibirsk, 630055, Russia
| | - Irina S Zakharova
- Federal Research Center, "Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences", Novosibirsk, 630090, Russia. .,Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia. .,E.N. Meshalkin National Medical Research Center, Ministry of Health Care of Russian Federation, Novosibirsk, 630055, Russia.
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31
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Paloviita P, Vuoristo S. The non-coding genome in early human development - Recent advancements. Semin Cell Dev Biol 2022; 131:4-13. [PMID: 35177347 DOI: 10.1016/j.semcdb.2022.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/08/2022] [Accepted: 02/08/2022] [Indexed: 12/14/2022]
Abstract
Not that long ago, the human genome was discovered to be mainly non-coding, that is comprised of DNA sequences that do not code for proteins. The initial paradigm that non-coding is also non-functional was soon overturned and today the work to uncover the functions of non-coding DNA and RNA in human early embryogenesis has commenced. Early human development is characterized by large-scale changes in genomic activity and the transcriptome that are partly driven by the coordinated activation and repression of repetitive DNA elements scattered across the genome. Here we provide examples of recent novel discoveries of non-coding DNA and RNA interactions and mechanisms that ensure accurate non-coding activity during human maternal-to-zygotic transition and lineage segregation. These include studies on small and long non-coding RNAs, transposable element regulation, and RNA tailing in human oocytes and early embryos. High-throughput approaches to dissect the non-coding regulatory networks governing early human development are a foundation for functional studies of specific genomic elements and molecules that has only begun and will provide a wider understanding of early human embryogenesis and causes of infertility.
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Affiliation(s)
- Pauliina Paloviita
- Department of Obstetrics and Gynaecology, University of Helsinki, 00014 Helsinki, Finland
| | - Sanna Vuoristo
- Department of Obstetrics and Gynaecology, University of Helsinki, 00014 Helsinki, Finland.
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32
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Li G, Duan JE. Dosage compensation: A new player in X chromosome upregulation. Curr Biol 2022; 32:R1030-R1032. [PMID: 36283351 DOI: 10.1016/j.cub.2022.09.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Dosage balance between sex chromosomes and autosomes can be achieved through diverse mechanisms across vertebrates and invertebrates. A new study discovers a key player that contributes to X chromosome upregulation (XCU) during early mouse development and associates the dysregulation of XCU with human bile duct cancer pathogenesis.
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Affiliation(s)
- Guangsheng Li
- Department of Animal Science, Cornell University, Ithaca, NY 14850, USA
| | - Jingyue Ellie Duan
- Department of Animal Science, Cornell University, Ithaca, NY 14850, USA.
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33
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Bouchereau W, Jouneau L, Archilla C, Aksoy I, Moulin A, Daniel N, Peynot N, Calderari S, Joly T, Godet M, Jaszczyszyn Y, Pratlong M, Severac D, Savatier P, Duranthon V, Afanassieff M, Beaujean N. Major transcriptomic, epigenetic and metabolic changes underlie the pluripotency continuum in rabbit preimplantation embryos. Development 2022; 149:276385. [DOI: 10.1242/dev.200538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 08/11/2022] [Indexed: 11/20/2022]
Abstract
ABSTRACT
Despite the growing interest in the rabbit model for developmental and stem cell biology, the characterization of embryos at the molecular level is still poorly documented. We conducted a transcriptome analysis of rabbit preimplantation embryos from E2.7 (morula stage) to E6.6 (early primitive streak stage) using bulk and single-cell RNA-sequencing. In parallel, we studied oxidative phosphorylation and glycolysis, and analysed active and repressive epigenetic modifications during blastocyst formation and expansion. We generated a transcriptomic, epigenetic and metabolic map of the pluripotency continuum in rabbit preimplantation embryos, and identified novel markers of naive pluripotency that might be instrumental for deriving naive pluripotent stem cell lines. Although the rabbit is evolutionarily closer to mice than to primates, we found that the transcriptome of rabbit epiblast cells shares common features with those of humans and non-human primates.
