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Espinosa-Martínez M, Alcázar-Fabra M, Landeira D. The molecular basis of cell memory in mammals: The epigenetic cycle. SCIENCE ADVANCES 2024; 10:eadl3188. [PMID: 38416817 PMCID: PMC10901381 DOI: 10.1126/sciadv.adl3188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 01/26/2024] [Indexed: 03/01/2024]
Abstract
Cell memory refers to the capacity of cells to maintain their gene expression program once the initiating environmental signal has ceased. This exceptional feature is key during the formation of mammalian organisms, and it is believed to be in part mediated by epigenetic factors that can endorse cells with the landmarks required to maintain transcriptional programs upon cell duplication. Here, we review current literature analyzing the molecular basis of epigenetic memory in mammals, with a focus on the mechanisms by which transcriptionally repressive chromatin modifications such as methylation of DNA and histone H3 are propagated through mitotic cell divisions. The emerging picture suggests that cellular memory is supported by an epigenetic cycle in which reversible activities carried out by epigenetic regulators in coordination with cell cycle transition create a multiphasic system that can accommodate both maintenance of cell identity and cell differentiation in proliferating stem cell populations.
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Affiliation(s)
- Mencía Espinosa-Martínez
- Centre for Genomics and Oncological Research (GENYO), Avenue de la Ilustración 114, 18016 Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
| | - María Alcázar-Fabra
- Centre for Genomics and Oncological Research (GENYO), Avenue de la Ilustración 114, 18016 Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
| | - David Landeira
- Centre for Genomics and Oncological Research (GENYO), Avenue de la Ilustración 114, 18016 Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
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2
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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.
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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.
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3
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Contreras A, Perea-Resa C. Transcriptional repression across mitosis: mechanisms and functions. Biochem Soc Trans 2024; 52:455-464. [PMID: 38372373 PMCID: PMC10903446 DOI: 10.1042/bst20231071] [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: 12/07/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/20/2024]
Abstract
Transcription represents a central aspect of gene expression with RNA polymerase machineries (RNA Pol) driving the synthesis of RNA from DNA template molecules. In eukaryotes, a total of three RNA Pol enzymes generate the plethora of RNA species and RNA Pol II is the one transcribing all protein-coding genes. A high number of cis- and trans-acting factors orchestrates RNA Pol II-mediated transcription by influencing the chromatin recruitment, activation, elongation, and/or termination steps. The levels of DNA accessibility, defining open-euchromatin versus close-heterochromatin, delimits RNA Pol II activity as well as the encounter with other factors acting on chromatin such as the DNA replication or DNA repair machineries. The stage of the cell cycle highly influences RNA Pol II activity with mitosis representing the major challenge. In fact, there is a massive inhibition of transcription during the mitotic entry coupled with chromatin dissociation of most of the components of the transcriptional machinery. Mitosis, as a consequence, highly compromises the transcriptional memory and the perpetuation of cellular identity. Once mitosis ends, transcription levels immediately recover to define the cell fate and to safeguard the proper progression of daughter cells through the cell cycle. In this review, we evaluate our current understanding of the transcriptional repression associated with mitosis with a special focus on the molecular mechanisms involved, on the potential function behind the general repression, and on the transmission of the transcriptional machinery into the daughter cells. We finally discuss the contribution that errors in the inheritance of the transcriptional machinery across mitosis might play in stem cell aging.
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Affiliation(s)
- A. Contreras
- Centro de Biología Molecular Severo Ochoa (CBMSO-CSIC), C/Nicolas Cabrera 1, 28049 Madrid, Spain
| | - C. Perea-Resa
- Centro de Biología Molecular Severo Ochoa (CBMSO-CSIC), C/Nicolas Cabrera 1, 28049 Madrid, Spain
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4
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Ramos-Alonso L, Chymkowitch P. Maintaining transcriptional homeostasis during cell cycle. Transcription 2024; 15:1-21. [PMID: 37655806 PMCID: PMC11093055 DOI: 10.1080/21541264.2023.2246868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 09/02/2023] Open
Abstract
The preservation of gene expression patterns that define cellular identity throughout the cell division cycle is essential to perpetuate cellular lineages. However, the progression of cells through different phases of the cell cycle severely disrupts chromatin accessibility, epigenetic marks, and the recruitment of transcriptional regulators. Notably, chromatin is transiently disassembled during S-phase and undergoes drastic condensation during mitosis, which is a significant challenge to the preservation of gene expression patterns between cell generations. This article delves into the specific gene expression and chromatin regulatory mechanisms that facilitate the preservation of transcriptional identity during replication and mitosis. Furthermore, we emphasize our recent findings revealing the unconventional role of yeast centromeres and mitotic chromosomes in maintaining transcriptional fidelity beyond mitosis.
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Affiliation(s)
- Lucía Ramos-Alonso
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Pierre Chymkowitch
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
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5
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Hayashi S, Seki-Omura R, Yamada S, Kamata T, Sato Y, Oe S, Koike T, Nakano Y, Iwashita H, Hirahara Y, Tanaka S, Sekijima T, Ito T, Yasukochi Y, Higasa K, Kitada M. OLIG2 translocates to chromosomes during mitosis via a temperature downshift: A novel neural cold response of mitotic bookmarking. Gene 2024; 891:147829. [PMID: 37748631 DOI: 10.1016/j.gene.2023.147829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 09/09/2023] [Accepted: 09/22/2023] [Indexed: 09/27/2023]
Affiliation(s)
- Shinichi Hayashi
- Department of Anatomy, Faculty of Medicine, Kansai Medical University, Shinmachi 2-5-1, Hirakata, Osaka, Japan.
| | - Ryohei Seki-Omura
- Department of Anatomy, Faculty of Medicine, Kansai Medical University, Shinmachi 2-5-1, Hirakata, Osaka, Japan
| | - Shintaro Yamada
- Department of Functional Neuroscience, Institute of Biomedical Science, Kansai Medical University, Shinmachi 2-5-1, Hirakata, Osaka, Japan
| | - Taito Kamata
- Graduate School of Science and Technology, Niigata University, 8050 Ikarashi 2-nocho, Niigata, Japan; Faculty of Agriculture, Niigata University, 8050 Ikarashi 2-nocho, Niigata, Japan
| | - Yuki Sato
- Department of Anatomy, Faculty of Medicine, Kansai Medical University, Shinmachi 2-5-1, Hirakata, Osaka, Japan
| | - Souichi Oe
- Department of Anatomy, Faculty of Medicine, Kansai Medical University, Shinmachi 2-5-1, Hirakata, Osaka, Japan
| | - Taro Koike
- Department of Anatomy, Faculty of Medicine, Kansai Medical University, Shinmachi 2-5-1, Hirakata, Osaka, Japan
| | - Yousuke Nakano
- Department of Anatomy, Faculty of Medicine, Kansai Medical University, Shinmachi 2-5-1, Hirakata, Osaka, Japan
| | - Hikaru Iwashita
- Department of Anatomy, Faculty of Medicine, Kansai Medical University, Shinmachi 2-5-1, Hirakata, Osaka, Japan
| | - Yukie Hirahara
- Department of Anatomy, Faculty of Medicine, Kansai Medical University, Shinmachi 2-5-1, Hirakata, Osaka, Japan; Faculty of Nursing, Kansai Medical University, Shinmachi 2-2-2, Hirakata, Osaka, Japan
| | - Susumu Tanaka
- Department of Anatomy, Faculty of Medicine, Kansai Medical University, Shinmachi 2-5-1, Hirakata, Osaka, Japan; Department of Anatomy and Physiology, Faculty of Nursing and Nutrition, University of Nagasaki, Manabino 1-1-1, Nagasaki, Japan
| | - Tsuneo Sekijima
- Faculty of Agriculture, Niigata University, 8050 Ikarashi 2-nocho, Niigata, Japan
| | - Takeshi Ito
- Department of Genome Analysis, Institute of Biomedical Science, Kansai Medical University, Shinmachi 2-5-1, Hirakata, Osaka, Japan
| | - Yoshiki Yasukochi
- Department of Genome Analysis, Institute of Biomedical Science, Kansai Medical University, Shinmachi 2-5-1, Hirakata, Osaka, Japan
| | - Koichiro Higasa
- Department of Genome Analysis, Institute of Biomedical Science, Kansai Medical University, Shinmachi 2-5-1, Hirakata, Osaka, Japan
| | - Masaaki Kitada
- Department of Anatomy, Faculty of Medicine, Kansai Medical University, Shinmachi 2-5-1, Hirakata, Osaka, Japan.
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6
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Rizvi S, Chhabra A, Tripathi A, Tyagi RK. Mitotic genome-bookmarking by nuclear hormone receptors: A novel dimension in epigenetic reprogramming and disease assessment. Mol Cell Endocrinol 2023; 578:112069. [PMID: 37730146 DOI: 10.1016/j.mce.2023.112069] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 09/07/2023] [Accepted: 09/12/2023] [Indexed: 09/22/2023]
Abstract
Arrival of multi-colored fluorescent proteins and advances in live cell imaging has immensely contributed to our understanding of intracellular trafficking of nuclear receptors and their roles in gene regulatory functions. These regulatory events need to be faithfully propagated from progenitor to progeny cells. This is corroborated by multiple converging mechanisms that include histone modifications and lately, the phenomenon of 'mitotic genome-bookmarking' by specific transcription factors. This phenomenon refers to the retention and feed-forward transmission of progenitor's architectural blueprint of active transcription status which is silenced and preserved during mitosis. Upon mitotic exit, this phenomenon ensures accurate reactivation of transcriptome, proteome, cellular traits and phenotypes in the progeny cells. In addition to diverse modes of genome-bookmarking by nuclear receptors, a correlation between disease-associated receptor polymorphism and disruption of this phenomenon is apparent. However, breakthrough technologies shall reveal finer details of this phenomenon to help achieve normalcy in receptor-specific diseases.
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Affiliation(s)
- Sheeba Rizvi
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Ayushi Chhabra
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Anjali Tripathi
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Rakesh K Tyagi
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, 110067, India.
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7
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Kiseleva AA, Poleshko A. The secret life of chromatin tethers. FEBS Lett 2023; 597:2782-2790. [PMID: 37339933 PMCID: PMC10730768 DOI: 10.1002/1873-3468.14685] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/05/2023] [Accepted: 06/12/2023] [Indexed: 06/22/2023]
Abstract
The nuclear envelope plays an essential role in organizing the genome inside of the nucleus. The inner nuclear membrane is coated with a meshwork of filamentous lamin proteins that provide a surface to organize a variety of cellular processes. A subset of nuclear lamina- and membrane-associated proteins functions as anchors to hold transcriptionally silent heterochromatin at the nuclear periphery. While most chromatin tethers are integral membrane proteins, a limited number are lamina-bound. One example is the mammalian proline-rich 14 (PRR14) protein. PRR14 is a recently characterized protein with unique function that is different from other known chromatin tethers. Here, we review our current understanding of PRR14 structure and function in organizing heterochromatin at the nuclear periphery.
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Affiliation(s)
- Anna A. Kiseleva
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Andrey Poleshko
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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8
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Treichel S, Filippi MD. Linking cell cycle to hematopoietic stem cell fate decisions. Front Cell Dev Biol 2023; 11:1231735. [PMID: 37645247 PMCID: PMC10461445 DOI: 10.3389/fcell.2023.1231735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 07/26/2023] [Indexed: 08/31/2023] Open
Abstract
Hematopoietic stem cells (HSCs) have the properties to self-renew and/or differentiate into any blood cell lineages. In order to balance the maintenance of the stem cell pool with supporting mature blood cell production, the fate decisions to self-renew or to commit to differentiation must be tightly controlled, as dysregulation of this process can lead to bone marrow failure or leukemogenesis. The contribution of the cell cycle to cell fate decisions has been well established in numerous types of stem cells, including pluripotent stem cells. Cell cycle length is an integral component of hematopoietic stem cell fate. Hematopoietic stem cells must remain quiescent to prevent premature replicative exhaustion. Yet, hematopoietic stem cells must be activated into cycle in order to produce daughter cells that will either retain stem cell properties or commit to differentiation. How the cell cycle contributes to hematopoietic stem cell fate decisions is emerging from recent studies. Hematopoietic stem cell functions can be stratified based on cell cycle kinetics and divisional history, suggesting a link between Hematopoietic stem cells activity and cell cycle length. Hematopoietic stem cell fate decisions are also regulated by asymmetric cell divisions and recent studies have implicated metabolic and organelle activity in regulating hematopoietic stem cell fate. In this review, we discuss the current understanding of the mechanisms underlying hematopoietic stem cell fate decisions and how they are linked to the cell cycle.
