1
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Abstract
Core histones package chromosomal DNA and regulate genomic transactions, with their nuclear import and deposition involving importin-β proteins and a dedicated repertoire of histone chaperones. Previously, a histone H3-H4 dimer has been isolated bound to importin-4 (Imp4) and the chaperone ASF1, suggesting that H3 and H4 fold together in the cytoplasm before nuclear import. However, other studies have shown the existence of monomeric H3 in the nucleus, indicating a post-import folding pathway. Here, we report that the predominant importin associated with cytoplasmic H3 is importin-5 (Imp5), which hands off its monomeric cargo to nuclear sNASP. Imp5, in contrast to Imp4, binds to both H3 and H4 containing constitutively monomeric mutations and binds to newly synthesised, monomeric H3 tethered in the cytoplasm. Constitutively monomeric H3 retains its interaction with NASP, whereas monomeric H4 retains interactions specifically with HAT1 and RBBP7. High-resolution separation of NASP interactors shows the 's' isoform but not the 't' isoform associates with monomeric H3, whilst both isoforms associate with H3-H4 dimers in at least three discrete multi-chaperoning complexes. In vitro binding experiments show mutual exclusivity between sNASP and Imp5 in binding H3, suggesting direct competition for interaction sites, with the GTP-bound form of Ran required for histone transfer. Finally, using pulse-chase analysis, we show that cytoplasm-tethered histones do not interact with endogenous NASP until they reach the nucleus, whereupon they bind rapidly. We propose an Imp5-specific import pathway for monomeric H3 that hands off to sNASP in the nucleus, with a parallel H4 pathway involving Imp5 and the HAT1-RBBP7 complex, followed by nuclear folding and hand-off to deposition factors.
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Affiliation(s)
- Alonso Javier Pardal
- Division of Biomedical Sciences, Warwick Medical School, University of WarwickCoventryUnited Kingdom
| | - Andrew James Bowman
- Division of Biomedical Sciences, Warwick Medical School, University of WarwickCoventryUnited Kingdom
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2
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Esteves de Lima J, Relaix F. Epigenetic Regulation of Myogenesis: Focus on the Histone Variants. Int J Mol Sci 2021; 22:ijms222312727. [PMID: 34884532 PMCID: PMC8657657 DOI: 10.3390/ijms222312727] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/16/2021] [Accepted: 11/19/2021] [Indexed: 01/04/2023] Open
Abstract
Skeletal muscle development and regeneration rely on the successive activation of specific transcription factors that engage cellular fate, promote commitment, and drive differentiation. Emerging evidence demonstrates that epigenetic regulation of gene expression is crucial for the maintenance of the cell differentiation status upon division and, therefore, to preserve a specific cellular identity. This depends in part on the regulation of chromatin structure and its level of condensation. Chromatin architecture undergoes remodeling through changes in nucleosome composition, such as alterations in histone post-translational modifications or exchange in the type of histone variants. The mechanisms that link histone post-translational modifications and transcriptional regulation have been extensively evaluated in the context of cell fate and differentiation, whereas histone variants have attracted less attention in the field. In this review, we discuss the studies that have provided insights into the role of histone variants in the regulation of myogenic gene expression, myoblast differentiation, and maintenance of muscle cell identity.
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3
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Esteves de Lima J, Bou Akar R, Machado L, Li Y, Drayton-Libotte B, Dilworth FJ, Relaix F. HIRA stabilizes skeletal muscle lineage identity. Nat Commun 2021; 12:3450. [PMID: 34103504 PMCID: PMC8187366 DOI: 10.1038/s41467-021-23775-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 05/17/2021] [Indexed: 12/26/2022] Open
Abstract
The epigenetic mechanisms coordinating the maintenance of adult cellular lineages and the inhibition of alternative cell fates remain poorly understood. Here we show that targeted ablation of the histone chaperone HIRA in myogenic cells leads to extensive transcriptional modifications, consistent with a role in maintaining skeletal muscle cellular identity. We demonstrate that conditional ablation of HIRA in muscle stem cells of adult mice compromises their capacity to regenerate and self-renew, leading to tissue repair failure. Chromatin analysis of Hira-deficient cells show a significant reduction of histone variant H3.3 deposition and H3K27ac modification at regulatory regions of muscle genes. Additionally, we find that genes from alternative lineages are ectopically expressed in Hira-mutant cells via MLL1/MLL2-mediated increase of H3K4me3 mark at silent promoter regions. Therefore, we conclude that HIRA sustains the chromatin landscape governing muscle cell lineage identity via incorporation of H3.3 at muscle gene regulatory regions, while preventing the expression of alternative lineage genes. The epigenetic mechanisms coordinating the maintenance of adult cellular lineages remain poorly understood. Here the authors demonstrate that HIRA, a H3.3 histone chaperone, establishes the chromatin landscape required for skeletal muscle cell identity.
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Affiliation(s)
| | - Reem Bou Akar
- Univ Paris Est Creteil, INSERM, EnvA, EFS, AP-HP, IMRB, F-94010, Creteil, France
| | - Léo Machado
- Univ Paris Est Creteil, INSERM, EnvA, EFS, AP-HP, IMRB, F-94010, Creteil, France
| | - Yuefeng Li
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada.,Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | | | - F Jeffrey Dilworth
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada.,Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Frédéric Relaix
- Univ Paris Est Creteil, INSERM, EnvA, EFS, AP-HP, IMRB, F-94010, Creteil, France.
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4
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Chen C, Sun X, Xie W, Chen S, Hu Y, Xing D, Xu J, Chen X, Zhao Z, Han Z, Xue X, Shen X, Lin K. Opposing biological functions of the cytoplasm and nucleus DAXX modified by SUMO-2/3 in gastric cancer. Cell Death Dis 2020; 11:514. [PMID: 32641734 PMCID: PMC7343808 DOI: 10.1038/s41419-020-2718-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 06/20/2020] [Accepted: 06/23/2020] [Indexed: 12/24/2022]
Abstract
Death domain-associated protein (DAXX) is a complex biological multifunctional protein and is involved in the tumorigenesis and progression of multiple cancers. The accumulation of DAXX in the nucleus is a common phenomenon in tumor cells. However, altering the subcellular localizations of DAXX results in different biological functions, and we also found that its nuclear/cytoplasmic ratio (NCR) was associated with poor prognosis in gastric cancer (GC). In this study, we investigated the effect of cytoplasmic and nuclear DAXX (cDAXX and nDAXX) in GC and the underlying mechanisms. Immunohistochemical detection performed in 323 GC tissues reveled that cDAXX was associated with a better survival, while high nDAXX expression suggested a poorer prognosis outcome. Upregulation of DAXX in the cytoplasm inhibited cell proliferation and promoted apoptosis, whereas downregulation of DAXX in the nucleus displayed opposite effects. Moreover, Transwell assays revealed that DAXX enhanced GC cell migration and invasion. Analysis from the Gene Expression Profile Interactive Analysis (GEPIA) database showed that the expression of DAXX was significantly associated with SUMO-2/3 in GC tissues. Co-immunoprecipitation combined with immunofluorescence analysis indicated that DAXX interacted directly with SUMO-2/3. Subsequently, down-regulating the expression of SUMO-2/3 resulted in altered subcellular localization of DAXX. Bioinformatics analysis showed that RanBP2 may act as SUMO E3 ligase to promote nuclear-plasma transport via combining with RanGAP1. Taken together, our results indicated that DAXX plays opposing roles in GC and suggest a new model whereby cDAXX, nDAXX, and SUMO-2/3 form a molecular network that regulates the subcellular localization of DAXX and thereby modulates its opposing biological effects. Thus, our findings provide a foundation for future studies of DAXX as a novel therapeutic target for patients with GC.