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Affiliation(s)
- Wilhelm Bouchereau
- Université Lyon 1, INSERM, Stem Cell and Brain Research Institute U1208, INRAE USC 1361 1 , F-69500 Bron , France
| | - Luc Jouneau
- Université Paris-Saclay, UVSQ, INRAE, BREED 2 , 78350 Jouy-en-Josas , France
- Ecole Nationale Vétérinaire d'Alfort, BREED 3 , 94700 Maisons-Alfort , France
| | - Catherine Archilla
- Université Paris-Saclay, UVSQ, INRAE, BREED 2 , 78350 Jouy-en-Josas , France
- Ecole Nationale Vétérinaire d'Alfort, BREED 3 , 94700 Maisons-Alfort , France
| | - Irène Aksoy
- Université Lyon 1, INSERM, Stem Cell and Brain Research Institute U1208, INRAE USC 1361 1 , F-69500 Bron , France
| | - Anais Moulin
- Université Lyon 1, INSERM, Stem Cell and Brain Research Institute U1208, INRAE USC 1361 1 , F-69500 Bron , France
| | - Nathalie Daniel
- Université Paris-Saclay, UVSQ, INRAE, BREED 2 , 78350 Jouy-en-Josas , France
- Ecole Nationale Vétérinaire d'Alfort, BREED 3 , 94700 Maisons-Alfort , France
| | - Nathalie Peynot
- Université Paris-Saclay, UVSQ, INRAE, BREED 2 , 78350 Jouy-en-Josas , France
- Ecole Nationale Vétérinaire d'Alfort, BREED 3 , 94700 Maisons-Alfort , France
| | - Sophie Calderari
- Université Paris-Saclay, UVSQ, INRAE, BREED 2 , 78350 Jouy-en-Josas , France
- Ecole Nationale Vétérinaire d'Alfort, BREED 3 , 94700 Maisons-Alfort , France
| | - Thierry Joly
- ISARA-Lyon 4 , F-69007 Lyon , France
- VetAgroSup, UPSP ICE 5 , F-69280 Marcy l'Etoile , France
| | - Murielle Godet
- Université Lyon 1, INSERM, Stem Cell and Brain Research Institute U1208, INRAE USC 1361 1 , F-69500 Bron , France
| | - Yan Jaszczyszyn
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC) 6 , 91198 Gif-sur-Yvette , France
| | - Marine Pratlong
- MGX, Université Montpellier, CNRS, INSERM 7 , 34094 Montpellier , France
| | - Dany Severac
- MGX, Université Montpellier, CNRS, INSERM 7 , 34094 Montpellier , France
| | - Pierre Savatier
- Université Lyon 1, INSERM, Stem Cell and Brain Research Institute U1208, INRAE USC 1361 1 , F-69500 Bron , France
| | - Véronique Duranthon
- Université Paris-Saclay, UVSQ, INRAE, BREED 2 , 78350 Jouy-en-Josas , France
- Ecole Nationale Vétérinaire d'Alfort, BREED 3 , 94700 Maisons-Alfort , France
| | - Marielle Afanassieff
- Université Lyon 1, INSERM, Stem Cell and Brain Research Institute U1208, INRAE USC 1361 1 , F-69500 Bron , France
| | - Nathalie Beaujean
- Université Lyon 1, INSERM, Stem Cell and Brain Research Institute U1208, INRAE USC 1361 1 , F-69500 Bron , France
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34
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Ma Z, Wang Y, Quan Y, Wang Z, Liu Y, Ding Z. Maternal obesity alters methylation level of cytosine in CpG island for epigenetic inheritance in fetal umbilical cord blood. Hum Genomics 2022; 16:34. [PMID: 36045397 PMCID: PMC9429776 DOI: 10.1186/s40246-022-00410-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 08/22/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Over the past few decades, global maternal obesity prevalence has rapidly increased. This condition may induce long-lasting pathophysiological effects on either fetal or infant health that could be attributable to unknown unique changes in the umbilical blood composition. METHODS A total of 34 overweight/obese and 32 normal-weight pregnant women were recruited. Fifteen umbilical blood samples including 8 overweight/obese subjects and 7 normal weight women were sequenced using Targeted Bisulfite Sequencing technology to detect the average methylation level of cytosine and identify the differentially methylated region (DMR). GO and KEGG analyses were then employed to perform pathway enrichment analysis of DMR-related genes and promoters. Moreover, the mRNA levels of methylation-related genes histone deacetylases (HDACs) and DNA methyltransferases (DNMTs) were characterized in the samples obtained from these two groups. RESULTS Average methylated cytosine levels in both the CpG islands (CGI) and promoter significantly decreased in overweight/obese groups. A total of 1669 DMRs exhibited differences in their DNA methylation status between the overweight/obese and control groups. GO and KEGG analyses revealed that DMR-related genes and promoters were enriched in the metabolism, cancer and cardiomyopathy signaling pathways. Furthermore, the HDACs and DNMTs mRNA levels trended to decline in overweight/obese groups. CONCLUSIONS Decreased methylated cytosine levels in overweight/obese women induce the gene expression activity at a higher level than in the control group. DMRs between these two groups in the fetal blood may contribute to the changes in gene transcription that underlie the increased risk of metabolic disorders, cancers and cardiomyopathy in their offspring.
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Affiliation(s)
- Zhuoyao Ma
- Department of Histology, Embryology, Genetics and Developmental Biology, Shanghai Key Laboratory for Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, No.280, Chongqing Road (South), Shanghai, 200025, China
| | - Yingjin Wang
- Department of Obstetrics and Gynecology, Shanghai Eighth People's Hospital, Shanghai, 200235, China
| | - Yanmei Quan
- Department of Histology, Embryology, Genetics and Developmental Biology, Shanghai Key Laboratory for Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, No.280, Chongqing Road (South), Shanghai, 200025, China
| | - Zhijie Wang
- Department of Obstetrics and Gynecology, Shanghai Eighth People's Hospital, Shanghai, 200235, China.
| | - Yue Liu
- Department of Histology, Embryology, Genetics and Developmental Biology, Shanghai Key Laboratory for Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, No.280, Chongqing Road (South), Shanghai, 200025, China.
| | - Zhide Ding
- Department of Histology, Embryology, Genetics and Developmental Biology, Shanghai Key Laboratory for Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, No.280, Chongqing Road (South), Shanghai, 200025, China.
