1
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Lerra L, Panatta M, Bär D, Zanini I, Tan JY, Pisano A, Mungo C, Baroux C, Panse VG, Marques AC, Santoro R. An RNA-dependent and phase-separated active subnuclear compartment safeguards repressive chromatin domains. Mol Cell 2024; 84:1667-1683.e10. [PMID: 38599210 PMCID: PMC11065421 DOI: 10.1016/j.molcel.2024.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 10/19/2023] [Accepted: 03/16/2024] [Indexed: 04/12/2024]
Abstract
The nucleus is composed of functionally distinct membraneless compartments that undergo phase separation (PS). However, whether different subnuclear compartments are connected remains elusive. We identified a type of nuclear body with PS features composed of BAZ2A that associates with active chromatin. BAZ2A bodies depend on RNA transcription and BAZ2A non-disordered RNA-binding TAM domain. Although BAZ2A and H3K27me3 occupancies anticorrelate in the linear genome, in the nuclear space, BAZ2A bodies contact H3K27me3 bodies. BAZ2A-body disruption promotes BAZ2A invasion into H3K27me3 domains, causing H3K27me3-body loss and gene upregulation. Weak BAZ2A-RNA interactions, such as with nascent transcripts, promote BAZ2A bodies, whereas the strong binder long non-coding RNA (lncRNA) Malat1 impairs them while mediating BAZ2A association to chromatin at nuclear speckles. In addition to unraveling a direct connection between nuclear active and repressive compartments through PS mechanisms, the results also showed that the strength of RNA-protein interactions regulates this process, contributing to nuclear organization and the regulation of chromatin and gene expression.
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Affiliation(s)
- Luigi Lerra
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, Zurich 8057, Switzerland; RNA Biology Program, Life Science Zurich Graduate School, University of Zurich, Zurich 8057, Switzerland
| | - Martina Panatta
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, Zurich 8057, Switzerland; RNA Biology Program, Life Science Zurich Graduate School, University of Zurich, Zurich 8057, Switzerland
| | - Dominik Bär
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, Zurich 8057, Switzerland
| | - Isabella Zanini
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, Zurich 8057, Switzerland
| | - Jennifer Yihong Tan
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland
| | - Agnese Pisano
- Institute of Medical Microbiology, University of Zurich, Zurich 8057, Switzerland
| | - Chiara Mungo
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, Zurich 8057, Switzerland; Molecular Life Science Program, Life Science Zurich Graduate School, University of Zurich, Zurich 8057, Switzerland
| | - Célia Baroux
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich 8057, Switzerland
| | - Vikram Govind Panse
- Institute of Medical Microbiology, University of Zurich, Zurich 8057, Switzerland
| | - Ana C Marques
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland
| | - Raffaella Santoro
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, Zurich 8057, Switzerland.
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2
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Beaujean N. Defining the chromatin signature of pluripotency. Nat Cell Biol 2024; 26:24-25. [PMID: 38228824 DOI: 10.1038/s41556-023-01268-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Affiliation(s)
- Nathalie Beaujean
- Université Lyon 1, INSERM, Stem Cell and Brain Research Institute U1208, INRAE USC 1361, Bron, France.
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3
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Canat A, Veillet A, Batrin R, Dubourg C, Lhoumaud P, Arnau-Romero P, Greenberg MVC, Bonhomme F, Arimondo PB, Illingworth R, Fabre E, Therizols P. DAXX safeguards heterochromatin formation in embryonic stem cells. J Cell Sci 2023; 136:jcs261092. [PMID: 37655670 DOI: 10.1242/jcs.261092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 08/25/2023] [Indexed: 09/02/2023] Open
Abstract
Genomes comprise a large fraction of repetitive sequences folded into constitutive heterochromatin, which protect genome integrity and cell identity. De novo formation of heterochromatin during preimplantation development is an essential step for preserving the ground-state of pluripotency and the self-renewal capacity of embryonic stem cells (ESCs). However, the molecular mechanisms responsible for the remodeling of constitutive heterochromatin are largely unknown. Here, we identify that DAXX, an H3.3 chaperone essential for the maintenance of mouse ESCs in the ground state, accumulates in pericentromeric regions independently of DNA methylation. DAXX recruits PML and SETDB1 to promote the formation of heterochromatin, forming foci that are hallmarks of ground-state ESCs. In the absence of DAXX or PML, the three-dimensional (3D) architecture and physical properties of pericentric and peripheral heterochromatin are disrupted, resulting in de-repression of major satellite DNA, transposable elements and genes associated with the nuclear lamina. Using epigenome editing tools, we observe that H3.3, and specifically H3.3K9 modification, directly contribute to maintaining pericentromeric chromatin conformation. Altogether, our data reveal that DAXX is crucial for the maintenance and 3D organization of the heterochromatin compartment and protects ESC viability.
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Affiliation(s)
- Antoine Canat
- Université de Paris, Laboratoire Génomes, Biologie Cellulaire et Thérapeutiques, CNRS UMR7212, INSERM U944, Institut de Recherche St Louis, F-75010 Paris, France
| | - Adeline Veillet
- Université de Paris, Laboratoire Génomes, Biologie Cellulaire et Thérapeutiques, CNRS UMR7212, INSERM U944, Institut de Recherche St Louis, F-75010 Paris, France
| | - Renaud Batrin
- Université de Paris, Laboratoire Génomes, Biologie Cellulaire et Thérapeutiques, CNRS UMR7212, INSERM U944, Institut de Recherche St Louis, F-75010 Paris, France
| | - Clara Dubourg
- Université de Paris, Laboratoire Génomes, Biologie Cellulaire et Thérapeutiques, CNRS UMR7212, INSERM U944, Institut de Recherche St Louis, F-75010 Paris, France
| | | | - Pol Arnau-Romero
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | | | - Frédéric Bonhomme
- Institut Pasteur, Université Paris Cité, CNRS, Epigenetic Chemical Biology, UMR 3523, F-75724 Paris, France
| | - Paola B Arimondo
- Institut Pasteur, Université Paris Cité, CNRS, Epigenetic Chemical Biology, UMR 3523, F-75724 Paris, France
| | - Robert Illingworth
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh BioQuarter, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Emmanuelle Fabre
- Université de Paris, Laboratoire Génomes, Biologie Cellulaire et Thérapeutiques, CNRS UMR7212, INSERM U944, Institut de Recherche St Louis, F-75010 Paris, France
| | - Pierre Therizols
- Université de Paris, Laboratoire Génomes, Biologie Cellulaire et Thérapeutiques, CNRS UMR7212, INSERM U944, Institut de Recherche St Louis, F-75010 Paris, France
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4
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Regulation, functions and transmission of bivalent chromatin during mammalian development. Nat Rev Mol Cell Biol 2023; 24:6-26. [PMID: 36028557 DOI: 10.1038/s41580-022-00518-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/05/2022] [Indexed: 12/25/2022]
Abstract
Cells differentiate and progress through development guided by a dynamic chromatin landscape that mediates gene expression programmes. During development, mammalian cells display a paradoxical chromatin state: histone modifications associated with gene activation (trimethylated histone H3 Lys4 (H3K4me3)) and with gene repression (trimethylated H3 Lys27 (H3K27me3)) co-occur at promoters of developmental genes. This bivalent chromatin modification state is thought to poise important regulatory genes for expression or repression during cell-lineage specification. In this Review, we discuss recent work that has expanded our understanding of the molecular basis of bivalent chromatin and its contributions to mammalian development. We describe the factors that establish bivalency, especially histone-lysine N-methyltransferase 2B (KMT2B) and Polycomb repressive complex 2 (PRC2), and consider evidence indicating that PRC1 shapes bivalency and may contribute to its transmission between generations. We posit that bivalency is a key feature of germline and embryonic stem cells, as well as other types of stem and progenitor cells. Finally, we discuss the relevance of bivalent chromtin to human development and cancer, and outline avenues of future research.
