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Fatima N, Saif Ur Rahman M, Qasim M, Ali Ashfaq U, Ahmed U, Masoud MS. Transcriptional Factors Mediated Reprogramming to Pluripotency. Curr Stem Cell Res Ther 2024; 19:367-388. [PMID: 37073151 DOI: 10.2174/1574888x18666230417084518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 04/20/2023]
Abstract
A unique kind of pluripotent cell, i.e., Induced pluripotent stem cells (iPSCs), now being targeted for iPSC synthesis, are produced by reprogramming animal and human differentiated cells (with no change in genetic makeup for the sake of high efficacy iPSCs formation). The conversion of specific cells to iPSCs has revolutionized stem cell research by making pluripotent cells more controllable for regenerative therapy. For the past 15 years, somatic cell reprogramming to pluripotency with force expression of specified factors has been a fascinating field of biomedical study. For that technological primary viewpoint reprogramming method, a cocktail of four transcription factors (TF) has required: Kruppel-like factor 4 (KLF4), four-octamer binding protein 34 (OCT3/4), MYC and SOX2 (together referred to as OSKM) and host cells. IPS cells have great potential for future tissue replacement treatments because of their ability to self-renew and specialize in all adult cell types, although factor-mediated reprogramming mechanisms are still poorly understood medically. This technique has dramatically improved performance and efficiency, making it more useful in drug discovery, disease remodeling, and regenerative medicine. Moreover, in these four TF cocktails, more than 30 reprogramming combinations were proposed, but for reprogramming effectiveness, only a few numbers have been demonstrated for the somatic cells of humans and mice. Stoichiometry, a combination of reprogramming agents and chromatin remodeling compounds, impacts kinetics, quality, and efficiency in stem cell research.
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Affiliation(s)
- Nazira Fatima
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China
| | - Muhammad Saif Ur Rahman
- Institute of Advanced Studies, Shenzhen University, Shenzhen, 518060, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Muhammad Qasim
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, 38000, Pakistan
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, 38000, Pakistan
| | - Uzair Ahmed
- EMBL Partnership Institute for Genome Editing Technologies, Vilnius University, Vilnius, 10257, Lithuania
| | - Muhammad Shareef Masoud
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, 38000, Pakistan
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2
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Altamirano-Pacheco L, Navarro P. A fork in the road to differentiation. Nat Genet 2023; 55:1422-1423. [PMID: 37666987 DOI: 10.1038/s41588-023-01489-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Affiliation(s)
- Luis Altamirano-Pacheco
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit, Paris, France
- Collège Doctoral, Sorbonne Université, 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.
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3
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Chervova A, Festuccia N, Altamirano‐Pacheco L, Dubois A, Navarro P. A gene subset requires CTCF bookmarking during the fast post-mitotic reactivation of mouse ES cells. EMBO Rep 2022; 24:e56075. [PMID: 36330771 PMCID: PMC9827546 DOI: 10.15252/embr.202256075] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/11/2022] [Accepted: 10/14/2022] [Indexed: 11/06/2022] Open
Abstract
Mitosis leads to global downregulation of transcription that then needs to be efficiently resumed. In somatic cells, this is mediated by a transient hyper-active state that first reactivates housekeeping and then cell identity genes. Here, we show that mouse embryonic stem cells, which display rapid cell cycles and spend little time in G1, also display accelerated reactivation dynamics. This uniquely fast global reactivation lacks specificity towards functional gene families, enabling the restoration of all regulatory functions before DNA replication. Genes displaying the fastest reactivation are bound by CTCF, a mitotic bookmarking transcription factor. In spite of this, the post-mitotic global burst is robust and largely insensitive to CTCF depletion. There are, however, around 350 genes that respond to CTCF depletion rapidly after mitotic exit. Remarkably, these are characterised by promoter-proximal mitotic bookmarking by CTCF. We propose that the structure of the cell cycle imposes distinct constrains to post-mitotic gene reactivation dynamics in different cell types, via mechanisms that are yet to be identified but that can be modulated by mitotic bookmarking factors.
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Affiliation(s)
- Almira Chervova
- Department of Developmental and Stem Cell BiologyInstitut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells UnitParisFrance,Equipe Labélisée Ligue Contre le CancerParisFrance
| | - Nicola Festuccia
- Department of Developmental and Stem Cell BiologyInstitut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells UnitParisFrance,Equipe Labélisée Ligue Contre le CancerParisFrance
| | - Luis Altamirano‐Pacheco
- Department of Developmental and Stem Cell BiologyInstitut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells UnitParisFrance,Equipe Labélisée Ligue Contre le CancerParisFrance,Collège DoctoralSorbonne UniversitéParisFrance
| | - Agnès Dubois
- Department of Developmental and Stem Cell BiologyInstitut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells UnitParisFrance,Equipe Labélisée Ligue Contre le CancerParisFrance
| | - Pablo Navarro
- Department of Developmental and Stem Cell BiologyInstitut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells UnitParisFrance,Equipe Labélisée Ligue Contre le CancerParisFrance
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4
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Dubois A, Vincenti L, Chervova A, Greenberg MVC, Vandormael-Pournin S, Bourc'his D, Cohen-Tannoudji M, Navarro P. H3K9 tri-methylation at Nanog times differentiation commitment and enables the acquisition of primitive endoderm fate. Development 2022; 149:276335. [PMID: 35976266 PMCID: PMC9482333 DOI: 10.1242/dev.201074] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/04/2022] [Indexed: 11/23/2022]
Abstract
Mouse embryonic stem cells have an inherent propensity to explore gene regulatory states associated with either self-renewal or differentiation. This property depends on ERK, which downregulates pluripotency genes such as Nanog. Here, we aimed at identifying repressive histone modifications that would mark Nanog for inactivation in response to ERK activity. We found that the transcription factor ZFP57, which binds methylated DNA to nucleate heterochromatin, is recruited upstream of Nanog, within a region enriched for histone H3 lysine 9 tri-methylation (H3K9me3). Whereas before differentiation H3K9me3 at Nanog depends on ERK, in somatic cells it becomes independent of ERK. Moreover, the loss of H3K9me3 at Nanog, induced by deleting the region or by knocking out DNA methyltransferases or Zfp57, is associated with reduced heterogeneity of NANOG, delayed commitment into differentiation and impaired ability to acquire a primitive endoderm fate. Hence, a network axis centred on DNA methylation, ZFP57 and H3K9me3 links Nanog regulation to ERK activity for the timely establishment of new cell identities. We suggest that establishment of irreversible H3K9me3 at specific master regulators allows the acquisition of particular cell fates during differentiation. Summary: A regulatory axis integrating ERK, ZFP57, DNA and H3K9 methylation underlies the transition of Nanog expression from heterogeneous and dynamic to irreversibly silenced, enabling differentiation commitment and primitive endoderm specification.