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Affiliation(s)
- Sydney Treichel
- Division of Experimental Hematology and Cancer Biology, Department of Pediatrics, Cincinnati Children’s Hospital Research Foundation, Cincinnati, OH, United States
- University of Cincinnati College of Medicine, Cincinnati, OH, United States
- Molecular and Development Biology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Marie-Dominique Filippi
- Division of Experimental Hematology and Cancer Biology, Department of Pediatrics, Cincinnati Children’s Hospital Research Foundation, Cincinnati, OH, United States
- University of Cincinnati College of Medicine, Cincinnati, OH, United States
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9
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Silvério-Alves R, Kurochkin I, Rydström A, Vazquez Echegaray C, Haider J, Nicholls M, Rode C, Thelaus L, Lindgren AY, Ferreira AG, Brandão R, Larsson J, de Bruijn MFTR, Martin-Gonzalez J, Pereira CF. GATA2 mitotic bookmarking is required for definitive haematopoiesis. Nat Commun 2023; 14:4645. [PMID: 37580379 PMCID: PMC10425459 DOI: 10.1038/s41467-023-40391-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 07/26/2023] [Indexed: 08/16/2023] Open
Abstract
In mitosis, most transcription factors detach from chromatin, but some are retained and bookmark genomic sites. Mitotic bookmarking has been implicated in lineage inheritance, pluripotency and reprogramming. However, the biological significance of this mechanism in vivo remains unclear. Here, we address mitotic retention of the hemogenic factors GATA2, GFI1B and FOS during haematopoietic specification. We show that GATA2 remains bound to chromatin throughout mitosis, in contrast to GFI1B and FOS, via C-terminal zinc finger-mediated DNA binding. GATA2 bookmarks a subset of its interphase targets that are co-enriched for RUNX1 and other regulators of definitive haematopoiesis. Remarkably, homozygous mice harbouring the cyclin B1 mitosis degradation domain upstream Gata2 partially phenocopy knockout mice. Degradation of GATA2 at mitotic exit abolishes definitive haematopoiesis at aorta-gonad-mesonephros, placenta and foetal liver, but does not impair yolk sac haematopoiesis. Our findings implicate GATA2-mediated mitotic bookmarking as critical for definitive haematopoiesis and highlight a dependency on bookmarkers for lineage commitment.
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Affiliation(s)
- Rita Silvério-Alves
- Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84, Lund, Sweden
- Wallenberg Centre for Molecular Medicine, Lund University, BMC A12, 221 84, Lund, Sweden
- CNC - Centre for Neuroscience and Cell Biology, University of Coimbra, Largo Marquês do Pombal, 3004-517, Coimbra, Portugal
- Doctoral Programme in Experimental Biology and Biomedicine, University of Coimbra, Largo Marquês do Pombal, 3004-517, Coimbra, Portugal
| | - Ilia Kurochkin
- Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84, Lund, Sweden
- Wallenberg Centre for Molecular Medicine, Lund University, BMC A12, 221 84, Lund, Sweden
| | - Anna Rydström
- Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84, Lund, Sweden
| | - Camila Vazquez Echegaray
- Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84, Lund, Sweden
- Wallenberg Centre for Molecular Medicine, Lund University, BMC A12, 221 84, Lund, Sweden
| | - Jakob Haider
- Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84, Lund, Sweden
- Wallenberg Centre for Molecular Medicine, Lund University, BMC A12, 221 84, Lund, Sweden
| | - Matthew Nicholls
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK
| | - Christina Rode
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK
| | - Louise Thelaus
- Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84, Lund, Sweden
- Wallenberg Centre for Molecular Medicine, Lund University, BMC A12, 221 84, Lund, Sweden
| | - Aida Yifter Lindgren
- Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84, Lund, Sweden
- Wallenberg Centre for Molecular Medicine, Lund University, BMC A12, 221 84, Lund, Sweden
| | - Alexandra Gabriela Ferreira
- Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84, Lund, Sweden
- Wallenberg Centre for Molecular Medicine, Lund University, BMC A12, 221 84, Lund, Sweden
- CNC - Centre for Neuroscience and Cell Biology, University of Coimbra, Largo Marquês do Pombal, 3004-517, Coimbra, Portugal
- Doctoral Programme in Experimental Biology and Biomedicine, University of Coimbra, Largo Marquês do Pombal, 3004-517, Coimbra, Portugal
| | - Rafael Brandão
- Core Facility for Transgenic Mice, Department of Experimental Medicine, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Jonas Larsson
- Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84, Lund, Sweden
- Wallenberg Centre for Molecular Medicine, Lund University, BMC A12, 221 84, Lund, Sweden
| | - Marella F T R de Bruijn
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS, Oxford, UK
| | - Javier Martin-Gonzalez
- Core Facility for Transgenic Mice, Department of Experimental Medicine, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Carlos-Filipe Pereira
- Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84, Lund, Sweden.
- Wallenberg Centre for Molecular Medicine, Lund University, BMC A12, 221 84, Lund, Sweden.
- CNC - Centre for Neuroscience and Cell Biology, University of Coimbra, Largo Marquês do Pombal, 3004-517, Coimbra, Portugal.
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10
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Zhu Z, Chen X, Guo A, Manzano T, Walsh PJ, Wills KM, Halliburton R, Radko-Juettner S, Carter RD, Partridge JF, Green DR, Zhang J, Roberts CWM. Mitotic bookmarking by SWI/SNF subunits. Nature 2023; 618:180-187. [PMID: 37225980 PMCID: PMC10303083 DOI: 10.1038/s41586-023-06085-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 04/14/2023] [Indexed: 05/26/2023]
Abstract
For cells to initiate and sustain a differentiated state, it is necessary that a 'memory' of this state is transmitted through mitosis to the daughter cells1-3. Mammalian switch/sucrose non-fermentable (SWI/SNF) complexes (also known as Brg1/Brg-associated factors, or BAF) control cell identity by modulating chromatin architecture to regulate gene expression4-7, but whether they participate in cell fate memory is unclear. Here we provide evidence that subunits of SWI/SNF act as mitotic bookmarks to safeguard cell identity during cell division. The SWI/SNF core subunits SMARCE1 and SMARCB1 are displaced from enhancers but are bound to promoters during mitosis, and we show that this binding is required for appropriate reactivation of bound genes after mitotic exit. Ablation of SMARCE1 during a single mitosis in mouse embryonic stem cells is sufficient to disrupt gene expression, impair the occupancy of several established bookmarks at a subset of their targets and cause aberrant neural differentiation. Thus, SWI/SNF subunit SMARCE1 has a mitotic bookmarking role and is essential for heritable epigenetic fidelity during transcriptional reprogramming.
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Affiliation(s)
- Zhexin Zhu
- Division of Molecular Oncology, Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA.
| | - Xiaolong Chen
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Ao Guo
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Trishabelle Manzano
- Division of Molecular Oncology, Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Patrick J Walsh
- Division of Molecular Oncology, Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Kendall M Wills
- Division of Molecular Oncology, Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Rebecca Halliburton
- Division of Molecular Oncology, Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Sandi Radko-Juettner
- Division of Molecular Oncology, Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
- St Jude Graduate School of Biomedical Sciences, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Raymond D Carter
- Division of Molecular Oncology, Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Janet F Partridge
- Division of Molecular Oncology, Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Douglas R Green
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Jinghui Zhang
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Charles W M Roberts
- Division of Molecular Oncology, Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA.
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11
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Maeda Y, Isomura A, Masaki T, Kageyama R. Differential cell-cycle control by oscillatory versus sustained Hes1 expression via p21. Cell Rep 2023; 42:112520. [PMID: 37200191 DOI: 10.1016/j.celrep.2023.112520] [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: 06/23/2022] [Revised: 01/06/2023] [Accepted: 05/02/2023] [Indexed: 05/20/2023] Open
Abstract
Oscillatory Hes1 expression activates cell proliferation, while high and sustained Hes1 expression induces quiescence, but the mechanism by which Hes1 differentially controls cell proliferation depending on its expression dynamics is unclear. Here, we show that oscillatory Hes1 expression down-regulates the expression of the cyclin-dependent kinase inhibitor p21 (Cdkn1a), which delays cell-cycle progression, and thereby activates the proliferation of mouse neural stem cells (NSCs). By contrast, sustained Hes1 overexpression up-regulates p21 expression and inhibits NSC proliferation, although it initially down-regulates p21 expression. Compared with Hes1 oscillation, sustained Hes1 overexpression represses Dusp7, a phosphatase for phosphorylated Erk (p-Erk), and increases the levels of p-Erk, which can up-regulate p21 expression. These results indicate that p21 expression is directly repressed by oscillatory Hes1 expression, but indirectly up-regulated by sustained Hes1 overexpression, suggesting that depending on its expression dynamics, Hes1 differentially controls NSC proliferation via p21.
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Affiliation(s)
- Yuki Maeda
- RIKEN Center for Brain Science, Wako 351-0198, Japan; Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | - Akihiro Isomura
- Institute for Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan; Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto 606-8501, Japan; Japan Science and Technology Agency, PRESTO, Saitama 332-0012, Japan
| | - Taimu Masaki
- RIKEN Center for Brain Science, Wako 351-0198, Japan
| | - Ryoichiro Kageyama
- RIKEN Center for Brain Science, Wako 351-0198, Japan; Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan; Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan.
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12
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Ye B, Shen W, Li Y, Wang D, Zhang Y, Li P, Yin M, Wang Y, Xie D, Shi S, Yao T, Chen J, Xu P, Zhao Z. FAIRE-MS reveals mitotic retention of transcriptional regulators on a proteome-wide scale. FASEB J 2023; 37:e22724. [PMID: 36583687 DOI: 10.1096/fj.202201038rrr] [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: 06/29/2022] [Revised: 12/01/2022] [Accepted: 12/08/2022] [Indexed: 12/31/2022]
Abstract
Mitosis entails global and dramatic alterations, such as higher-order chromatin organization disruption, concomitant with global transcription downregulation. Cells reliably re-establishing gene expression patterns upon mitotic exit and maintaining cellular identities remain poorly understood. Previous studies indicated that certain transcription factors (TFs) remain associated with individual loci during mitosis and serve as mitotic bookmarkers. However, it is unclear which regulatory factors remain bound to the compacted mitotic chromosomes. We developed formaldehyde-assisted isolation of regulatory elements-coupled mass spectrometry (FAIRE-MS) that combines FAIRE-based open chromatin-associated protein pull-down and mass spectrometry (MS) to quantify the open chromatin-associated proteome during the interphase and mitosis. We identified 189 interphase and mitosis maintained (IM) regulatory factors using FAIRE-MS and found intrinsically disordered proteins and regions (IDP(R)s) are highly enriched, which plays a crucial role in liquid-liquid phase separation (LLPS) and chromatin organization during the cell cycle. Notably, in these IDP(R)s, we identified mitotic bookmarkers, such as CEBPB, HMGB1, and TFAP2A, and several factors, including MAX, HMGB3, hnRNP A2/B1, FUS, hnRNP D, and TIAL1, which are at least partially bound to the mitotic chromosome. Furthermore, it will be essential to study whether these IDP(R)s through LLPS helps cells transit from mitosis to the G1 phase during the cell cycle.