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5
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Randall RS, Jourdain C, Nowicka A, Kaduchová K, Kubová M, Ayoub MA, Schubert V, Tatout C, Colas I, Kalyanikrishna, Desset S, Mermet S, Boulaflous-Stevens A, Kubalová I, Mandáková T, Heckmann S, Lysak MA, Panatta M, Santoro R, Schubert D, Pecinka A, Routh D, Baroux C. Image analysis workflows to reveal the spatial organization of cell nuclei and chromosomes. Nucleus 2022; 13:277-299. [PMID: 36447428 PMCID: PMC9754023 DOI: 10.1080/19491034.2022.2144013] [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] [Indexed: 12/03/2022] Open
Abstract
Nucleus, chromatin, and chromosome organization studies heavily rely on fluorescence microscopy imaging to elucidate the distribution and abundance of structural and regulatory components. Three-dimensional (3D) image stacks are a source of quantitative data on signal intensity level and distribution and on the type and shape of distribution patterns in space. Their analysis can lead to novel insights that are otherwise missed in qualitative-only analyses. Quantitative image analysis requires specific software and workflows for image rendering, processing, segmentation, setting measurement points and reference frames and exporting target data before further numerical processing and plotting. These tasks often call for the development of customized computational scripts and require an expertise that is not broadly available to the community of experimental biologists. Yet, the increasing accessibility of high- and super-resolution imaging methods fuels the demand for user-friendly image analysis workflows. Here, we provide a compendium of strategies developed by participants of a training school from the COST action INDEPTH to analyze the spatial distribution of nuclear and chromosomal signals from 3D image stacks, acquired by diffraction-limited confocal microscopy and super-resolution microscopy methods (SIM and STED). While the examples make use of one specific commercial software package, the workflows can easily be adapted to concurrent commercial and open-source software. The aim is to encourage biologists lacking custom-script-based expertise to venture into quantitative image analysis and to better exploit the discovery potential of their images.Abbreviations: 3D FISH: three-dimensional fluorescence in situ hybridization; 3D: three-dimensional; ASY1: ASYNAPTIC 1; CC: chromocenters; CO: Crossover; DAPI: 4',6-diamidino-2-phenylindole; DMC1: DNA MEIOTIC RECOMBINASE 1; DSB: Double-Strand Break; FISH: fluorescence in situ hybridization; GFP: GREEN FLUORESCENT PROTEIN; HEI10: HUMAN ENHANCER OF INVASION 10; NCO: Non-Crossover; NE: Nuclear Envelope; Oligo-FISH: oligonucleotide fluorescence in situ hybridization; RNPII: RNA Polymerase II; SC: Synaptonemal Complex; SIM: structured illumination microscopy; ZMM (ZIP: MSH4: MSH5 and MER3 proteins); ZYP1: ZIPPER-LIKE PROTEIN 1.
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Affiliation(s)
- Ricardo S Randall
- Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | | | - Anna Nowicka
- Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), Institute of Experimental Botany, v. v. i. (IEB), Olomouc, Czech Republic
| | - Kateřina Kaduchová
- Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), Institute of Experimental Botany, v. v. i. (IEB), Olomouc, Czech Republic
| | - Michaela Kubová
- Central European Institute of Technology (CEITEC) and Department of Experimental Biology, Masaryk University, Brno, Czech Republic
| | - Mohammad A. Ayoub
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466Seeland, Germany
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466Seeland, Germany
| | - Christophe Tatout
- Institut Génétique, Reproduction et Développement (GReD), Université Clermont Auvergne, CNRS, INSERM, 63001Clermont-Ferrand, France
| | - Isabelle Colas
- The James Hutton Institute, Errol Road, Invergowrie, DD2 5DA, Scotland UK
| | | | - Sophie Desset
- Institut Génétique, Reproduction et Développement (GReD), Université Clermont Auvergne, CNRS, INSERM, 63001Clermont-Ferrand, France
| | - Sarah Mermet
- Institut Génétique, Reproduction et Développement (GReD), Université Clermont Auvergne, CNRS, INSERM, 63001Clermont-Ferrand, France
| | - Aurélia Boulaflous-Stevens
- Institut Génétique, Reproduction et Développement (GReD), Université Clermont Auvergne, CNRS, INSERM, 63001Clermont-Ferrand, France
| | - Ivona Kubalová
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466Seeland, Germany
| | - Terezie Mandáková
- Central European Institute of Technology (CEITEC) and Department of Experimental Biology, Masaryk University, Brno, Czech Republic
| | - Stefan Heckmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466Seeland, Germany
| | - Martin A. Lysak
- Central European Institute of Technology (CEITEC) and National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
| | - Martina Panatta
- Department of Molecular Mechanisms of Disease, DMMD, University of Zürich, Zürich, Switzerland
| | - Raffaella Santoro
- Department of Molecular Mechanisms of Disease, DMMD, University of Zürich, Zürich, Switzerland
| | | | - Ales Pecinka
- Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), Institute of Experimental Botany, v. v. i. (IEB), Olomouc, Czech Republic
| | - Devin Routh
- Service and Support for Science IT (S3IT), Universität Zürich, Zürich, Switzerland
| | - Célia Baroux
- Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland,CONTACT Célia Baroux Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
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6
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H3K27me3 at pericentromeric heterochromatin is a defining feature of the early mouse blastocyst. Sci Rep 2022; 12:13908. [PMID: 35974030 PMCID: PMC9381757 DOI: 10.1038/s41598-022-17730-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 07/29/2022] [Indexed: 11/09/2022] Open
Abstract
Early mouse development is characterized by structural and epigenetic changes while cells progress towards differentiation. At blastocyst stage, the segregation of the three primordial lineages is accompanied by establishment of differential patterns of DNA methylation and post-translational modifications of histones, such as H3K27me3. Here, we analysed the dynamics of H3K27me3 at pericentromeric heterochromatin (PCH) during early development. We also followed the localization of EZH2 and BEND3, previously shown in ESCs to drive PRC2 to hypomethylated PCH. We show that the location of H3K27me3 at PCH, in addition to H3K9me3, is a defining feature of embryonic cells in vivo. Moreover, it may play an important role in structuring PCH and preserving genomic integrity at a time of globally relaxed chromatin. At peri-implantation stages, while DNA methylation is still low, EZH2 and then H3K27me3, leave PCH in epiblast progenitors at the time of their spatial segregation from primitive endoderm cells, while BEND3 remains there up to implantation. The comparison with stem cells (ESCs and TSCs) reveals that the epigenetic marks (i.e. H3K9me3 and H3K27me3) of PCH are reset during in vitro derivation and only partially restored thereafter. This highlights possible divergences between in vitro and "in embryo" epigenetic regulation regarding constitutive heterochromatin.