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Affiliation(s)
- Agnès Dubois
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit 1 Department of Developmental and Stem Cell Biology , , F-75015 Paris , France
| | - Loris Vincenti
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit 1 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 1 Department of Developmental and Stem Cell Biology , , F-75015 Paris , France
| | - Maxim V. C. Greenberg
- Department of Genetics and Developmental Biology, Institut Curie, PSL Research University, INSERM, CNRS 2 , 75005 Paris , France
- Université Paris Cité, CNRS, Institut Jacques Monod 3 , F-75013 Paris , France
| | - Sandrine Vandormael-Pournin
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit 1 Department of Developmental and Stem Cell Biology , , F-75015 Paris , France
| | - Déborah Bourc'his
- Department of Genetics and Developmental Biology, Institut Curie, PSL Research University, INSERM, CNRS 2 , 75005 Paris , France
| | - Michel Cohen-Tannoudji
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit 1 Department of Developmental and Stem Cell Biology , , F-75015 Paris , France
| | - Pablo Navarro
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit 1 Department of Developmental and Stem Cell Biology , , F-75015 Paris , France
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5
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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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6
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Nishio M, Matsuura T, Hibi S, Ohta S, Oka C, Sasai N, Ishida Y, Matsuda E. Heterozygous loss of Zbtb38 leads to early embryonic lethality via the suppression of Nanog and Sox2 expression. Cell Prolif 2022; 55:e13215. [PMID: 35297517 PMCID: PMC9055898 DOI: 10.1111/cpr.13215] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 02/17/2022] [Accepted: 02/22/2022] [Indexed: 01/27/2023] Open
Abstract
Objectives Mammalian DNA methyltransferases are essential to re‐establish global DNA methylation patterns during implantation, which is critical for transmitting epigenetic information to the next generation. In contrast, the significance of methyl‐CpG binding proteins (MBPs) that bind methylated CpG remains almost unknown at this stage. We previously demonstrated that Zbtb38 (also known as CIBZ)—a zinc finger type of MBP—is required for mouse embryonic stem (ES) cell proliferation by positively regulating Nanog expression. However, the physiological function of Zbtb38 in vivo remains unclear. Materials and Methods This study used the Cre‐loxP system to generate conditional Zbtb38 knockout mice. Cell proliferation and apoptosis were studied by immunofluorescence staining. Quantitative real‐time PCR, immunoblotting and immunofluorescence were performed to investigate the molecular mechanisms. Results Germline loss of the Zbtb38 single allele resulted in decreased epiblast cell proliferation and increased apoptosis shortly after implantation, leading to early embryonic lethality. Heterozygous loss of Zbtb38 reduced the expression of Nanog, Sox2, and the genes responsible for epiblast proliferation, differentiation, and cell viability. Although this early lethal phenotype, Zbtb38 is dispensable for ES cell establishment and identity. Conclusions These findings indicate that Zbtb38 is essential for early embryonic development via the suppression of Nanog and Sox2 expression.
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Affiliation(s)
- Miki Nishio
- Functional Genomics and Medicine, Nara Institute of Science and Technology, Ikoma, Japan.,Cosmo Bio Co., Ltd., Tokyo, Japan
| | - Takuya Matsuura
- Functional Genomics and Medicine, Nara Institute of Science and Technology, Ikoma, Japan
| | - Shunya Hibi
- Functional Genomics and Medicine, Nara Institute of Science and Technology, Ikoma, Japan
| | - Shiomi Ohta
- Functional Genomics and Medicine, Nara Institute of Science and Technology, Ikoma, Japan
| | - Chio Oka
- Functional Genomics and Medicine, Nara Institute of Science and Technology, Ikoma, Japan
| | - Noriaki Sasai
- Development Biomedical Science, Nara Institute of Science and Technology, Ikoma, Japan
| | - Yasumasa Ishida
- Functional Genomics and Medicine, Nara Institute of Science and Technology, Ikoma, Japan
| | - Eishou Matsuda
- Functional Genomics and Medicine, Nara Institute of Science and Technology, Ikoma, Japan
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7
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Carlini V, Policarpi C, Hackett JA. Epigenetic inheritance is gated by naïve pluripotency and Dppa2. EMBO J 2022; 41:e108677. [PMID: 35199868 PMCID: PMC8982627 DOI: 10.15252/embj.2021108677] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 01/12/2022] [Accepted: 01/17/2022] [Indexed: 12/14/2022] Open
Abstract
Environmental factors can trigger cellular responses that propagate across mitosis or even generations. Perturbations to the epigenome could underpin such acquired changes, however, the extent and contexts in which modified chromatin states confer heritable memory in mammals is unclear. Here, we exploit a precision epigenetic editing strategy and forced Xist activity to programme de novo heterochromatin domains (epialleles) at endogenous loci and track their inheritance in a developmental model. We find that naïve pluripotent phases systematically erase ectopic domains of heterochromatin via active mechanisms, which likely acts as an intergenerational safeguard against transmission of epialleles. Upon lineage specification, however, acquired chromatin states can be probabilistically inherited under selectively favourable conditions, including propagation of p53 silencing through in vivo development. Using genome‐wide CRISPR screening, we identify molecular factors that restrict heritable memory of epialleles in naïve pluripotent cells, and demonstrate that removal of chromatin factor Dppa2 unlocks the potential for epigenetic inheritance uncoupled from DNA sequence. Our study outlines a mechanistic basis for how epigenetic inheritance is constrained in mammals, and reveals genomic and developmental contexts in which heritable memory is feasible.