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Affiliation(s)
- Chenbin Chen
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital & Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, P.R. China
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, P.R. China
| | - Xiangwei Sun
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital & Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, P.R. China
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, P.R. China
| | - Wangkai Xie
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital & Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, P.R. China
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, P.R. China
| | - Sian Chen
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital & Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, P.R. China
| | - Yuanbo Hu
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital & Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, P.R. China
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, P.R. China
| | - Dong Xing
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, P.R. China
| | - Jianfeng Xu
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital & Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, P.R. China
| | - Xiaodong Chen
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital & Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, P.R. China
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, P.R. China
| | - Zhiguang Zhao
- Department of Pathology, the Second Affiliated Hospital & Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, P.R. China
| | - Zheng Han
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital & Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, P.R. China
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, P.R. China
| | - Xiangyang Xue
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, P.R. China.
| | - Xian Shen
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital & Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, P.R. China.
| | - Kezhi Lin
- Morphology Laboratory, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, P.R. China.
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5
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Abstract
Background: Epigenetic alterations comprise key regulatory events that dynamically alter gene expression and their deregulation is commonly linked to the pathogenesis of various diseases, including cancer. Unlike DNA mutations, epigenetic alterations involve modifications to proteins and nucleic acids that regulate chromatin structure without affecting the underlying DNA sequence, altering the accessibility of the transcriptional machinery to the DNA, thus modulating gene expression. In cancer cells, this often involves the silencing of tumor suppressor genes or the increased expression of genes involved in oncogenesis. Advances in laboratory medicine have made it possible to map critical epigenetic events, including histone modifications and DNA methylation, on a genome-wide scale. Like the identification of genetic mutations, mapping of changes to the epigenetic landscape has increased our understanding of cancer progression. However, in contrast to irreversible genetic mutations, epigenetic modifications are flexible and dynamic, thereby making them promising therapeutic targets. Ongoing studies are evaluating the use of epigenetic drugs in chemotherapy sensitization and immune system modulation. With the preclinical success of drugs that modify epigenetics, along with the FDA approval of epigenetic drugs including the DNA methyltransferase 1 (DNMT1) inhibitor 5-azacitidine and the histone deacetylase (HDAC) inhibitor vorinostat, there has been a rise in the number of drugs that target epigenetic modulators over recent years. Conclusion: We provide an overview of epigenetic modulations, particularly those involved in cancer, and discuss the recent advances in drug development that target these chromatin-modifying events, primarily focusing on novel strategies to regulate the epigenome.
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Affiliation(s)
- Jasmine Kaur
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina, United States
| | - Abdelkader Daoud
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina, United States
| | - Scott T Eblen
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina, United States
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Ko TY, Kim JI, Park ES, Mun JM, Park SD. The Clinical Implications of Death Domain-Associated Protein (DAXX) Expression. Korean J Thorac Cardiovasc Surg 2018; 51:187-194. [PMID: 29854663 PMCID: PMC5973215 DOI: 10.5090/kjtcs.2018.51.3.187] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 11/01/2017] [Accepted: 11/01/2017] [Indexed: 01/10/2023]
Abstract
Background Death domain-associated protein (DAXX), originally identified as a pro-apoptotic protein, is now understood to be either a pro-apoptotic or an anti-apoptotic factor with a chromatin remodeler, depending on the cell type and context. This study evaluated DAXX expression and its clinical implications in squamous cell carcinoma of the esophagus. Methods Paraffin-embedded tissues from 60 cases of esophageal squamous carcinoma were analyzed immunohistochemically. An immune reaction with more than 10% of tumor cells was interpreted as positive. Positive reactions were sorted into 2 groups: reactions in 11%–50% of tumor cells and reactions in more than 51% of tumor cells, and the correlations between expression and survival and clinical prognosticators were analyzed. Results Forty-three of the 60 cases (71.7%) showed strong nuclear DAXX expression, among which 19 cases showed a positive reaction (31.7%) in 11%–50% of tumor cells, and 24 cases (40.0%) showed a positive reaction in more than 51% of tumor cells. A negative reaction was found in 17 cases (28.3%). These patterns of immunostaining were significantly associated with the N stage (p=0.005) and American Joint Committee on Cancer stage (p=0.001), but overall survival showed no significant difference. There were no correlations of DAXX expression with age, gender, or T stage. However, in stage IIB (p=0.046) and stage IV (p=0.014) disease, DAXX expression was significantly correlated with survival. Conclusion This investigation found upregulation of DAXX in esophageal cancer, with a 71.7% expression rate. DAXX immunostaining could be used in clinical practice to predict aggressive tumors with lymph node metastasis in advanced-stage disease, especially in stages IIB and IV.
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Affiliation(s)
- Taek Yong Ko
- Department of Thoracic and Cardiovascular Surgery, Kosin University Gospel Hospital, Kosin University College of Medicine
| | - Jong In Kim
- Department of Thoracic and Cardiovascular Surgery, Kosin University Gospel Hospital, Kosin University College of Medicine
| | - Eok Sung Park
- Department of Thoracic and Cardiovascular Surgery, Haeundae Bumin Hospital
| | - Jeong Min Mun
- Department of Thoracic and Cardiovascular Surgery, Kosin University Gospel Hospital, Kosin University College of Medicine
| | - Sung Dal Park
- Department of Thoracic and Cardiovascular Surgery, Kosin University Gospel Hospital, Kosin University College of Medicine
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7
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Yang S, Liu L, Cao C, Song N, Wang Y, Ma S, Zhang Q, Yu N, Ding X, Yang F, Tian S, Zhang K, Sun T, Yang J, Yao Z, Wu S, Shi L. USP52 acts as a deubiquitinase and promotes histone chaperone ASF1A stabilization. Nat Commun 2018; 9:1285. [PMID: 29599486 DOI: 10.1038/s41467-018-03588-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 02/22/2018] [Indexed: 12/31/2022] Open
Abstract
Histone chaperone ASF1A has been reported to be dysregulated in multiple tumors; however, the underlying molecular mechanism that how the abundance and function of ASF1A are regulated remains unclear. Here we report that ASF1A is physically associated with USP52, which is previously identified as a pseudo-deubiquitinase. Interestingly, we demonstrate that USP52 is a bona fide ubiquitin-specific protease, and USP52 promotes ASF1A deubiquitination and stabilization. USP52-promoted ASF1A stabilization facilitates chromatin assembly and favors cell cycle progression. Additionally, we find that USP52 is overexpressed in breast carcinomas, and its level of expression correlates with that of ASF1A. Moreover, we reveal that impairment of USP52-promoted ASF1A stabilization results in growth arrest of breast cancer cells and sensitizes these cells to DNA damage. Our experiments identify USP52 as a truly protein deubiquitinase, uncover a molecular mechanism of USP52 in chromatin assembly, and reveal a potential role of USP52 in breast carcinogenesis. Histone chaperone ASF1A is often dysregulated in cancers, however the regulation of its abundance is unclear. Here, the authors show that USP52 promotes ASF1A stability through deubiquitination while impairment of this stability reduces breast tumorigenesis and confers sensitivity to DNA damage.