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7
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Epigenetics as "conductor" in "orchestra" of pluripotent states. Cell Tissue Res 2022; 390:141-172. [PMID: 35838826 DOI: 10.1007/s00441-022-03667-0] [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: 12/30/2021] [Accepted: 07/01/2022] [Indexed: 11/02/2022]
Abstract
Pluripotent character is described as the potency of cells to differentiate into all three germ layers. The best example to reinstate the term lies in the context of embryonic stem cells (ESCs). Pluripotent ESC describes the in vitro status of those cells that originate during the complex process of embryogenesis. Pre-implantation to post-implantation development of embryo embrace cells with different levels of stemness. Currently, four states of pluripotency have been recognized, in the progressing order of "naïve," "poised," "formative," and "primed." Epigenetics act as the "conductor" in this "orchestra" of transition in pluripotent states. With a distinguishable gene expression profile, these four states associate with different epigenetic signatures, sometimes distinct while otherwise overlapping. The present review focuses on how epigenetic factors, including DNA methylation, bivalent chromatin, chromatin remodelers, chromatin/nuclear architecture, and microRNA, could dictate pluripotent states and their transition among themselves.
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8
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Bernard LD, Dubois A, Heurtier V, Fischer V, Gonzalez I, Chervova A, Tachtsidi A, Gil N, Owens N, Bates L, Vandormael-Pournin S, Silva JCR, Ulitsky I, Cohen-Tannoudji M, Navarro P. OCT4 activates a Suv39h1-repressive antisense lncRNA to couple histone H3 Lysine 9 methylation to pluripotency. Nucleic Acids Res 2022; 50:7367-7379. [PMID: 35762231 PMCID: PMC9303268 DOI: 10.1093/nar/gkac550] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 06/08/2022] [Accepted: 06/24/2022] [Indexed: 12/17/2022] Open
Abstract
Histone H3 Lysine 9 (H3K9) methylation, a characteristic mark of heterochromatin, is progressively implemented during development to contribute to cell fate restriction as differentiation proceeds. Accordingly, in undifferentiated and pluripotent mouse Embryonic Stem (ES) cells the global levels of H3K9 methylation are rather low and increase only upon differentiation. How global H3K9 methylation levels are coupled with the loss of pluripotency remains largely unknown. Here, we identify SUV39H1, a major H3K9 di- and tri-methylase, as an indirect target of the pluripotency network of Transcription Factors (TFs). We find that pluripotency TFs, principally OCT4, activate the expression of Suv39h1as, an antisense long non-coding RNA to Suv39h1. In turn, Suv39h1as downregulates Suv39h1 transcription in cis via a mechanism involving the modulation of the chromatin status of the locus. The targeted deletion of the Suv39h1as promoter region triggers increased SUV39H1 expression and H3K9me2 and H3K9me3 levels, affecting all heterochromatic regions, particularly peri-centromeric major satellites and retrotransposons. This increase in heterochromatinization efficiency leads to accelerated and more efficient commitment into differentiation. We report, therefore, a simple genetic circuitry coupling the genetic control of pluripotency with the global efficiency of H3K9 methylation associated with a major cell fate restriction, the irreversible loss of pluripotency.
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Affiliation(s)
- Laure D Bernard
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit, Department of Developmental and Stem Cell Biology, F-75015 Paris, France
- Sorbonne Université, Collège doctoral, F-75005 Paris, France
| | - Agnès Dubois
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit, Department of Developmental and Stem Cell Biology, F-75015 Paris, France
| | - Victor Heurtier
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit, Department of Developmental and Stem Cell Biology, F-75015 Paris, France
- Sorbonne Université, Collège doctoral, F-75005 Paris, France
| | - Véronique Fischer
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit, Department of Developmental and Stem Cell Biology, F-75015 Paris, France
| | - Inma Gonzalez
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit, Department of Developmental and Stem Cell Biology, F-75015 Paris, France
| | - Almira Chervova
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit, Department of Developmental and Stem Cell Biology, F-75015 Paris, France
| | - Alexandra Tachtsidi
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit, Department of Developmental and Stem Cell Biology, F-75015 Paris, France
- Sorbonne Université, Collège doctoral, F-75005 Paris, France
| | - Noa Gil
- Department of Immunology and Regenerative Biology and Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Nick Owens
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit, Department of Developmental and Stem Cell Biology, F-75015 Paris, France
| | - Lawrence E Bates
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Sandrine Vandormael-Pournin
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit, Department of Developmental and Stem Cell Biology, F-75015 Paris, France
| | - José C R Silva
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou510005, Guangdong Province, China
| | - Igor Ulitsky
- Department of Immunology and Regenerative Biology and Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Michel Cohen-Tannoudji
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit, Department of Developmental and Stem Cell Biology, F-75015 Paris, France
| | - Pablo Navarro
- To whom correspondence should be addressed. Tel: +33 145688285;
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9
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Novo CL, Wong EV, Hockings C, Poudel C, Sheekey E, Wiese M, Okkenhaug H, Boulton SJ, Basu S, Walker S, Kaminski Schierle GS, Narlikar GJ, Rugg-Gunn PJ. Satellite repeat transcripts modulate heterochromatin condensates and safeguard chromosome stability in mouse embryonic stem cells. Nat Commun 2022; 13:3525. [PMID: 35725842 PMCID: PMC9209518 DOI: 10.1038/s41467-022-31198-3] [Citation(s) in RCA: 2] [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: 02/02/2021] [Accepted: 06/07/2022] [Indexed: 12/25/2022] Open
Abstract
Heterochromatin maintains genome integrity and function, and is organised into distinct nuclear domains. Some of these domains are proposed to form by phase separation through the accumulation of HP1ɑ. Mouse heterochromatin contains noncoding major satellite repeats (MSR), which are highly transcribed in mouse embryonic stem cells (ESCs). Here, we report that MSR transcripts can drive the formation of HP1ɑ droplets in vitro, and modulate heterochromatin into dynamic condensates in ESCs, contributing to the formation of large nuclear domains that are characteristic of pluripotent cells. Depleting MSR transcripts causes heterochromatin to transition into a more compact and static state. Unexpectedly, changing heterochromatin's biophysical properties has severe consequences for ESCs, including chromosome instability and mitotic defects. These findings uncover an essential role for MSR transcripts in modulating the organisation and properties of heterochromatin to preserve genome stability. They also provide insights into the processes that could regulate phase separation and the functional consequences of disrupting the properties of heterochromatin condensates.