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Affiliation(s)
- Bingyu Ye
- Beijing Institute of Biotechnology, Beijing, China.,State Key Laboratory of Cell Differentiation and Regulation, College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Wenlong Shen
- Beijing Institute of Biotechnology, Beijing, China
| | - Yanchang Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Institute of Lifeomics, Beijing, China
| | - Dong Wang
- Beijing Institute of Biotechnology, Beijing, China
| | - Yan Zhang
- Beijing Institute of Biotechnology, Beijing, China
| | - Ping Li
- Beijing Institute of Biotechnology, Beijing, China
| | - Man Yin
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yahao Wang
- Beijing Institute of Biotechnology, Beijing, China
| | - Dejian Xie
- Beijing Institute of Biotechnology, Beijing, China
| | - Shu Shi
- Beijing Institute of Biotechnology, Beijing, China
| | - Tao Yao
- Beijing Institute of Biotechnology, Beijing, China
| | - Juncai Chen
- Beijing Institute of Biotechnology, Beijing, China
| | - Ping Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Institute of Lifeomics, Beijing, China
| | - Zhihu Zhao
- Beijing Institute of Biotechnology, Beijing, China
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13
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Alvarez V, Bandau S, Jiang H, Rios-Szwed D, Hukelmann J, Garcia-Wilson E, Wiechens N, Griesser E, Ten Have S, Owen-Hughes T, Lamond A, Alabert C. Proteomic profiling reveals distinct phases to the restoration of chromatin following DNA replication. Cell Rep 2023; 42:111996. [PMID: 36680776 DOI: 10.1016/j.celrep.2023.111996] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 08/12/2022] [Accepted: 01/03/2023] [Indexed: 01/21/2023] Open
Abstract
Chromatin organization must be maintained during cell proliferation to preserve cellular identity and genome integrity. However, DNA replication results in transient displacement of DNA-bound proteins, and it is unclear how they regain access to newly replicated DNA. Using quantitative proteomics coupled to Nascent Chromatin Capture or isolation of Proteins on Nascent DNA, we provide time-resolved binding kinetics for thousands of proteins behind replisomes within euchromatin and heterochromatin in human cells. This shows that most proteins regain access within minutes to newly replicated DNA. In contrast, 25% of the identified proteins do not, and this delay cannot be inferred from their known function or nuclear abundance. Instead, chromatin organization and G1 phase entry affect their reassociation. Finally, DNA replication not only disrupts but also promotes recruitment of transcription factors and chromatin remodelers, providing a significant advance in understanding how DNA replication could contribute to programmed changes of cell memory.
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Affiliation(s)
- Vanesa Alvarez
- Division of Molecular, Cell, and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Susanne Bandau
- Division of Molecular, Cell, and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Hao Jiang
- Laboratory of Quantitative Proteomics, Division of Molecular, Cell, and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Diana Rios-Szwed
- Division of Molecular, Cell, and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Jens Hukelmann
- Laboratory of Quantitative Proteomics, Division of Molecular, Cell, and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Elisa Garcia-Wilson
- Division of Molecular, Cell, and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Nicola Wiechens
- Laboratory of Chromatin Remodelling and Cancer Epigenetics, Division of Molecular, Cell & Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Eva Griesser
- Laboratory of Quantitative Proteomics, Division of Molecular, Cell, and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Sara Ten Have
- Laboratory of Quantitative Proteomics, Division of Molecular, Cell, and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Tom Owen-Hughes
- Laboratory of Chromatin Remodelling and Cancer Epigenetics, Division of Molecular, Cell & Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Angus Lamond
- Laboratory of Quantitative Proteomics, Division of Molecular, Cell, and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Constance Alabert
- Division of Molecular, Cell, and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK.
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14
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Yu Q, Liu X, Fang J, Wu H, Guo C, Zhang W, Liu N, Jiang C, Sha Q, Yuan X, Wang Z, Qu K. Dynamics and regulation of mitotic chromatin accessibility bookmarking at single-cell resolution. SCIENCE ADVANCES 2023; 9:eadd2175. [PMID: 36696508 PMCID: PMC9876548 DOI: 10.1126/sciadv.add2175] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 12/29/2022] [Indexed: 06/17/2023]
Abstract
Although mitotic chromosomes are highly compacted and transcriptionally inert, some active chromatin features are retained during mitosis to ensure the proper postmitotic reestablishment of maternal transcriptional programs, a phenomenon termed "mitotic bookmarking." However, the dynamics and regulation of mitotic bookmarking have not been systemically surveyed. Using single-cell transposase-accessible chromatin sequencing (scATAC-seq), we examined 6538 mitotic L02 human liver cells of variable stages and found that chromatin accessibility remained changing throughout cell division, with a constant decrease until metaphase and a gradual increase as chromosomes segregated. In particular, a subset of chromatin regions were identified to remain open throughout mitosis, and genes associated with these bookmarked regions are primarily linked to rapid reactivation upon mitotic exit. We also demonstrated that nuclear transcription factor Y subunit α (NF-YA) preferentially occupied bookmarked regions and contributed to transcriptional reactivation after mitosis. Our study uncovers the dynamic and regulatory blueprint of mitotic bookmarking.
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Affiliation(s)
- Qiaoni Yu
- MOE Key Laboratory for Cellular Dynamics, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230021, China
| | - Xu Liu
- MOE Key Laboratory for Cellular Dynamics, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
- Keck Center for Organoids Plasticity, Morehouse School of Medicine, Atlanta, GA, USA
| | - Jingwen Fang
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China
- HanGene Biotech, Xiaoshan Innovation Polis, Hangzhou, Zhejiang 311200, China
| | - Huihui Wu
- MOE Key Laboratory for Cellular Dynamics, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
- Keck Center for Organoids Plasticity, Morehouse School of Medicine, Atlanta, GA, USA
| | - Chuang Guo
- MOE Key Laboratory for Cellular Dynamics, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Wen Zhang
- MOE Key Laboratory for Cellular Dynamics, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Nianping Liu
- MOE Key Laboratory for Cellular Dynamics, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Chen Jiang
- MOE Key Laboratory for Cellular Dynamics, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Qing Sha
- MOE Key Laboratory for Cellular Dynamics, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Xiao Yuan
- MOE Key Laboratory for Cellular Dynamics, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
- Keck Center for Organoids Plasticity, Morehouse School of Medicine, Atlanta, GA, USA
| | - Zhikai Wang
- MOE Key Laboratory for Cellular Dynamics, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
- Keck Center for Organoids Plasticity, Morehouse School of Medicine, Atlanta, GA, USA
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China
| | - Kun Qu
- MOE Key Laboratory for Cellular Dynamics, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230021, China
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China
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15
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Madrigal P, Deng S, Feng Y, Militi S, Goh KJ, Nibhani R, Grandy R, Osnato A, Ortmann D, Brown S, Pauklin S. Epigenetic and transcriptional regulations prime cell fate before division during human pluripotent stem cell differentiation. Nat Commun 2023; 14:405. [PMID: 36697417 PMCID: PMC9876972 DOI: 10.1038/s41467-023-36116-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 01/17/2023] [Indexed: 01/26/2023] Open
Abstract
Stem cells undergo cellular division during their differentiation to produce daughter cells with a new cellular identity. However, the epigenetic events and molecular mechanisms occurring between consecutive cell divisions have been insufficiently studied due to technical limitations. Here, using the FUCCI reporter we developed a cell-cycle synchronised human pluripotent stem cell (hPSC) differentiation system for uncovering epigenome and transcriptome dynamics during the first two divisions leading to definitive endoderm. We observed that transcription of key differentiation markers occurs before cell division, while chromatin accessibility analyses revealed the early inhibition of alternative cell fates. We found that Activator protein-1 members controlled by p38/MAPK signalling are necessary for inducing endoderm while blocking cell fate shifting toward mesoderm, and that enhancers are rapidly established and decommissioned between different cell divisions. Our study has practical biomedical utility for producing hPSC-derived patient-specific cell types since p38/MAPK induction increased the differentiation efficiency of insulin-producing pancreatic beta-cells.
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Affiliation(s)
- Pedro Madrigal
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0SZ, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Siwei Deng
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Old Road, University of Oxford, Headington, Oxford, OX3 7LD, UK
| | - Yuliang Feng
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Old Road, University of Oxford, Headington, Oxford, OX3 7LD, UK
| | - Stefania Militi
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Old Road, University of Oxford, Headington, Oxford, OX3 7LD, UK
| | - Kim Jee Goh
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
- The Francis Crick Institute, London, NW1 1AT, UK
| | - Reshma Nibhani
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Old Road, University of Oxford, Headington, Oxford, OX3 7LD, UK
| | - Rodrigo Grandy
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Anna Osnato
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Daniel Ortmann
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Stephanie Brown
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Siim Pauklin
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Old Road, University of Oxford, Headington, Oxford, OX3 7LD, UK.
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16
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Huang Y, Gao BQ, Meng Q, Yang LZ, Ma XK, Wu H, Pan YH, Yang L, Li D, Chen LL. CRISPR-dCas13-tracing reveals transcriptional memory and limited mRNA export in developing zebrafish embryos. Genome Biol 2023; 24:15. [PMID: 36658633 PMCID: PMC9854193 DOI: 10.1186/s13059-023-02848-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 01/04/2023] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Understanding gene transcription and mRNA-protein (mRNP) dynamics in single cells in a multicellular organism has been challenging. The catalytically dead CRISPR-Cas13 (dCas13) system has been used to visualize RNAs in live cells without genetic manipulation. We optimize this system to track developmentally expressed mRNAs in zebrafish embryos and to understand features of endogenous transcription kinetics and mRNP export. RESULTS We report that zygotic microinjection of purified CRISPR-dCas13-fluorescent proteins and modified guide RNAs allows single- and dual-color tracking of developmentally expressed mRNAs in zebrafish embryos from zygotic genome activation (ZGA) until early segmentation period without genetic manipulation. Using this approach, we uncover non-synchronized de novo transcription between inter-alleles, synchronized post-mitotic re-activation in pairs of alleles, and transcriptional memory as an extrinsic noise that potentially contributes to synchronized post-mitotic re-activation. We also reveal rapid dCas13-engaged mRNP movement in the nucleus with a corralled and diffusive motion, but a wide varying range of rate-limiting mRNP export, which can be shortened by Alyref and Nxf1 overexpression. CONCLUSIONS This optimized dCas13-based toolkit enables robust spatial-temporal tracking of endogenous mRNAs and uncovers features of transcription and mRNP motion, providing a powerful toolkit for endogenous RNA visualization in a multicellular developmental organism.
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Affiliation(s)
- Youkui Huang
- grid.410726.60000 0004 1797 8419State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, China
| | - Bao-Qing Gao
- grid.410726.60000 0004 1797 8419CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Quan Meng
- grid.418856.60000 0004 1792 5640National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China ,grid.410726.60000 0004 1797 8419College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Liang-Zhong Yang
- grid.410726.60000 0004 1797 8419State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, China
| | - Xu-Kai Ma
- grid.8547.e0000 0001 0125 2443Center for Molecular Medicine, Children’s Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Hao Wu
- grid.410726.60000 0004 1797 8419State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, China
| | - Yu-Hang Pan
- grid.410726.60000 0004 1797 8419State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, China
| | - Li Yang
- grid.8547.e0000 0001 0125 2443Center for Molecular Medicine, Children’s Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Dong Li
- grid.418856.60000 0004 1792 5640National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China ,grid.410726.60000 0004 1797 8419College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ling-Ling Chen
- grid.410726.60000 0004 1797 8419State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, China ,grid.440637.20000 0004 4657 8879School of Life Science and Technology, ShanghaiTech University, Shanghai, China ,grid.410726.60000 0004 1797 8419School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
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17
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Changes in PRC1 activity during interphase modulate lineage transition in pluripotent cells. Nat Commun 2023; 14:180. [PMID: 36635295 PMCID: PMC9837203 DOI: 10.1038/s41467-023-35859-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 01/05/2023] [Indexed: 01/14/2023] Open
Abstract
The potential of pluripotent cells to respond to developmental cues and trigger cell differentiation is enhanced during the G1 phase of the cell cycle, but the molecular mechanisms involved are poorly understood. Variations in polycomb activity during interphase progression have been hypothesized to regulate the cell-cycle-phase-dependent transcriptional activation of differentiation genes during lineage transition in pluripotent cells. Here, we show that recruitment of Polycomb Repressive Complex 1 (PRC1) and associated molecular functions, ubiquitination of H2AK119 and three-dimensional chromatin interactions, are enhanced during S and G2 phases compared to the G1 phase. In agreement with the accumulation of PRC1 at target promoters upon G1 phase exit, cells in S and G2 phases show firmer transcriptional repression of developmental regulator genes that is drastically perturbed upon genetic ablation of the PRC1 catalytic subunit RING1B. Importantly, depletion of RING1B during retinoic acid stimulation interferes with the preference of mouse embryonic stem cells (mESCs) to induce the transcriptional activation of differentiation genes in G1 phase. We propose that incremental enrolment of polycomb repressive activity during interphase progression reduces the tendency of cells to respond to developmental cues during S and G2 phases, facilitating activation of cell differentiation in the G1 phase of the pluripotent cell cycle.