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8
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Sakaue T, Maekawa M, Nakayama H, Higashiyama S. Prospect of divergent roles for the CUL3 system in vascular endothelial cell function and angiogenesis. J Biochem 2017; 162:237-245. [PMID: 28981750 DOI: 10.1093/jb/mvx051] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 06/05/2017] [Indexed: 11/14/2022] Open
Abstract
Tissue remodelling and regeneration in various pathophysiological conditions (e.g. the processes of development, pregnancy, inflammation, wound healing, tissue regeneration, tumor growth, etc.) require angiogenesis, a dynamically coordinated response to stimuli from the extracellular microenvironment. During angiogenic and angiostatic responses, endothelial cells play a central role in the blood vessel formation and regression. Angiostatic responses, which are evoked by crucial factors such as VEGF and DLL4, have been elucidated. However, it has not been revealed, how endothelial cells process these conflicting signals. The study of VEGFR-Notch cross-signalling provided some clues. We discuss here the potential roles of cullin 3-based ubiquitin E3 ligases as key players in the process of various signals in endothelial cell function and angiogenesis. Our recent findings show that they function as units to process conflicting signalling crosstalk, epigenetic regulation of key factors, and functional barrier maintenance. We also expect more divergent roles of cullin 3-based ubiquitin E3 ligases in endothelial cell function and angiogenesis, and for their potential use as therapeutic targets.
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Affiliation(s)
- Tomohisa Sakaue
- Division of Cell Growth and Tumor Regulation, Proteo-Science Center, Ehime University, Ehime, Japan.,Department of Cardiovascular and Thoracic Surgery, Ehime University Graduate School of Medicine, Ehime, Japan.,Department of Biochemistry and Molecular Genetics, Ehime University Graduate School of Medicine, Toon, Shitsukawa, Ehime 791-0295, Japan
| | - Masashi Maekawa
- Division of Cell Growth and Tumor Regulation, Proteo-Science Center, Ehime University, Ehime, Japan.,Department of Biochemistry and Molecular Genetics, Ehime University Graduate School of Medicine, Toon, Shitsukawa, Ehime 791-0295, Japan
| | - Hironao Nakayama
- Division of Cell Growth and Tumor Regulation, Proteo-Science Center, Ehime University, Ehime, Japan.,Department of Biochemistry and Molecular Genetics, Ehime University Graduate School of Medicine, Toon, Shitsukawa, Ehime 791-0295, Japan
| | - Shigeki Higashiyama
- Division of Cell Growth and Tumor Regulation, Proteo-Science Center, Ehime University, Ehime, Japan.,Department of Biochemistry and Molecular Genetics, Ehime University Graduate School of Medicine, Toon, Shitsukawa, Ehime 791-0295, Japan
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9
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Kovatcheva M, Liao W, Klein ME, Robine N, Geiger H, Crago AM, Dickson MA, Tap WD, Singer S, Koff A. ATRX is a regulator of therapy induced senescence in human cells. Nat Commun 2017; 8:386. [PMID: 28855512 PMCID: PMC5577318 DOI: 10.1038/s41467-017-00540-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 07/07/2017] [Indexed: 01/24/2023] Open
Abstract
Senescence is a state of stable cell cycle exit with important implications for development and disease. Here, we demonstrate that the chromatin remodeling enzyme ATRX is required for therapy-induced senescence. ATRX accumulates in nuclear foci and is required for therapy-induced senescence in multiple types of transformed cells exposed to either DNA damaging agents or CDK4 inhibitors. Mobilization into foci depends on the ability of ATRX to interact with H3K9me3 histone and HP1. Foci form soon after cells exit the cell cycle, before other hallmarks of senescence appear. Eliminating ATRX in senescent cells destabilizes the senescence-associated heterochromatic foci. Additionally, ATRX binds to and suppresses expression from the HRAS locus; repression of HRAS is sufficient to promote the transition of quiescent cells into senescence and preventing repression blocks progression into senescence. Thus ATRX is a critical regulator of therapy-induced senescence and acts in multiple ways to drive cells into this state. Therapy induced senescence (TIS) is a growth suppressive program activated by cytostatic agents in some cancer cells. Here the authors show that the chromatin remodeling enzyme ATRX is a regulator of TIS and drives cells into this state via multiple mechanisms.
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Affiliation(s)
- Marta Kovatcheva
- The Louis V. Gerstner Graduate School of Biomedical Sciences, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, 10065, USA.,Program in Molecular Biology, Memorial Sloan Kettering Cancer Center, New York, 10065, USA
| | - Will Liao
- The New York Genome Center, New York, 10013, USA
| | - Mary E Klein
- The Louis V. Gerstner Graduate School of Biomedical Sciences, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, 10065, USA.,Program in Molecular Biology, Memorial Sloan Kettering Cancer Center, New York, 10065, USA
| | | | | | - Aimee M Crago
- Program in Molecular Biology, Memorial Sloan Kettering Cancer Center, New York, 10065, USA.,Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, 10065, USA
| | - Mark A Dickson
- Department of Medicine, Weill College of Medicine, Cornell University, New York, 10065, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, 10065, USA
| | - William D Tap
- Department of Medicine, Weill College of Medicine, Cornell University, New York, 10065, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, 10065, USA
| | - Samuel Singer
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, 10065, USA
| | - Andrew Koff
- The Louis V. Gerstner Graduate School of Biomedical Sciences, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, 10065, USA. .,Program in Molecular Biology, Memorial Sloan Kettering Cancer Center, New York, 10065, USA.
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10
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Jenull S, Tscherner M, Gulati M, Nobile CJ, Chauhan N, Kuchler K. The Candida albicans HIR histone chaperone regulates the yeast-to-hyphae transition by controlling the sensitivity to morphogenesis signals. Sci Rep 2017; 7:8308. [PMID: 28814742 DOI: 10.1038/s41598-017-08239-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 07/10/2017] [Indexed: 01/01/2023] Open
Abstract
Morphological plasticity such as the yeast-to-hyphae transition is a key virulence factor of the human fungal pathogen Candida albicans. Hyphal formation is controlled by a multilayer regulatory network composed of environmental sensing, signaling, transcriptional modulators as well as chromatin modifications. Here, we demonstrate a novel role for the replication-independent HIR histone chaperone complex in fungal morphogenesis. HIR operates as a crucial modulator of hyphal development, since genetic ablation of the HIR complex subunit Hir1 decreases sensitivity to morphogenetic stimuli. Strikingly, HIR1-deficient cells display altered transcriptional amplitudes upon hyphal initiation, suggesting that Hir1 affects transcription by establishing transcriptional thresholds required for driving morphogenetic cell-fate decisions. Furthermore, ectopic expression of the transcription factor Ume6, which facilitates hyphal maintenance, rescues filamentation defects of hir1Δ/Δ cells, suggesting that Hir1 impacts the early phase of hyphal initiation. Hence, chromatin chaperone-mediated fine-tuning of transcription is crucial for driving morphogenetic conversions in the fungal pathogen C. albicans.
