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Ouasti F, Audin M, Fréon K, Quivy JP, Tachekort M, Cesard E, Thureau A, Ropars V, Fernández Varela P, Moal G, Soumana-Amadou I, Uryga A, Legrand P, Andreani J, Guerois R, Almouzni G, Lambert S, Ochsenbein F. Disordered regions and folded modules in CAF-1 promote histone deposition in Schizosaccharomyces pombe. eLife 2024; 12:RP91461. [PMID: 38376141 PMCID: PMC10942606 DOI: 10.7554/elife.91461] [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] [Indexed: 02/21/2024] Open
Abstract
Genome and epigenome integrity in eukaryotes depends on the proper coupling of histone deposition with DNA synthesis. This process relies on the evolutionary conserved histone chaperone CAF-1 for which the links between structure and functions are still a puzzle. While studies of the Saccharomyces cerevisiae CAF-1 complex enabled to propose a model for the histone deposition mechanism, we still lack a framework to demonstrate its generality and in particular, how its interaction with the polymerase accessory factor PCNA is operating. Here, we reconstituted a complete SpCAF-1 from fission yeast. We characterized its dynamic structure using NMR, SAXS and molecular modeling together with in vitro and in vivo functional studies on rationally designed interaction mutants. Importantly, we identify the unfolded nature of the acidic domain which folds up when binding to histones. We also show how the long KER helix mediates DNA binding and stimulates SpCAF-1 association with PCNA. Our study highlights how the organization of CAF-1 comprising both disordered regions and folded modules enables the dynamics of multiple interactions to promote synthesis-coupled histone deposition essential for its DNA replication, heterochromatin maintenance, and genome stability functions.
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Affiliation(s)
- Fouad Ouasti
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Institute JoliotGif-sur-YvetteFrance
| | - Maxime Audin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Institute JoliotGif-sur-YvetteFrance
| | - Karine Fréon
- Institut Curie, PSL Research University, CNRS UMR 3348, INSERM U1278, Université Paris-Saclay, Equipe labellisée Ligue contre le CancerOrsayFrance
| | - Jean-Pierre Quivy
- Institut Curie, PSL Research University, CNRS, Sorbonne Université,CNRS UMR3664, Nuclear Dynamics Unit, Équipe Labellisée Ligue contre le CancerParisFrance
| | - Mehdi Tachekort
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Institute JoliotGif-sur-YvetteFrance
| | - Elizabeth Cesard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Institute JoliotGif-sur-YvetteFrance
| | - Aurélien Thureau
- Synchrotron SOLEIL, HelioBio group, l'Orme des MerisiersSaint-AubinFrance
| | - Virginie Ropars
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Institute JoliotGif-sur-YvetteFrance
| | - Paloma Fernández Varela
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Institute JoliotGif-sur-YvetteFrance
| | - Gwenaelle Moal
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Institute JoliotGif-sur-YvetteFrance
| | - Ibrahim Soumana-Amadou
- Institut Curie, PSL Research University, CNRS UMR 3348, INSERM U1278, Université Paris-Saclay, Equipe labellisée Ligue contre le CancerOrsayFrance
| | - Aleksandra Uryga
- Institut Curie, PSL Research University, CNRS UMR 3348, INSERM U1278, Université Paris-Saclay, Equipe labellisée Ligue contre le CancerOrsayFrance
| | - Pierre Legrand
- Synchrotron SOLEIL, HelioBio group, l'Orme des MerisiersSaint-AubinFrance
| | - Jessica Andreani
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Institute JoliotGif-sur-YvetteFrance
| | - Raphaël Guerois
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Institute JoliotGif-sur-YvetteFrance
| | - Geneviève Almouzni
- Institut Curie, PSL Research University, CNRS, Sorbonne Université,CNRS UMR3664, Nuclear Dynamics Unit, Équipe Labellisée Ligue contre le CancerParisFrance
| | - Sarah Lambert
- Institut Curie, PSL Research University, CNRS UMR 3348, INSERM U1278, Université Paris-Saclay, Equipe labellisée Ligue contre le CancerOrsayFrance
| | - Francoise Ochsenbein
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Institute JoliotGif-sur-YvetteFrance
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Torres-Arciga K, Flores-León M, Ruiz-Pérez S, Trujillo-Pineda M, González-Barrios R, Herrera LA. Histones and their chaperones: Adaptive remodelers of an ever-changing chromatinic landscape. Front Genet 2022; 13:1057846. [PMID: 36468032 PMCID: PMC9709290 DOI: 10.3389/fgene.2022.1057846] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/02/2022] [Indexed: 07/29/2023] Open
Abstract
Chromatin maintenance and remodeling are processes that take place alongside DNA repair, replication, or transcription to ensure the survival and adaptability of a cell. The environment and the needs of the cell dictate how chromatin is remodeled; particularly where and which histones are deposited, thus changing the canonical histone array to regulate chromatin structure and gene expression. Chromatin is highly dynamic, and histone variants and their chaperones play a crucial role in maintaining the epigenetic regulation at different genomic regions. Despite the large number of histone variants reported to date, studies on their roles in physiological processes and pathologies are emerging but continue to be scarce. Here, we present recent advances in the research on histone variants and their chaperones, with a focus on their importance in molecular mechanisms such as replication, transcription, and DNA damage repair. Additionally, we discuss the emerging role they have in transposable element regulation, aging, and chromatin remodeling syndromes. Finally, we describe currently used methods and their limitations in the study of these proteins and highlight the importance of improving the experimental approaches to further understand this epigenetic machinery.