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35
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Mu J, Zhou Z, Sang Q, Wang L. The physiological and pathological mechanisms of early embryonic development. FUNDAMENTAL RESEARCH 2022. [DOI: 10.1016/j.fmre.2022.08.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022] Open
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36
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Wanigasuriya I, Kinkel SA, Beck T, Roper EA, Breslin K, Lee HJ, Keniry A, Ritchie ME, Blewitt ME, Gouil Q. Maternal SMCHD1 controls both imprinted Xist expression and imprinted X chromosome inactivation. Epigenetics Chromatin 2022; 15:26. [PMID: 35843975 PMCID: PMC9290310 DOI: 10.1186/s13072-022-00458-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 06/21/2022] [Indexed: 12/13/2022] Open
Abstract
Embryonic development is dependent on the maternal supply of proteins through the oocyte, including factors setting up the adequate epigenetic patterning of the zygotic genome. We previously reported that one such factor is the epigenetic repressor SMCHD1, whose maternal supply controls autosomal imprinted expression in mouse preimplantation embryos and mid-gestation placenta. In mouse preimplantation embryos, X chromosome inactivation is also an imprinted process. Combining genomics and imaging, we show that maternal SMCHD1 is required not only for the imprinted expression of Xist in preimplantation embryos, but also for the efficient silencing of the inactive X in both the preimplantation embryo and mid-gestation placenta. These results expand the role of SMCHD1 in enforcing the silencing of Polycomb targets. The inability of zygotic SMCHD1 to fully restore imprinted X inactivation further points to maternal SMCHD1’s role in setting up the appropriate chromatin environment during preimplantation development, a critical window of epigenetic remodelling.
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Affiliation(s)
- Iromi Wanigasuriya
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,The Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Sarah A Kinkel
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,The Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Tamara Beck
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,The Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Ellise A Roper
- The School of Biomedical Sciences and Pharmacy, The University of Newcastle, Newcastle, Australia
| | - Kelsey Breslin
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,The Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Heather J Lee
- The School of Biomedical Sciences and Pharmacy, The University of Newcastle, Newcastle, Australia
| | - Andrew Keniry
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,The Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Matthew E Ritchie
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,The Department of Medical Biology, The University of Melbourne, Parkville, Australia.,The Department of Mathematics and Statistics, The University of Melbourne, Parkville, Australia
| | - Marnie E Blewitt
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia. .,The Department of Medical Biology, The University of Melbourne, Parkville, Australia.
| | - Quentin Gouil
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia. .,The Department of Medical Biology, The University of Melbourne, Parkville, Australia.
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37
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Glanzner WG, de Macedo MP, Gutierrez K, Bordignon V. Enhancement of Chromatin and Epigenetic Reprogramming in Porcine SCNT Embryos—Progresses and Perspectives. Front Cell Dev Biol 2022; 10:940197. [PMID: 35898400 PMCID: PMC9309298 DOI: 10.3389/fcell.2022.940197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 06/20/2022] [Indexed: 12/12/2022] Open
Abstract
Over the last 25 years, cloned animals have been produced by transferring somatic cell nuclei into enucleated oocytes (SCNT) in more than 20 mammalian species. Among domestic animals, pigs are likely the leading species in the number of clones produced by SCNT. The greater interest in pig cloning has two main reasons, its relevance for food production and as its use as a suitable model in biomedical applications. Recognized progress in animal cloning has been attained over time, but the overall efficiency of SCNT in pigs remains very low, based on the rate of healthy, live born piglets following embryo transfer. Accumulating evidence from studies in mice and other species indicate that new strategies for promoting chromatin and epigenetic reprogramming may represent the beginning of a new era for pig cloning.
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38
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Chlamydas S, Markouli M, Strepkos D, Piperi C. Epigenetic mechanisms regulate sex-specific bias in disease manifestations. J Mol Med (Berl) 2022; 100:1111-1123. [PMID: 35764820 PMCID: PMC9244100 DOI: 10.1007/s00109-022-02227-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/02/2022] [Accepted: 06/20/2022] [Indexed: 12/15/2022]
Abstract
Abstract Sex presents a vital determinant of a person’s physiology, anatomy, and development. Recent clinical studies indicate that sex is also involved in the differential manifestation of various diseases, affecting both clinical outcome as well as response to therapy. Genetic and epigenetic changes are implicated in sex bias and regulate disease onset, including the inactivation of the X chromosome as well as sex chromosome aneuploidy. The differential expression of X-linked genes, along with the presence of sex-specific hormones, exhibits a significant impact on immune system function. Several studies have revealed differences between the two sexes in response to infections, including respiratory diseases and COVID-19 infection, autoimmune disorders, liver fibrosis, neuropsychiatric diseases, and cancer susceptibility, which can be explained by sex-biased immune responses. In the present review, we explore the input of genetic and epigenetic interplay in the sex bias underlying disease manifestation and discuss their effects along with sex hormones on disease development and progression, aiming to reveal potential new therapeutic targets. Key messages Sex is involved in the differential manifestation of various diseases. Epigenetic modifications influence X-linked gene expression, affecting immune response to infections, including COVID-19. Epigenetic mechanisms are responsible for the sex bias observed in several respiratory and autoimmune disorders, liver fibrosis, neuropsychiatric diseases, and cancer.