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11
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Abstract
Inheritance of the DNA sequence and its proper organization into chromatin is fundamental for genome stability and function. Therefore, how specific chromatin structures are restored on newly synthesized DNA and transmitted through cell division remains a central question to understand cell fate choices and self-renewal. Propagation of genetic information and chromatin-based information in cycling cells entails genome-wide disruption and restoration of chromatin, coupled with faithful replication of DNA. In this chapter, we describe how cells duplicate the genome while maintaining its proper organization into chromatin. We reveal how specialized replication-coupled mechanisms rapidly assemble newly synthesized DNA into nucleosomes, while the complete restoration of chromatin organization including histone marks is a continuous process taking place throughout the cell cycle. Because failure to reassemble nucleosomes at replication forks blocks DNA replication progression in higher eukaryotes and leads to genomic instability, we further underline the importance of the mechanistic link between DNA replication and chromatin duplication.
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Affiliation(s)
- Constance Alabert
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Zuzana Jasencakova
- Biotech Research and Innovation Centre (BRIC), Health and Medical Faculty, University of Copenhagen, Copenhagen, Denmark
| | - Anja Groth
- Biotech Research and Innovation Centre (BRIC), Health and Medical Faculty, University of Copenhagen, Copenhagen, Denmark.
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12
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Albright ER, Kalejta RF. Canonical and Variant Forms of Histone H3 Are Deposited onto the Human Cytomegalovirus Genome during Lytic and Latent Infections. J Virol 2016; 90:10309-20. [PMID: 27605676 DOI: 10.1128/JVI.01220-16] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 08/30/2016] [Indexed: 01/16/2023] Open
Abstract
Chromatin is the nucleoprotein complex that protects and compacts eukaryotic genomes. It is responsible for a large part of the epigenetic control of transcription. The genomes of DNA viruses such as human cytomegalovirus (HCMV) are devoid of histones within virions but are chromatinized and epigenetically regulated following delivery to the host cell nucleus. How chromatin is initially assembled on viral genomes and which variant forms of the core histone proteins are deposited are incompletely understood. We monitored the deposition of both ectopically expressed and endogenous histones H3.1 and H3.2 (collectively, H3.1/2) and H3.3 during lytic and latent HCMV infections. Here, we show that they are deposited on HCMV genomes during lytic and latent infections, suggesting similar mechanisms of viral chromatin assembly during the different infection types and indicating that both canonical and variant core histones may be important modulators of infecting viral genomes. We further show that association of both H3.1/2 and H3.3 occurs independent of viral DNA synthesis or de novo viral gene expression, implicating cellular factors and/or virion components in the formation of chromatin on virion-delivered genomes during both lytic and latent infections. IMPORTANCE It is well established that infecting herpesvirus genomes are chromatinized upon entry into the host cell nucleus. Why or how this occurs is a mystery. It is important to know why they are chromatinized in order to better understand cellular pathogen recognition (DNA sensing) pathways and viral fate determinations (lytic or latent) and to anticipate how artificially modulating chromatinization may impact viral infections. It is important to know how the genomes are chromatinized in order to potentially modulate the process for therapeutic effect. Our work showing that HCMV genomes are loaded with canonical and variant H3 histones during both lytic and latent infections strengthens the hypothesis that chromatinization pathways are similar between the two infection types, implicates virion or cellular factors in this process, and exposes the possibility that histone variants, in addition to posttranslational modification, may impact viral gene expression. These revelations are important to understanding and intelligently intervening in herpesvirus infections.
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13
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Horard B, Loppin B. Histone storage and deposition in the early Drosophila embryo. Chromosoma 2015; 124:163-75. [PMID: 25563491 DOI: 10.1007/s00412-014-0504-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 12/17/2014] [Accepted: 12/18/2014] [Indexed: 12/18/2022]
Abstract
Drosophila development initiates with the formation of a diploid zygote followed by the rapid division of embryonic nuclei. This syncytial phase of development occurs almost entirely under maternal control and ends when the blastoderm embryo cellularizes and activates its zygotic genome. The biosynthesis and storage of histones in quantity sufficient for chromatin assembly of several thousands of genome copies represent a unique challenge for the developing embryo. In this article, we have reviewed our current understanding of the mechanisms involved in the production, storage, and deposition of histones in the fertilized egg and during the exponential amplification of cleavage nuclei.