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18
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Hayashi S, Oe S, Koike T, Seki-Omura R, Nakano Y, Hirahara Y, Tanaka S, Ito T, Yasukochi Y, Higasa K, Kitada M. OLIG2 is an in vivo bookmarking transcription factor in the developing neural tube in mouse. J Neurochem 2022; 165:303-317. [PMID: 36547371 DOI: 10.1111/jnc.15746] [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: 06/17/2022] [Revised: 10/24/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022]
Abstract
Cells possess intrinsic features that are inheritable via epigenetic regulation, such as DNA methylation and histone modification. These inheritable features maintain a unique gene expression pattern, underlying cellular memory. Because of the degradation or displacement of mitotic chromosomes, most transcription factors do not contribute to cellular memory. However, accumulating in vitro evidence indicates that some transcription factors can be retained in mitotic chromosomes called as bookmarking. Such transcription factors may contribute to a novel third mechanism of cellular memory. Since most findings of transcription factor bookmarking have been reported in vitro, little is currently known in vivo. In the neural tube of mouse embryos, we discovered that OLIG2, a basic helix loop helix (bHLH) transcription factor that regulates proliferation of neural progenitors and the cell fate of motoneurons and oligodendrocytes, binds to chromatin through every cell cycle including M-phase. OLIG2 chromosomal localization coincides with mitotic cell features such as the phosphorylation of histone H3, KI67, and nuclear membrane breakdown. Chromosomal localization of OLIG2 is regulated by an N-terminus triple serine motif. Photobleaching analysis revealed slow OLIG2 mobility, suggesting a high affinity of OLIG2 to DNA. In Olig2 N-terminal deletion mutant mice, motoneurons and oligodendrocyte progenitor numbers are reduced in the neural tube, suggesting that the bookmarking regulatory domain is important for OLIG2 function. We conclude that OLIG2 is a de novo in vivo bookmarking transcription factor. Our results demonstrate the presence of in vivo bookmarking in a living organism and illustrate a novel function of transcription factors.
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Affiliation(s)
- Shinichi Hayashi
- Faculty of Medicine, Department of Anatomy, Kansai Medical University, Osaka, Japan
| | - Souichi Oe
- Faculty of Medicine, Department of Anatomy, Kansai Medical University, Osaka, Japan
| | - Taro Koike
- Faculty of Medicine, Department of Anatomy, Kansai Medical University, Osaka, Japan
| | - Ryohei Seki-Omura
- Faculty of Medicine, Department of Anatomy, Kansai Medical University, Osaka, Japan
| | - Yosuke Nakano
- Faculty of Medicine, Department of Anatomy, Kansai Medical University, Osaka, Japan
| | - Yukie Hirahara
- Faculty of Medicine, Department of Anatomy, Kansai Medical University, Osaka, Japan.,Faculty of Nursing, Kansai Medical University, Osaka, Japan
| | - Susumu Tanaka
- Faculty of Medicine, Department of Anatomy, Kansai Medical University, Osaka, Japan.,Faculty of Nursing and Nutrition, Department of Anatomy and Physiology, University of Nagasaki, Nagasaki, Japan
| | - Takeshi Ito
- Department of Genome Analysis, Institute of Biomedical Science, Kansai Medical University, Osaka, Japan
| | - Yoshiki Yasukochi
- Department of Genome Analysis, Institute of Biomedical Science, Kansai Medical University, Osaka, Japan
| | - Koichiro Higasa
- Department of Genome Analysis, Institute of Biomedical Science, Kansai Medical University, Osaka, Japan
| | - Masaaki Kitada
- Faculty of Medicine, Department of Anatomy, Kansai Medical University, Osaka, Japan
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19
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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: 5] [Impact Index Per Article: 2.5] [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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20
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Soares MAF, Oliveira RA, Castro DS. Function and regulation of transcription factors during mitosis-to-G1 transition. Open Biol 2022; 12:220062. [PMID: 35642493 PMCID: PMC9157305 DOI: 10.1098/rsob.220062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
During cell division, drastic cellular changes characteristic of mitosis result in the inactivation of the transcriptional machinery, and global downregulation of transcription. Sequence-specific transcription factors (TFs) have thus been considered mere bystanders, devoid of any regulatory function during mitosis. This view changed significantly in recent years, upon the conclusion that many TFs associate with condensed chromosomes during cell division, even occupying a fraction of their genomic target sites in mitotic chromatin. This finding was at the origin of the concept of mitotic bookmarking by TFs, proposed as a mechanism to propagate gene regulatory information across cell divisions, by facilitating the reactivation of specific bookmarked genes. While the underlying mechanisms and biological significance of this model remain elusive, recent developments in this fast-moving field have cast new light into TF activity during mitosis, beyond a bookmarking role. Here, we start by reviewing the most recent findings on the complex nature of TF-chromatin interactions during mitosis, and on mechanisms that may regulate them. Next, and in light of recent reports describing how transcription is reinitiated in temporally distinct waves during mitosis-to-G1 transition, we explore how TFs may contribute to defining this hierarchical gene expression process. Finally, we discuss how TF activity during mitotic exit may impact the acquisition of cell identity upon cell division, and propose a model that integrates dynamic changes in TF-chromatin interactions during this cell-cycle period, with the execution of cell-fate decisions.
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Affiliation(s)
- Mário A. F. Soares
- i3S Instituto de Investigação e Inovação em Saúde, IBMC Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
| | | | - Diogo S. Castro
- i3S Instituto de Investigação e Inovação em Saúde, IBMC Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
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21
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Bellec M, Dufourt J, Hunt G, Lenden-Hasse H, Trullo A, Zine El Aabidine A, Lamarque M, Gaskill MM, Faure-Gautron H, Mannervik M, Harrison MM, Andrau JC, Favard C, Radulescu O, Lagha M. The control of transcriptional memory by stable mitotic bookmarking. Nat Commun 2022; 13:1176. [PMID: 35246556 PMCID: PMC8897465 DOI: 10.1038/s41467-022-28855-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 02/15/2022] [Indexed: 01/23/2023] Open
Abstract
To maintain cellular identities during development, gene expression profiles must be faithfully propagated through cell generations. The reestablishment of gene expression patterns upon mitotic exit is mediated, in part, by transcription factors (TF) mitotic bookmarking. However, the mechanisms and functions of TF mitotic bookmarking during early embryogenesis remain poorly understood. In this study, taking advantage of the naturally synchronized mitoses of Drosophila early embryos, we provide evidence that GAGA pioneer factor (GAF) acts as a stable mitotic bookmarker during zygotic genome activation. We show that, during mitosis, GAF remains associated to a large fraction of its interphase targets, including at cis-regulatory sequences of key developmental genes with both active and repressive chromatin signatures. GAF mitotic targets are globally accessible during mitosis and are bookmarked via histone acetylation (H4K8ac). By monitoring the kinetics of transcriptional activation in living embryos, we report that GAF binding establishes competence for rapid activation upon mitotic exit.
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Affiliation(s)
- Maëlle Bellec
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS-UMR 5535, 1919 Route de Mende, Montpellier, 34293, Cedex 5, France
| | - Jérémy Dufourt
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS-UMR 5535, 1919 Route de Mende, Montpellier, 34293, Cedex 5, France
| | - George Hunt
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691, Stockholm, Sweden
| | - Hélène Lenden-Hasse
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS-UMR 5535, 1919 Route de Mende, Montpellier, 34293, Cedex 5, France
| | - Antonio Trullo
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS-UMR 5535, 1919 Route de Mende, Montpellier, 34293, Cedex 5, France
| | - Amal Zine El Aabidine
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS-UMR 5535, 1919 Route de Mende, Montpellier, 34293, Cedex 5, France
| | - Marie Lamarque
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS-UMR 5535, 1919 Route de Mende, Montpellier, 34293, Cedex 5, France
| | - Marissa M Gaskill
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Heloïse Faure-Gautron
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS-UMR 5535, 1919 Route de Mende, Montpellier, 34293, Cedex 5, France
| | - Mattias Mannervik
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691, Stockholm, Sweden
| | - Melissa M Harrison
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Jean-Christophe Andrau
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS-UMR 5535, 1919 Route de Mende, Montpellier, 34293, Cedex 5, France
| | - Cyril Favard
- Institut de Recherche en Infectiologie de Montpellier, CNRS UMR 9004, University of Montpellier, 1919 Route de Mende, Montpellier, 34293, Cedex 5, France
| | - Ovidiu Radulescu
- LPHI, UMR CNRS 5235, University of Montpellier, Place E. Bataillon - Bât. 24 cc 107, Montpellier, 34095, Cedex 5, France
| | - Mounia Lagha
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS-UMR 5535, 1919 Route de Mende, Montpellier, 34293, Cedex 5, France.
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22
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Li Y, Darabi R. Role of epigenetics in cellular reprogramming; from iPSCs to disease modeling and cell therapy. J Cell Biochem 2022; 123:147-154. [PMID: 34668236 PMCID: PMC8860854 DOI: 10.1002/jcb.30164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 08/31/2021] [Accepted: 10/08/2021] [Indexed: 02/03/2023]
Abstract
Epigenetics play a fundamental role in induced pluripotent stem cell (iPSC) technology due to their effect on iPSC's reprogramming efficiency and their subsequent role in iPSC differentiation toward a specific lineage. Epigenetics can skew the differentiation course of iPSCs toward a specific lineage based on the epigenetic memory of the source cells, or even lead to acquisition of new cell phenotypes, due to its aberrations during reprogramming. This viewpoint discusses key features of the epigenetic process during iPSC reprogramming/differentiation and outlines important epigenetic factors that need to be considered for successful generation and differentiation of iPSCs for downstream applications.
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Affiliation(s)
- Yong Li
- Department of Orthopaedic Surgery, BioMedical Engineering, Western Michigan University Homer Stryker M.D. School of Medicine, Kalamazoo, Michigan, USA
| | - Radbod Darabi
- Center for Stem Cell and Regenerative Medicine (CSCRM), The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases (IMM), McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
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23
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Shvedunova M, Akhtar A. Modulation of cellular processes by histone and non-histone protein acetylation. Nat Rev Mol Cell Biol 2022; 23:329-349. [PMID: 35042977 DOI: 10.1038/s41580-021-00441-y] [Citation(s) in RCA: 269] [Impact Index Per Article: 134.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/25/2021] [Indexed: 12/12/2022]
Abstract
Lysine acetylation is a widespread and versatile protein post-translational modification. Lysine acetyltransferases and lysine deacetylases catalyse the addition or removal, respectively, of acetyl groups at both histone and non-histone targets. In this Review, we discuss several features of acetylation and deacetylation, including their diversity of targets, rapid turnover, exquisite sensitivity to the concentrations of the cofactors acetyl-CoA, acyl-CoA and NAD+, and tight interplay with metabolism. Histone acetylation and non-histone protein acetylation influence a myriad of cellular and physiological processes, including transcription, phase separation, autophagy, mitosis, differentiation and neural function. The activity of lysine acetyltransferases and lysine deacetylases can, in turn, be regulated by metabolic states, diet and specific small molecules. Histone acetylation has also recently been shown to mediate cellular memory. These features enable acetylation to integrate the cellular state with transcriptional output and cell-fate decisions.
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Affiliation(s)
- Maria Shvedunova
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Asifa Akhtar
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany.