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Affiliation(s)
- Karla Torres-Arciga
- Doctorado en Ciencias Biológicas, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología (INCan)-Instituto de Investigaciones Biomédicas (IIBO), Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Manuel Flores-León
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas (IIBO), Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Samuel Ruiz-Pérez
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología (INCan)-Instituto de Investigaciones Biomédicas (IIBO), Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Magalli Trujillo-Pineda
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología (INCan)-Instituto de Investigaciones Biomédicas (IIBO), Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Rodrigo González-Barrios
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología (INCan)-Instituto de Investigaciones Biomédicas (IIBO), Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Luis A. Herrera
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología (INCan)-Instituto de Investigaciones Biomédicas (IIBO), Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
- Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
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3
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FACT modulates the conformations of histone H2A and H2B N-terminal tails within nucleosomes. Commun Biol 2022; 5:814. [PMID: 35963897 PMCID: PMC9376062 DOI: 10.1038/s42003-022-03785-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 08/01/2022] [Indexed: 11/09/2022] Open
Abstract
Gene expression is regulated by the modification and accessibility of histone tails within nucleosomes. The histone chaperone FACT (facilitate chromatin transcription), comprising SPT16 and SSRP1, interacts with nucleosomes through partial replacement of DNA with the phosphorylated acidic intrinsically disordered (pAID) segment of SPT16; pAID induces an accessible conformation of the proximal histone H3 N-terminal tail (N-tail) in the unwrapped nucleosome with FACT. Here, we use NMR to probe the histone H2A and H2B tails in the unwrapped nucleosome. Consequently, both the H2A and H2B N-tails on the pAID-proximal side bind to pAID with robust interactions, which are important for nucleosome assembly with FACT. Furthermore, the conformations of these N-tails on the distal DNA-contact site are altered from those in the canonical nucleosome. Our findings highlight that FACT both proximally and distally regulates the conformations of the H2A and H2B N-tails in the asymmetrically unwrapped nucleosome.
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Liu Y, Li Y, Bao H, Liu Y, Chen L, Huang H. Epstein-Barr Virus Tegument Protein BKRF4 is a Histone Chaperone. J Mol Biol 2022; 434:167756. [PMID: 35870648 DOI: 10.1016/j.jmb.2022.167756] [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: 06/17/2022] [Revised: 07/18/2022] [Accepted: 07/18/2022] [Indexed: 11/18/2022]
Abstract
Histone chaperones, which constitute an interaction and functional network involved in all aspects of histone metabolism, have to date been identified only in eukaryotes. The Epstein-Barr virus tegument protein BKRF4 is a histone-binding protein that engages histones H2A-H2B and H3-H4, and cellular chromatin, inhibiting the host DNA damage response. Here, we identified BKRF4 as a bona fide viral histone chaperone whose histone-binding domain (HBD) forms a co-chaperone complex with the human histone chaperone ASF1 in vitro. We determined the crystal structures of the quaternary complex of the BKRF4 HBD with human H3-H4 dimer and the histone chaperone ASF1b and the ternary complex of the BKRF4 HBD with human H2A-H2B dimer. Through structural and biochemical studies, we elucidated the molecular basis for H3-H4 and H2A-H2B recognition by BKRF4. We also revealed two conserved motifs, D/EL and DEF/Y/W, within the BKRF4 HBD, which may represent common motifs through which histone chaperones target H3-H4 and H2A-H2B, respectively. In conclusion, our results identify BKRF4 as a histone chaperone encoded by the Epstein-Barr virus, representing a typical histone chaperone found in a non-eukaryote. We envision that more histone chaperones await identification and characterization in DNA viruses and even archaea.