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Affiliation(s)
- Béatrice Horard
- Centre de Génétique et de Physiologie Moléculaire et Cellulaire-CNRS UMR5534, Université Claude Bernard Lyon 1, University of Lyon, 69100, Villeurbanne, France
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14
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Torigoe SE, Patel A, Khuong MT, Bowman GD, Kadonaga JT. ATP-dependent chromatin assembly is functionally distinct from chromatin remodeling. eLife 2013; 2:e00863. [PMID: 23986862 PMCID: PMC3748710 DOI: 10.7554/elife.00863] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 07/16/2013] [Indexed: 11/23/2022] Open
Abstract
Chromatin assembly involves the combined action of ATP-dependent motor proteins and histone chaperones. Because motor proteins in chromatin assembly also function as chromatin remodeling factors, we investigated the relationship between ATP-driven chromatin assembly and chromatin remodeling in the generation of periodic nucleosome arrays. We found that chromatin remodeling-defective Chd1 motor proteins are able to catalyze ATP-dependent chromatin assembly. The resulting nucleosomes are not, however, spaced in periodic arrays. Wild-type Chd1, but not chromatin remodeling-defective Chd1, can catalyze the conversion of randomly-distributed nucleosomes into periodic arrays. These results reveal a functional distinction between ATP-dependent nucleosome assembly and chromatin remodeling, and suggest a model for chromatin assembly in which randomly-distributed nucleosomes are formed by the nucleosome assembly function of Chd1, and then regularly-spaced nucleosome arrays are generated by the chromatin remodeling activity of Chd1. These findings uncover an unforeseen level of specificity in the role of motor proteins in chromatin assembly. DOI:http://dx.doi.org/10.7554/eLife.00863.001 In many cells, genomic DNA is wrapped around proteins known as histones to produce particles called nucleosomes. These particles then join together—like beads on a string—to form a highly periodic structure called chromatin. In the nucleus, chromatin is further folded and condensed into chromosomes. However, many important processes, including the replication of DNA and the transcription of genes, require access to the DNA. The cell must therefore be able to disassemble chromatin and remove the histones, and then, once these processes are complete, to reassemble the chromatin. Enzymes known as chromatin assembly factors are responsible for the disassembly and reassembly of chromatin. There are two main types of chromatin assembly factors in eukaryotic cells (i.e., cells with nuclei)—histone chaperones and motor proteins. The histone chaperones escort histones from the cytoplasm, where they are made, to the nucleus. The motor proteins—using energy supplied by ATP molecules—then catalyze the formation of nucleosomes. This involves two activities: the motor proteins assemble nucleosomes by helping the DNA to wrap around the histones, and they also remodel chromatin by altering the positions of nucleosomes along the DNA to ensure that they are periodic—that is, regularly spaced. A conserved motor protein called Chd1 performs chromatin assembly and remodeling in eukaryotic cells. Chd1 works in conjunction with histone chaperones—both are needed for chromatin assembly, and so are DNA, histones and ATP. However, whether or not chromatin assembly and chromatin remodeling by Chd1 are identical or distinct processes is not well understood. Torigoe et al. have now discovered a mutant Chd1 protein that has nucleosome assembly activity (i.e., it can make nucleosomes) but cannot remodel chromatin (i.e., it is unable to move nucleosomes), and thus have demonstrated that these two processes are functionally distinct. Torigoe et al. additionally have found that the mutant Chd1 proteins produce randomly distributed nucleosomes rather than the periodic arrays normally found in chromatin. Further analysis then revealed that the wild-type Chd1 protein, which can remodel chromatin, is able to convert randomly distributed nucleosomes into periodic arrays. These findings have led to a new model for chromatin assembly in which Chd1 initially generates randomly distributed nucleosomes (via its assembly function), and then converts them into periodic arrays of nucleosomes (via its remodeling function). Together, these studies shed light on the mechanisms by which chromatin is created and manipulated in cells. DOI:http://dx.doi.org/10.7554/eLife.00863.002
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Affiliation(s)
- Sharon E Torigoe
- Section of Molecular Biology , University of California, San Diego , La Jolla , United States
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15
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Abstract
Chromatin assembly involves the combined action of ATP-dependent motor proteins and histone chaperones. Because motor proteins in chromatin assembly also function as chromatin remodeling factors, we investigated the relationship between ATP-driven chromatin assembly and chromatin remodeling in the generation of periodic nucleosome arrays. We found that chromatin remodeling-defective Chd1 motor proteins are able to catalyze ATP-dependent chromatin assembly. The resulting nucleosomes are not, however, spaced in periodic arrays. Wild-type Chd1, but not chromatin remodeling-defective Chd1, can catalyze the conversion of randomly-distributed nucleosomes into periodic arrays. These results reveal a functional distinction between ATP-dependent nucleosome assembly and chromatin remodeling, and suggest a model for chromatin assembly in which randomly-distributed nucleosomes are formed by the nucleosome assembly function of Chd1, and then regularly-spaced nucleosome arrays are generated by the chromatin remodeling activity of Chd1. These findings uncover an unforeseen level of specificity in the role of motor proteins in chromatin assembly. DOI:http://dx.doi.org/10.7554/eLife.00863.001.
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Affiliation(s)
- Sharon E Torigoe
- Section of Molecular Biology , University of California, San Diego , La Jolla , United States
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16
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Abstract
Phosphorylation of histone H4 serine 47 (H4S47ph) is catalyzed by Pak2, a member of the p21-activated serine/threonine protein kinase (Pak) family and regulates the deposition of histone variant H3.3. However, the phosphatase(s) involved in the regulation of H4S47ph levels was unknown. Here, we show that three phosphatases (PP1α, PP1β and Wip1) regulate H4S47ph levels and H3.3 deposition. Depletion of each of the three phosphatases results in increased H4S47ph levels. Moreover, PP1α, PP1β and Wip1 bind H3-H4 in vitro and in vivo, whereas only PP1α and PP1β, but not Wip1, interact with Pak2 in vivo. These results suggest that PP1α, PP1β and Wip1 regulate the levels of H4S47ph through directly acting on H4S47ph, with PP1α and PP1β also likely regulating the activity of Pak2. Finally, depletion of PP1α, PP1β and Wip1 leads to increased H3.3 occupancy at candidate genes tested, elevated H3.3 deposition and enhanced association of H3.3 with its chaperones HIRA and Daxx. These results reveal a novel role of three phosphatases in chromatin dynamics in mammalian cells.
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Affiliation(s)
- Hui Zhang
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
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17
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Zizzi A, Montironi MA, Mazzucchelli R, Scarpelli M, Lopez-Beltran A, Cheng L, Paone N, Castellini P, Montironi R. Immunohistochemical analysis of chromatin remodeler DAXX in high grade urothelial carcinoma. Diagn Pathol 2013; 8:111. [PMID: 23819605 PMCID: PMC3751668 DOI: 10.1186/1746-1596-8-111] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2013] [Accepted: 06/25/2013] [Indexed: 01/06/2023] Open
Abstract
Background/Aims The chromatin remodeler DAXX, a predominantly nuclear protein, regulates the status of chromatin organization. The aim of this exploratory immunohistochemical study was to evaluate DAXX protein expression in high grade invasive urothelial carcinoma (UC) of the bladder as a biological regulator of aggressiveness. Methods Quantitative analysis was made on DAXX immunostained nuclei in tissue sections from 5 cases of bladder normal urothelium (NU) and 5 cases of bladder pT1 UC. Carcinoma in situ (CIS) and high grade papillary carcinoma (HGPCa) were identified in 2 out of 5 UC cases. Results The nuclei in UC show an open configuration of the chromatin composed of granules varying in size and distribution and a mean nuclear area 1.7 times greater than that in NU (UC: mean and SD 24.4 ± 11.4 square microns; NU: 14.8 6.5 square microns. The differences are statistically significant). 70% of the NU nuclei are immunostained, whereas 90% of UC nuclei are positive. The mean gray level value in UC, related to the intensity of nuclear immunostaining, is lower than in NU by a factor of 0.94 (UC: mean and SD 100 ± 15; NU: 106 ± 15. The differences are statistically significant). In particular, the value in the nuclei adjacent to the stroma in UC is slightly lower than in the intermediate cell layers by factor of 0.98, whereas in NU it is slightly greater by a factor 1.02 and 1.04 compared to the intermediate and superficial cell layers. The values in CIS and HGPCa are similar to those in UC. Conclusions The quantitative immunohistochemical analysis shows an altered protein expression of chromatin remodeler DAXX in UC and in its preinvasive phases, when compared to NU. DAXX evaluation, if associated with markers related to global DNA methylation and histone acetylation, could be used in clinical practice as a marker of aggressiveness. Virtual slides The virtual slides for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1398457297102379
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Affiliation(s)
- Antonio Zizzi
- Section of Pathological Anatomy, Polytechnic University of the Marche Region, School of Medicine, United Hospitals, Via Conca 71, 60126, Torrette Ancona, Italy
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18
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Newhart A, Rafalska-Metcalf IU, Yang T, Joo LM, Powers SL, Kossenkov AV, Lopez-Jones M, Singer RH, Showe LC, Skordalakes E, Janicki SM. Single cell analysis of RNA-mediated histone H3.3 recruitment to a cytomegalovirus promoter-regulated transcription site. J Biol Chem 2013; 288:19882-99. [PMID: 23689370 DOI: 10.1074/jbc.m113.473181] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Unlike the core histones, which are incorporated into nucleosomes concomitant with DNA replication, histone H3.3 is synthesized throughout the cell cycle and utilized for replication-independent (RI) chromatin assembly. The RI incorporation of H3.3 into nucleosomes is highly conserved and occurs at both euchromatin and heterochromatin. However, neither the mechanism of H3.3 recruitment nor its essential function is well understood. Several different chaperones regulate H3.3 assembly at distinct sites. The H3.3 chaperone, Daxx, and the chromatin-remodeling factor, ATRX, are required for H3.3 incorporation and heterochromatic silencing at telomeres, pericentromeres, and the cytomegalovirus (CMV) promoter. By evaluating H3.3 dynamics at a CMV promoter-regulated transcription site in a genetic background in which RI chromatin assembly is blocked, we have been able to decipher the regulatory events upstream of RI nucleosomal deposition. We find that at the activated transcription site, H3.3 accumulates with sense and antisense RNA, suggesting that it is recruited through an RNA-mediated mechanism. Sense and antisense transcription also increases after H3.3 knockdown, suggesting that the RNA signal is amplified when chromatin assembly is blocked and attenuated by nucleosomal deposition. Additionally, we find that H3.3 is still recruited after Daxx knockdown, supporting a chaperone-independent recruitment mechanism. Sequences in the H3.3 N-terminal tail and αN helix mediate both its recruitment to RNA at the activated transcription site and its interaction with double-stranded RNA in vitro. Interestingly, the H3.3 gain-of-function pediatric glioblastoma mutations, G34R and K27M, differentially affect H3.3 affinity in these assays, suggesting that disruption of an RNA-mediated regulatory event could drive malignant transformation.