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Affiliation(s)
- Sarantis Chlamydas
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 75 M. Asias Street Bldg 16, 11527, Athens, Greece.,Olink Proteomics, Uppsala, Sweden
| | - Mariam Markouli
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 75 M. Asias Street Bldg 16, 11527, Athens, Greece
| | - Dimitrios Strepkos
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 75 M. Asias Street Bldg 16, 11527, Athens, Greece
| | - Christina Piperi
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 75 M. Asias Street Bldg 16, 11527, Athens, Greece.
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39
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A lifelong duty: how Xist maintains the inactive X chromosome. Curr Opin Genet Dev 2022; 75:101927. [PMID: 35717799 PMCID: PMC9472561 DOI: 10.1016/j.gde.2022.101927] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 05/10/2022] [Accepted: 05/14/2022] [Indexed: 11/22/2022]
Abstract
Female eutherians transcriptionally silence one X chromosome to balance gene dosage between the sexes. X-chromosome inactivation (XCI) is initiated by the lncRNA Xist, which assembles many proteins within the inactive X chromosome (Xi) to trigger gene silencing and heterochromatin formation. It is well established that gene silencing on the Xi is maintained through repressive epigenetic processes, including histone deacetylation and DNA methylation. Recent studies revealed a new mechanism where RNA-binding proteins that interact directly with the RNA contribute to the maintenance of Xist localization and gene silencing. In addition, a surprising plasticity of the Xi was uncovered with many genes becoming upregulated upon experimental deletion of Xist. Intriguingly, immune cells normally lose Xist from the Xi, suggesting that thisXist dependence is utilized in vivo to dynamically regulate gene expression from the Xi. These new studies expose fundamental regulatory mechanisms for the chromatin association of RNAs, highlight the need for studying the maintenance of XCI and Xist localization in a gene- and cell-type-specific manner, and are likely to have clinical impact.
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40
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Cloutier M, Kumar S, Buttigieg E, Keller L, Lee B, Williams A, Mojica-Perez S, Erliandri I, Rocha AMD, Cadigan K, Smith GD, Kalantry S. Preventing erosion of X-chromosome inactivation in human embryonic stem cells. Nat Commun 2022; 13:2516. [PMID: 35523820 PMCID: PMC9076865 DOI: 10.1038/s41467-022-30259-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 04/11/2022] [Indexed: 12/12/2022] Open
Abstract
X-chromosome inactivation is a paradigm of epigenetic transcriptional regulation. Female human embryonic stem cells (hESCs) often undergo erosion of X-inactivation upon prolonged culture. Here, we investigate the sources of X-inactivation instability by deriving new primed pluripotent hESC lines. We find that culture media composition dramatically influenced the expression of XIST lncRNA, a key regulator of X-inactivation. hESCs cultured in a defined xenofree medium stably maintained XIST RNA expression and coating, whereas hESCs cultured in the widely used mTeSR1 medium lost XIST RNA expression. We pinpointed lithium chloride in mTeSR1 as a cause of XIST RNA loss. The addition of lithium chloride or inhibitors of GSK-3 proteins that are targeted by lithium to the defined hESC culture medium impeded XIST RNA expression. GSK-3 inhibition in differentiating female mouse embryonic stem cells and epiblast stem cells also resulted in a loss of XIST RNA expression. Together, these data may reconcile observed variations in X-inactivation in hESCs and inform the faithful culture of pluripotent stem cells.
