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Bakail M, Gaubert A, Andreani J, Moal G, Pinna G, Boyarchuk E, Gaillard MC, Courbeyrette R, Mann C, Thuret JY, Guichard B, Murciano B, Richet N, Poitou A, Frederic C, Le Du MH, Agez M, Roelants C, Gurard-Levin ZA, Almouzni G, Cherradi N, Guerois R, Ochsenbein F. Design on a Rational Basis of High-Affinity Peptides Inhibiting the Histone Chaperone ASF1. Cell Chem Biol 2019; 26:1573-1585.e10. [PMID: 31543461 DOI: 10.1016/j.chembiol.2019.09.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 06/12/2019] [Accepted: 09/03/2019] [Indexed: 12/16/2022]
Abstract
Anti-silencing function 1 (ASF1) is a conserved H3-H4 histone chaperone involved in histone dynamics during replication, transcription, and DNA repair. Overexpressed in proliferating tissues including many tumors, ASF1 has emerged as a promising therapeutic target. Here, we combine structural, computational, and biochemical approaches to design peptides that inhibit the ASF1-histone interaction. Starting from the structure of the human ASF1-histone complex, we developed a rational design strategy combining epitope tethering and optimization of interface contacts to identify a potent peptide inhibitor with a dissociation constant of 3 nM. When introduced into cultured cells, the inhibitors impair cell proliferation, perturb cell-cycle progression, and reduce cell migration and invasion in a manner commensurate with their affinity for ASF1. Finally, we find that direct injection of the most potent ASF1 peptide inhibitor in mouse allografts reduces tumor growth. Our results open new avenues to use ASF1 inhibitors as promising leads for cancer therapy.
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Affiliation(s)
- May Bakail
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Albane Gaubert
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France
| | - Jessica Andreani
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Gwenaëlle Moal
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Guillaume Pinna
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Ekaterina Boyarchuk
- Institut Curie, Paris Sciences et Lettres (PSL) Research University, CNRS, UMR3664, Equipe Labellisée Ligue Contre le Cancer, 75005 Paris, France; Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3664, 75005 Paris, France
| | - Marie-Cécile Gaillard
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Regis Courbeyrette
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Carl Mann
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Jean-Yves Thuret
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Bérengère Guichard
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France
| | - Brice Murciano
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France
| | - Nicolas Richet
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France
| | - Adeline Poitou
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France
| | - Claire Frederic
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France
| | - Marie-Hélène Le Du
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Morgane Agez
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France
| | - Caroline Roelants
- Institut National de la Santé et de la Recherche Médicale, Unité 1036, 38000 Grenoble, France; Commissariat à l'Energie Atomique, Institut de Recherche Interdisciplinaire de Grenoble, Biologie du Cancer et de l'Infection, 38000 Grenoble, France; Université Grenoble Alpes, Unité Mixte de Recherche-S1036, 38000 Grenoble, France
| | - Zachary A Gurard-Levin
- Institut Curie, Paris Sciences et Lettres (PSL) Research University, CNRS, UMR3664, Equipe Labellisée Ligue Contre le Cancer, 75005 Paris, France; Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3664, 75005 Paris, France
| | - Geneviève Almouzni
- Institut Curie, Paris Sciences et Lettres (PSL) Research University, CNRS, UMR3664, Equipe Labellisée Ligue Contre le Cancer, 75005 Paris, France; Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3664, 75005 Paris, France
| | - Nadia Cherradi
- Institut National de la Santé et de la Recherche Médicale, Unité 1036, 38000 Grenoble, France; Commissariat à l'Energie Atomique, Institut de Recherche Interdisciplinaire de Grenoble, Biologie du Cancer et de l'Infection, 38000 Grenoble, France; Université Grenoble Alpes, Unité Mixte de Recherche-S1036, 38000 Grenoble, France
| | - Raphael Guerois
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France.
| | - Françoise Ochsenbein
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France.
