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Serra-Bardenys G, Blanco E, Escudero-Iriarte C, Serra-Camprubí Q, Querol J, Pascual-Reguant L, Morancho B, Escorihuela M, Tissera NS, Sabé A, Martín L, Segura-Bayona S, Verde G, Aiese Cigliano R, Millanes-Romero A, Jerónimo C, Cebrià-Costa JP, Nuciforo P, Simonetti S, Viaplana C, Dienstmann R, Oliveira M, Peg V, Stracker TH, Arribas J, Canals F, Villanueva J, Di Croce L, García de Herreros A, Tian TV, Peiró S. LOXL2-mediated chromatin compaction is required to maintain the oncogenic properties of triple-negative breast cancer cells. FEBS J 2024; 291:2423-2448. [PMID: 38451841 DOI: 10.1111/febs.17112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 01/02/2024] [Accepted: 02/23/2024] [Indexed: 03/09/2024]
Abstract
Oxidation of histone H3 at lysine 4 (H3K4ox) is catalyzed by lysyl oxidase homolog 2 (LOXL2). This histone modification is enriched in heterochromatin in triple-negative breast cancer (TNBC) cells and has been linked to the maintenance of compacted chromatin. However, the molecular mechanism underlying this maintenance is still unknown. Here, we show that LOXL2 interacts with RuvB-Like 1 (RUVBL1), RuvB-Like 2 (RUVBL2), Actin-like protein 6A (ACTL6A), and DNA methyltransferase 1associated protein 1 (DMAP1), a complex involved in the incorporation of the histone variant H2A.Z. Our experiments indicate that this interaction and the active form of RUVBL2 are required to maintain LOXL2-dependent chromatin compaction. Genome-wide experiments showed that H2A.Z, RUVBL2, and H3K4ox colocalize in heterochromatin regions. In the absence of LOXL2 or RUVBL2, global levels of the heterochromatin histone mark H3K9me3 were strongly reduced, and the ATAC-seq signal in the H3K9me3 regions was increased. Finally, we observed that the interplay between these series of events is required to maintain H3K4ox-enriched heterochromatin regions, which in turn is key for maintaining the oncogenic properties of the TNBC cell line tested (MDA-MB-231).
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Affiliation(s)
- Gemma Serra-Bardenys
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Institut Bonanova FP Sanitaria, Consorci Mar Parc de Salut de Barcelona, Spain
| | - Enrique Blanco
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Spain
| | | | | | - Jessica Querol
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Laura Pascual-Reguant
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Spain
| | | | | | | | - Anna Sabé
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Luna Martín
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | | | - Gaetano Verde
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | | | - Alba Millanes-Romero
- Institute for Research in Biomedicine (IRB Barcelona) and Barcelona Institute of Science and Technology, Spain
| | - Celia Jerónimo
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Spain
- Institut de Recherches Cliniques de Montréal, Canada
| | | | - Paolo Nuciforo
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Sara Simonetti
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | | | | | - Mafalda Oliveira
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Medical Oncology Department, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Vicente Peg
- Medical Oncology Department, Vall d'Hebron University Hospital, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Oncología (CIBERONC), Barcelona, Spain
- Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Travis H Stracker
- Radiation Oncology Branch, National Cancer Institute, Bethesda, MD, USA
| | - Joaquín Arribas
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Programa de Recerca en Càncer, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain
| | - Francesc Canals
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | | | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Antonio García de Herreros
- Programa de Recerca en Càncer, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Tian V Tian
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Sandra Peiró
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
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2
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Kirkiz E, Meers O, Grebien F, Buschbeck M. Histone Variants and Their Chaperones in Hematological Malignancies. Hemasphere 2023; 7:e927. [PMID: 37449197 PMCID: PMC10337764 DOI: 10.1097/hs9.0000000000000927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 06/13/2023] [Indexed: 07/18/2023] Open
Abstract
Epigenetic regulation occurs on the level of compacting DNA into chromatin. The functional unit of chromatin is the nucleosome, which consists of DNA wrapped around a core of histone proteins. While canonical histone proteins are incorporated into chromatin through a replication-coupled process, structural variants of histones, commonly named histone variants, are deposited into chromatin in a replication-independent manner. Specific chaperones and chromatin remodelers mediate the locus-specific deposition of histone variants. Although histone variants comprise one of the least understood layers of epigenetic regulation, it has been proposed that they play an essential role in directly regulating gene expression in health and disease. Here, we review the emerging evidence suggesting that histone variants have a role at different stages of hematopoiesis, with a particular focus on the histone variants H2A, H3, and H1. Moreover, we discuss the current knowledge on how the dysregulation of histone variants can contribute to hematopoietic malignancies.