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Affiliation(s)
- Marissa Cloutier
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Surinder Kumar
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Emily Buttigieg
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Laura Keller
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Obstetrics & Gynecology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Brandon Lee
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Aaron Williams
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Sandra Mojica-Perez
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Obstetrics & Gynecology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Indri Erliandri
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Obstetrics & Gynecology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Andre Monteiro Da Rocha
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Obstetrics & Gynecology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Internal Medicine & Cardiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Kenneth Cadigan
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Gary D Smith
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Obstetrics & Gynecology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Sundeep Kalantry
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
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41
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Matoba S, Kozuka C, Miura K, Inoue K, Kumon M, Hayashi R, Ohhata T, Ogura A, Inoue A. Noncanonical imprinting sustains embryonic development and restrains placental overgrowth. Genes Dev 2022; 36:483-494. [PMID: 35483741 PMCID: PMC9067403 DOI: 10.1101/gad.349390.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 04/08/2022] [Indexed: 01/23/2023]
Abstract
In this study, Matoba et al. use a combinatorial maternal KO of Xist, a noncanonical imprinted gene whose LOI causes aberrant transient maternal X-chromosome inactivation (XCI) at preimplantation, and show that prevention of the transient maternal XCI greatly restores the development of Eed matKO embryos. Their findings provide evidence that Xist imprinting sustains embryonic development and that autosomal noncanonical imprinting restrains placental overgrowth. Genomic imprinting regulates parental origin-dependent monoallelic gene expression. It is mediated by either germline differential methylation of DNA (canonical imprinting) or oocyte-derived H3K27me3 (noncanonical imprinting) in mice. Depletion of Eed, an essential component of Polycomb repressive complex 2, results in genome-wide loss of H3K27me3 in oocytes, which causes loss of noncanonical imprinting (LOI) in embryos. Although Eed maternal KO (matKO) embryos show partial lethality after implantation, it is unknown whether LOI itself contributes to the developmental phenotypes of these embryos, which makes it unclear whether noncanonical imprinting is developmentally relevant. Here, by combinatorial matKO of Xist, a noncanonical imprinted gene whose LOI causes aberrant transient maternal X-chromosome inactivation (XCI) at preimplantation, we show that prevention of the transient maternal XCI greatly restores the development of Eed matKO embryos. Moreover, we found that the placentae of Eed matKO embryos are remarkably enlarged in a manner independent of Xist LOI. Heterozygous deletion screening of individual autosomal noncanonical imprinted genes suggests that LOI of the Sfmbt2 miRNA cluster chromosome 2 miRNA cluster (C2MC), solute carrier family 38 member 4 (Slc38a4), and Gm32885 contributes to the placental enlargement. Taken together, our study provides evidence that Xist imprinting sustains embryonic development and that autosomal noncanonical imprinting restrains placental overgrowth.
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Affiliation(s)
- Shogo Matoba
- Bioresource Engineering Division, RIKEN Bioresource Research Center, Tsukuba 305-0074, Japan.,Cooperative Division of Veterinary Sciences, Tokyo University of Agriculture and Technology, Fuchu 183-8509, Japan
| | - Chisayo Kozuka
- Young Chief Investigator (YCI) Laboratory for Metabolic Epigenetics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Kento Miura
- Bioresource Engineering Division, RIKEN Bioresource Research Center, Tsukuba 305-0074, Japan.,Department of Disease Model, Research Institute of Radiation Biology and Medicine, Hiroshima University, Hiroshima 734-8553, Japan
| | - Kimiko Inoue
- Bioresource Engineering Division, RIKEN Bioresource Research Center, Tsukuba 305-0074, Japan.,Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan
| | - Mami Kumon
- Young Chief Investigator (YCI) Laboratory for Metabolic Epigenetics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Ryoya Hayashi
- Young Chief Investigator (YCI) Laboratory for Metabolic Epigenetics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Tokyo Metropolitan University, Hachioji 192-0397, Japan
| | - Tatsuya Ohhata
- Department of Molecular Biology, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan
| | - Atsuo Ogura
- Bioresource Engineering Division, RIKEN Bioresource Research Center, Tsukuba 305-0074, Japan.,Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan.,The Center for Disease Biology and Integrative Medicine, Faculty of Medicine, University of Tokyo, Tokyo 113-0033, Japan.,RIKEN Cluster for Pioneering Research, Wako 351-0198, Japan
| | - Azusa Inoue
- Young Chief Investigator (YCI) Laboratory for Metabolic Epigenetics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Tokyo Metropolitan University, Hachioji 192-0397, Japan
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42
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Li J, Ming Z, Yang L, Wang T, Liu G, Ma Q. Long noncoding RNA XIST: Mechanisms for X chromosome inactivation, roles in sex-biased diseases, and therapeutic opportunities. Genes Dis 2022; 9:1478-1492. [PMID: 36157489 PMCID: PMC9485286 DOI: 10.1016/j.gendis.2022.04.007] [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: 02/21/2022] [Revised: 04/16/2022] [Accepted: 04/18/2022] [Indexed: 11/30/2022] Open
Abstract
Sexual dimorphism has been reported in various human diseases including autoimmune diseases, neurological diseases, pulmonary arterial hypertension, and some types of cancers, although the underlying mechanisms remain poorly understood. The long noncoding RNA (lncRNA) X-inactive specific transcript (XIST) is involved in X chromosome inactivation (XCI) in female placental mammals, a process that ensures the balanced expression dosage of X-linked genes between sexes. XIST is abnormally expressed in many sex-biased diseases. In addition, escape from XIST-mediated XCI and skewed XCI also contribute to sex-biased diseases. Therefore, its expression or modification can be regarded as a biomarker for the diagnosis and prognosis of many sex-biased diseases. Genetic manipulation of XIST expression can inhibit the progression of some of these diseases in animal models, and therefore XIST has been proposed as a potential therapeutic target. In this manuscript, we summarize the current knowledge about the mechanisms for XIST-mediated XCI and the roles of XIST in sex-biased diseases, and discuss potential therapeutic strategies targeting XIST.
