1
|
Chervova A, Molliex A, Baymaz HI, Coux RX, Papadopoulou T, Mueller F, Hercul E, Fournier D, Dubois A, Gaiani N, Beli P, Festuccia N, Navarro P. Mitotic bookmarking redundancy by nuclear receptors in pluripotent cells. Nat Struct Mol Biol 2024; 31:513-522. [PMID: 38196033 PMCID: PMC10948359 DOI: 10.1038/s41594-023-01195-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 11/30/2023] [Indexed: 01/11/2024]
Abstract
Mitotic bookmarking transcription factors (TFs) are thought to mediate rapid and accurate reactivation after mitotic gene silencing. However, the loss of individual bookmarking TFs often leads to the deregulation of only a small proportion of their mitotic targets, raising doubts on the biological significance and importance of their bookmarking function. Here we used targeted proteomics of the mitotic bookmarking TF ESRRB, an orphan nuclear receptor, to discover a large redundancy in mitotic binding among members of the protein super-family of nuclear receptors. Focusing on the nuclear receptor NR5A2, which together with ESRRB is essential in maintaining pluripotency in mouse embryonic stem cells, we demonstrate conjoint bookmarking activity of both factors on promoters and enhancers of a large fraction of active genes, particularly those most efficiently reactivated in G1. Upon fast and simultaneous degradation of both factors during mitotic exit, hundreds of mitotic targets of ESRRB/NR5A2, including key players of the pluripotency network, display attenuated transcriptional reactivation. We propose that redundancy in mitotic bookmarking TFs, especially nuclear receptors, confers robustness to the reestablishment of gene regulatory networks after mitosis.
Collapse
Affiliation(s)
- Almira Chervova
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit, Paris, France
- Equipe Labéllisée Ligue Contre le cancer, Paris, France
| | - Amandine Molliex
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit, Paris, France
- Equipe Labéllisée Ligue Contre le cancer, Paris, France
| | | | - Rémi-Xavier Coux
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit, Paris, France
- Equipe Labéllisée Ligue Contre le cancer, Paris, France
| | - Thaleia Papadopoulou
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit, Paris, France
- Equipe Labéllisée Ligue Contre le cancer, Paris, France
| | - Florian Mueller
- Department of Computational Biology, Institut Pasteur, Université Paris Cité, CNRS UMR3691, Imaging and Modeling Unit, Paris, France
| | - Eslande Hercul
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit, Paris, France
- Equipe Labéllisée Ligue Contre le cancer, Paris, France
| | - David Fournier
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit, Paris, France
- Equipe Labéllisée Ligue Contre le cancer, Paris, France
| | - Agnès Dubois
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit, Paris, France
- Equipe Labéllisée Ligue Contre le cancer, Paris, France
| | - Nicolas Gaiani
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit, Paris, France
- Equipe Labéllisée Ligue Contre le cancer, Paris, France
| | - Petra Beli
- Institute of Molecular Biology, Mainz, Germany
- Institute of Developmental Biology and Neurobiology, Johannes Gutenberg-Universität, Mainz, Germany
| | - Nicola Festuccia
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit, Paris, France.
- Equipe Labéllisée Ligue Contre le cancer, Paris, France.
| | - Pablo Navarro
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit, Paris, France.
- Equipe Labéllisée Ligue Contre le cancer, Paris, France.
| |
Collapse
|
2
|
Yelagandula R, Stecher K, Novatchkova M, Michetti L, Michlits G, Wang J, Hofbauer P, Vainorius G, Pribitzer C, Isbel L, Mendjan S, Schübeler D, Elling U, Brennecke J, Bell O. ZFP462 safeguards neural lineage specification by targeting G9A/GLP-mediated heterochromatin to silence enhancers. Nat Cell Biol 2023; 25:42-55. [PMID: 36604593 PMCID: PMC10038669 DOI: 10.1038/s41556-022-01051-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 11/10/2022] [Indexed: 01/07/2023]
Abstract
ZNF462 haploinsufficiency is linked to Weiss-Kruszka syndrome, a genetic disorder characterized by neurodevelopmental defects, including autism. Though conserved in vertebrates and essential for embryonic development, the molecular functions of ZNF462 remain unclear. We identified its murine homologue ZFP462 in a screen for mediators of epigenetic gene silencing. Here we show that ZFP462 safeguards neural lineage specification of mouse embryonic stem cells (ESCs) by targeting the H3K9-specific histone methyltransferase complex G9A/GLP to silence meso-endodermal genes. ZFP462 binds to transposable elements that are potential enhancers harbouring pluripotency and meso-endoderm transcription factor binding sites. Recruiting G9A/GLP, ZFP462 seeds heterochromatin, restricting transcription factor binding. Loss of ZFP462 in ESCs results in increased chromatin accessibility at target sites and ectopic expression of meso-endodermal genes. Taken together, ZFP462 confers lineage and locus specificity to the broadly expressed epigenetic regulator G9A/GLP. Our results suggest that aberrant activation of lineage non-specific genes in the neuronal lineage underlies ZNF462-associated neurodevelopmental pathology.