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24
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Hill SL, Rogan PK, Wang YX, Knoll JHM. Differentially accessible, single copy sequences form contiguous domains along metaphase chromosomes that are conserved among multiple tissues. Mol Cytogenet 2021; 14:49. [PMID: 34670606 PMCID: PMC8527651 DOI: 10.1186/s13039-021-00567-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 09/08/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND During mitosis, chromatin engages in a dynamic cycle of condensation and decondensation. Condensation into distinct units to ensure high fidelity segregation is followed by rapid and reproducible decondensation to produce functional daughter cells. Factors contributing to the reproducibility of chromatin structure between cell generations are not well understood. We investigated local metaphase chromosome condensation along mitotic chromosomes within genomic intervals showing differential accessibility (DA) between homologs. DA was originally identified using short sequence-defined single copy (sc) DNA probes of < 5 kb in length by fluorescence in situ hybridization (scFISH) in peripheral lymphocytes. These structural differences between metaphase homologs are non-random, stable, and heritable epigenetic marks which have led to the proposed function of DA as a marker of chromatin memory. Here, we characterize the organization of DA intervals into chromosomal domains by identifying multiple DA loci in close proximity to each other and examine the conservation of DA between tissues. RESULTS We evaluated multiple adjacent scFISH probes at 6 different DA loci from chromosomal regions 2p23, 3p24, 12p12, 15q22, 15q24 and 20q13 within peripheral blood T-lymphocytes. DA was organized within domains that extend beyond the defined boundaries of individual scFISH probes. Based on hybridizations of 2 to 4 scFISH probes per domain, domains ranged in length from 16.0 kb to 129.6 kb. Transcriptionally inert chromosomal DA regions in T-lymphocytes also demonstrated conservation of DA in bone marrow and fibroblast cells. CONCLUSIONS We identified novel chromosomal regions with allelic differences in metaphase chromosome accessibility and demonstrated that these accessibility differences appear to be aggregated into contiguous domains extending beyond individual scFISH probes. These domains are encompassed by previously established topologically associated domain (TAD) boundaries. DA appears to be a conserved feature of human metaphase chromosomes across different stages of lymphocyte differentiation and germ cell origin, consistent with its proposed role in maintenance of intergenerational cellular chromosome memory.
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Affiliation(s)
- Seana L Hill
- Department of Pathology & Laboratory Medicine, Schulich School of Medicine & Dentistry, University of Western Ontario, London, Canada
| | - Peter K Rogan
- Departments of Biochemistry and Oncology, Schulich School of Medicine & Dentistry, University of Western Ontario, London, Canada
- Cytognomix Inc., London, ON, Canada
| | - Yi Xuan Wang
- Department of Pathology & Laboratory Medicine, Schulich School of Medicine & Dentistry, University of Western Ontario, London, Canada
| | - Joan H M Knoll
- Department of Pathology & Laboratory Medicine, Schulich School of Medicine & Dentistry, University of Western Ontario, London, Canada.
- Cytognomix Inc., London, ON, Canada.
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25
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Sarnataro S, Riba A, Molina N. Regulation of transcription reactivation dynamics exiting mitosis. PLoS Comput Biol 2021; 17:e1009354. [PMID: 34606497 PMCID: PMC8516288 DOI: 10.1371/journal.pcbi.1009354] [Citation(s) in RCA: 3] [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: 01/22/2021] [Revised: 10/14/2021] [Accepted: 08/17/2021] [Indexed: 11/23/2022] Open
Abstract
Proliferating cells experience a global reduction of transcription during mitosis, yet their cell identity is maintained and regulatory information is propagated from mother to daughter cells. Mitotic bookmarking by transcription factors has been proposed as a potential mechanism to ensure the reactivation of transcription at the proper set of genes exiting mitosis. Recently, mitotic transcription and waves of transcription reactivation have been observed in synchronized populations of human hepatoma cells. However, the study did not consider that mitotic-arrested cell populations progressively desynchronize leading to measurements of gene expression on a mixture of cells at different internal cell-cycle times. Moreover, it is not well understood yet what is the precise role of mitotic bookmarking on mitotic transcription as well as on the transcription reactivation waves. Ultimately, the core gene regulatory network driving the precise transcription reactivation dynamics remains to be identified. To address these questions, we developed a mathematical model to correct for the progressive desynchronization of cells and estimate gene expression dynamics with respect to a cell-cycle pseudotime. Furthermore, we used a multiple linear regression model to infer transcription factor activity dynamics. Our analysis allows us to characterize waves of transcription factor activities exiting mitosis and predict a core gene regulatory network responsible of the transcription reactivation dynamics. Moreover, we identified more than 60 transcription factors that are highly active during mitosis and represent new candidates of mitotic bookmarking factors which could be relevant therapeutic targets to control cell proliferation. Specific gene expression patterns confer particular identities to cells. During proliferation, cells undergo mitosis when chromosomes are formed and segregated into two new cells leading to a global downregulation of gene expression. Yet, cell identity is propagated from mother to daughter cells by the reactivation of gene expression at the appropriate set of genes once mitosis is completed. Mitotic bookmarking has been proposed as a mechanism to regulate this process. Indeed certain regulatory factors tag genes during mitosis to promote gene reactivation in the next cycle. Here we analyze gene expression over time measured on synchronized cell populations by using a new generation sequencing technique. To do so, we proposed a mathematical model to obtain the exact gene expression dynamics with respect to the cell-cycle progression and identified waves of genes reactivation during mitosis and the transition to the next cycle. Also, we developed a computational method that allowed us to predict key regulatory factors that drive this process and predict new candidates that could be involved in mitotic bookmarking. These regulatory factors could be relevant therapeutic targets to control cell proliferation.
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Affiliation(s)
- Sergio Sarnataro
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) Université de Strasbourg – CNRS – INSERM, Illkirch, France
| | - Andrea Riba
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) Université de Strasbourg – CNRS – INSERM, Illkirch, France
| | - Nacho Molina
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) Université de Strasbourg – CNRS – INSERM, Illkirch, France
- * E-mail:
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26
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Lan HC, Du TH, Yao YL, Yang WM. Ocular disease-associated mutations diminish the mitotic chromosome retention ability of PAX6. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2021; 1864:194751. [PMID: 34500082 DOI: 10.1016/j.bbagrm.2021.194751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 08/25/2021] [Accepted: 08/25/2021] [Indexed: 10/20/2022]
Abstract
Transcription factors play a key role in maintaining cell identity. One mechanism of such cell memory after multiple rounds of cell division cycles is through persistent mitotic chromosome binding, although how individual transcription factors achieve mitotic chromosome retention is not completely understood. Here we show that PAX6, a lineage-determining transcription factor, coats mitotic chromosomes. Using deletion and point mutants associated with human ocular diseases in live-cell imaging analysis, we identified two regions, MCR-D1 and MCR-D2, that were responsible for mitotic chromosome retention of PAX6. We also identified three nuclear localization signals (NLSs) that contributed to mitotic chromosome retention independent of their nuclear import functions. Full mitotic chromosome retention required the presence of DNA-binding domains as well as NLSs within MCR-Ds. Furthermore, disease-associated mutations and NLS mutations changed the distribution of intrinsically disordered regions (IDRs) in PAX6. Our findings not only identify PAX6 as a novel mitotic chromosome retention factor but also demonstrate that the mechanism of mitotic chromosome retention involves sequence-specific DNA binding, NLSs, and molecular conformation determined by IDRs. These findings link mitotic chromosome retention with PAX6-related pathogenesis and imply similar mechanisms for other lineage-determining factors in the PAX family.
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Affiliation(s)
- Hsin-Chi Lan
- Institute of Molecular Biology, National Chung Hsing University, Taichung 40227, Taiwan
| | - Ting-Huei Du
- Institute of Molecular Biology, National Chung Hsing University, Taichung 40227, Taiwan
| | - Ya-Li Yao
- Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung 41354, Taiwan.
| | - Wen-Ming Yang
- Institute of Molecular Biology, National Chung Hsing University, Taichung 40227, Taiwan; Ph.D. Program in Translational Medicine, National Chung Hsing University, Taichung 40227, Taiwan.
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27
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Weinhouse C. The roles of inducible chromatin and transcriptional memory in cellular defense system responses to redox-active pollutants. Free Radic Biol Med 2021; 170:85-108. [PMID: 33789123 PMCID: PMC8382302 DOI: 10.1016/j.freeradbiomed.2021.03.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 03/12/2021] [Accepted: 03/15/2021] [Indexed: 12/17/2022]
Abstract
People are exposed to wide range of redox-active environmental pollutants. Air pollution, heavy metals, pesticides, and endocrine disrupting chemicals can disrupt cellular redox status. Redox-active pollutants in our environment all trigger their own sets of specific cellular responses, but they also activate a common set of general stress responses that buffer the cell against homeostatic insults. These cellular defense system (CDS) pathways include the heat shock response, the oxidative stress response, the hypoxia response, the unfolded protein response, the DNA damage response, and the general stress response mediated by the stress-activated p38 mitogen-activated protein kinase. Over the past two decades, the field of environmental epigenetics has investigated epigenetic responses to environmental pollutants, including redox-active pollutants. Studies of these responses highlight the role of chromatin modifications in controlling the transcriptional response to pollutants and the role of transcriptional memory, often referred to as "epigenetic reprogramming", in predisposing previously exposed individuals to more potent transcriptional responses on secondary challenge. My central thesis in this review is that high dose or chronic exposure to redox-active pollutants leads to transcriptional memories at CDS target genes that influence the cell's ability to mount protective responses. To support this thesis, I will: (1) summarize the known chromatin features required for inducible gene activation; (2) review the known forms of transcriptional memory; (3) discuss the roles of inducible chromatin and transcriptional memory in CDS responses that are activated by redox-active environmental pollutants; and (4) propose a conceptual framework for CDS pathway responsiveness as a readout of total cellular exposure to redox-active pollutants.
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Affiliation(s)
- Caren Weinhouse
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR, 97214, USA.
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28
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Soares MAF, Soares DS, Teixeira V, Heskol A, Bressan RB, Pollard SM, Oliveira RA, Castro DS. Hierarchical reactivation of transcription during mitosis-to-G1 transition by Brn2 and Ascl1 in neural stem cells. Genes Dev 2021; 35:1020-1034. [PMID: 34168041 PMCID: PMC8247608 DOI: 10.1101/gad.348174.120] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 05/19/2021] [Indexed: 12/19/2022]
Abstract
During mitosis, chromatin condensation is accompanied by a global arrest of transcription. Recent studies suggest transcriptional reactivation upon mitotic exit occurs in temporally coordinated waves, but the underlying regulatory principles have yet to be elucidated. In particular, the contribution of sequence-specific transcription factors (TFs) remains poorly understood. Here we report that Brn2, an important regulator of neural stem cell identity, associates with condensed chromatin throughout cell division, as assessed by live-cell imaging of proliferating neural stem cells. In contrast, the neuronal fate determinant Ascl1 dissociates from mitotic chromosomes. ChIP-seq analysis reveals that Brn2 mitotic chromosome binding does not result in sequence-specific interactions prior to mitotic exit, relying mostly on electrostatic forces. Nevertheless, surveying active transcription using single-molecule RNA-FISH against immature transcripts reveals differential reactivation kinetics for key targets of Brn2 and Ascl1, with transcription onset detected in early (anaphase) versus late (early G1) phases, respectively. Moreover, by using a mitotic-specific dominant-negative approach, we show that competing with Brn2 binding during mitotic exit reduces the transcription of its target gene Nestin Our study shows an important role for differential binding of TFs to mitotic chromosomes, governed by their electrostatic properties, in defining the temporal order of transcriptional reactivation during mitosis-to-G1 transition.
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Affiliation(s)
- Mário A F Soares
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
- i3S Instituto de Investigação e Inovação em Saúde, IBMC Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
| | - Diogo S Soares
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
- i3S Instituto de Investigação e Inovação em Saúde, IBMC Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
| | - Vera Teixeira
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | - Abeer Heskol
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
- i3S Instituto de Investigação e Inovação em Saúde, IBMC Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
| | - Raul Bardini Bressan
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, United Kingdom
| | - Steven M Pollard
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, United Kingdom
| | | | - Diogo S Castro
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
- i3S Instituto de Investigação e Inovação em Saúde, IBMC Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
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29
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Taguchi YH, Turki T. Unsupervised tensor decomposition-based method to extract candidate transcription factors as histone modification bookmarks in post-mitotic transcriptional reactivation. PLoS One 2021; 16:e0251032. [PMID: 34032804 PMCID: PMC8148352 DOI: 10.1371/journal.pone.0251032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 04/17/2021] [Indexed: 11/25/2022] Open
Abstract
The histone group added to a gene sequence must be removed during mitosis to halt transcription during the DNA replication stage of the cell cycle. However, the detailed mechanism of this transcription regulation remains unclear. In particular, it is not realistic to reconstruct all appropriate histone modifications throughout the genome from scratch after mitosis. Thus, it is reasonable to assume that there might be a type of “bookmark” that retains the positions of histone modifications, which can be readily restored after mitosis. We developed a novel computational approach comprising tensor decomposition (TD)-based unsupervised feature extraction (FE) to identify transcription factors (TFs) that bind to genes associated with reactivated histone modifications as candidate histone bookmarks. To the best of our knowledge, this is the first application of TD-based unsupervised FE to the cell division context and phases pertaining to the cell cycle in general. The candidate TFs identified with this approach were functionally related to cell division, suggesting the suitability of this method and the potential of the identified TFs as bookmarks for histone modification during mitosis.