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Affiliation(s)
- Alyshia Newhart
- Molecular and Cellular Oncogenesis Program, Wistar Institute, Philadelphia, Pennsylvania 19104, USA
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19
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Song Y, Seol JH, Yang JH, Kim HJ, Han JW, Youn HD, Cho EJ. Dissecting the roles of the histone chaperones reveals the evolutionary conserved mechanism of transcription-coupled deposition of H3.3. Nucleic Acids Res 2013; 41:5199-209. [PMID: 23563152 PMCID: PMC3664809 DOI: 10.1093/nar/gkt220] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The mammalian genome encodes multiple variants of histone H3 including H3.1/H3.2 and H3.3. In contrast to H3.1/H3.2, H3.3 is enriched in the actively transcribed euchromatin and the telomeric heterochromatins. However, the mechanism for H3.3 to incorporate into the different domains of chromatin is not known. Here, taking the advantage of well-defined transcription analysis system of yeast, we attempted to understand the molecular mechanism of selective deposition of human H3.3 into actively transcribed genes. We show that there are systemic H3 substrate-selection mechanisms operating even in yeasts, which encode a single type of H3. Yeast HIR complex mediated H3-specific recognition specificity for deposition of H3.3 in the transcribed genes. A critical component of this process was the H3 A-IG code composed of amino acids 87, 89 and 90. The preference toward H3.3 was completely lost when HIR subunits were absent and partially suppressed by human HIRA. Asf1 allows the influx of H3, regardless of H3 type. We propose that H3.3 is introduced into the active euchromatin by targeting the recycling pathway that is mediated by HIRA (or HIR), and this H3-selection mechanism is highly conserved through the evolution. These results also uncover an unexpected role of RI chaperones in evolution of variant H3s.
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Affiliation(s)
- Yunkyoung Song
- School of Pharmacy, Sungkyunkwan University, Suwon, Gyeonggi-do 440-746, Republic of Korea
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20
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Liu CP, Xiong C, Wang M, Yu Z, Yang N, Chen P, Zhang Z, Li G, Xu RM. Structure of the variant histone H3.3-H4 heterodimer in complex with its chaperone DAXX. Nat Struct Mol Biol 2012; 19:1287-92. [PMID: 23142979 DOI: 10.1038/nsmb.2439] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 10/12/2012] [Indexed: 11/08/2022]
Abstract
Mammalian histone H3.3 is a variant of the canonical H3.1 essential for genome reprogramming in fertilized eggs and maintenance of chromatin structure in neuronal cells. An H3.3-specific histone chaperone, DAXX, directs the deposition of H3.3 onto pericentric and telomeric heterochromatin. H3.3 differs from H3.1 by only five amino acids, yet DAXX can distinguish the two with high precision. By a combination of structural, biochemical and cell-based targeting analyses, we show that Ala87 and Gly90 are the principal determinants of human H3.3 specificity. DAXX uses a shallow hydrophobic pocket to accommodate the small hydrophobic Ala87 of H3.3, whereas a polar binding environment in DAXX prefers Gly90 in H3.3 over the hydrophobic Met90 in H3.1. An H3.3-H4 heterodimer is bound by the histone-binding domain of DAXX, which makes extensive contacts with both H3.3 and H4.
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21
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Finn RM, Ellard K, Eirín-López JM, Ausió J. Vertebrate nucleoplasmin and NASP: egg histone storage proteins with multiple chaperone activities. FASEB J 2012; 26:4788-804. [PMID: 22968912 DOI: 10.1096/fj.12-216663] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Recent reviews have focused on the structure and function of histone chaperones involved in different aspects of somatic cell chromatin metabolism. One of the most dramatic chromatin remodeling processes takes place immediately after fertilization and is mediated by egg histone storage chaperones. These include members of the nucleoplasmin (NPM2/NPM3), which are preferentially associated with histones H2A-H2B in the egg and the nuclear autoantigenic sperm protein (NASP) families. Interestingly, in addition to binding and providing storage to H3/H4 in the egg and in somatic cells, NASP has been shown to be a unique genuine chaperone for histone H1. This review revolves around the structural and functional roles of these two families of chaperones whose activity is modulated by their own post-translational modifications (PTMs), particularly phosphorylation. Beyond their important role in the remodeling of paternal chromatin in the early stages of embryogenesis, NPM and NASP members can interact with a plethora of proteins in addition to histones in somatic cells and play a critical role in processes of functional cell alteration, such as in cancer. Despite their common presence in the egg, these two histone chaperones appear to be evolutionarily unrelated. In contrast to members of the NPM family, which share a common monophyletic evolutionary origin, the different types of NASP appear to have evolved recurrently within different taxa.