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Affiliation(s)
- Valentina Carlini
- Epigenetics & Neurobiology Unit, European Molecular Biology Laboratory (EMBL), Rome, Italy.,Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Heidelberg, Germany
| | - Cristina Policarpi
- Epigenetics & Neurobiology Unit, European Molecular Biology Laboratory (EMBL), Rome, Italy
| | - Jamie A Hackett
- Epigenetics & Neurobiology Unit, European Molecular Biology Laboratory (EMBL), Rome, Italy
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8
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Fischer V, Plassard D, Ye T, Reina-San-Martin B, Stierle M, Tora L, Devys D. The related coactivator complexes SAGA and ATAC control embryonic stem cell self-renewal through acetyltransferase-independent mechanisms. Cell Rep 2021; 36:109598. [PMID: 34433046 PMCID: PMC8430043 DOI: 10.1016/j.celrep.2021.109598] [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: 01/27/2021] [Revised: 06/17/2021] [Accepted: 08/03/2021] [Indexed: 01/10/2023] Open
Abstract
SAGA (Spt-Ada-Gcn5 acetyltransferase) and ATAC (Ada-two-A-containing) are two related coactivator complexes, sharing the same histone acetyltransferase (HAT) subunit. The HAT activities of SAGA and ATAC are required for metazoan development, but the role of these complexes in RNA polymerase II transcription is less understood. To determine whether SAGA and ATAC have redundant or specific functions, we compare the effects of HAT inactivation in each complex with that of inactivation of either SAGA or ATAC core subunits in mouse embryonic stem cells (ESCs). We show that core subunits of SAGA or ATAC are required for complex assembly and mouse ESC growth and self-renewal. Surprisingly, depletion of HAT module subunits causes a global decrease in histone H3K9 acetylation, but does not result in significant phenotypic or transcriptional defects. Thus, our results indicate that SAGA and ATAC are differentially required for self-renewal of mouse ESCs by regulating transcription through different pathways in a HAT-independent manner.
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Affiliation(s)
- Veronique Fischer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch Cedex, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch Cedex, France; Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch Cedex, France; Université de Strasbourg, 67000 Strasbourg, France
| | - Damien Plassard
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch Cedex, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch Cedex, France; Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch Cedex, France; Université de Strasbourg, 67000 Strasbourg, France; Plateforme GenomEast, infrastructure France Génomique, Illkirch, France
| | - Tao Ye
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch Cedex, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch Cedex, France; Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch Cedex, France; Université de Strasbourg, 67000 Strasbourg, France; Plateforme GenomEast, infrastructure France Génomique, Illkirch, France
| | - Bernardo Reina-San-Martin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch Cedex, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch Cedex, France; Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch Cedex, France; Université de Strasbourg, 67000 Strasbourg, France
| | - Matthieu Stierle
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch Cedex, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch Cedex, France; Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch Cedex, France; Université de Strasbourg, 67000 Strasbourg, France
| | - Laszlo Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch Cedex, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch Cedex, France; Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch Cedex, France; Université de Strasbourg, 67000 Strasbourg, France
| | - Didier Devys
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch Cedex, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch Cedex, France; Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch Cedex, France; Université de Strasbourg, 67000 Strasbourg, France.
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9
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Wang F, El-Saafin F, Ye T, Stierle M, Negroni L, Durik M, Fischer V, Devys D, Vincent SD, Tora L. Histone H2Bub1 deubiquitylation is essential for mouse development, but does not regulate global RNA polymerase II transcription. Cell Death Differ 2021; 28:2385-2403. [PMID: 33731875 PMCID: PMC8329007 DOI: 10.1038/s41418-021-00759-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 02/18/2021] [Accepted: 02/23/2021] [Indexed: 01/31/2023] Open
Abstract
Co-activator complexes dynamically deposit post-translational modifications (PTMs) on histones, or remove them, to regulate chromatin accessibility and/or to create/erase docking surfaces for proteins that recognize histone PTMs. SAGA (Spt-Ada-Gcn5 Acetyltransferase) is an evolutionary conserved multisubunit co-activator complex with modular organization. The deubiquitylation module (DUB) of mammalian SAGA complex is composed of the ubiquitin-specific protease 22 (USP22) and three adaptor proteins, ATXN7, ATXN7L3 and ENY2, which are all needed for the full activity of the USP22 enzyme to remove monoubiquitin (ub1) from histone H2B. Two additional USP22-related ubiquitin hydrolases (called USP27X or USP51) have been described to form alternative DUBs with ATXN7L3 and ENY2, which can also deubiquitylate H2Bub1. Here we report that USP22 and ATXN7L3 are essential for normal embryonic development of mice, however their requirements are not identical during this process, as Atxn7l3-/- embryos show developmental delay already at embryonic day (E) 7.5, while Usp22-/- embryos are normal at this stage, but die at E14.5. Global histone H2Bub1 levels were only slightly affected in Usp22 null embryos, in contrast H2Bub1 levels were strongly increased in Atxn7l3 null embryos and derived cell lines. Our transcriptomic analyses carried out from wild type and Atxn7l3-/- mouse embryonic stem cells (mESCs), or primary mouse embryonic fibroblasts (MEFs) suggest that the ATXN7L3-related DUB activity regulates only a subset of genes in both cell types. However, the gene sets and the extent of their deregulation were different in mESCs and MEFs. Interestingly, the strong increase of H2Bub1 levels observed in the Atxn7l3-/- mESCs, or Atxn7l3-/- MEFs, does not correlate with the modest changes in RNA Polymerase II (Pol II) occupancy and lack of changes in Pol II elongation observed in the two Atxn7l3-/- cellular systems. These observations together indicate that deubiquitylation of histone H2Bub1 does not directly regulate global Pol II transcription elongation.