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Affiliation(s)
- Ecem Kirkiz
- Institute for Medical Biochemistry, University of Veterinary Medicine, Vienna, Austria
| | - Oliver Meers
- Cancer and Leukaemia Epigenetics and Biology Program, Josep Carreras Leukaemia Research Institute (IJC), Campus Can Ruti, Badalona, Spain
- PhD Programme in Biomedicine, University of Barcelona, Spain
| | - Florian Grebien
- Institute for Medical Biochemistry, University of Veterinary Medicine, Vienna, Austria
- St. Anna Children’s Cancer Research Institute (CCRI), Vienna, Austria
| | - Marcus Buschbeck
- Cancer and Leukaemia Epigenetics and Biology Program, Josep Carreras Leukaemia Research Institute (IJC), Campus Can Ruti, Badalona, Spain
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
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3
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Interplay Between the Histone Variant H2A.Z and the Epigenome in Pancreatic Cancer. Arch Med Res 2022; 53:840-858. [PMID: 36470770 DOI: 10.1016/j.arcmed.2022.11.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/25/2022] [Accepted: 11/18/2022] [Indexed: 12/03/2022]
Abstract
BACKGROUND The oncogenic process is orchestrated by a complex network of chromatin remodeling elements that shape the cancer epigenome. Histone variant H2A.Z regulates DNA control elements such as promoters and enhancers in different types of cancer; however, the interplay between H2A.Z and the pancreatic cancer epigenome is unknown. OBJECTIVE This study analyzed the role of H2A.Z in different DNA regulatory elements. METHODS We performed Chromatin Immunoprecipitation Sequencing assays (ChiP-seq) with total H2A.Z and acetylated H2A.Z (acH2A.Z) antibodies and analyzed published data from ChIP-seq, RNA-seq, bromouridine labeling-UV and sequencing (BruUV-seq), Hi-C and ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) in the pancreatic cancer cell line PANC-1. RESULTS The results indicate that total H2A.Z facilitates the recruitment of RNA polymerase II and transcription factors at promoters and enhancers allowing the expression of pro-oncogenic genes. Interestingly, we demonstrated that H2A.Z is enriched in super-enhancers (SEs) contributing to the transcriptional activation of key genes implicated in tumor development. Importantly, we established that H2A.Z contributes to the three-dimensional (3D) genome organization of pancreatic cancer and that it is a component of the Topological Associated Domains (TADs) boundaries in PANC-1 and that total H2A.Z and acH2A.Z are associated with A and B compartments, respectively. CONCLUSIONS H2A.Z participates in the biology and development of pancreatic cancer by generating a pro-oncogenic transcriptome through its posttranslational modifications, interactions with different partners, and regulatory elements, contributing to the oncogenic 3D genome organization. These data allow us to understand the molecular mechanisms that promote an oncogenic transcriptome in pancreatic cancer mediated by H2A.Z.