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Affiliation(s)
- Clara Lopes Novo
- Epigenetics Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.
- Tommy's National Miscarriage Research Centre at Imperial College London, London, W12 0NN, UK.
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
| | - Emily V Wong
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Colin Hockings
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, CB3 0AS, UK
| | - Chetan Poudel
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, CB3 0AS, UK
| | - Eleanor Sheekey
- Epigenetics Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Meike Wiese
- Wellcome - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 1QR, UK
| | - Hanneke Okkenhaug
- Imaging Facility, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Simon J Boulton
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Artios Pharma Ltd., B940, Babraham Research Campus, Cambridge, CB22 3FH, UK
| | - Srinjan Basu
- Wellcome - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 1QR, UK
| | - Simon Walker
- Imaging Facility, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | | | - Geeta J Narlikar
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Peter J Rugg-Gunn
- Epigenetics Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.
- Wellcome - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 1QR, UK.
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10
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Transcriptional Activation of Heterochromatin by Recruitment of dCas9 Activators. Methods Mol Biol 2021; 2351:307-320. [PMID: 34382197 DOI: 10.1007/978-1-0716-1597-3_17] [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: 03/29/2023]
Abstract
The transition from silenced heterochromatin to a biologically active state and vice versa is a fundamental part of the implementation of cell type-specific gene expression programs. To reveal structure-function relationships and dissect the underlying mechanisms, experiments that ectopically induce transcription are highly informative. In particular, the approach to perturb chromatin states by recruiting fusions of the catalytically inactive dCas9 protein in a sequence-specific manner to a locus of interest has been used in numerous applications. Here, we describe how this approach can be applied to activate pericentric heterochromatin (PCH) in mouse cells as a prototypic silenced state by providing protocols for the following workflow: (a) Recruitment of dCas9 fusion constructs with the strong transcriptional activator VPR to PCH. (b) Analysis of the resulting changes in chromatin compaction, epigenetic marks, and active transcription by fluorescence microscopy-based readouts. (c) Automated analysis of the resulting images with a set of scripts in the R programming language. Furthermore, we discuss how parameters for chromatin decondensation and active transcription are extracted from these experiments and can be combined with other readouts to gain insights into PCH activation.
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11
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Franek M, Kilar A, Fojtík P, Olšinová M, Benda A, Rotrekl V, Dvořáčková M, Fajkus J. Super-resolution microscopy of chromatin fibers and quantitative DNA methylation analysis of DNA fiber preparations. J Cell Sci 2021; 134:jcs258374. [PMID: 34350964 DOI: 10.1242/jcs.258374] [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: 01/06/2021] [Accepted: 07/05/2021] [Indexed: 11/20/2022] Open
Abstract
Analysis of histone variants and epigenetic marks is dominated by genome-wide approaches in the form of chromatin immunoprecipitation-sequencing (ChIP-seq) and related methods. Although uncontested in their value for single-copy genes, mapping the chromatin of DNA repeats is problematic for biochemical techniques that involve averaging of cell populations or analysis of clusters of tandem repeats in a single-cell analysis. Extending chromatin and DNA fibers allows us to study the epigenetics of individual repeats in their specific chromosomal context, and thus constitutes an important tool for gaining a complete understanding of the epigenetic organization of genomes. We report that using an optimized fiber extension protocol is essential in order to obtain more reproducible data and to minimize the clustering of fibers. We also demonstrate that the use of super-resolution microscopy is important for reliable evaluation of the distribution of histone modifications on individual fibers. Furthermore, we introduce a custom script for the analysis of methylation levels on DNA fibers and apply it to map the methylation of telomeres, ribosomal genes and centromeres.
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Affiliation(s)
- Michal Franek
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Agata Kilar
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-61137 Brno, Czech Republic
| | - Petr Fojtík
- International Clinical Research Center (ICRC) at St. Anne's University Hospital, Pekařská 53, CZ-65691 Brno, Czech Republic
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Marie Olšinová
- Charles University, Faculty of Science, Biology Section, Imaging methods core facility at BIOCEV, Průmyslová 595, 252 50 Vestec, Czech Republic
| | - Aleš Benda
- Charles University, Faculty of Science, Biology Section, Imaging methods core facility at BIOCEV, Průmyslová 595, 252 50 Vestec, Czech Republic
| | - Vladimír Rotrekl
- International Clinical Research Center (ICRC) at St. Anne's University Hospital, Pekařská 53, CZ-65691 Brno, Czech Republic
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Martina Dvořáčková
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Jíří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-61137 Brno, Czech Republic
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12
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Fu H, Zhang W, Li N, Yang J, Ye X, Tian C, Lu X, Liu L. Elevated retrotransposon activity and genomic instability in primed pluripotent stem cells. Genome Biol 2021; 22:201. [PMID: 34243810 PMCID: PMC8268579 DOI: 10.1186/s13059-021-02417-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 06/24/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Naïve and primed pluripotent stem cells (PSCs) represent two different pluripotent states. Primed PSCs following in vitro culture exhibit lower developmental potency as evidenced by failure in germline chimera assays, unlike mouse naïve PSCs. However, the molecular mechanisms underlying the lower developmental competency of primed PSCs remain elusive. RESULTS We examine the regulation of telomere maintenance, retrotransposon activity, and genomic stability of primed PSCs and compare them with naïve PSCs. Surprisingly, primed PSCs only minimally maintain telomeres and show fragile telomeres, associated with declined DNA recombination and repair activity, in contrast to naïve PSCs that robustly elongate telomeres. Also, we identify LINE1 family integrant L1Md_T as naïve-specific retrotransposon and ERVK family integrant IAPEz to define primed PSCs, and their transcription is differentially regulated by heterochromatic histones and Dnmt3b. Notably, genomic instability of primed PSCs is increased, in association with aberrant retrotransposon activity. CONCLUSIONS Our data suggest that fragile telomere, retrotransposon-associated genomic instability, and declined DNA recombination repair, together with reduced function of cell cycle and mitochondria, increased apoptosis, and differentiation properties may link to compromised developmental potency of primed PSCs, noticeably distinguishable from naïve PSCs.