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Affiliation(s)
- Fang Wang
- grid.420255.40000 0004 0638 2716Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France ,grid.4444.00000 0001 2112 9282Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404 Illkirch, France ,grid.7429.80000000121866389Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404 Illkirch, France ,grid.420255.40000 0004 0638 2716Université de Strasbourg, 67404 Illkirch, France
| | - Farrah El-Saafin
- grid.420255.40000 0004 0638 2716Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France ,grid.4444.00000 0001 2112 9282Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404 Illkirch, France ,grid.7429.80000000121866389Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404 Illkirch, France ,grid.420255.40000 0004 0638 2716Université de Strasbourg, 67404 Illkirch, France ,grid.482637.cPresent Address: Olivia Newton-John Cancer Research Institute, Melbourne, VIC Australia
| | - Tao Ye
- grid.420255.40000 0004 0638 2716Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France ,grid.4444.00000 0001 2112 9282Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404 Illkirch, France ,grid.7429.80000000121866389Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404 Illkirch, France ,grid.420255.40000 0004 0638 2716Université de Strasbourg, 67404 Illkirch, France ,Plateforme GenomEast, infrastructure France Génomique, 67404 Illkirch, France
| | - Matthieu Stierle
- grid.420255.40000 0004 0638 2716Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France ,grid.4444.00000 0001 2112 9282Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404 Illkirch, France ,grid.7429.80000000121866389Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404 Illkirch, France ,grid.420255.40000 0004 0638 2716Université de Strasbourg, 67404 Illkirch, France
| | - Luc Negroni
- grid.420255.40000 0004 0638 2716Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France ,grid.4444.00000 0001 2112 9282Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404 Illkirch, France ,grid.7429.80000000121866389Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404 Illkirch, France ,grid.420255.40000 0004 0638 2716Université de Strasbourg, 67404 Illkirch, France
| | - Matej Durik
- grid.420255.40000 0004 0638 2716Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France ,grid.4444.00000 0001 2112 9282Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404 Illkirch, France ,grid.7429.80000000121866389Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404 Illkirch, France ,grid.420255.40000 0004 0638 2716Université de Strasbourg, 67404 Illkirch, France
| | - Veronique Fischer
- grid.420255.40000 0004 0638 2716Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France ,grid.4444.00000 0001 2112 9282Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404 Illkirch, France ,grid.7429.80000000121866389Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404 Illkirch, France ,grid.420255.40000 0004 0638 2716Université de Strasbourg, 67404 Illkirch, France
| | - Didier Devys
- grid.420255.40000 0004 0638 2716Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France ,grid.4444.00000 0001 2112 9282Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404 Illkirch, France ,grid.7429.80000000121866389Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404 Illkirch, France ,grid.420255.40000 0004 0638 2716Université de Strasbourg, 67404 Illkirch, France
| | - Stéphane D. Vincent
- grid.420255.40000 0004 0638 2716Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France ,grid.4444.00000 0001 2112 9282Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404 Illkirch, France ,grid.7429.80000000121866389Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404 Illkirch, France ,grid.420255.40000 0004 0638 2716Université de Strasbourg, 67404 Illkirch, France
| | - László Tora
- grid.420255.40000 0004 0638 2716Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France ,grid.4444.00000 0001 2112 9282Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404 Illkirch, France ,grid.7429.80000000121866389Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404 Illkirch, France ,grid.420255.40000 0004 0638 2716Université de Strasbourg, 67404 Illkirch, France
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10
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Posfai E, Lanner F, Mulas C, Leitch HG. All models are wrong, but some are useful: Establishing standards for stem cell-based embryo models. Stem Cell Reports 2021; 16:1117-1141. [PMID: 33979598 PMCID: PMC8185978 DOI: 10.1016/j.stemcr.2021.03.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 03/17/2021] [Accepted: 03/17/2021] [Indexed: 02/06/2023] Open
Abstract
Detailed studies of the embryo allow an increasingly mechanistic understanding of development, which has proved of profound relevance to human disease. The last decade has seen in vitro cultured stem cell-based models of embryo development flourish, which provide an alternative to the embryo for accessible experimentation. However, the usefulness of any stem cell-based embryo model will be determined by how accurately it reflects in vivo embryonic development, and/or the extent to which it facilitates new discoveries. Stringent benchmarking of embryo models is thus an important consideration for this growing field. Here we provide an overview of means to evaluate both the properties of stem cells, the building blocks of most embryo models, as well as the usefulness of current and future in vitro embryo models.