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Affiliation(s)
- Y-h. Taguchi
- Department of Physics, Chuo University, Tokyo, Japan
- * E-mail:
| | - Turki Turki
- Department of Computer Science, King Abdulaziz University, Jeddah, Saudi Arabia
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30
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Alicea B, Parent J, Singh U. Periodicity in the embryo: Emergence of order in space, diffusion of order in time. Biosystems 2021; 204:104405. [PMID: 33746021 DOI: 10.1016/j.biosystems.2021.104405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 03/07/2021] [Accepted: 03/08/2021] [Indexed: 02/02/2023]
Abstract
Does embryonic development exhibit characteristic temporal features? This is apparent in evolution, where evolutionary change has been shown to occur in bursts of activity. Using two animal models (Nematode, Caenorhabditis elegans and Zebrafish, Danio rerio) and simulated data, we demonstrate that temporal heterogeneity exists in embryogenesis at the cellular level, and may have functional consequences. Cell proliferation and division from cell tracking data is subject to analysis to characterize specific features in each model species. Simulated data is then used to understand what role this variation might play in producing phenotypic variation in the adult phenotype. This goes beyond a molecular characterization of developmental regulation to provide a quantitative result at the phenotypic scale of complexity.
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Affiliation(s)
- Bradly Alicea
- OpenWorm Foundation, Boston, MA, USA; Orthogonal Research and Education Laboratory, Champaign, IL, USA.
| | - Jesse Parent
- Orthogonal Research and Education Laboratory, Champaign, IL, USA
| | - Ujjwal Singh
- OpenWorm Foundation, Boston, MA, USA; IIIT Delhi, Delhi, India
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31
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Mammalian SWI/SNF continuously restores local accessibility to chromatin. Nat Genet 2021; 53:279-287. [PMID: 33558757 DOI: 10.1038/s41588-020-00768-w] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 12/16/2020] [Indexed: 01/30/2023]
Abstract
Chromatin accessibility is a hallmark of regulatory regions, entails transcription factor (TF) binding and requires nucleosomal reorganization. However, it remains unclear how dynamic this process is. In the present study, we use small-molecule inhibition of the catalytic subunit of the mouse SWI/SNF remodeler complex to show that accessibility and reduced nucleosome presence at TF-binding sites rely on persistent activity of nucleosome remodelers. Within minutes of remodeler inhibition, accessibility and TF binding decrease. Although this is irrespective of TF function, we show that the activating TF OCT4 (POU5F1) exhibits a faster response than the repressive TF REST. Accessibility, nucleosome depletion and gene expression are rapidly restored on inhibitor removal, suggesting that accessible chromatin is regenerated continuously and in a largely cell-autonomous fashion. We postulate that TF binding to chromatin and remodeler-mediated nucleosomal removal do not represent a stable situation, but instead accessible chromatin reflects an average of a dynamic process under continued renewal.
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Wadkin LE, Orozco-Fuentes S, Neganova I, Lako M, Barrio RA, Baggaley AW, Parker NG, Shukurov A. OCT4 expression in human embryonic stem cells: spatio-temporal dynamics and fate transitions. Phys Biol 2021; 18:026003. [PMID: 33296887 DOI: 10.1088/1478-3975/abd22b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The improved in vitro regulation of human embryonic stem cell (hESC) pluripotency and differentiation trajectories is required for their promising clinical applications. The temporal and spatial quantification of the molecular interactions controlling pluripotency is also necessary for the development of successful mathematical and computational models. Here we use time-lapse experimental data of OCT4-mCherry fluorescence intensity to quantify the temporal and spatial dynamics of the pluripotency transcription factor OCT4 in a growing hESC colony in the presence and absence of BMP4. We characterise the internal self-regulation of OCT4 using the Hurst exponent and autocorrelation analysis, quantify the intra-cellular fluctuations and consider the diffusive nature of OCT4 evolution for individual cells and pairs of their descendants. We find that OCT4 abundance in the daughter cells fluctuates sub-diffusively, showing anti-persistent self-regulation. We obtain the stationary probability distributions governing hESC transitions amongst the different cell states and establish the times at which pro-fate cells (which later give rise to pluripotent or differentiated cells) cluster in the colony. By quantifying the similarities between the OCT4 expression amongst neighbouring cells, we show that hESCs express similar OCT4 to cells within their local neighbourhood within the first two days of the experiment and before BMP4 treatment. Our framework allows us to quantify the relevant properties of proliferating hESC colonies and the procedure is widely applicable to other transcription factors and cell populations.
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Affiliation(s)
- L E Wadkin
- School of Mathematics, Statistics and Physics, Newcastle University, Newcastle upon Tyne, United Kingdom
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Nucleosome Positioning and Spacing: From Mechanism to Function. J Mol Biol 2021; 433:166847. [PMID: 33539878 DOI: 10.1016/j.jmb.2021.166847] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 01/16/2021] [Accepted: 01/22/2021] [Indexed: 02/08/2023]
Abstract
Eukaryotes associate their genomes with histone proteins, forming nucleosome particles. Nucleosomes regulate and protect the genetic information. They often assemble into evenly spaced arrays of nucleosomes. These regular nucleosome arrays cover significant portions of the genome, in particular over genes. The presence of these evenly spaced nucleosome arrays is highly conserved throughout the entire eukaryotic domain. Here, we review the mechanisms behind the establishment of this primary structure of chromatin with special emphasis on the biogenesis of evenly spaced nucleosome arrays. We highlight the roles that transcription, nucleosome remodelers, DNA sequence, and histone density play towards the formation of evenly spaced nucleosome arrays and summarize our current understanding of their cellular functions. We end with key unanswered questions that remain to be explored to obtain an in-depth understanding of the biogenesis and function of the nucleosome landscape.
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Elsherbiny A, Dobreva G. Epigenetic memory of cell fate commitment. Curr Opin Cell Biol 2021; 69:80-87. [PMID: 33535129 DOI: 10.1016/j.ceb.2020.12.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/15/2020] [Accepted: 12/22/2020] [Indexed: 12/23/2022]
Abstract
During development, discrete cell fates are established in precise spatiotemporal order guided by morphogen signals. These signals converge in the nucleus to induce transcriptional and epigenetic programming that determines cell fate. Once cell identity is established, cell programs have to be accurately sustained through multiple rounds of cell division, during which DNA replication serves as a window of opportunity for altering cell fate. In this review, we summarize recent advances in understanding the molecular players that underlie epigenetic memory of cell fate decisions, with a particular focus on histone modifications and mitotic bookmarking factors. We also discuss the different mechanisms of inheritance of repressed and active chromatin states.
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Affiliation(s)
- Adel Elsherbiny
- Department of Anatomy and Developmental Biology, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany; German Centre for Cardiovascular Research (DZHK), Germany
| | - Gergana Dobreva
- Department of Anatomy and Developmental Biology, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany; German Centre for Cardiovascular Research (DZHK), Germany.
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35
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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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36
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Pelham-Webb B, Murphy D, Apostolou E. Dynamic 3D Chromatin Reorganization during Establishment and Maintenance of Pluripotency. Stem Cell Reports 2020; 15:1176-1195. [PMID: 33242398 PMCID: PMC7724465 DOI: 10.1016/j.stemcr.2020.10.012] [Citation(s) in RCA: 17] [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: 07/09/2020] [Revised: 10/25/2020] [Accepted: 10/27/2020] [Indexed: 12/12/2022] Open
Abstract
Higher-order chromatin structure is tightly linked to gene expression and therefore cell identity. In recent years, the chromatin landscape of pluripotent stem cells has become better characterized, and unique features at various architectural levels have been revealed. However, the mechanisms that govern establishment and maintenance of these topological characteristics and the temporal and functional relationships with transcriptional or epigenetic features are still areas of intense study. Here, we will discuss progress and limitations of our current understanding regarding how the 3D chromatin topology of pluripotent stem cells is established during somatic cell reprogramming and maintained during cell division. We will also discuss evidence and theories about the driving forces of topological reorganization and the functional links with key features and properties of pluripotent stem cell identity.
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Affiliation(s)
- Bobbie Pelham-Webb
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY 10021, USA
| | - Dylan Murphy
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - Effie Apostolou
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA.
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37
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Jirawatnotai S, Dalton S, Wattanapanitch M. Role of cyclins and cyclin-dependent kinases in pluripotent stem cells and their potential as a therapeutic target. Semin Cell Dev Biol 2020; 107:63-71. [PMID: 32417217 PMCID: PMC7554155 DOI: 10.1016/j.semcdb.2020.05.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/30/2020] [Accepted: 05/02/2020] [Indexed: 02/09/2023]
Abstract
Over the last 15 years connections between cell cycle control, maintenance of pluripotency, and control of cell fate decisions have been firmly established. With the emergence of powerful tools, such as highly-specific small molecule inhibitors for cyclin-dependent protein kinase (CDK) activity and single-cell imaging technologies, the mechanistic links between cyclins, CDKs and regulation in PSCs in mechanistic detail has been made possible. In this review, we discuss new developments that mechanistically link the CDK regulatory network to control of cell fate decisions, including maintenance of the pluripotent state. Overall, these findings have potential to impact the translational applications of stem cells in regenerative medicine, drug discovery and cancer treatment.
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Affiliation(s)
- Siwanon Jirawatnotai
- Siriraj Center of Research for Excellence for Systems Pharmacology, Department of Pharmacology, Faculty of Medicine, Siriraj Medical School, Mahidol University, Bangkok, 10700, Thailand
| | - Stephen Dalton
- Center for Molecular Medicine and Department of Biochemistry and Molecular Biology, 325 Riverbend Road, The University of Georgia, Athens, GA, 30602, USA
| | - Methichit Wattanapanitch
- Siriraj Center for Regenerative Medicine, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.
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Coux RX, Owens NDL, Navarro P. Chromatin accessibility and transcription factor binding through the perspective of mitosis. Transcription 2020; 11:236-240. [PMID: 33054514 PMCID: PMC7714440 DOI: 10.1080/21541264.2020.1825907] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Chromatin accessibility is generally perceived as a common property of active regulatory elements where transcription factors are recruited via DNA-specific interactions and other physico-chemical properties to regulate gene transcription. Recent work in the context of mitosis provides less trivial and potentially more interesting relationships than previously anticipated.
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Affiliation(s)
- Rémi-Xavier Coux
- Epigenomics, Proliferation and the Identity of Cells, Department of Development and Stem Cell Biology, Institut Pasteur , Paris, France
| | - Nick D L Owens
- Institute of Biomedical and Clinical Science, University of Exeter Medical School , Exeter, UK
| | - Pablo Navarro
- Epigenomics, Proliferation and the Identity of Cells, Department of Development and Stem Cell Biology, Institut Pasteur , Paris, France
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39
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Hwang Y, Hidalgo D, Socolovsky M. The shifting shape and functional specializations of the cell cycle during lineage development. WIREs Mech Dis 2020; 13:e1504. [PMID: 32916032 DOI: 10.1002/wsbm.1504] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 06/29/2020] [Accepted: 07/08/2020] [Indexed: 12/12/2022]
Abstract
Essentially all cell cycling in multicellular organisms in vivo takes place in the context of lineage differentiation. This notwithstanding, the regulation of the cell cycle is often assumed to be generic, independent of tissue or developmental stage. Here we review developmental-stage-specific cell cycle adaptations that may influence developmental decisions, in mammalian erythropoiesis and in other lineages. The length of the cell cycle influences the balance between self-renewal and differentiation in multiple tissues, and may determine lineage fate. Shorter cycles contribute to the efficiency of reprogramming somatic cells into induced pluripotency stem cells and help maintain the pluripotent state. While the plasticity of G1 length is well established, the speed of S phase is emerging as a novel regulated parameter that may influence cell fate transitions in the erythroid lineage, in neural tissue and in embryonic stem cells. A slow S phase may stabilize the self-renewal state, whereas S phase shortening may favor a cell fate change. In the erythroid lineage, functional approaches and single-cell RNA-sequencing show that a key transcriptional switch, at the transition from self-renewal to differentiation, is synchronized with and dependent on S phase. This specific S phase is shorter, as a result of a genome-wide increase in the speed of replication forks. Furthermore, there is progressive shortening in G1 in the period preceding this switch. Together these studies suggest an integrated regulatory landscape of the cycle and differentiation programs, where cell cycle adaptations are controlled by, and in turn feed back on, the propagation of developmental trajectories. This article is categorized under: Biological Mechanisms > Cell Fates Developmental Biology > Stem Cell Biology and Regeneration Developmental Biology > Lineages.