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Affiliation(s)
- Ron M Finn
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada V8W 3P6
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22
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Abstract
The eukaryotic processes of nucleosome assembly and disassembly govern chromatin dynamics, in which histones exchange in a highly regulated manner to promote genome accessibility for all DNA-dependent processes. This regulation is partly carried out by histone chaperones, which serve multifaceted roles in co-ordinating the interactions of histone proteins with modification enzymes, nucleosome remodellers, other histone chaperones and nucleosomal DNA. The molecular details of the processes by which histone chaperones promote delivery of histones among their many functional partners are still largely undefined, but promise to offer insights into epigenome maintenance. In the present paper, we review recent findings on the histone chaperone interactions that guide the assembly of histones H3 and H4 into chromatin. This evidence supports the concepts of histone post-translational modifications and specific histone chaperone interactions as guiding principles for histone H3/H4 transactions during chromatin assembly.
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Ethier SD, Miura H, Dostie J. Discovering genome regulation with 3C and 3C-related technologies. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 2012; 1819:401-10. [DOI: 10.1016/j.bbagrm.2011.12.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Revised: 12/05/2011] [Accepted: 12/06/2011] [Indexed: 10/14/2022]
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Morozov VM, Gavrilova EV, Ogryzko VV, Ishov AM. Dualistic function of Daxx at centromeric and pericentromeric heterochromatin in normal and stress conditions. Nucleus 2012; 3:276-85. [PMID: 22572957 DOI: 10.4161/nucl.20180] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Nuclear structures ND10/PML NBs are linked to multiple processes, including the maintenance of intranuclear homeostasis by sequestering proteins into "nuclear depot." This function presumes release of proteins from PML NBs and their redistribution to the alternative, supposedly "active" locations, in response to the external stress application. To further investigate this nuclear depot function, we focused on the intranuclear distribution of protein Daxx that in normal conditions is mainly accumulated at PML NBs, and has a minor association with centromeres and pericentromeres (CEN/periCEN). Here we report that application of physiological Heat Shock (HS) changes this balance forcing very robust and reversible accumulation of Daxx on CEN/periCEN heterochromatin. Heterochromatin architecture is essential for the proper orchestration of nuclear processes, while transcription from this part of genome is required for its maintenance. To understand functional consequences of Daxx deposition at CEN/periCEN, we tested for Daxx-dependency of heterochromatin transcription. Depletion of Daxx reduces accumulation of CEN RNA in normal conditions and periCEN RNA after HS application. Searching for the mechanism of Daxx-dependent regulation of heterochromatin transcription, we found that depletion of Daxx decreases incorporation of transcription-associated histone H3 variant, H3.3, into both CEN and periCEN. Surprisingly, HS-induced deposition of Daxx does not further elevate incorporation of H3.3 into CEN/periCEN that remained steady during stress and recovery. Instead, depletion of Daxx leads to HS-induced changes in the balance of epigenetic modifications at heterochromatin, most dramatically elevating levels of active H3K4Me2 modification at periCEN. We propose dualistic function of Daxx-containing complexes at CEN/periCEN: (1) regulation of H3.3 loading in normal conditions and (2) protection of epigenetic status upon stress-induced accumulation, thus collectively guarding epigenetic identity of CEN/periCEN heterochromatin.
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Affiliation(s)
- Viacheslav M Morozov
- University of Florida, Cancer & Genetics Research Complex and Department of Anatomy and Cell Biology, Gainesville, FL, USA
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25
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Keck KM, Pemberton LF. Histone chaperones link histone nuclear import and chromatin assembly. Biochim Biophys Acta 2012; 1819:277-89. [PMID: 22015777 PMCID: PMC3272145 DOI: 10.1016/j.bbagrm.2011.09.007] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Revised: 09/08/2011] [Accepted: 09/12/2011] [Indexed: 12/12/2022]
Abstract
Histone chaperones are proteins that shield histones from nonspecific interactions until they are assembled into chromatin. After their synthesis in the cytoplasm, histones are bound by different histone chaperones, subjected to a series of posttranslational modifications and imported into the nucleus. These evolutionarily conserved modifications, including acetylation and methylation, can occur in the cytoplasm, but their role in regulating import is not well understood. As part of histone import complexes, histone chaperones may serve to protect the histones during transport, or they may be using histones to promote their own nuclear localization. In addition, there is evidence that histone chaperones can play an active role in the import of histones. Histone chaperones have also been shown to regulate the localization of important chromatin modifying enzymes. This review is focused on the role histone chaperones play in the early biogenesis of histones, the distinct cytoplasmic subcomplexes in which histone chaperones have been found in both yeast and mammalian cells and the importins/karyopherins and nuclear localization signals that mediate the nuclear import of histones. We also address the role that histone chaperone localization plays in human disease. This article is part of a Special Issue entitled: Histone chaperones and chromatin assembly.
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Affiliation(s)
- Kristin M. Keck
- Center for Cell Signaling, Department of Microbiology, Immunology and Cancer Biology University of Virginia, Charlottesville, VA 22908, USA
| | - Lucy F. Pemberton
- Center for Cell Signaling, Department of Microbiology, Immunology and Cancer Biology University of Virginia, Charlottesville, VA 22908, USA
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26
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Abstract
Chromatin is organized into distinct functional domains. During mitotic cell division, both genetic information encoded in DNA sequence and epigenetic information embedded in chromatin structure must be faithfully duplicated. The inheritance of epigenetic states is critical in maintaining the genome integrity and gene expression state. In this review, we will discuss recent progress on how proteins known to be involved in DNA replication and DNA replication-coupled nucleosome assembly impact on the inheritance and maintenance of heterochromatin, a tightly compact chromatin structure that silences gene transcription. As heterochromatin is important in regulating gene expression and maintaining genome stability, understanding how heterochromatin states are inherited during S phase of the cell cycle is of fundamental importance.
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27
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Cook A, Gurard-levin Z, Vassias I, Almouzni G. A Specific Function for the Histone Chaperone NASP to Fine-Tune a Reservoir of Soluble H3-H4 in the Histone Supply Chain. Mol Cell 2011; 44:918-27. [DOI: 10.1016/j.molcel.2011.11.021] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Revised: 08/31/2011] [Accepted: 11/21/2011] [Indexed: 11/30/2022]
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28
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Torigoe SE, Urwin DL, Ishii H, Smith DE, Kadonaga JT. Identification of a rapidly formed nonnucleosomal histone-DNA intermediate that is converted into chromatin by ACF. Mol Cell 2011; 43:638-48. [PMID: 21855802 DOI: 10.1016/j.molcel.2011.07.017] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Revised: 05/27/2011] [Accepted: 07/15/2011] [Indexed: 10/17/2022]
Abstract
Chromatin assembly involves the combined action of histone chaperones and ATP-dependent motor proteins. Here, we investigate the mechanism of nucleosome assembly with a purified chromatin assembly system containing the histone chaperone NAP1 and the ATP-dependent motor protein ACF. These studies revealed the rapid formation of a stable nonnucleosomal histone-DNA intermediate that is converted into canonical nucleosomes by ACF. The histone-DNA intermediate does not supercoil DNA like a canonical nucleosome, but has a nucleosome-like appearance by atomic force microscopy. This intermediate contains all four core histones, lacks NAP1, and is formed by the initial deposition of histones H3-H4. Conversion of the intermediate into histone H1-containing chromatin results in increased resistance to micrococcal nuclease digestion. These findings suggest that the histone-DNA intermediate corresponds to nascent nucleosome-like structures, such as those observed at DNA replication forks. Related complexes might be formed during other chromatin-directed processes such as transcription, DNA repair, and histone exchange.