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Affiliation(s)
- Eszter Posfai
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
| | - Fredrik Lanner
- Department of Clinical Sciences, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden; Division of Obstetrics and Gynecology, Karolinska Universitetssjukhuset, Stockholm, Sweden; Ming Wai Lau Center for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden
| | - Carla Mulas
- Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Harry G Leitch
- MRC London Institute of Medical Sciences, London, UK; Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, UK; Centre for Paediatrics and Child Health, Faculty of Medicine, Imperial College London, London W2 1PG, UK
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11
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Ancona M, Michieletto D, Marenduzzo D. Competition between local erasure and long-range spreading of a single biochemical mark leads to epigenetic bistability. Phys Rev E 2021; 101:042408. [PMID: 32422714 DOI: 10.1103/physreve.101.042408] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 02/19/2020] [Indexed: 11/07/2022]
Abstract
The mechanism through which cells determine their fate is intimately related to the spreading of certain biochemical (so-called epigenetic) marks along their genome. The mechanisms behind mark spreading and maintenance are not yet fully understood, and current models often assume a long-range infectionlike process for the dynamics of marks, due to the polymeric nature of the chromatin fiber which allows looping between distant sites. While these existing models typically consider antagonizing marks, here we propose a qualitatively different scenario which analyses the spreading of a single mark. We define a one-dimensional stochastic model in which mark spreading/infection occurs as a long-range process whereas mark erasure/recovery is a local process, with an enhanced rate at boundaries of infected domains. In the limiting case where our model exhibits absorbing states, we find a first-order-like transition separating the marked/infected phase from the unmarked/recovered phase. This suggests that our model, in this limit, belongs to the long-range compact directed percolation universality class. The abrupt nature of the transition is retained in a more biophysically realistic situation when a basal infection/recovery rate is introduced (thereby removing absorbing states). Close to the transition there is a range of bistability where both the marked/infected and unmarked/recovered states are metastable and long lived, which provides a possible avenue for controlling fate decisions in cells. Increasing the basal infection/recovery rate, we find a second transition between a coherent (marked or unmarked) phase, and a mixed, or random, one.
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Affiliation(s)
- Marco Ancona
- SUPA, School of Physics and Astronomy, University of Edinburgh, Edinburgh EH9 3FD, United Kingdom
| | - Davide Michieletto
- SUPA, School of Physics and Astronomy, University of Edinburgh, Edinburgh EH9 3FD, United Kingdom.,MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom.,Centre for Mathematical Biology, and Department of Mathematical Sciences, University of Bath, North Road, Bath BA2 7AY, United Kingdom
| | - Davide Marenduzzo
- SUPA, School of Physics and Astronomy, University of Edinburgh, Edinburgh EH9 3FD, United Kingdom
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12
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Gonzalez I, Molliex A, Navarro P. Mitotic memories of gene activity. Curr Opin Cell Biol 2021; 69:41-47. [PMID: 33454629 DOI: 10.1016/j.ceb.2020.12.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/08/2020] [Accepted: 12/13/2020] [Indexed: 11/28/2022]
Abstract
When cells enter mitosis, they undergo series of dramatic changes in their structure and function that severely hamper gene regulatory processes and gene transcription. This raises the question of how daughter cells efficiently recapitulate the gene expression profile of their mother such that cell identity can be preserved. Here, we review recent evidence supporting the view that distinct chromatin-associated mechanisms of gene-regulatory inheritance assist daughter cells in the postmitotic reestablishment of gene activity with increased fidelity.
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Affiliation(s)
- Inma Gonzalez
- Epigenomics, Proliferation and the Identity of Cells, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS, UMR3738, Paris, France
| | - Amandine Molliex
- Epigenomics, Proliferation and the Identity of Cells, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS, UMR3738, Paris, France
| | - Pablo Navarro
- Epigenomics, Proliferation and the Identity of Cells, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS, UMR3738, Paris, France.
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13
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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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14
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Owens N, Papadopoulou T, Festuccia N, Tachtsidi A, Gonzalez I, Dubois A, Vandormael-Pournin S, Nora EP, Bruneau BG, Cohen-Tannoudji M, Navarro P. CTCF confers local nucleosome resiliency after DNA replication and during mitosis. eLife 2019; 8:e47898. [PMID: 31599722 PMCID: PMC6844645 DOI: 10.7554/elife.47898] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 10/09/2019] [Indexed: 12/20/2022] Open
Abstract
The access of Transcription Factors (TFs) to their cognate DNA binding motifs requires a precise control over nucleosome positioning. This is especially important following DNA replication and during mitosis, both resulting in profound changes in nucleosome organization over TF binding regions. Using mouse Embryonic Stem (ES) cells, we show that the TF CTCF displaces nucleosomes from its binding site and locally organizes large and phased nucleosomal arrays, not only in interphase steady-state but also immediately after replication and during mitosis. Correlative analyses suggest this is associated with fast gene reactivation following replication and mitosis. While regions bound by other TFs (Oct4/Sox2), display major rearrangement, the post-replication and mitotic nucleosome positioning activity of CTCF is not unique: Esrrb binding regions are also characterized by persistent nucleosome positioning. Therefore, selected TFs such as CTCF and Esrrb act as resilient TFs governing the inheritance of nucleosome positioning at regulatory regions throughout the cell-cycle.