Collapse
Affiliation(s)
- Ramesh Yelagandula
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria.
- Department of Biochemistry and Molecular Medicine and Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA.
| | - Karin Stecher
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Vienna, Austria
| | - Maria Novatchkova
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Luca Michetti
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Università Vita-Salute San Raffaele, Milan, Italy
| | - Georg Michlits
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Jingkui Wang
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Pablo Hofbauer
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Gintautas Vainorius
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Carina Pribitzer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Luke Isbel
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Sasha Mendjan
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Dirk Schübeler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Ulrich Elling
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Julius Brennecke
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Oliver Bell
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria.
- Department of Biochemistry and Molecular Medicine and Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA.
| |
Collapse
|
3
|
Ishii S. The Role of Histone Deacetylase 3 Complex in Nuclear Hormone Receptor Action. Int J Mol Sci 2021; 22:ijms22179138. [PMID: 34502048 PMCID: PMC8431225 DOI: 10.3390/ijms22179138] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/18/2021] [Accepted: 08/19/2021] [Indexed: 11/16/2022] Open
Abstract
Nuclear hormone receptors (NRs) regulate transcription of the target genes in a ligand-dependent manner in either a positive or negative direction, depending on the case. Deacetylation of histone tails is associated with transcriptional repression. A nuclear receptor corepressor (N-CoR) and a silencing mediator for retinoid and thyroid hormone receptors (SMRT) are the main corepressors responsible for gene suppression mediated by NRs. Among numerous histone deacetylases (HDACs), HDAC3 is the core component of the N-CoR/SMRT complex, and plays a central role in NR-dependent repression. Here, the roles of HDAC3 in ligand-independent repression, gene repression by orphan NRs, NRs antagonist action, ligand-induced repression, and the activation of a transcriptional coactivator are reviewed. In addition, some perspectives regarding the non-canonical mechanisms of HDAC3 action are discussed.
Collapse
Affiliation(s)
- Sumiyasu Ishii
- Department of Integrative Physiology, Gunma University Graduate School of Medicine, Maebashi 371-8501, Japan
| |
Collapse
|
4
|
Olivieri D, Paramanathan S, Bardet AF, Hess D, Smallwood SA, Elling U, Betschinger J. The BTB-domain transcription factor ZBTB2 recruits chromatin remodelers and a histone chaperone during the exit from pluripotency. J Biol Chem 2021; 297:100947. [PMID: 34270961 PMCID: PMC8350017 DOI: 10.1016/j.jbc.2021.100947] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 06/21/2021] [Accepted: 07/08/2021] [Indexed: 12/12/2022] Open
Abstract
Transcription factors (TFs) harboring broad-complex, tramtrack, and bric-a-brac (BTB) domains play important roles in development and disease. These BTB domains are thought to recruit transcriptional modulators to target DNA regions. However, a systematic molecular understanding of the mechanism of action of this TF family is lacking. Here, we identify the zinc finger BTB-TF Zbtb2 from a genetic screen for regulators of exit from pluripotency and demonstrate that its absence perturbs embryonic stem cell differentiation and the gene expression dynamics underlying peri-implantation development. We show that ZBTB2 binds the chromatin remodeler Ep400 to mediate downstream transcription. Independently, the BTB domain directly interacts with nucleosome remodeling and deacetylase and histone chaperone histone regulator A. Nucleosome remodeling and deacetylase recruitment is a common feature of BTB TFs, and based on phylogenetic analysis, we propose that this is a conserved evolutionary property. Binding to UBN2, in contrast, is specific to ZBTB2 and requires a C-terminal extension of the BTB domain. Taken together, this study identifies a BTB-domain TF that recruits chromatin modifiers and a histone chaperone during a developmental cell state transition and defines unique and shared molecular functions of the BTB-domain TF family.