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Affiliation(s)
- Haifeng Fu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
- Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin, China
| | - Weiyu Zhang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
- College of Pharmacy, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Niannian Li
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
- Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin, China
| | - Jiao Yang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
- Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin, China
| | - Xiaoying Ye
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
- Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin, China
| | - Chenglei Tian
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
- Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin, China
| | - Xinyi Lu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
- College of Pharmacy, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Lin Liu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China.
- Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin, China.
- The Key Laboratory of Bioactive Materials Ministry of Education, Nankai University, Tianjin, China.
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13
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Macrae TA, Ramalho-Santos M. The deubiquitinase Usp9x regulates PRC2-mediated chromatin reprogramming during mouse development. Nat Commun 2021; 12:1865. [PMID: 33767158 PMCID: PMC7994559 DOI: 10.1038/s41467-021-21910-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 02/19/2021] [Indexed: 01/31/2023] Open
Abstract
Pluripotent cells of the mammalian embryo undergo extensive chromatin rewiring to prepare for lineage commitment after implantation. Repressive H3K27me3, deposited by Polycomb Repressive Complex 2 (PRC2), is reallocated from large blankets in pre-implantation embryos to mark promoters of developmental genes. The regulation of this global redistribution of H3K27me3 is poorly understood. Here we report a post-translational mechanism that destabilizes PRC2 to constrict H3K27me3 during lineage commitment. Using an auxin-inducible degron system, we show that the deubiquitinase Usp9x is required for mouse embryonic stem (ES) cell self-renewal. Usp9x-high ES cells have high PRC2 levels and bear a chromatin and transcriptional signature of the pre-implantation embryo, whereas Usp9x-low ES cells resemble the post-implantation, gastrulating epiblast. We show that Usp9x interacts with, deubiquitinates and stabilizes PRC2. Deletion of Usp9x in post-implantation embryos results in the derepression of genes that normally gain H3K27me3 after gastrulation, followed by the appearance of morphological abnormalities at E9.5, pointing to a recurrent link between Usp9x and PRC2 during development. Usp9x is a marker of "stemness" and is mutated in various neurological disorders and cancers. Our results unveil a Usp9x-PRC2 regulatory axis that is critical at peri-implantation and may be redeployed in other stem cell fate transitions and disease states.
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Affiliation(s)
- Trisha A Macrae
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
- Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Miguel Ramalho-Santos
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA.
- Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA.
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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14
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Abstract
Organoids are three-dimensional structures that are derived from the self-organization of stem cells as they differentiate in vitro. The plasticity of stem cells is one of the major criteria for generating organoids most similar to the tissue structures they intend to mimic. Stem cells are cells with unique properties of self-renewal and differentiation. Depending on their origin, a distinction is made between pluripotent (embryonic) stem cells (PSCs), adult (or tissue) stem cells (ASCs), and those obtained by somatic reprogramming, so-called induced pluripotent stem cells (iPSCs). While most data since the 1980s have been acquired in the mouse model, and then from the late 1990s in humans, the process of somatic reprogammation has revolutionized the field of stem cell research. For domestic animals, numerous attempts have been made to obtain PSCs and iPSCs, an approach that makes it possible to omit the use of embryos to derive the cells. Even if the plasticity of the cells obtained is not always optimal, the recent progress in obtaining reprogrammed cells is encouraging. Along with PSCs and iPSCs, many organoid derivations in animal species are currently obtained from ASCs. In this study, we present state-of-the-art stem cell research according to their origins in the various animal models developed.
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Affiliation(s)
- Bertrand Pain
- Univ Lyon, Université Lyon 1, INSERM, INRAE, Stem Cell and Brain Research Institute, U1208, CSC USC1361, Bron, France.
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15
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Takei Y, Yun J, Zheng S, Ollikainen N, Pierson N, White J, Shah S, Thomassie J, Suo S, Eng CHL, Guttman M, Yuan GC, Cai L. Integrated spatial genomics reveals global architecture of single nuclei. Nature 2021; 590:344-350. [PMID: 33505024 PMCID: PMC7878433 DOI: 10.1038/s41586-020-03126-2] [Citation(s) in RCA: 188] [Impact Index Per Article: 62.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 12/16/2020] [Indexed: 12/11/2022]
Abstract
Identifying the relationships between chromosome structures, nuclear bodies, chromatin states, and gene expression is an overarching goal of nuclear organization studies1–4. Because individual cells appear to be highly variable at all these levels5, it is essential to map different modalities in the same cells. Here, we report the imaging of 3,660 chromosomal loci in single mouse embryonic stem cells (mESCs) by DNA seqFISH+, along with 17 chromatin marks and subnuclear structures by sequential immunofluorescence (IF) and the expression profile of 70 RNAs. We found many loci were invariantly associated with IF marks in single mESCs. These loci form “fixed points” in the nuclear organizations in single cells and often appear on the surfaces of nuclear bodies and zones defined by combinatorial chromatin marks. Furthermore, highly expressed genes appear to be pre-positioned to active nuclear zones, independent of bursting dynamics in single cells. Our analysis also uncovered several distinct mESCs subpopulations with characteristic combinatorial chromatin states. Using clonal analysis, we show that the global levels of some chromatin marks, such as H3K27me3 and macroH2A1 (mH2A1), are heritable over at least 3–4 generations, whereas other marks fluctuate on a faster time scale. This seqFISH+ based spatial multimodal approach can be used to explore nuclear organization and cell states in diverse biological systems.
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Affiliation(s)
- Yodai Takei
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jina Yun
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Shiwei Zheng
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H.Chan School of Public Health, Boston, MA, USA.,Department of Genetics and Genomic Sciences and Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Noah Ollikainen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Nico Pierson
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jonathan White
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Sheel Shah
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Julian Thomassie
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Shengbao Suo
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H.Chan School of Public Health, Boston, MA, USA.,Department of Genetics and Genomic Sciences and Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Chee-Huat Linus Eng
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Guo-Cheng Yuan
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H.Chan School of Public Health, Boston, MA, USA.,Department of Genetics and Genomic Sciences and Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Long Cai
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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16
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Thanuthanakhun N, Kino-Oka M, Borwornpinyo S, Ito Y, Kim MH. The impact of culture dimensionality on behavioral epigenetic memory contributing to pluripotent state of iPS cells. J Cell Physiol 2020; 236:4985-4996. [PMID: 33305410 DOI: 10.1002/jcp.30211] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/24/2020] [Accepted: 11/25/2020] [Indexed: 12/12/2022]
Abstract
Three-dimensional (3D) culture platforms have been explored to establish physiologically relevant cell culture environment and permit expansion scalability; however, little is known about the mechanisms underlying the regulation of pluripotency of human induced pluripotent stem cells (hiPSCs). This study elucidated epigenetic modifications contributing to pluripotency of hiPSCs in response to 3D culture. Unlike two-dimensional (2D) monolayer cultures, 3D cultured cells aggregated with each other to form ball-like aggregates. 2D cultured cells expressed elevated levels of Rac1 and RhoA; however, Rac1 level was significantly lower while RhoA level was persisted in 3D aggregates. Compared with 2D monolayers, the 3D aggregates also exhibited significantly lower myosin phosphorylation. Histone methylation analysis revealed remarkable H3K4me3 upregulation and H3K27me3 maintenance throughout the duration of 3D culture; in addition, we observed the existence of naïve pluripotency signatures in cells grown in 3D culture. These results demonstrated that hiPSCs adapted to 3D culture through alteration of the Rho-Rho kinase-phospho-myosin pathway, influencing the epigenetic modifications and transcriptional expression of pluripotency-associated factors. These results may help design culture environments for stable and high-quality hiPSCs.