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Affiliation(s)
- Nick Owens
- Epigenomics, Proliferation, and the Identity of Cells, Department of Developmental and Stem Cell BiologyInstitut Pasteur, CNRS UMR3738ParisFrance
- Equipe Labellisée LIGUE Contre le CancerParisFrance
| | - Thaleia Papadopoulou
- Epigenomics, Proliferation, and the Identity of Cells, Department of Developmental and Stem Cell BiologyInstitut Pasteur, CNRS UMR3738ParisFrance
- Equipe Labellisée LIGUE Contre le CancerParisFrance
| | - Nicola Festuccia
- Epigenomics, Proliferation, and the Identity of Cells, Department of Developmental and Stem Cell BiologyInstitut Pasteur, CNRS UMR3738ParisFrance
- Equipe Labellisée LIGUE Contre le CancerParisFrance
| | - Alexandra Tachtsidi
- Epigenomics, Proliferation, and the Identity of Cells, Department of Developmental and Stem Cell BiologyInstitut Pasteur, CNRS UMR3738ParisFrance
- Equipe Labellisée LIGUE Contre le CancerParisFrance
- Sorbonne Université, Collège DoctoralParisFrance
| | - Inma Gonzalez
- Epigenomics, Proliferation, and the Identity of Cells, Department of Developmental and Stem Cell BiologyInstitut Pasteur, CNRS UMR3738ParisFrance
- Equipe Labellisée LIGUE Contre le CancerParisFrance
| | - Agnes Dubois
- Epigenomics, Proliferation, and the Identity of Cells, Department of Developmental and Stem Cell BiologyInstitut Pasteur, CNRS UMR3738ParisFrance
- Equipe Labellisée LIGUE Contre le CancerParisFrance
| | - Sandrine Vandormael-Pournin
- Epigenomics, Proliferation, and the Identity of Cells, Department of Developmental and Stem Cell BiologyInstitut Pasteur, CNRS UMR3738ParisFrance
- Early Mammalian Development and Stem Cell Biology, Department of Developmental and Stem Cell BiologyInstitut Pasteur, CNRS UMR 3738ParisFrance
| | - Elphège P Nora
- Gladstone InstitutesSan FranciscoUnited States
- Cardiovascular Research InstituteUniversity of California, San FranciscoSan FranciscoUnited States
| | - Benoit G Bruneau
- Gladstone InstitutesSan FranciscoUnited States
- Cardiovascular Research InstituteUniversity of California, San FranciscoSan FranciscoUnited States
- Department of PediatricsUniversity of California, San FranciscoSan FranciscoUnited States
| | - Michel Cohen-Tannoudji
- Epigenomics, Proliferation, and the Identity of Cells, Department of Developmental and Stem Cell BiologyInstitut Pasteur, CNRS UMR3738ParisFrance
- Early Mammalian Development and Stem Cell Biology, Department of Developmental and Stem Cell BiologyInstitut Pasteur, CNRS UMR 3738ParisFrance
| | - Pablo Navarro
- Epigenomics, Proliferation, and the Identity of Cells, Department of Developmental and Stem Cell BiologyInstitut Pasteur, CNRS UMR3738ParisFrance
- Equipe Labellisée LIGUE Contre le CancerParisFrance
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15
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Ferrari A, Longo R, Silva R, Mitro N, Caruso D, De Fabiani E, Crestani M. Epigenome modifiers and metabolic rewiring: New frontiers in therapeutics. Pharmacol Ther 2019; 193:178-193. [DOI: 10.1016/j.pharmthera.2018.08.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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16
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Pennings S, Revuelta A, McLaughlin KA, Abd Hadi NA, Petchreing P, Ottaviano R, Meehan RR. Dynamics and Mechanisms of DNA Methylation Reprogramming. EPIGENETICS AND REGENERATION 2019:19-45. [DOI: 10.1016/b978-0-12-814879-2.00002-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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17
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Fabbrizi MR, Warshowsky KE, Zobel CL, Hallahan DE, Sharma GG. Molecular and epigenetic regulatory mechanisms of normal stem cell radiosensitivity. Cell Death Discov 2018; 4:117. [PMID: 30588339 PMCID: PMC6299079 DOI: 10.1038/s41420-018-0132-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 11/01/2018] [Accepted: 11/20/2018] [Indexed: 12/14/2022] Open
Abstract
Ionizing radiation (IR) therapy is a major cancer treatment modality and an indispensable auxiliary treatment for primary and metastatic cancers, but invariably results in debilitating organ dysfunctions. IR-induced depletion of neural stem/progenitor cells in the subgranular zone of the dentate gyrus in the hippocampus where neurogenesis occurs is considered largely responsible for deficiencies such as learning, memory, and spatial information processing in patients subjected to cranial irradiation. Similarly, IR therapy-induced intestinal injuries such as diarrhea and malabsorption are common side effects in patients with gastrointestinal tumors and are believed to be caused by intestinal stem cell drop out. Hematopoietic stem cell transplantation is currently used to reinstate blood production in leukemia patients and pre-clinical treatments show promising results in other organs such as the skin and kidney, but ethical issues and logistic problems make this route difficult to follow. An alternative way to restore the injured tissue is to preserve the stem cell pool located in that specific tissue/organ niche, but stem cell response to ionizing radiation is inadequately understood at the molecular mechanistic level. Although embryonic and fetal hypersensity to IR has been very well known for many decades, research on embryonic stem cell models in culture concerning molecular mechanisms have been largely inconclusive and often in contradiction of the in vivo observations. This review will summarize the latest discoveries on stem cell radiosensitivity, highlighting the possible molecular and epigenetic mechanism(s) involved in DNA damage response and programmed cell death after ionizing radiation therapy specific to normal stem cells. Finally, we will analyze the possible contribution of stem cell-specific chromatin's epigenetic constitution in promoting normal stem cell radiosensitivity.