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Affiliation(s)
- Yung Hwang
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Daniel Hidalgo
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Merav Socolovsky
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
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40
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Abstract
The hierarchical three-dimensional folding of the mammalian genome constitutes an important regulatory layer of gene expression and cell fate control during processes such as development and tumorigenesis. Accumulating evidence supports the existence of complex topological assemblies in which multiple genes and regulatory elements are frequently interacting with each other in the 3D nucleus. Here, we will discuss the nature, organizational principles, and potential function of such assemblies, including the recently reported enhancer “hubs,” “cliques,” and FIREs (frequently interacting regions) as well as multi-contact hubs. We will also review recent studies that investigate the role of transcription factors (TFs) in driving the topological genome reorganization and hub formation in the context of cell fate transitions and cancer. Finally, we will highlight technological advances that enabled these studies, current limitations, and future directions necessary to advance our understating in the field.
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Affiliation(s)
- Dafne Campigli Di Giammartino
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine , New York, NY, USA
| | - Alexander Polyzos
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine , New York, NY, USA
| | - Effie Apostolou
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine , New York, NY, USA
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41
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Scott WA, Campos EI. Interactions With Histone H3 & Tools to Study Them. Front Cell Dev Biol 2020; 8:701. [PMID: 32850821 PMCID: PMC7411163 DOI: 10.3389/fcell.2020.00701] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 07/10/2020] [Indexed: 01/12/2023] Open
Abstract
Histones are an integral part of chromatin and thereby influence its structure, dynamics, and functions. The effects of histone variants, posttranslational modifications, and binding proteins is therefore of great interest. From the moment that they are deposited on chromatin, nucleosomal histones undergo dynamic changes in function of the cell cycle, and as DNA is transcribed and replicated. In the process, histones are not only modified and bound by various proteins, but also shuffled, evicted, or replaced. Technologies and tools to study such dynamic events continue to evolve and better our understanding of chromatin and of histone proteins proper. Here, we provide an overview of H3.1 and H3.3 histone dynamics throughout the cell cycle, while highlighting some of the tools used to study their protein–protein interactions. We specifically discuss how histones are chaperoned, modified, and bound by various proteins at different stages of the cell cycle. Established and select emerging technologies that furthered (or have a high potential of furthering) our understanding of the dynamic histone–protein interactions are emphasized. This includes experimental tools to investigate spatiotemporal changes on chromatin, the role of histone chaperones, histone posttranslational modifications, and histone-binding effector proteins.
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Affiliation(s)
- William A Scott
- Genetics & Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Eric I Campos
- Genetics & Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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Rose JT, Moskovitz E, Boyd JR, Gordon JA, Bouffard NA, Fritz AJ, Illendula A, Bushweller JH, Lian JB, Stein JL, Zaidi SK, Stein GS. Inhibition of the RUNX1-CBFβ transcription factor complex compromises mammary epithelial cell identity: a phenotype potentially stabilized by mitotic gene bookmarking. Oncotarget 2020; 11:2512-2530. [PMID: 32655837 PMCID: PMC7335667 DOI: 10.18632/oncotarget.27637] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 05/20/2020] [Indexed: 12/12/2022] Open
Abstract
RUNX1 has recently been shown to play an important role in determination of mammary epithelial cell identity. However, mechanisms by which loss of the RUNX1 transcription factor in mammary epithelial cells leads to epithelial-to-mesenchymal transition (EMT) are not known. Here, we report that interaction between RUNX1 and its heterodimeric partner CBFβ is essential for sustaining mammary epithelial cell identity. Disruption of RUNX1-CBFβ interaction, DNA binding, and association with mitotic chromosomes alters cell morphology, global protein synthesis, and phenotype-related gene expression. During interphase, RUNX1 is organized as punctate, predominantly nuclear, foci that are dynamically redistributed during mitosis, with a subset localized to mitotic chromosomes. Genome-wide RUNX1 occupancy profiles for asynchronous, mitotically enriched, and early G1 breast epithelial cells reveal RUNX1 associates with RNA Pol II-transcribed protein coding and long non-coding RNA genes and RNA Pol I-transcribed ribosomal genes critical for mammary epithelial proliferation, growth, and phenotype maintenance. A subset of these genes remains occupied by the protein during the mitosis to G1 transition. Together, these findings establish that the RUNX1-CBFβ complex is required for maintenance of the normal mammary epithelial phenotype and its disruption leads to EMT. Importantly, our results suggest, for the first time, that RUNX1 mitotic bookmarking of a subset of epithelial-related genes may be an important epigenetic mechanism that contributes to stabilization of the mammary epithelial cell identity.
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Affiliation(s)
- Joshua T. Rose
- Department of Biochemistry and University of Vermont Cancer Center, Robert Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
- These authors contributed equally to this work
| | - Eliana Moskovitz
- Department of Biochemistry and University of Vermont Cancer Center, Robert Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
- These authors contributed equally to this work
| | - Joseph R. Boyd
- Department of Biochemistry and University of Vermont Cancer Center, Robert Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Jonathan A. Gordon
- Department of Biochemistry and University of Vermont Cancer Center, Robert Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Nicole A. Bouffard
- Microscopy Imaging Center at the Robert Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Andrew J. Fritz
- Department of Biochemistry and University of Vermont Cancer Center, Robert Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Anuradha Illendula
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - John H. Bushweller
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - Jane B. Lian
- Department of Biochemistry and University of Vermont Cancer Center, Robert Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Janet L. Stein
- Department of Biochemistry and University of Vermont Cancer Center, Robert Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Sayyed K. Zaidi
- Department of Biochemistry and University of Vermont Cancer Center, Robert Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Gary S. Stein
- Department of Biochemistry and University of Vermont Cancer Center, Robert Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
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Kori S, Jimenji T, Ekimoto T, Sato M, Kusano F, Oda T, Unoki M, Ikeguchi M, Arita K. Serine 298 Phosphorylation in Linker 2 of UHRF1 Regulates Ligand-Binding Property of Its Tandem Tudor Domain. J Mol Biol 2020; 432:4061-4075. [PMID: 32428527 DOI: 10.1016/j.jmb.2020.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 05/11/2020] [Accepted: 05/13/2020] [Indexed: 01/26/2023]
Abstract
Ubiquitin-like with PHD and RING finger domains 1 (UHRF1) is an essential factor for the maintenance of mammalian DNA methylation and harbors several reader modules for recognizing epigenetic marks. The tandem Tudor domain (TTD) of UHRF1 has a peptide-binding groove that functions as a binding platform for intra- or intermolecular interactions. Besides the groove interacting with unphosphorylated linker 2 and spacer of UHRF1, it also interacts with di/tri-methylated histone H3 at Lys9 and DNA ligase 1 (LIG1) at Lys126. Here we focus on the phosphorylation of Ser298 in linker 2, which was implied to regulate the ligand-binding property of the TTD. Although the protein expression level of UHRF1 is unchanged throughout the cell cycle, Ser298 phosphorylated form of UHRF1 is notably increased in the G2/M phase, which is revealed by immunoprecipitation followed by Western blotting. Molecularly, while unphosphorylated linker 2 covers the peptide-binding groove to prevent access of other interactors, small-angle X-ray scattering, thermal stability assay and molecular dynamics simulation revealed that the phosphate group of Ser298 dissociates linker 2 from the peptide-binding groove of the TTD to permit the other interactors to access to the groove. Our data reveal a mechanism in which Ser298 phosphorylation in linker 2 triggers a change of the TTD's structure and may affect multiple functions of UHRF1 by facilitating associations with LIG1 at DNA replication sites and histone H3K9me2/me3 at heterochromatic regions.
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Affiliation(s)
- Satomi Kori
- Structure Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Tomohiro Jimenji
- Structure Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Toru Ekimoto
- Computational Life Science Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Miwa Sato
- Mitsui Knowledge Industry, 2-5-1 Atago, Minato-ku, Tokyo 105-6215, Japan
| | - Fumie Kusano
- Structure Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Takashi Oda
- Structure Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Motoko Unoki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| | - Mitsunori Ikeguchi
- Computational Life Science Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; RIKEN Medical Sciences Innovation Hub Program, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Kyohei Arita
- Structure Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.
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44
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Cappelli C, Sepulveda H, Rivas S, Pola V, Urzúa U, Donoso G, Sagredo E, Carrero D, Casanova-Ortiz E, Sagredo A, González M, Manterola M, Nardocci G, Armisén R, Montecino M, Marcelain K. Ski Is Required for Tri-Methylation of H3K9 in Major Satellite and for Repression of Pericentromeric Genes: Mmp3, Mmp10 and Mmp13, in Mouse Fibroblasts. J Mol Biol 2020; 432:3222-3238. [PMID: 32198114 DOI: 10.1016/j.jmb.2020.03.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 02/23/2020] [Accepted: 03/11/2020] [Indexed: 11/27/2022]
Abstract
Several mechanisms directing a rapid transcriptional reactivation of genes immediately after mitosis have been described. However, little is known about the maintenance of repressive signals during mitosis. In this work, we address the role of Ski in the repression of gene expression during M/G1 transition in mouse embryonic fibroblasts (MEFs). We found that Ski localises as a distinct pair of dots at the pericentromeric region of mitotic chromosomes, and the absence of the protein is related to high acetylation and low tri-methylation of H3K9 in pericentromeric major satellite. Moreover, differential expression assays in early G1 cells showed that the presence of Ski is significantly associated with repression of genes localised nearby to pericentromeric DNA. In mitotic cells, chromatin immunoprecipitation assays confirmed the association of Ski to major satellite and the promoters of the most repressed genes: Mmp3, Mmp10 and Mmp13. These genes are at pericentromeric region of chromosome 9. In these promoters, the presence of Ski resulted in increased H3K9 tri-methylation levels. This Ski-dependent regulation is also observed during interphase. Consequently, Mmp activity is augmented in Ski-/- MEFs. Altogether, these data indicate that association of Ski with the pericentromeric region of chromosomes during mitosis is required to maintain the silencing bookmarks of underlying chromatin.
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Affiliation(s)
- Claudio Cappelli
- Departamento de Oncología Básico Clínica. Facultad de Medicina, Universidad de Chile, Santiago, Chile; Instituto de Bioquimica y Microbiologia, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Hugo Sepulveda
- Instituto de Ciencias Biomédicas, Facultad de Medicina y Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Solange Rivas
- Departamento de Oncología Básico Clínica. Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Víctor Pola
- Departamento de Oncología Básico Clínica. Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Ulises Urzúa
- Departamento de Oncología Básico Clínica. Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Gerardo Donoso
- Departamento de Oncología Básico Clínica. Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Eduardo Sagredo
- Departamento de Oncología Básico Clínica. Facultad de Medicina, Universidad de Chile, Santiago, Chile; Centro de Genética y Genómica, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - David Carrero
- Departamento de Oncología Básico Clínica. Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Emmanuel Casanova-Ortiz
- Departamento de Oncología Básico Clínica. Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Alfredo Sagredo
- Departamento de Oncología Básico Clínica. Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Marisel González
- Departamento de Oncología Básico Clínica. Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Marcia Manterola
- Instituto de Ciencias Biomédicas. Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Gino Nardocci
- Instituto de Ciencias Biomédicas, Facultad de Medicina y Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile; FONDAP Center for Genome Regulation, Santiago, Chile
| | - Ricardo Armisén
- Departamento de Oncología Básico Clínica. Facultad de Medicina, Universidad de Chile, Santiago, Chile; Centro de Genética y Genómica, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Martin Montecino
- Instituto de Ciencias Biomédicas, Facultad de Medicina y Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile; FONDAP Center for Genome Regulation, Santiago, Chile
| | - Katherine Marcelain
- Departamento de Oncología Básico Clínica. Facultad de Medicina, Universidad de Chile, Santiago, Chile.