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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] [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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Sales-Gil R, Kommer DC, de Castro IJ, Amin HA, Vinciotti V, Sisu C, Vagnarelli P. Non-redundant functions of H2A.Z.1 and H2A.Z.2 in chromosome segregation and cell cycle progression. EMBO Rep 2021; 22:e52061. [PMID: 34423893 PMCID: PMC8567233 DOI: 10.15252/embr.202052061] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 07/26/2021] [Accepted: 08/03/2021] [Indexed: 12/30/2022] Open
Abstract
H2A.Z is a H2A‐type histone variant essential for many aspects of cell biology, ranging from gene expression to genome stability. From deuterostomes, H2A.Z evolved into two paralogues, H2A.Z.1 and H2A.Z.2, that differ by only three amino acids and are encoded by different genes (H2AFZ and H2AFV, respectively). Despite the importance of this histone variant in development and cellular homeostasis, very little is known about the individual functions of each paralogue in mammals. Here, we have investigated the distinct roles of the two paralogues in cell cycle regulation and unveiled non‐redundant functions for H2A.Z.1 and H2A.Z.2 in cell division. Our findings show that H2A.Z.1 regulates the expression of cell cycle genes such as Myc and Ki‐67 and its depletion leads to a G1 arrest and cellular senescence. On the contrary, H2A.Z.2, in a transcription‐independent manner, is essential for centromere integrity and sister chromatid cohesion regulation, thus playing a key role in chromosome segregation.
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Affiliation(s)
- Raquel Sales-Gil
- College of Health, Medicine and Life Science, Brunel University London, London, UK
| | - Dorothee C Kommer
- College of Health, Medicine and Life Science, Brunel University London, London, UK
| | - Ines J de Castro
- College of Health, Medicine and Life Science, Brunel University London, London, UK
| | - Hasnat A Amin
- College of Health, Medicine and Life Science, Brunel University London, London, UK
| | - Veronica Vinciotti
- College of Engineering, Design and Physical Sciences, Research Institute for Environment Health and Society, Brunel University London, London, UK
| | - Cristina Sisu
- College of Health, Medicine and Life Science, Brunel University London, London, UK
| | - Paola Vagnarelli
- College of Health, Medicine and Life Science, Brunel University London, London, UK
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Salmerón-Bárcenas EG, Zacapala-Gómez AE, Lozano-Amado D, Castro-Muñoz LJ, Leyva-Vázquez MA, Manzo-Merino J, Ávila-López PA. Comprehensive bioinformatic analysis reveals oncogenic role of H2A.Z isoforms in cervical cancer progression. IRANIAN JOURNAL OF BASIC MEDICAL SCIENCES 2021; 24:1470-1481. [PMID: 35317119 PMCID: PMC8917839 DOI: 10.22038/ijbms.2021.58287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 09/11/2021] [Indexed: 12/20/2022]
Abstract
Objectives Cervical cancer ranks as the fourth most common neoplasia in women worldwide in which epigenetic alterations play an important role. Several studies have reported pro-oncogenic role of the histone variant H2A.Z in different types of cancer; however, the role of H2A.Z in cervical cancer remains poorly studied. This study aimed to determine the potential role of H2A.Z in cervical cancer through a bioinformatic approach. Materials and Methods H2A.Z expression was analyzed in The Human Protein Atlas, The Cancer Genome Atlas, and Gene Expression Omnibus datasets. The promoter regions of H2AZ1 and H2AZ2 genes were downloaded from Expasy, and the prediction of transcription factor binding motifs was performed using CONSITE, Alibaba, and ALGGEN. ChIP-seq and RNA-seq data from HeLa-S3 cells were downloaded from ENCODE. The discovery motif was investigated using MEME-ChIP. The functional annotation was examined in Enrich. Results The expression of H2A.Z is elevated in cervical cancer. Interestingly, DNA methylation, copy number, and transcription factors AP2α and ELK1 are involved in H2A.Z overexpression. Additionally, H2A.Z is enriched on promoter and enhancer regions of genes involved in pathways associated with cancer development. In these regions, H2A.Z enables the recruitment of transcription factors such as NRF1, NFYA, and RNA Pol II. Finally, H2A.Z allows the expression of genes associated with proliferation in patients with cervical cancer. Conclusion Our findings suggest that H2A.Z overexpression and its presence in promoters and enhancers could be regulating the transcription of genes involved in cervical carcinogenesis.