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Affiliation(s)
- Maria Rita Fabbrizi
- Cancer Biology Division, Department of Radiation Oncology, Washington University School of Medicine, 4511 Forest Park, Saint Louis, MO 63108 USA
| | - Kacie E. Warshowsky
- Cancer Biology Division, Department of Radiation Oncology, Washington University School of Medicine, 4511 Forest Park, Saint Louis, MO 63108 USA
| | - Cheri L. Zobel
- Cancer Biology Division, Department of Radiation Oncology, Washington University School of Medicine, 4511 Forest Park, Saint Louis, MO 63108 USA
| | - Dennis E. Hallahan
- Cancer Biology Division, Department of Radiation Oncology, Washington University School of Medicine, 4511 Forest Park, Saint Louis, MO 63108 USA
- Siteman Cancer Center, Washington University School of Medicine, Saint Louis, MO 63108 USA
| | - Girdhar G. Sharma
- Cancer Biology Division, Department of Radiation Oncology, Washington University School of Medicine, 4511 Forest Park, Saint Louis, MO 63108 USA
- Siteman Cancer Center, Washington University School of Medicine, Saint Louis, MO 63108 USA
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18
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Festuccia N, Halbritter F, Corsinotti A, Gagliardi A, Colby D, Tomlinson SR, Chambers I. Esrrb extinction triggers dismantling of naïve pluripotency and marks commitment to differentiation. EMBO J 2018; 37:e95476. [PMID: 30275266 PMCID: PMC6213284 DOI: 10.15252/embj.201695476] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 08/24/2018] [Accepted: 08/27/2018] [Indexed: 11/25/2022] Open
Abstract
Self-renewal of embryonic stem cells (ESCs) cultured in LIF/fetal calf serum (FCS) is incomplete with some cells initiating differentiation. While this is reflected in heterogeneous expression of naive pluripotency transcription factors (TFs), the link between TF heterogeneity and differentiation is not fully understood. Here, we purify ESCs with distinct TF expression levels from LIF/FCS cultures to uncover early events during commitment from naïve pluripotency. ESCs carrying fluorescent Nanog and Esrrb reporters show Esrrb downregulation only in Nanoglow cells. Independent Esrrb reporter lines demonstrate that Esrrbnegative ESCs cannot effectively self-renew. Upon Esrrb loss, pre-implantation pluripotency gene expression collapses. ChIP-Seq identifies different regulatory element classes that bind both OCT4 and NANOG in Esrrbpositive cells. Class I elements lose NANOG and OCT4 binding in Esrrbnegative ESCs and associate with genes expressed preferentially in naïve ESCs. In contrast, Class II elements retain OCT4 but not NANOG binding in ESRRB-negative cells and associate with more broadly expressed genes. Therefore, mechanistic differences in TF function act cumulatively to restrict potency during exit from naïve pluripotency.
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Affiliation(s)
- Nicola Festuccia
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Florian Halbritter
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Andrea Corsinotti
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Alessia Gagliardi
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Douglas Colby
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Simon R Tomlinson
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Ian Chambers
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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19
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Chuang JH, Yarmishyn AA, Hwang DK, Hsu CC, Wang ML, Yang YP, Chien KH, Chiou SH, Peng CH, Chen SJ. Expression profiling of cell-intrinsic regulators in the process of differentiation of human iPSCs into retinal lineages. Stem Cell Res Ther 2018; 9:140. [PMID: 29751772 PMCID: PMC5948821 DOI: 10.1186/s13287-018-0848-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 03/06/2018] [Accepted: 03/16/2018] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Differentiation of human induced pluripotent stem cells (hiPSCs) into retinal lineages offers great potential for medical application. Therefore, it is of crucial importance to know the key intrinsic regulators of differentiation and the specific biomarker signatures of cell lineages. METHODS In this study, we used microarrays to analyze transcriptomes of terminally differentiated retinal ganglion cell (RGC) and retinal pigment epithelium (RPE) lineages, as well as intermediate retinal progenitor cells of optic vesicles (OVs) derived from hiPSCs. In our analysis, we specifically focused on the classes of transcripts that encode intrinsic regulators of gene expression: the transcription factors (TFs) and epigenetic chromatin state regulators. We applied two criteria for the selection of potentially important regulators and markers: firstly, the magnitude of fold-change of upregulation; secondly, the contrasted pattern of differential expression between OV, RGC and RPE lineages. RESULTS We found that among the most highly overexpressed TF-encoding genes in the OV/RGC lineage were three members of the Collier/Olfactory-1/Early B-cell family: EBF1, EBF2 and EBF3. Knockdown of EBF1 led to significant impairment of differentiation of hiPSCs into RGCs. EBF1 was shown to act upstream of ISL1 and BRN3A, the well-characterized regulators of RGC lineage specification. TF-encoding genes DLX1, DLX2 and INSM1 were the most highly overexpressed genes in the OVs, indicating their important role in the early stages of retinal differentiation. Along with MITF, the two paralogs, BHLHE41 and BHLHE40, were the most robust TF markers of RPE cells. The markedly contrasted expression of ACTL6B, encoding the component of chromatin remodeling complex SWI/SNF, discriminated hiPSC-derived OV/RGC and RPE lineages. CONCLUSIONS We identified novel, potentially important intrinsic regulators of RGC and RPE cell lineage specification in the process of differentiation from hiPSCs. We demonstrated the crucial role played by EBF1 in differentiation of RGCs. We identified intrinsic regulator biomarker signatures of these two retinal cell types that can be applied with high confidence to confirm the cell lineage identities.
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Affiliation(s)
- Jen-Hua Chuang
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan.,Institute of Pharmacology, National Yang-Ming University, Taipei, Taiwan
| | - Aliaksandr A Yarmishyn
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan.,Institute of Pharmacology, National Yang-Ming University, Taipei, Taiwan
| | - De-Kuang Hwang
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei, Taiwan.,School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Chih-Chien Hsu
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan.,School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Mong-Lien Wang
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan.,Institute of Pharmacology, National Yang-Ming University, Taipei, Taiwan.,School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Yi-Ping Yang
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan.,Institute of Pharmacology, National Yang-Ming University, Taipei, Taiwan
| | - Ke-Hung Chien
- Department of Ophthalmology, Tri-Service General Hospital & National Defense Medical Center, Taipei, Taiwan
| | - Shih-Hwa Chiou
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan.,Institute of Pharmacology, National Yang-Ming University, Taipei, Taiwan.,School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Chi-Hsien Peng
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei, Taiwan. .,Department of Ophthalmology, Shin Kong Wu Ho-Su Memorial Hospital and Fu Jen Catholic University, Taipei, Taiwan.
| | - Shih-Jen Chen
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei, Taiwan. .,Department of Ophthalmology, Tri-Service General Hospital & National Defense Medical Center, Taipei, Taiwan. .,School of Medicine, National Yang-Ming University, Taipei, Taiwan.