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45
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Nevil M, Gibson TJ, Bartolutti C, Iyengar A, Harrison MM. Establishment of chromatin accessibility by the conserved transcription factor Grainy head is developmentally regulated. Development 2020; 147:dev185009. [PMID: 32098765 PMCID: PMC10624965 DOI: 10.1242/dev.185009] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 02/07/2020] [Indexed: 12/18/2022]
Abstract
The dramatic changes in gene expression required for development necessitate the establishment of cis-regulatory modules defined by regions of accessible chromatin. Pioneer transcription factors have the unique property of binding closed chromatin and facilitating the establishment of these accessible regions. Nonetheless, much of how pioneer transcription factors coordinate changes in chromatin accessibility during development remains unknown. To determine whether pioneer-factor function is intrinsic to the protein or whether pioneering activity is developmentally modulated, we studied the highly conserved, essential transcription factor Grainy head (Grh). Prior work established that Grh is expressed throughout Drosophila development and is a pioneer factor in the larva. We demonstrated that Grh remains bound to mitotic chromosomes, a property shared with other pioneer factors. By assaying chromatin accessibility in embryos lacking maternal and/or zygotic Grh at three stages of development, we discovered that Grh is not required for chromatin accessibility in early embryogenesis, in contrast to its essential functions later in development. Our data reveal that the pioneering activity of Grh is temporally regulated and likely influenced by additional factors expressed at a given developmental stage.
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Affiliation(s)
- Markus Nevil
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Tyler J Gibson
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Constantine Bartolutti
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Anusha Iyengar
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Melissa M Harrison
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA
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46
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Shoaib M, Nair N, Sørensen CS. Chromatin Landscaping At Mitotic Exit Orchestrates Genome Function. Front Genet 2020; 11:103. [PMID: 32158468 PMCID: PMC7052122 DOI: 10.3389/fgene.2020.00103] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 01/29/2020] [Indexed: 11/23/2022] Open
Abstract
Chromatin architecture is highly dynamic during different phases of cell cycle to accommodate DNA-based processes. This is particularly obvious during mitotic exit, where highly condensed rod-like chromatids need to be rapidly decondensed. Such chromatin structural transitions are tightly controlled and organized as any perturbance in this dynamic process can lead to genome dysfunction which may culminate in loss of cellular fitness. However, the mechanisms underlying cell cycle-dependent chromatin structural changes are not fully understood. In this mini review, we highlight our current knowledge of chromatin structural organization, focusing on mitotic exit. In this regard, we examine how nuclear processes are orchestrated during chromatin unfolding and compartmentalization and discuss the critical importance of cell cycle-controlled chromatin landscaping in maintaining genome integrity.
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Affiliation(s)
- Muhammad Shoaib
- Biotech Research and Innovation Centre (BRIC), Faculty of Medical and Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nidhi Nair
- Biotech Research and Innovation Centre (BRIC), Faculty of Medical and Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Claus Storgaard Sørensen
- Biotech Research and Innovation Centre (BRIC), Faculty of Medical and Health Sciences, University of Copenhagen, Copenhagen, Denmark
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47
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Laner-Plamberger S, Oeller M, Mrazek C, Hartl A, Sonderegger A, Rohde E, Strunk D, Schallmoser K. Upregulation of mitotic bookmarking factors during enhanced proliferation of human stromal cells in human platelet lysate. J Transl Med 2019; 17:432. [PMID: 31888679 PMCID: PMC6936143 DOI: 10.1186/s12967-019-02183-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 12/20/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Innovative human stromal cell therapeutics require xeno-free culture conditions. Various formulations of human platelet lysate (HPL) are efficient alternatives for fetal bovine serum (FBS). However, a consistent lack of standardized manufacturing protocols and quality criteria hampers comparability of HPL-products. Aim of this study was to compare the biochemical composition of three differential HPL-preparations with FBS and to investigate their impact on stromal cell biology. METHODS Stromal cells were isolated from bone marrow (BM), white adipose tissue (WAT) and umbilical cord (UC) and cultured in medium supplemented with pooled HPL (pHPL), fibrinogen-depleted serum-converted pHPL (pHPLS), mechanically fibrinogen-depleted pHPL (mcpHPL) and FBS. Biochemical parameters were analyzed in comparison to standard values in whole blood. Distinct growth factors and cytokines were measured by bead-based multiplex technology. Flow cytometry of stromal cell immunophenotype, in vitro differentiation, and mRNA expression analysis of transcription factors SOX2, KLF4, cMYC, OCT4 and NANOG were performed. RESULTS Biochemical parameters were comparable in all pHPL preparations, but to some extent different to FBS. Total protein, glucose, cholesterol and Na+ were elevated in pHPL preparations, K+ and Fe3+ levels were higher in FBS. Compared to FBS, pHPL-based media significantly enhanced stromal cell propagation. Characteristic immunophenotype and in vitro differentiation potential were maintained in all four culture conditions. The analysis of growth factors and cytokines revealed distinct levels depending on the pre-existence in pHPL, consumption or secretion by the stromal cells. Interestingly, mRNA expression of the transcription and mitotic bookmarking factors cMYC and KLF4 was significantly enhanced in a source dependent manner in stromal cells cultured in pHPL- compared to FBS-supplemented media. SOX2 mRNA expression of all stromal cell types was increased in all pHPL culture conditions. CONCLUSION All pHPL-supplemented media equally supported proliferation of WAT- and UC-derived stromal cells significantly better than FBS. Mitotic bookmarking factors, known to enable a quick re-entry to the cell cycle, were significantly enhanced in pHPL-expanded cells. Our results support a better characterization and standardization of humanized culture media for stromal cell-based medicinal products.
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Affiliation(s)
- Sandra Laner-Plamberger
- Department of Transfusion Medicine, University Hospital of Salzburg (SALK), Paracelsus Medical University, Salzburg, Austria.,Spinal Cord Injury and Tissue Regeneration Center Salzburg (SCI-TReCS), Paracelsus Medical University, Strubergasse 21, 5020, Salzburg, Austria
| | - Michaela Oeller
- Department of Transfusion Medicine, University Hospital of Salzburg (SALK), Paracelsus Medical University, Salzburg, Austria.,Spinal Cord Injury and Tissue Regeneration Center Salzburg (SCI-TReCS), Paracelsus Medical University, Strubergasse 21, 5020, Salzburg, Austria
| | - Cornelia Mrazek
- Department of Laboratory Medicine, University Hospital of Salzburg (SALK), Paracelsus Medical University, Salzburg, Austria
| | - Arnulf Hartl
- Institute of Ecomedicine, Paracelsus Medical University, Salzburg, Austria
| | - Alina Sonderegger
- Spinal Cord Injury and Tissue Regeneration Center Salzburg (SCI-TReCS), Paracelsus Medical University, Strubergasse 21, 5020, Salzburg, Austria.,Cell Therapy Institute, Paracelsus Medical University, Salzburg, Austria
| | - Eva Rohde
- Department of Transfusion Medicine, University Hospital of Salzburg (SALK), Paracelsus Medical University, Salzburg, Austria.,Spinal Cord Injury and Tissue Regeneration Center Salzburg (SCI-TReCS), Paracelsus Medical University, Strubergasse 21, 5020, Salzburg, Austria
| | - Dirk Strunk
- Spinal Cord Injury and Tissue Regeneration Center Salzburg (SCI-TReCS), Paracelsus Medical University, Strubergasse 21, 5020, Salzburg, Austria.,Cell Therapy Institute, Paracelsus Medical University, Salzburg, Austria
| | - Katharina Schallmoser
- Department of Transfusion Medicine, University Hospital of Salzburg (SALK), Paracelsus Medical University, Salzburg, Austria. .,Spinal Cord Injury and Tissue Regeneration Center Salzburg (SCI-TReCS), Paracelsus Medical University, Strubergasse 21, 5020, Salzburg, Austria.
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48
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Dreval K, Lake RJ, Fan HY. HDAC1 negatively regulates selective mitotic chromatin binding of the Notch effector RBPJ in a KDM5A-dependent manner. Nucleic Acids Res 2019; 47:4521-4538. [PMID: 30916347 PMCID: PMC6511865 DOI: 10.1093/nar/gkz178] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 02/28/2019] [Accepted: 03/07/2019] [Indexed: 01/25/2023] Open
Abstract
Faithful propagation of transcription programs through cell division underlies cell-identity maintenance. Transcriptional regulators selectively bound on mitotic chromatin are emerging critical elements for mitotic transcriptional memory; however, mechanisms governing their site-selective binding remain elusive. By studying how protein-protein interactions impact mitotic chromatin binding of RBPJ, the major downstream effector of the Notch signaling pathway, we found that histone modifying enzymes HDAC1 and KDM5A play critical, regulatory roles in this process. We found that HDAC1 knockdown or inactivation leads to increased RBPJ occupancy on mitotic chromatin in a site-specific manner, with a concomitant increase of KDM5A occupancy at these sites. Strikingly, the presence of KDM5A is essential for increased RBPJ occupancy. Our results uncover a regulatory mechanism in which HDAC1 negatively regulates RBPJ binding on mitotic chromatin in a KDM5A-dependent manner. We propose that relative chromatin affinity of a minimal regulatory complex, reflecting a specific transcription program, renders selective RBPJ binding on mitotic chromatin.
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Affiliation(s)
- Kostiantyn Dreval
- From the Department of Internal Medicine, Division of Molecular Medicine, Program in Cancer Genetics, Epigenetics and Genomics, University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87131, USA
| | - Robert J Lake
- From the Department of Internal Medicine, Division of Molecular Medicine, Program in Cancer Genetics, Epigenetics and Genomics, University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87131, USA
| | - Hua-Ying Fan
- From the Department of Internal Medicine, Division of Molecular Medicine, Program in Cancer Genetics, Epigenetics and Genomics, University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87131, USA
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49
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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: 46] [Impact Index Per Article: 9.2] [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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50
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Poleshko A, Smith CL, Nguyen SC, Sivaramakrishnan P, Wong KG, Murray JI, Lakadamyali M, Joyce EF, Jain R, Epstein JA. H3K9me2 orchestrates inheritance of spatial positioning of peripheral heterochromatin through mitosis. eLife 2019; 8:49278. [PMID: 31573510 PMCID: PMC6795522 DOI: 10.7554/elife.49278] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 09/30/2019] [Indexed: 12/16/2022] Open
Abstract
Cell-type-specific 3D organization of the genome is unrecognizable during mitosis. It remains unclear how essential positional information is transmitted through cell division such that a daughter cell recapitulates the spatial genome organization of the parent. Lamina-associated domains (LADs) are regions of repressive heterochromatin positioned at the nuclear periphery that vary by cell type and contribute to cell-specific gene expression and identity. Here we show that histone 3 lysine 9 dimethylation (H3K9me2) is an evolutionarily conserved, specific mark of nuclear peripheral heterochromatin and that it is retained through mitosis. During mitosis, phosphorylation of histone 3 serine 10 temporarily shields the H3K9me2 mark allowing for dissociation of chromatin from the nuclear lamina. Using high-resolution 3D immuno-oligoFISH, we demonstrate that H3K9me2-enriched genomic regions, which are positioned at the nuclear lamina in interphase cells prior to mitosis, re-associate with the forming nuclear lamina before mitotic exit. The H3K9me2 modification of peripheral heterochromatin ensures that positional information is safeguarded through cell division such that individual LADs are re-established at the nuclear periphery in daughter nuclei. Thus, H3K9me2 acts as a 3D architectural mitotic guidepost. Our data establish a mechanism for epigenetic memory and inheritance of spatial organization of the genome.
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Affiliation(s)
- Andrey Poleshko
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Cheryl L Smith
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Son C Nguyen
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Priya Sivaramakrishnan
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Karen G Wong
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - John Isaac Murray
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Melike Lakadamyali
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Eric F Joyce
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Rajan Jain
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States.,Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States.,Penn Cardiovascular Institute and Institute of Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Jonathan A Epstein
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States.,Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States.,Penn Cardiovascular Institute and Institute of Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
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