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Affiliation(s)
- Naruchit Thanuthanakhun
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
| | - Masahiro Kino-Oka
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
| | - Suparerk Borwornpinyo
- Department of Biotechnology, Faculty of Science, Mahidol University, Ratchathewi, Bangkok, Thailand
| | - Yuzuru Ito
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Mee-Hae Kim
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
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17
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Genet M, Torres-Padilla ME. The molecular and cellular features of 2-cell-like cells: a reference guide. Development 2020; 147:147/16/dev189688. [PMID: 32847823 DOI: 10.1242/dev.189688] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Currently, two main cell culture models predominate pluripotent stem cell research: embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs). Thanks to their ability to contribute to and form all tissues within the body, ESCs and iPSCs have proven invaluable in understanding pluripotent states, early embryonic development and cell differentiation, as well as in devising strategies for regenerative medicine. Comparatively little is known about totipotency - a cellular state with greater developmental potential. In mice, only the zygote and the blastomeres of the 2-cell-stage embryo are truly totipotent, as they alone can develop to form the embryo and all of its supportive extra-embryonic tissues. However, the discovery of a rare subpopulation of cells in murine ESC cultures, possessing features of 2-cell embryo blastomeres and expanded cell fate potential, has provided a biochemically tractable model to enable the in vitro study of totipotency. Here, we summarize current known features of these 2-cell-like cells (2CLCs) in an effort to provide a reference for the community, and to clarify what we know about their identity so far.
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Affiliation(s)
- Marion Genet
- Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München, D-81377, Germany
| | - Maria-Elena Torres-Padilla
- Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München, D-81377, Germany .,Faculty of Biology, Ludwig-Maximilians Universität, 82152 Martinsried, Germany
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18
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Shukla R, Mjoseng HK, Thomson JP, Kling S, Sproul D, Dunican DS, Ramsahoye B, Wongtawan T, Treindl F, Templin MF, Adams IR, Pennings S, Meehan RR. Activation of transcription factor circuity in 2i-induced ground state pluripotency is independent of repressive global epigenetic landscapes. Nucleic Acids Res 2020; 48:7748-7766. [PMID: 32585002 PMCID: PMC7641322 DOI: 10.1093/nar/gkaa529] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 06/02/2020] [Accepted: 06/15/2020] [Indexed: 01/07/2023] Open
Abstract
Mouse embryonic stem cells (mESCs) cultured with MEK/ERK and GSK3β (2i) inhibitors transition to ground state pluripotency. Gene expression changes, redistribution of histone H3K27me3 profiles and global DNA hypomethylation are hallmarks of 2i exposure, but it is unclear whether epigenetic alterations are required to achieve and maintain ground state or occur as an outcome of 2i signal induced changes. Here we show that ESCs with three epitypes, WT, constitutively methylated, or hypomethylated, all undergo comparable morphological, protein expression and transcriptome changes independently of global alterations of DNA methylation levels or changes in H3K27me3 profiles. Dazl and Fkbp6 expression are induced by 2i in all three epitypes, despite exhibiting hypermethylated promoters in constitutively methylated ESCs. We identify a number of activated gene promoters that undergo 2i dependent loss of H3K27me3 in all three epitypes, however genetic and pharmaceutical inhibition experiments show that H3K27me3 is not required for their silencing in non-2i conditions. By separating and defining their contributions, our data suggest that repressive epigenetic systems play minor roles in mESC self-renewal and naïve ground state establishment by core sets of dominant pluripotency associated transcription factor networks, which operate independently from these epigenetic processes.
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Affiliation(s)
- Ruchi Shukla
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, WGH, University of Edinburgh, Edinburgh EH4 2XU, UK
- Newcastle University Centre for Cancer, Biosciences Institute, Newcastle University, Newcastle-upon-Tyne NE2 4HH, UK
| | - Heidi K Mjoseng
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, WGH, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - John P Thomson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, WGH, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Simon Kling
- NMI Natural and Medical Sciences Institute, Tübingen University, Reutlingen, Germany
| | - Duncan Sproul
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, WGH, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Donncha S Dunican
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, WGH, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Bernard Ramsahoye
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, WGH, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Tuempong Wongtawan
- Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Fridolin Treindl
- NMI Natural and Medical Sciences Institute, Tübingen University, Reutlingen, Germany
- Pharmaceutical Biotechnology, Tübingen University, Tübingen, Germany
| | - Markus F Templin
- NMI Natural and Medical Sciences Institute, Tübingen University, Reutlingen, Germany
- Pharmaceutical Biotechnology, Tübingen University, Tübingen, Germany
| | - Ian R Adams
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, WGH, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Sari Pennings
- Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Richard R Meehan
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, WGH, University of Edinburgh, Edinburgh EH4 2XU, UK
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19
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Neagu A, van Genderen E, Escudero I, Verwegen L, Kurek D, Lehmann J, Stel J, Dirks RAM, van Mierlo G, Maas A, Eleveld C, Ge Y, den Dekker AT, Brouwer RWW, van IJcken WFJ, Modic M, Drukker M, Jansen JH, Rivron NC, Baart EB, Marks H, ten Berge D. In vitro capture and characterization of embryonic rosette-stage pluripotency between naive and primed states. Nat Cell Biol 2020; 22:534-545. [DOI: 10.1038/s41556-020-0508-x] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 03/20/2020] [Indexed: 12/13/2022]
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20
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Untargeted histone profiling during naive conversion uncovers conserved modification markers between mouse and human. Sci Rep 2019; 9:17240. [PMID: 31754138 PMCID: PMC6872658 DOI: 10.1038/s41598-019-53681-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 10/25/2019] [Indexed: 11/08/2022] Open
Abstract
Recent progress has enabled the conversion of primed human embryonic stem cells (hESCs) to the naive state of pluripotency, resembling the well-characterized naive mouse ESCs (mESCs). However, a thorough histone epigenetic characterization of this conversion process is currently lacking, while its likeness to the mouse model has not been clearly established. Here, we profile the histone epigenome of hESCs during conversion in a time-resolved experimental design, using an untargeted mass spectrometry-based approach. In total, 23 histone post-translational modifications (hPTMs) changed significantly over time. H3K27Me3 was the most prominently increasing marker hPTM in naive hESCs. This is in line with previous reports in mouse, prompting us to compare all the shared hPTM fold changes between mouse and human, revealing a set of conserved hPTM markers for the naive state. Principally, we present the first roadmap of the changing human histone epigenome during the conversion of hESCs from the primed to the naive state. This further revealed similarities with mouse, which hint at a conserved mammalian epigenetic signature of the ground state of pluripotency.