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20
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Michieletto D, Chiang M, Colì D, Papantonis A, Orlandini E, Cook PR, Marenduzzo D. Shaping epigenetic memory via genomic bookmarking. Nucleic Acids Res 2018; 46:83-93. [PMID: 29190361 PMCID: PMC5758908 DOI: 10.1093/nar/gkx1200] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 11/06/2017] [Accepted: 11/19/2017] [Indexed: 12/18/2022] Open
Abstract
Reconciling the stability of epigenetic patterns with the rapid turnover of histone modifications and their adaptability to external stimuli is an outstanding challenge. Here, we propose a new biophysical mechanism that can establish and maintain robust yet plastic epigenetic domains via genomic bookmarking (GBM). We model chromatin as a recolourable polymer whose segments bear non-permanent histone marks (or colours) which can be modified by 'writer' proteins. The three-dimensional chromatin organisation is mediated by protein bridges, or 'readers', such as Polycomb Repressive Complexes and Transcription Factors. The coupling between readers and writers drives spreading of biochemical marks and sustains the memory of local chromatin states across replication and mitosis. In contrast, GBM-targeted perturbations destabilise the epigenetic patterns. Strikingly, we demonstrate that GBM alone can explain the full distribution of Polycomb marks in a whole Drosophila chromosome. We finally suggest that our model provides a starting point for an understanding of the biophysics of cellular differentiation and reprogramming.
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Affiliation(s)
- Davide Michieletto
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK
| | - Michael Chiang
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK
| | - Davide Colì
- Dipartimento di Fisica e Astronomia and Sezione INFN, Università di Padova, Via Marzolo 8, Padova 35131, Italy
| | - Argyris Papantonis
- Centre for Molecular Medicine, University of Cologne, Robert-Koch-Str. 21, D-50931, Cologne, DE, Germany
| | - Enzo Orlandini
- Dipartimento di Fisica e Astronomia and Sezione INFN, Università di Padova, Via Marzolo 8, Padova 35131, Italy
| | - Peter R Cook
- The Sir William Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, UK
| | - Davide Marenduzzo
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK
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21
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Festuccia N, Gonzalez I, Owens N, Navarro P. Mitotic bookmarking in development and stem cells. Development 2017; 144:3633-3645. [DOI: 10.1242/dev.146522] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The changes imposed on the nucleus, chromatin and its regulators during mitosis lead to the dismantlement of most gene regulatory processes. However, an increasing number of transcriptional regulators are being identified as capable of binding their genomic targets during mitosis. These so-called ‘mitotic bookmarking factors’ encompass transcription factors and chromatin modifiers that are believed to convey gene regulatory information from mother to daughter cells. In this Primer, we review mitotic bookmarking processes in development and stem cells and discuss the interest and potential importance of this concept with regard to epigenetic regulation and cell fate transitions involving cellular proliferation.
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Affiliation(s)
- Nicola Festuccia
- Epigenetics of Stem Cells, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR3738, 25 rue du Docteur Roux, 75015 Paris, France
| | - Inma Gonzalez
- Epigenetics of Stem Cells, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR3738, 25 rue du Docteur Roux, 75015 Paris, France
| | - Nick Owens
- Epigenetics of Stem Cells, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR3738, 25 rue du Docteur Roux, 75015 Paris, France
| | - Pablo Navarro
- Epigenetics of Stem Cells, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR3738, 25 rue du Docteur Roux, 75015 Paris, France
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22
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Festuccia N, Owens N, Navarro P. Esrrb, an estrogen-related receptor involved in early development, pluripotency, and reprogramming. FEBS Lett 2017; 592:852-877. [DOI: 10.1002/1873-3468.12826] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 08/11/2017] [Accepted: 08/19/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Nicola Festuccia
- Epigenetics of Stem Cells; Department of Developmental and Stem Cell Biology; Institut Pasteur; CNRS UMR3738; Paris France
| | - Nick Owens
- Epigenetics of Stem Cells; Department of Developmental and Stem Cell Biology; Institut Pasteur; CNRS UMR3738; Paris France
| | - Pablo Navarro
- Epigenetics of Stem Cells; Department of Developmental and Stem Cell Biology; Institut Pasteur; CNRS UMR3738; Paris France
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23
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Findlay GM, David L, Beyer TA. Molecular Mechanisms of Stem Cell Pluripotency and Cell Fate Specification. J Mol Biol 2017; 429:1439-1440. [PMID: 28302388 DOI: 10.1016/j.jmb.2017.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Greg M Findlay
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, The University of Dundee, Dundee DD1 5EH, UK.
| | - Laurent David
- INSERM UMS 016, SFR Francois Bonamy, iPSC Core Facility, Nantes F-44000, France; CNRS UMS 3556, Nantes F-44000, France; Université de Nantes, Nantes F-44000, France; CHU de Nantes, Nantes F-44000, France; INSERM, Center for Research in Transplantation and Immunology (CRTI) U1064, Nantes F-44000, France; Université de Nantes, UMR 1064, Nantes F-44000, France.
| | - Tobias A Beyer
- Institute for Molecular Health Sciences, Department of Biology, ETH Zurich, Switzerland.
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