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43
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Mechanisms of Choice in X-Chromosome Inactivation. Cells 2022; 11:cells11030535. [PMID: 35159344 PMCID: PMC8833938 DOI: 10.3390/cells11030535] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/30/2022] [Accepted: 01/31/2022] [Indexed: 12/04/2022] Open
Abstract
Early in development, placental and marsupial mammals harbouring at least two X chromosomes per nucleus are faced with a choice that affects the rest of their lives: which of those X chromosomes to transcriptionally inactivate. This choice underlies phenotypical diversity in the composition of tissues and organs and in their response to the environment, and can determine whether an individual will be healthy or affected by an X-linked disease. Here, we review our current understanding of the process of choice during X-chromosome inactivation and its implications, focusing on the strategies evolved by different mammalian lineages and on the known and unknown molecular mechanisms and players involved.
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44
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Gene regulation in time and space during X-chromosome inactivation. Nat Rev Mol Cell Biol 2022; 23:231-249. [PMID: 35013589 DOI: 10.1038/s41580-021-00438-7] [Citation(s) in RCA: 65] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2021] [Indexed: 12/21/2022]
Abstract
X-chromosome inactivation (XCI) is the epigenetic mechanism that ensures X-linked dosage compensation between cells of females (XX karyotype) and males (XY). XCI is essential for female embryos to survive through development and requires the accurate spatiotemporal regulation of many different factors to achieve remarkable chromosome-wide gene silencing. As a result of XCI, the active and inactive X chromosomes are functionally and structurally different, with the inactive X chromosome undergoing a major conformational reorganization within the nucleus. In this Review, we discuss the multiple layers of genetic and epigenetic regulation that underlie initiation of XCI during development and then maintain it throughout life, in light of the most recent findings in this rapidly advancing field. We discuss exciting new insights into the regulation of X inactive-specific transcript (XIST), the trigger and master regulator of XCI, and into the mechanisms and dynamics that underlie the silencing of nearly all X-linked genes. Finally, given the increasing interest in understanding the impact of chromosome organization on gene regulation, we provide an overview of the factors that are thought to reshape the 3D structure of the inactive X chromosome and of the relevance of such structural changes for XCI establishment and maintenance.
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45
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Mahadik K, Rougeulle C. Study of X Chromosome Activity Status in Human Naive Pluripotent Stem Cells Using RNA-FISH. Methods Mol Biol 2022; 2416:239-255. [PMID: 34870840 DOI: 10.1007/978-1-0716-1908-7_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
X chromosome activity is a defining attribute of naive pluripotency, with naive pluripotency being a rare context in which both X chromosomes of females are active. RNA-fluorescence in situ hybridization (RNA-FISH) is a powerful tool to determine the transcriptional status of specific genes with allelic and single-cell resolution and has been widely used in the context of X chromosome inactivation, the process ensuring dosage compensation for X-linked genes between sexes in mammals. RNA-FISH using genomic or intronic probes allows the detection of newly synthesized transcripts at the site of transcription. This technique is invaluable for appreciating the putative heterogeneity in the expression profiles within cell populations. RNA-FISH has the added advantage of allowing the visualization of gene transcription in a spatial perspective. Here, we provide a detailed protocol describing the application of RNA-FISH to detect nascent X-linked transcripts in female naive human embryonic stem cells to assess their X chromosome status, along with another complementary technique, DNA-FISH.
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Affiliation(s)
- Kasturi Mahadik
- Université de Paris, Epigenetics and Cell Fate, CNRS, F-75006, Paris, France
| | - Claire Rougeulle
- Université de Paris, Epigenetics and Cell Fate, CNRS, F-75006, Paris, France.
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46
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Schall PZ, Latham KE. Cross-species meta-analysis of transcriptome changes during the morula-to-blastocyst transition: metabolic and physiological changes take center stage. Am J Physiol Cell Physiol 2021; 321:C913-C931. [PMID: 34669511 DOI: 10.1152/ajpcell.00318.2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The morula-to-blastocyst transition (MBT) culminates with formation of inner cell mass (ICM) and trophectoderm (TE) lineages. Recent studies identified signaling pathways driving lineage specification, but some features of these pathways display significant species divergence. To better understand evolutionary conservation of the MBT, we completed a meta-analysis of RNA sequencing data from five model species and ICMTE differences from four species. Although many genes change in expression during the MBT within any given species, the number of shared differentially expressed genes (DEGs) is comparatively small, and the number of shared ICMTE DEGs is even smaller. DEGs related to known lineage determining pathways (e.g., POU5F1) are seen, but the most prominent pathways and functions associated with shared DEGs or shared across individual species DEG lists impact basic physiological and metabolic activities, such as TCA cycle, unfolded protein response, oxidative phosphorylation, sirtuin signaling, mitotic roles of polo-like kinases, NRF2-mediated oxidative stress, estrogen receptor signaling, apoptosis, necrosis, lipid and fatty acid metabolism, cholesterol biosynthesis, endocytosis, AMPK signaling, homeostasis, transcription, and cell death. We also observed prominent differences in transcriptome regulation between ungulates and nonungulates, particularly for ICM- and TE-enhanced mRNAs. These results extend our understanding of shared mechanisms of the MBT and formation of the ICM and TE and should better inform the selection of model species for particular applications.