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21
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Szczerbinska I, Gonzales KAU, Cukuroglu E, Ramli MNB, Lee BPG, Tan CP, Wong CK, Rancati GI, Liang H, Göke J, Ng HH, Chan YS. A Chemically Defined Feeder-free System for the Establishment and Maintenance of the Human Naive Pluripotent State. Stem Cell Reports 2019; 13:612-626. [PMID: 31522974 PMCID: PMC6829768 DOI: 10.1016/j.stemcr.2019.08.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 08/12/2019] [Accepted: 08/15/2019] [Indexed: 01/28/2023] Open
Abstract
The distinct states of pluripotency in the pre- and post-implantation embryo can be captured in vitro as naive and primed pluripotent stem cell cultures, respectively. The study and application of the naive state remains hampered, particularly in humans, partially due to current culture protocols relying on extraneous undefined factors such as feeders. Here we performed a small-molecule screen to identify compounds that facilitate chemically defined establishment and maintenance of human feeder-independent naive embryonic (FINE) stem cells. The expression profile in genic and repetitive elements of FINE cells resembles the 8-cell-to-morula stage in vivo, and only differs from feeder-dependent naive cells in genes involved in cell-cell/cell-matrix interactions. FINE cells offer several technical advantages, such as increased amenability to transfection and a longer period of genomic stability, compared with feeder-dependent cells. Thus, FINE cells will serve as an accessible and useful system for scientific and translational applications of naïve pluripotent stem cells. High-throughput screen identifies small molecules modulating human naive pluripotency Induction and culture of human feeder-independent naive embryonic (FINE) stem cells FINE cells are molecularly equivalent to 4iLA hESCs FINE cells offer enhanced genomic stability and amenability to exogenous DNA uptake
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Affiliation(s)
- Iwona Szczerbinska
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore; Department of Biochemistry, National University of Singapore, Singapore 117559, Singapore
| | - Kevin Andrew Uy Gonzales
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore; Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, 1230 York Avenue, New York City, NY 10065, USA
| | - Engin Cukuroglu
- Computational and Systems Biology, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore
| | - Muhammad Nadzim Bin Ramli
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore; NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
| | - Bertha Pei Ge Lee
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore
| | - Cheng Peow Tan
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore
| | - Cheng Kit Wong
- Institute of Medical Biology, A(∗)STAR, 8A Biomedical Grove, Immunos #05, Singapore 138648, Singapore
| | - Giulia Irene Rancati
- Institute of Medical Biology, A(∗)STAR, 8A Biomedical Grove, Immunos #05, Singapore 138648, Singapore
| | - Hongqing Liang
- Division of Human Reproduction and Developmental Genetics, the Women's Hospital, Zhejiang University School of Medicine, Yuhangtang Road 866, Hangzhou, Zhejiang 310012, China; Institute of Genetics and Department of Genetics, Zhejiang University School of Medicine, Yuhangtang Road 866, Hangzhou, Zhejiang 310012, China
| | - Jonathan Göke
- Computational and Systems Biology, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore
| | - Huck-Hui Ng
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore; Department of Biochemistry, National University of Singapore, Singapore 117559, Singapore; Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117597, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 639798, Singapore.
| | - Yun-Shen Chan
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore.
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22
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van Mierlo G, Wester RA, Marks H. A Mass Spectrometry Survey of Chromatin-Associated Proteins in Pluripotency and Early Lineage Commitment. Proteomics 2019; 19:e1900047. [PMID: 31219242 DOI: 10.1002/pmic.201900047] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 06/07/2019] [Indexed: 12/12/2022]
Abstract
Pluripotency can be captured in vitro in the form of Embryonic Stem Cells (ESCs). These ESCs can be either maintained in the unrestricted "naïve" state of pluripotency, adapted to developmentally more constrained "primed" pluripotency or differentiated towards each of the three germ layers. Epigenetic protein complexes and transcription factors have been shown to specify and instruct transitions from ESCs to distinct cell states. In this study, proteomic profiling of the chromatin landscape by chromatin enrichment for proteomics (ChEP) is used in mouse naive pluripotent ESCs, primed pluripotent Epiblast stem cells (EpiSCs), and cells in early stages of differentiation. A comprehensive overview of epigenetic protein complexes associated with the chromatin is provided and proteins associated with the maintenance and loss of pluripotency are identified. The data reveal major compositional alterations of epigenetic complexes during priming and differentiation of naïve pluripotent ESCs. These results contribute to the understanding of ESC differentiation and provide a framework for future studies of lineage commitment of ESCs.
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Affiliation(s)
- Guido van Mierlo
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, Nijmegen, 6525GA, The Netherlands.,Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University, Nijmegen, 6525GA, The Netherlands
| | - Roelof Alexander Wester
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, Nijmegen, 6525GA, The Netherlands
| | - Hendrik Marks
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, Nijmegen, 6525GA, The Netherlands
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23
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Epigenetic modulation of a hardwired 3D chromatin landscape in two naive states of pluripotency. Nat Cell Biol 2019; 21:568-578. [PMID: 31036938 DOI: 10.1038/s41556-019-0310-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 03/11/2019] [Indexed: 01/09/2023]
Abstract
The mechanisms underlying enhancer activation and the extent to which enhancer-promoter rewiring contributes to spatiotemporal gene expression are not well understood. Using integrative and time-resolved analyses we show that the extensive transcriptome and epigenome resetting during the conversion between 'serum' and '2i' states of mouse embryonic stem cells (ESCs) takes place with minimal enhancer-promoter rewiring that becomes more evident in primed-state pluripotency. Instead, differential gene expression is strongly linked to enhancer activation via H3K27ac. Conditional depletion of transcription factors and allele-specific enhancer analysis reveal an essential role for Esrrb in H3K27 acetylation and activation of 2i-specific enhancers. Restoration of a polymorphic ESRRB motif using CRISPR-Cas9 in a hybrid ESC line restores ESRRB binding and enhancer H3K27ac in an allele-specific manner but has no effect on chromatin interactions. Our study shows that enhancer activation in serum- and 2i-ESCs is largely driven by transcription factor binding and epigenetic marking in a hardwired network of chromatin interactions.