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3
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Abstract
Nucleosomes compact and organize genetic material on a structural level. However, they also alter local chromatin accessibility through changes in their position, through the incorporation of histone variants, and through a vast array of histone posttranslational modifications. The dynamic nature of chromatin requires histone chaperones to process, deposit, and evict histones in different tissues and at different times in the cell cycle. This review focuses on the molecular details of canonical and variant H3-H4 histone chaperone pathways that lead to histone deposition on DNA as they are currently understood. Emphasis is placed on the most established pathways beginning with the folding, posttranslational modification, and nuclear import of newly synthesized H3-H4 histones. Next, we review the deposition of replication-coupled H3.1-H4 in S-phase and replication-independent H3.3-H4 via alternative histone chaperone pathways. Highly specialized histone chaperones overseeing the deposition of histone variants are also briefly discussed.
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Affiliation(s)
- Prerna Grover
- Genetics & Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada;
| | - Jonathon S Asa
- Department of Molecular Genetics, The University of Toronto, Toronto, Ontario M5G 0A4, Canada
| | - Eric I Campos
- Genetics & Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada; .,Department of Molecular Genetics, The University of Toronto, Toronto, Ontario M5G 0A4, Canada
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4
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Bowman A, Koide A, Goodman JS, Colling ME, Zinne D, Koide S, Ladurner AG. sNASP and ASF1A function through both competitive and compatible modes of histone binding. Nucleic Acids Res 2016; 45:643-656. [PMID: 28123037 PMCID: PMC5314797 DOI: 10.1093/nar/gkw892] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 09/19/2016] [Accepted: 10/04/2016] [Indexed: 02/07/2023] Open
Abstract
Histone chaperones are proteins that interact with histones to regulate the thermodynamic process of nucleosome assembly. sNASP and ASF1 are conserved histone chaperones that interact with histones H3 and H4 and are found in a multi-chaperoning complex in vivo. Previously we identified a short peptide motif within H3 that binds to the TPR domain of sNASP with nanomolar affinity. Interestingly, this peptide motif is sequestered within the known ASF1–H3–H4 interface, raising the question of how these two proteins are found in complex together with histones when they share the same binding site. Here, we show that sNASP contains at least two additional histone interaction sites that, unlike the TPR–H3 peptide interaction, are compatible with ASF1A binding. These surfaces allow ASF1A to form a quaternary complex with both sNASP and H3–H4. Furthermore, we demonstrate that sNASP makes a specific complex with H3 on its own in vitro, but not with H4, suggesting that it could work upstream of ASF1A. Further, we show that sNASP and ASF1A are capable of folding an H3–H4 dimer in vitro under native conditions. These findings reveal a network of binding events that may promote the entry of histones H3 and H4 into the nucleosome assembly pathway.
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Affiliation(s)
- Andrew Bowman
- Biomedical Center Munich, Physiological Chemistry, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Planegg-Martinsried, Germany
| | - Akiko Koide
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
- Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY 10016, USA
| | - Jay S Goodman
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Meaghan E Colling
- Biomedical Center Munich, Physiological Chemistry, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Planegg-Martinsried, Germany
| | - Daria Zinne
- Biomedical Center Munich, Physiological Chemistry, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Planegg-Martinsried, Germany
| | - Shohei Koide
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
- Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY 10016, USA
| | - Andreas G Ladurner
- Biomedical Center Munich, Physiological Chemistry, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Planegg-Martinsried, Germany
- Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Butenandt Str. 5-13, 81377 Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Ludwig-Maximilians-Universität München, Feodor Lynen Str. 17, 81377 Munich, Germany
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5
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Liu WH, Roemer SC, Zhou Y, Shen ZJ, Dennehey BK, Balsbaugh JL, Liddle JC, Nemkov T, Ahn NG, Hansen KC, Tyler JK, Churchill ME. The Cac1 subunit of histone chaperone CAF-1 organizes CAF-1-H3/H4 architecture and tetramerizes histones. eLife 2016; 5. [PMID: 27690308 PMCID: PMC5045291 DOI: 10.7554/elife.18023] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 08/25/2016] [Indexed: 01/16/2023] Open