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Affiliation(s)
- Sharon E Torigoe
- Section of Molecular Biology, University of California, San Diego, La Jolla, CA 92093-0347, USA
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29
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Avvakumov N, Nourani A, Côté J. Histone chaperones: modulators of chromatin marks. Mol Cell 2011; 41:502-14. [PMID: 21362547 DOI: 10.1016/j.molcel.2011.02.013] [Citation(s) in RCA: 154] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2010] [Revised: 01/26/2011] [Accepted: 02/09/2011] [Indexed: 10/18/2022]
Abstract
The many factors that control chromatin biology play key roles in essential nuclear functions like transcription, DNA damage response and repair, recombination, and replication and are critical for proper cell-cycle progression, stem cell renewal, differentiation, and development. These players belong to four broad classes: histone modifiers, chromatin remodelers, histone variants, and histone chaperones. A large number of studies have established the existence of an intricate functional crosstalk between the different factors, not only within a single class but also between different classes. In light of this, while many recent reviews have focused on structure and functions of histone chaperones, the current text highlights novel and striking links that have been established between these proteins and posttranslational modifications of histones and discusses the functional consequences of this crosstalk. These findings feed a current hot question of how cell memory may be maintained through epigenetic mechanisms involving histone chaperones.
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Affiliation(s)
- Nikita Avvakumov
- Laval University Cancer Research Center, Hôtel-Dieu de Québec (CHUQ), 9 McMahon Street, Quebec City, Quebec G1R 2J6, Canada
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30
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Abstract
Much progress has been made concerning histone function in the nucleus; however, following their synthesis, how their marking and subcellular trafficking are regulated remains to be explored. To gain an insight into these issues, we focused on soluble histones and analyzed endogenous and tagged H3 histones in parallel. We distinguished six complexes that we could place to account for maturation events occurring on histones H3 and H4 from their synthesis onward. In each complex, a different set of chaperones is involved, and we found specific post-translational modifications. Interestingly, we revealed that histones H3 and H4 are transiently poly(ADP-ribosylated). The impact of these marks in histone metabolism proved to be important as we found that acetylation of lysines 5 and 12 on histone H4 stimulated its nuclear translocation. Furthermore, we showed that, depending on particular histone H3 modifications, the balance in the presence of the different translocation complexes changes. Therefore, our results enabled us to propose a regulatory means of these marks for controlling cytoplasmic/nuclear shuttling and the establishment of early modification patterns.
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Yang JH, Choi JH, Jang H, Park JY, Han JW, Youn HD, Cho EJ. Histone chaperones cooperate to mediate Mef2-targeted transcriptional regulation during skeletal myogenesis. Biochem Biophys Res Commun 2011; 407:541-7. [PMID: 21414300 DOI: 10.1016/j.bbrc.2011.03.055] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Accepted: 03/11/2011] [Indexed: 11/17/2022]
Abstract
Histone chaperones function in histone transfer and regulate the nucleosome occupancy and the activity of genes. HIRA is a replication-independent (RI) histone chaperone that is linked to transcription and various developmental processes. Here, we show that HIRA interacts with Mef2 and contributes to the activation of Mef2-target genes during muscle differentiation. Asf1 cooperated with HIRA and was indispensable for Mef2-dependent transcription. The HIRA R460A mutant, which is defective in Asf1 binding, lost the transcriptional co-activation. In addition, the role of Cabin1, previously reported as a Mef2 repressor and as one of the components of the HIRA-containing complex, was delineated in Mef2/HIRA-mediated transcription. Cabin1 associated with the C-terminus of HIRA via its N-terminal domain and suppressed Mef2/HIRA-mediated transcription. Expression of Cabin1 was dramatically reduced upon myoblast differentiation, which may allow Mef2 and HIRA/Asf1 to resume their transcriptional activity. HIRA led to more permeable chromatin structure marked by active histone modifications around the myogenin promoter. Our results suggest that histone chaperone complex components contribute to the regulation of Mef2 target genes for muscle differentiation.
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Affiliation(s)
- Jae-Hyun Yang
- School of Pharmacy, Sungkyunkwan University, Suwon, Gyeonggi-do 440-746, Republic of Korea
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Abstract
Chromatin is disassembled and reassembled during DNA repair. To assay chromatin reassembly accompanying DNA double strand break repair, ChIP analysis can be used to monitor the presence of histone H3 near the lesion. The chromatin assembly factor Asf1p, as well as the acetylation of histone H3 lysine 56, have been shown to promote chromatin reassembly when DNA double strand break repair is complete. Using Gal-HO-mediated double strand break repair, we have tested each of the components of the nuclear Hat1p-containing type B histone acetyltransferase complex (NuB4) and have found that they can affect repair-linked chromatin reassembly but that their contributions are not equivalent. In particular, deletion of the catalytic subunit, Hat1p, caused a significant defect in chromatin reassembly. In addition, loss of the histone chaperone Hif1p, when combined with an allele of H3 that mutates lysines 14 and 23 to arginine, has a pronounced effect on chromatin reassembly that is similar to that observed in an asf1Δ. The role of Hat1p and Hif1p is at least partially redundant with the role of Asf1p. Consistent with a more prominent role for Hif1p in chromatin reassembly than either Hat1p or Hat2p, Hif1p exists in complex(es) independent of Hat1p and Hat2p and influences the activity of an H3-specific histone acetyltransferase activity. Our data directly demonstrate the role of the nuclear HAT1 complex (NuB4) components in DNA repair-linked chromatin reassembly.
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Affiliation(s)
- Zhongqi Ge
- Department of Molecular and Cellular Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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Abstract
Genomic DNA in the eukaryotic nucleus is hierarchically packaged by histones into chromatin to fit inside the nucleus. The dynamics of higher-order chromatin compaction play a crucial role in transcription and other biological processes inherent to DNA. Many factors, including histone variants, histone modifications, DNA methylation, and the binding of non-histone architectural proteins regulate the structure of chromatin. Although the structure of nucleosomes, the fundamental repeating unit of chromatin, is clear, there is still much discussion on the higher-order levels of chromatin structure. In this review, we focus on the recent progress in elucidating the structure of the 30-nm chromatin fiber. We also discuss the structural plasticity/dynamics and epigenetic inheritance of higher-order chromatin and the roles of chromatin higher-order organization in eukaryotic gene regulation.
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Abstract
A new study in this issue of Molecular Cell (Yamane et al., 2010) demonstrates how chromatin assembly proteins HIRA/Asf1 help enforce transcriptional gene silencing in heterochromatin by bridging interactions between HP1 and histone deacetylase complexes.
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Affiliation(s)
- Paul D Kaufman
- Program in Gene Function and Expression, University of Massachusetts Medical School, 364 Plantation Street, LRB506, Worcester, MA 01605, USA.
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