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24
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Zhang J, Chen Y, Gao M, Wang Z, Liu R, Xia T, Liu S. Silver Nanoparticles Compromise Female Embryonic Stem Cell Differentiation through Disturbing X Chromosome Inactivation. ACS NANO 2019; 13:2050-2061. [PMID: 30650303 DOI: 10.1021/acsnano.8b08604] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The widespread use of silver nanoparticles (AgNPs) has raised substantial health risks to human beings. Despite a wealth of progress on toxicity studies, the understanding of the adverse effects on fetuses, embryos, and early stage cells is still rather limited, particularly under low-dose exposure settings. Moreover, nearly all previous studies ascribed AgNP-induced toxic effects to oxidative stress. Differently, we here unearthed a mechanism, namely, interruption of X chromosome inactivation (XCI) in female mouse embryonic stem cells (mESCs). Albeit with no observable cytotoxicity, significant differentiation retardation was found in female mESCs upon low-dose AgNP exposure. Mechanistic investigations uncovered expedited inactivation for the inactive X chromosome (Xi) and attenuated maintenance of the active X chromosome (Xa) state during mESC differentiation upon the challenge of low-dose AgNPs, indicative of disordered XCI. Thereby, a few X-linked genes (which are closely involved in orchestrating ESC differentiation) were found to be repressed, partially attributable to reinforced enrichment of histone modification ( e. g., histone 3 lysine 27 trimethylation, H3K27me3) on their promoter regions, as the result of disordered XCI. In stark contrast to female mESCs, no impairment of differentiation was observed in male mESCs under low-dose AgNP exposure. All considered, our data unearthed that AgNPs at low concentrations compromised the differentiation program of female mESCs through disturbing XCI. Thus, this work would provide a model for the type of studies necessary to advance the understandings on AgNP-induced developmental toxicity.
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Affiliation(s)
- Jie Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology , Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Yongjiu Chen
- State Key Laboratory of Environmental Chemistry and Ecotoxicology , Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Ming Gao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology , Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Zhe Wang
- School of Public Health , Xinxiang Medical University , Xinxiang , Henan Province 453003 , China
| | - Rui Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology , Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Tian Xia
- State Key Laboratory of Environmental Chemistry and Ecotoxicology , Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085 , China
- Division of NanoMedicine, Department of Medicine , University of California Los Angeles , Los Angeles , California 90095 , United States
| | - Sijin Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology , Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
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25
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Festuccia N, Owens N, Papadopoulou T, Gonzalez I, Tachtsidi A, Vandoermel-Pournin S, Gallego E, Gutierrez N, Dubois A, Cohen-Tannoudji M, Navarro P. Transcription factor activity and nucleosome organization in mitosis. Genome Res 2019; 29:250-260. [PMID: 30655337 PMCID: PMC6360816 DOI: 10.1101/gr.243048.118] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 12/05/2018] [Indexed: 12/23/2022]
Abstract
Mitotic bookmarking transcription factors (BFs) maintain the capacity to bind to their targets during mitosis, despite major rearrangements of the chromatin. While they were thought to propagate gene regulatory information through mitosis by statically occupying their DNA targets, it has recently become clear that BFs are highly dynamic in mitotic cells. This represents both a technical and a conceptual challenge to study and understand the function of BFs: First, formaldehyde has been suggested to be unable to efficiently capture these transient interactions, leading to profound contradictions in the literature; and second, if BFs are not permanently bound to their targets during mitosis, it becomes unclear how they convey regulatory information to daughter cells. Here, comparing formaldehyde to alternative fixatives we clarify the nature of the chromosomal association of previously proposed BFs in embryonic stem cells: While ESRRB can be considered as a canonical BF that binds at selected regulatory regions in mitosis, SOX2 and POU5F1 (also known as OCT4) establish DNA sequence-independent interactions with the mitotic chromosomes, either throughout the chromosomal arms (SOX2) or at pericentromeric regions (POU5F1). Moreover, we show that ordered nucleosomal arrays are retained during mitosis at ESRRB bookmarked sites, whereas regions losing transcription factor binding display a profound loss of order. By maintaining nucleosome positioning during mitosis, ESRRB might ensure the rapid post-mitotic re-establishment of functional regulatory complexes at selected enhancers and promoters. Our results provide a mechanistic framework that reconciles dynamic mitotic binding with the transmission of gene regulatory information across cell division.
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Affiliation(s)
- Nicola Festuccia
- Epigenetics of Stem Cells, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR3738, 75015 Paris, France.,Equipe Labellisée LIGUE Contre le Cancer
| | - Nick Owens
- Epigenetics of Stem Cells, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR3738, 75015 Paris, France.,Equipe Labellisée LIGUE Contre le Cancer
| | - Thaleia Papadopoulou
- Epigenetics of Stem Cells, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR3738, 75015 Paris, France.,Equipe Labellisée LIGUE Contre le Cancer
| | - Inma Gonzalez
- Epigenetics of Stem Cells, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR3738, 75015 Paris, France.,Equipe Labellisée LIGUE Contre le Cancer
| | - Alexandra Tachtsidi
- Epigenetics of Stem Cells, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR3738, 75015 Paris, France.,Equipe Labellisée LIGUE Contre le Cancer.,Sorbonne Université, Collège Doctoral, F-75005 Paris, France
| | - Sandrine Vandoermel-Pournin
- Mouse Functional Genetics, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR 3738, 75015 Paris, France
| | - Elena Gallego
- Epigenetics of Stem Cells, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR3738, 75015 Paris, France.,Equipe Labellisée LIGUE Contre le Cancer
| | - Nancy Gutierrez
- Epigenetics of Stem Cells, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR3738, 75015 Paris, France.,Equipe Labellisée LIGUE Contre le Cancer
| | - Agnès Dubois
- Epigenetics of Stem Cells, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR3738, 75015 Paris, France.,Equipe Labellisée LIGUE Contre le Cancer
| | - Michel Cohen-Tannoudji
- Mouse Functional Genetics, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR 3738, 75015 Paris, France
| | - Pablo Navarro
- Epigenetics of Stem Cells, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR3738, 75015 Paris, France.,Equipe Labellisée LIGUE Contre le Cancer
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26
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Schlesinger S, Meshorer E. Open Chromatin, Epigenetic Plasticity, and Nuclear Organization in Pluripotency. Dev Cell 2019; 48:135-150. [DOI: 10.1016/j.devcel.2019.01.003] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 10/30/2018] [Accepted: 12/31/2018] [Indexed: 12/27/2022]
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