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Affiliation(s)
- Yongrui Liu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China.
| | - Yue Li
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Hongyu Bao
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China.
| | - Yanhong Liu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Liu Chen
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Hongda Huang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China.
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Chen X, Li M, Tang Y, Liang Q, Hua C, He H, Song Y, Cheng H. Gene Expression Profile Analysis of Human Epidermal Keratinocytes Expressing Human Papillomavirus Type 8 E7. Pathol Oncol Res 2022; 28:1610176. [PMID: 35665406 PMCID: PMC9156622 DOI: 10.3389/pore.2022.1610176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 04/21/2022] [Indexed: 11/13/2022]
Abstract
Background: Human papillomavirus type 8 (HPV8) has been implicated in the progress of non-melanoma skin cancers and their precursor lesions. The HPV8 E7 oncoprotein plays a key role in the tumorigenesis of HPV-associated cutaneous tumors. However, the exact role of HPV8 E7 in human epidermal carcinogenesis has not been fully elucidated. Methods: To investigate the potential carcinogenic effects of HPV8 E7 on epithelial cells, we used RNA-sequencing technology to analyze the gene expression profile of HPV8 E7-overexpressed normal human epidermal keratinocytes (NHEKs). Results: RNA-sequencing revealed 831 differentially expressed genes (DEGs) between HPV8 E7-expressing NHEKs and control cells, among which, 631 genes were significantly upregulated, and 200 were downregulated. Gene ontology annotation enrichment analysis showed that HPV8 E7 mainly affected the expression of genes associated with protein heterodimerization activity, DNA binding, nucleosomes, and nucleosome assembly. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis revealed that overexpression of HPV8 E7 affected the expression of gene clusters associated with viral carcinogenesis and transcriptional misregulation in cancer and necroptosis signaling pathways that reportedly play crucial roles in HPV infection promotion and cancer progression. We also found the DEGs, such as HKDC1 and TNFAIP3, were associated with epigenetic modifications, immune regulation, and metabolic pathways. Conclusion: Our results demonstrate that the pro-carcinogenic effect of HPV8 expression in epithelial cells may be attributed to the regulatory effect of oncogene E7 on gene expression associated with epigenetic modifications and immune and metabolic status-associated gene expression. Although our data are based on an in vitro experiment, it provides the theoretical evidence that the development of squamous cell carcinoma can be caused by HPV.
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Affiliation(s)
- Xianzhen Chen
- Department of Dermatology and Venereology, Zhejiang University School of Medicine Sir Run Run Shaw Hospital, Hangzhou, China
| | - Ma Li
- Department of Dermatology and Venereology, Zhejiang University School of Medicine Sir Run Run Shaw Hospital, Hangzhou, China
| | - Yi Tang
- Department of Dermatology and Venereology, Zhejiang University School of Medicine Sir Run Run Shaw Hospital, Hangzhou, China.,Department of Dermatology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - Qichang Liang
- Department of Dermatology and Venereology, Zhejiang University School of Medicine Sir Run Run Shaw Hospital, Hangzhou, China
| | - Chunting Hua
- Department of Dermatology and Venereology, Zhejiang University School of Medicine Sir Run Run Shaw Hospital, Hangzhou, China
| | - Huiqin He
- Department of Gastroenterology, Zhejiang University School of Medicine Sir Run Run Shaw Hospital, Hangzhou, China
| | - Yinjing Song
- Department of Dermatology and Venereology, Zhejiang University School of Medicine Sir Run Run Shaw Hospital, Hangzhou, China
| | - Hao Cheng
- Department of Dermatology and Venereology, Zhejiang University School of Medicine Sir Run Run Shaw Hospital, Hangzhou, China
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