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Affiliation(s)
- Peter Z Schall
- Department of Animal Science, Michigan State University, East Lansing, Michigan.,Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan.,Comparative Medicine and Integrative Biology Program, Michigan State University, East Lansing, Michigan
| | - Keith E Latham
- Department of Animal Science, Michigan State University, East Lansing, Michigan.,Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan.,Department of Obstetrics, Gynecology, & Reproductive Biology, Michigan State University, East Lansing, Michigan
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Abstract
[Figure: see text].
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Affiliation(s)
- Edith Heard
- Director's Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Claire Rougeulle
- Department of Epigenetics and Cell Fate, Université de Paris, CNRS, F-75006 Paris, France
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48
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Okamoto I, Nakamura T, Sasaki K, Yabuta Y, Iwatani C, Tsuchiya H, Nakamura SI, Ema M, Yamamoto T, Saitou M. The X chromosome dosage compensation program during the development of cynomolgus monkeys. Science 2021; 374:eabd8887. [PMID: 34793202 DOI: 10.1126/science.abd8887] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Ikuhiro Okamoto
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Tomonori Nakamura
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Hakubi Center for Advanced Research, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kotaro Sasaki
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yukihiro Yabuta
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Chizuru Iwatani
- Research Center for Animal Life Science, Shiga University of Medical Science, Seta-Tsukinowa-cho, Otsu, Shiga 520-2192, Japan
| | - Hideaki Tsuchiya
- Research Center for Animal Life Science, Shiga University of Medical Science, Seta-Tsukinowa-cho, Otsu, Shiga 520-2192, Japan
| | - Shin-Ichiro Nakamura
- Research Center for Animal Life Science, Shiga University of Medical Science, Seta-Tsukinowa-cho, Otsu, Shiga 520-2192, Japan
| | - Masatsugu Ema
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Research Center for Animal Life Science, Shiga University of Medical Science, Seta-Tsukinowa-cho, Otsu, Shiga 520-2192, Japan
| | - Takuya Yamamoto
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan.,AMED-CREST, AMED, 1-7-1 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan.,Medical-Risk Avoidance Based on iPS Cells Team, RIKEN Center for Advanced Intelligence Project (AIP), Kyoto 606-8507, Japan
| | - Mitinori Saitou
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
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49
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Talon I, Janiszewski A, Theeuwes B, Lefevre T, Song J, Bervoets G, Vanheer L, De Geest N, Poovathingal S, Allsop R, Marine JC, Rambow F, Voet T, Pasque V. Enhanced chromatin accessibility contributes to X chromosome dosage compensation in mammals. Genome Biol 2021; 22:302. [PMID: 34724962 PMCID: PMC8558763 DOI: 10.1186/s13059-021-02518-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 10/13/2021] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Precise gene dosage of the X chromosomes is critical for normal development and cellular function. In mice, XX female somatic cells show transcriptional X chromosome upregulation of their single active X chromosome, while the other X chromosome is inactive. Moreover, the inactive X chromosome is reactivated during development in the inner cell mass and in germ cells through X chromosome reactivation, which can be studied in vitro by reprogramming of somatic cells to pluripotency. How chromatin processes and gene regulatory networks evolved to regulate X chromosome dosage in the somatic state and during X chromosome reactivation remains unclear. RESULTS Using genome-wide approaches, allele-specific ATAC-seq and single-cell RNA-seq, in female embryonic fibroblasts and during reprogramming to pluripotency, we show that chromatin accessibility on the upregulated mammalian active X chromosome is increased compared to autosomes. We further show that increased accessibility on the active X chromosome is erased by reprogramming, accompanied by erasure of transcriptional X chromosome upregulation and the loss of increased transcriptional burst frequency. In addition, we characterize gene regulatory networks during reprogramming and X chromosome reactivation, revealing changes in regulatory states. Our data show that ZFP42/REX1, a pluripotency-associated gene that evolved specifically in placental mammals, targets multiple X-linked genes, suggesting an evolutionary link between ZFP42/REX1, X chromosome reactivation, and pluripotency. CONCLUSIONS Our data reveal the existence of intrinsic compensatory mechanisms that involve modulation of chromatin accessibility to counteract X-to-Autosome gene dosage imbalances caused by evolutionary or in vitro X chromosome loss and X chromosome inactivation in mammalian cells.