Collapse
Affiliation(s)
- Daniel Olivieri
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
| | | | - Anaïs F Bardet
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; CNRS, University of Strasbourg, UMR7242 Biotechnology and Cell Signaling, Illkirch, France
| | - Daniel Hess
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | | | - Ulrich Elling
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Joerg Betschinger
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
| |
Collapse
|
5
|
Olivieri D, Castelli E, Kawamura YK, Papasaikas P, Lukonin I, Rittirsch M, Hess D, Smallwood SA, Stadler MB, Peters AHFM, Betschinger J. Cooperation between HDAC3 and DAX1 mediates lineage restriction of embryonic stem cells. EMBO J 2021; 40:e106818. [PMID: 33909924 PMCID: PMC8204867 DOI: 10.15252/embj.2020106818] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 03/13/2021] [Accepted: 03/17/2021] [Indexed: 12/11/2022] Open
Abstract
Mouse embryonic stem cells (mESCs) are biased toward producing embryonic rather than extraembryonic endoderm fates. Here, we identify the mechanism of this barrier and report that the histone deacetylase Hdac3 and the transcriptional corepressor Dax1 cooperatively limit the lineage repertoire of mESCs by silencing an enhancer of the extraembryonic endoderm-specifying transcription factor Gata6. This restriction is opposed by the pluripotency transcription factors Nr5a2 and Esrrb, which promote cell type conversion. Perturbation of the barrier extends mESC potency and allows formation of 3D spheroids that mimic the spatial segregation of embryonic epiblast and extraembryonic endoderm in early embryos. Overall, this study shows that transcriptional repressors stabilize pluripotency by biasing the equilibrium between embryonic and extraembryonic lineages that is hardwired into the mESC transcriptional network.
Collapse
Affiliation(s)
- Daniel Olivieri
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
| | - Eleonora Castelli
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
- Faculty of SciencesUniversity of BaselBaselSwitzerland
| | - Yumiko K Kawamura
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
| | - Panagiotis Papasaikas
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
- Swiss Institute of BioinformaticsBaselSwitzerland
| | - Ilya Lukonin
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
| | - Melanie Rittirsch
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
| | - Daniel Hess
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
| | | | - Michael B Stadler
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
- Swiss Institute of BioinformaticsBaselSwitzerland
| | - Antoine H F M Peters
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
- Faculty of SciencesUniversity of BaselBaselSwitzerland
| | - Joerg Betschinger
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
| |
Collapse
|
6
|
Janiszewski A, Georgolopoulos G, Balli M, Athanasouli P, Lluis F, Pasque V. Keep the fate: how chromatin regulators safeguard embryonic stem cell identity. EMBO J 2021; 40:e108437. [PMID: 33998023 DOI: 10.15252/embj.2021108437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 04/19/2021] [Indexed: 12/13/2022] Open
Abstract
Segregation of cells that form the embryo from those that produce the surrounding extra-embryonic tissues is critical for early mammalian development, but the regulatory layers governing these first cell fate decisions remain poorly understood. Recent work in The EMBO Journal identifies two chromatin regulators, Hdac3 and Dax1, that synergistically restrict the developmental potential of mouse embryonic stem cells and act as a lineage barrier to primitive endoderm formation.
Collapse
Affiliation(s)
- Adrian Janiszewski
- Department of Development and Regeneration, KU Leuven-University of Leuven, Leuven, Belgium.,KU Leuven Institute for Single Cell Omics (LISCO), Leuven, Belgium.,Leuven Stem Cell Institute, Leuven, Belgium
| | - Grigorios Georgolopoulos
- Department of Development and Regeneration, KU Leuven-University of Leuven, Leuven, Belgium.,KU Leuven Institute for Single Cell Omics (LISCO), Leuven, Belgium.,Leuven Stem Cell Institute, Leuven, Belgium
| | - Martina Balli
- Department of Development and Regeneration, KU Leuven-University of Leuven, Leuven, Belgium.,Leuven Stem Cell Institute, Leuven, Belgium
| | - Paraskevi Athanasouli
- Department of Development and Regeneration, KU Leuven-University of Leuven, Leuven, Belgium.,Leuven Stem Cell Institute, Leuven, Belgium
| | - Frederic Lluis
- Department of Development and Regeneration, KU Leuven-University of Leuven, Leuven, Belgium.,Leuven Stem Cell Institute, Leuven, Belgium
| | - Vincent Pasque
- Department of Development and Regeneration, KU Leuven-University of Leuven, Leuven, Belgium.,KU Leuven Institute for Single Cell Omics (LISCO), Leuven, Belgium.,Leuven Stem Cell Institute, Leuven, Belgium
| |
Collapse
|