Abstract
The histone chaperone Chromatin Assembly Factor 1 (CAF-1) deposits tetrameric (H3/H4)2 histones onto newly-synthesized DNA during DNA replication. To understand the mechanism of the tri-subunit CAF-1 complex in this process, we investigated the protein-protein interactions within the CAF-1-H3/H4 architecture using biophysical and biochemical approaches. Hydrogen/deuterium exchange and chemical cross-linking coupled to mass spectrometry reveal interactions that are essential for CAF-1 function in budding yeast, and importantly indicate that the Cac1 subunit functions as a scaffold within the CAF-1-H3/H4 complex. Cac1 alone not only binds H3/H4 with high affinity, but also promotes histone tetramerization independent of the other subunits. Moreover, we identify a minimal region in the C-terminus of Cac1, including the structured winged helix domain and glutamate/aspartate-rich domain, which is sufficient to induce (H3/H4)2 tetramerization. These findings reveal a key role of Cac1 in histone tetramerization, providing a new model for CAF-1-H3/H4 architecture and function during eukaryotic replication. DOI:http://dx.doi.org/10.7554/eLife.18023.001 The DNA of a human, yeast or other eukaryotic cell is bound to proteins called histones to form repeating units called nucleosomes. Every time a eukaryotic cell divides, it must duplicate its DNA. Old histones are first removed from the nucleosomes before being re-assembled onto the newly duplicated DNA along with new histone proteins, producing a full complement of nucleosomes. A group of proteins called the chromatin assembly factor 1 (or CAF-1 for short) helps to assemble the histones onto the DNA. CAF-1 is made up of three proteins, and binds to two copies of each of the histones known as H3 and H4. These are the first histones to be assembled onto the nucleosomes. It was not clear how the components of CAF-1 are organized, or how CAF-1 recognizes histones. Liu et al. have now investigated the structure of CAF-1 and its interactions with the H3 and H4 histones by studying yeast proteins and cells. Yeast is a good model system because yeast CAF-1 is smaller and easier to isolate than human CAF-1, yet still performs the same essential activities. Using a combination of biochemical and biophysical techniques, Liu et al. found that one of the three proteins that makes up yeast CAF-1 – called Cac1 – forms a scaffold that supports the other CAF-1 proteins and histones H3 and H4. Moreover, a specific part of Cac1 is able to bind to these histones and assemble two copies of each of them to prepare for efficient nucleosome assembly. Further experiments revealed the specific areas where the CAF-1 proteins interact with each other and with the histones, determined how strong those interactions are, and confirmed that these interactions play important roles in yeast. Overall, the results presented by Liu et al. provide new insights into the structure of CAF-1 bound to H3 and H4. In order to understand in detail how CAF-1 helps to assemble histones onto DNA, future work needs to capture three-dimensional snapshots of the different steps in this process. Further investigation is also needed to discover how CAF-1 cooperates with other factors that promote DNA duplication. DOI:http://dx.doi.org/10.7554/eLife.18023.002
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Affiliation(s)
- Wallace H Liu
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, United States
| | - Sarah C Roemer
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, United States
| | - Yeyun Zhou
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, United States
| | - Zih-Jie Shen
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, United States
| | - Briana K Dennehey
- Department of Epigenetics and Molecular Carcinogenesis, MD Anderson Cancer Center, Houston, United States
| | - Jeremy L Balsbaugh
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Boulder, United States.,BioFrontiers Institute, University of Colorado, Boulder, Boulder, United States
| | - Jennifer C Liddle
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Boulder, United States.,BioFrontiers Institute, University of Colorado, Boulder, Boulder, United States
| | - Travis Nemkov
- Program in Structural Biology and Biochemistry, University of Colorado School of Medicine, Aurora, United States
| | - Natalie G Ahn
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Boulder, United States.,BioFrontiers Institute, University of Colorado, Boulder, Boulder, United States
| | - Kirk C Hansen
- Program in Structural Biology and Biochemistry, University of Colorado School of Medicine, Aurora, United States
| | - Jessica K Tyler
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, United States.,Department of Epigenetics and Molecular Carcinogenesis, MD Anderson Cancer Center, Houston, United States
| | - Mair Ea Churchill
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, United States.,Program in Structural Biology and Biochemistry, University of Colorado School of Medicine, Aurora, United States
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