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Affiliation(s)
- Irene Talon
- Department of Development and Regeneration, Laboratory of Cellular Reprogramming and Epigenetic Regulation, KU Leuven – University of Leuven, Herestraat 49, 3000 Leuven, Belgium
- KU Leuven Institute for Single Cell Omics (LISCO), 3000 Leuven, Belgium
- Leuven Stem Cell Institute (SCIL), 3000 Leuven, Belgium
| | - Adrian Janiszewski
- Department of Development and Regeneration, Laboratory of Cellular Reprogramming and Epigenetic Regulation, KU Leuven – University of Leuven, Herestraat 49, 3000 Leuven, Belgium
- KU Leuven Institute for Single Cell Omics (LISCO), 3000 Leuven, Belgium
- Leuven Stem Cell Institute (SCIL), 3000 Leuven, Belgium
| | - Bart Theeuwes
- Department of Development and Regeneration, Laboratory of Cellular Reprogramming and Epigenetic Regulation, KU Leuven – University of Leuven, Herestraat 49, 3000 Leuven, Belgium
- Leuven Stem Cell Institute (SCIL), 3000 Leuven, Belgium
| | - Thomas Lefevre
- Laboratory of Reproductive Genomics, Centre for Human Genetics, KU Leuven, 3000 Leuven, Belgium
| | - Juan Song
- Department of Development and Regeneration, Laboratory of Cellular Reprogramming and Epigenetic Regulation, KU Leuven – University of Leuven, Herestraat 49, 3000 Leuven, Belgium
- Leuven Stem Cell Institute (SCIL), 3000 Leuven, Belgium
| | - Greet Bervoets
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, VIB, 3000 Leuven, Belgium
- Department of Oncology, Laboratory for Molecular Cancer Biology, KU Leuven, 3000 Leuven, Belgium
| | - Lotte Vanheer
- Department of Development and Regeneration, Laboratory of Cellular Reprogramming and Epigenetic Regulation, KU Leuven – University of Leuven, Herestraat 49, 3000 Leuven, Belgium
- KU Leuven Institute for Single Cell Omics (LISCO), 3000 Leuven, Belgium
- Leuven Stem Cell Institute (SCIL), 3000 Leuven, Belgium
| | - Natalie De Geest
- Department of Development and Regeneration, Laboratory of Cellular Reprogramming and Epigenetic Regulation, KU Leuven – University of Leuven, Herestraat 49, 3000 Leuven, Belgium
- Leuven Stem Cell Institute (SCIL), 3000 Leuven, Belgium
| | - Suresh Poovathingal
- KU Leuven Institute for Single Cell Omics (LISCO), 3000 Leuven, Belgium
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium
| | - Ryan Allsop
- Department of Development and Regeneration, Laboratory of Cellular Reprogramming and Epigenetic Regulation, KU Leuven – University of Leuven, Herestraat 49, 3000 Leuven, Belgium
- KU Leuven Institute for Single Cell Omics (LISCO), 3000 Leuven, Belgium
- Leuven Stem Cell Institute (SCIL), 3000 Leuven, Belgium
| | - Jean-Christophe Marine
- KU Leuven Institute for Single Cell Omics (LISCO), 3000 Leuven, Belgium
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, VIB, 3000 Leuven, Belgium
- Department of Oncology, Laboratory for Molecular Cancer Biology, KU Leuven, 3000 Leuven, Belgium
| | - Florian Rambow
- KU Leuven Institute for Single Cell Omics (LISCO), 3000 Leuven, Belgium
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, VIB, 3000 Leuven, Belgium
| | - Thierry Voet
- KU Leuven Institute for Single Cell Omics (LISCO), 3000 Leuven, Belgium
- Laboratory of Reproductive Genomics, Centre for Human Genetics, KU Leuven, 3000 Leuven, Belgium
| | - Vincent Pasque
- Department of Development and Regeneration, Laboratory of Cellular Reprogramming and Epigenetic Regulation, KU Leuven – University of Leuven, Herestraat 49, 3000 Leuven, Belgium
- KU Leuven Institute for Single Cell Omics (LISCO), 3000 Leuven, Belgium
- Leuven Stem Cell Institute (SCIL), 3000 Leuven, Belgium
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50
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Christians JK. The Placenta's Role in Sexually Dimorphic Fetal Growth Strategies. Reprod Sci 2021; 29:1895-1907. [PMID: 34699045 DOI: 10.1007/s43032-021-00780-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 10/19/2021] [Indexed: 12/27/2022]
Abstract
Fetal sex affects the risk of pregnancy complications and the long-term effects of prenatal environment on health. Some have hypothesized that growth strategies differ between the sexes, whereby males prioritize growth whereas females are more responsive to their environment. This review evaluates the role of the placenta in such strategies, focusing on (1) mechanisms underlying sexual dimorphism in gene expression, (2) the nature and extent of sexual dimorphism in placental gene expression, (3) sexually dimorphic responses to nutrient supply, and (4) sexual dimorphism in morphology and histopathology. The sex chromosomes contribute to sex differences in placental gene expression, and fetal hormones may play a role later in development. Sexually dimorphic placental gene expression may contribute to differences in the prevalence of complications such as preeclampsia, although this link is not clear. Placental responses to nutrient supply frequently show sexual dimorphism, but there is no consistent pattern where one sex is more responsive. There are sex differences in the prevalence of placental histopathologies, and placental changes in pregnancy complications, but also many similarities. Overall, no clear patterns support the hypothesis that females are more responsive to the maternal environment, or that males prioritize growth. While male fetuses are at greater risk of a variety of complications, total prenatal mortality is higher in females, such that males exposed to early insults may be more likely to survive and be observed in studies of adverse outcomes. Going forward, robust statistical approaches to test for sex-dependent effects must be more widely adopted to reduce the incidence of spurious results.
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Affiliation(s)
- Julian K Christians
- Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada. .,Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, BC, Canada. .,British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada. .,Women's Health Research Institute, BC Women's Hospital and Health Centre, Vancouver, BC, Canada.
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