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Affiliation(s)
- Eric G. Salmerón-Bárcenas
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. Instituto
| | - Ana E. Zacapala-Gómez
- Politécnico Nacional 2508, Col. San Pedro Zacatenco, Delegación Gustavo A. Madero, Ciudad de México
| | - Daniela Lozano-Amado
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico-Biológicas, Universidad Autónoma de Guerrero, Chilpancingo, 39090, Gro
| | | | - Marco A. Leyva-Vázquez
- Politécnico Nacional 2508, Col. San Pedro Zacatenco, Delegación Gustavo A. Madero, Ciudad de México
| | | | - Pedro A. Ávila-López
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. Instituto ,Corresponding author: Pedro A. Ávila-López. Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Delegación Gustavo A. Madero, Ciudad de México. Tel: +52 55 6098 2694;
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Colino-Sanguino Y, Clark SJ, Valdes-Mora F. The H2A.Z-nuclesome code in mammals: emerging functions. Trends Genet 2021; 38:273-289. [PMID: 34702577 DOI: 10.1016/j.tig.2021.10.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/30/2021] [Accepted: 10/04/2021] [Indexed: 12/12/2022]
Abstract
H2A.Z is a histone variant that provides specific structural and docking-side properties to the nucleosome, resulting in diverse and specialised molecular and cellular functions. In this review, we discuss the latest studies uncovering new functional aspects of mammalian H2A.Z in gene transcription, including pausing and elongation of RNA polymerase II (RNAPII) and enhancer activity; DNA repair; DNA replication; and 3D chromatin structure. We also review the recently described role of H2A.Z in embryonic development, cell differentiation, neurodevelopment, and brain function. In conclusion, our cumulative knowledge of H2A.Z over the past 40 years, in combination with the implementation of novel molecular technologies, is unravelling an unexpected and complex role of histone variants in gene regulation and disease.
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Affiliation(s)
- Yolanda Colino-Sanguino
- Cancer Epigenetics Biology and Therapeutics, Precision Medicine Theme, Children's Cancer Institute, Sydney, NSW, Australia; School of Children and Women Health, University of NSW Sydney, Sydney, NSW, Australia.
| | - Susan J Clark
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, Australia; St. Vincent's Clinical School, University of NSW Sydney, Sydney, NSW, Australia
| | - Fatima Valdes-Mora
- Cancer Epigenetics Biology and Therapeutics, Precision Medicine Theme, Children's Cancer Institute, Sydney, NSW, Australia; School of Children and Women Health, University of NSW Sydney, Sydney, NSW, Australia.
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Lone IN, Sengez B, Hamiche A, Dimitrov S, Alotaibi H. The Role of Histone Variants in the Epithelial-To-Mesenchymal Transition. Cells 2020; 9:cells9112499. [PMID: 33213091 PMCID: PMC7698467 DOI: 10.3390/cells9112499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 11/13/2020] [Accepted: 11/14/2020] [Indexed: 11/16/2022] Open
Abstract
The epithelial-to-mesenchymal transition (EMT) is a physiological process activated during early embryogenesis, which continues to shape tissues and organs later on. It is also hijacked by tumor cells during metastasis. The regulation of EMT has been the focus of many research groups culminating in the last few years and resulting in an elaborate transcriptional network buildup. However, the implication of epigenetic factors in the control of EMT is still in its infancy. Recent discoveries pointed out that histone variants, which are key epigenetic players, appear to be involved in EMT control. This review summarizes the available data on histone variants' function in EMT that would contribute to a better understanding of EMT itself and EMT-related diseases.
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Affiliation(s)
- Imtiaz Nisar Lone
- Izmir Biomedicine and Genome Center, Izmir 35340, Turkey; (I.N.L.); (B.S.); (S.D.)
| | - Burcu Sengez
- Izmir Biomedicine and Genome Center, Izmir 35340, Turkey; (I.N.L.); (B.S.); (S.D.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir 35340, Turkey
| | - Ali Hamiche
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, 67400 Illkirch, France;
| | - Stefan Dimitrov
- Izmir Biomedicine and Genome Center, Izmir 35340, Turkey; (I.N.L.); (B.S.); (S.D.)
- Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences (IAB), Site Santé-Allée des Alpes, 38700 La Tronche, France
| | - Hani Alotaibi
- Izmir Biomedicine and Genome Center, Izmir 35340, Turkey; (I.N.L.); (B.S.); (S.D.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir 35340, Turkey
- Correspondence: ; Tel.: +90-232-299-4100 (ext. 5071)
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Martire S, Banaszynski LA. The roles of histone variants in fine-tuning chromatin organization and function. Nat Rev Mol Cell Biol 2020; 21:522-541. [PMID: 32665685 PMCID: PMC8245300 DOI: 10.1038/s41580-020-0262-8] [Citation(s) in RCA: 200] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/28/2020] [Indexed: 12/15/2022]
Abstract
Histones serve to both package and organize DNA within the nucleus. In addition to histone post-translational modification and chromatin remodelling complexes, histone variants contribute to the complexity of epigenetic regulation of the genome. Histone variants are characterized by a distinct protein sequence and a selection of designated chaperone systems and chromatin remodelling complexes that regulate their localization in the genome. In addition, histone variants can be enriched with specific post-translational modifications, which in turn can provide a scaffold for recruitment of variant-specific interacting proteins to chromatin. Thus, through these properties, histone variants have the capacity to endow specific regions of chromatin with unique character and function in a regulated manner. In this Review, we provide an overview of recent advances in our understanding of the contribution of histone variants to chromatin function in mammalian systems. First, we discuss new molecular insights into chaperone-mediated histone variant deposition. Next, we discuss mechanisms by which histone variants influence chromatin properties such as nucleosome stability and the local chromatin environment both through histone variant sequence-specific effects and through their role in recruiting different chromatin-associated complexes. Finally, we focus on histone variant function in the context of both embryonic development and human disease, specifically developmental syndromes and cancer.
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Affiliation(s)
- Sara Martire
- Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Laura A Banaszynski
- Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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Abstract
Histone variants regulate chromatin accessibility and gene transcription. Given their distinct properties and functions, histone varint substitutions allow for profound alteration of nucleosomal architecture and local chromatin landscape. Skeletal myogenesis driven by the key transcription factor MyoD is characterized by precise temporal regulation of myogenic genes. Timed substitution of variants within the nucleosomes provides a powerful means to ensure sequential expression of myogenic genes. Indeed, growing evidence has shown H3.3, H2A.Z, macroH2A, and H1b to be critical for skeletal myogenesis. However, the relative importance of various histone variants and their associated chaperones in myogenesis is not fully appreciated. In this review, we summarize the role that histone variants play in altering chromatin landscape to ensure proper muscle differentiation. The temporal regulation and cross talk between histones variants and their chaperones in conjunction with other forms of epigenetic regulation could be critical to understanding myogenesis and their involvement in myopathies.
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Affiliation(s)
- Nandini Karthik
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore , Singapore
| | - Reshma Taneja
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore , Singapore
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11
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Scacchetti A, Schauer T, Reim A, Apostolou Z, Campos Sparr A, Krause S, Heun P, Wierer M, Becker PB. Drosophila SWR1 and NuA4 complexes are defined by DOMINO isoforms. eLife 2020; 9:e56325. [PMID: 32432549 PMCID: PMC7239659 DOI: 10.7554/elife.56325] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 04/23/2020] [Indexed: 12/11/2022] Open
Abstract
Histone acetylation and deposition of H2A.Z variant are integral aspects of active transcription. In Drosophila, the single DOMINO chromatin regulator complex is thought to combine both activities via an unknown mechanism. Here we show that alternative isoforms of the DOMINO nucleosome remodeling ATPase, DOM-A and DOM-B, directly specify two distinct multi-subunit complexes. Both complexes are necessary for transcriptional regulation but through different mechanisms. The DOM-B complex incorporates H2A.V (the fly ortholog of H2A.Z) genome-wide in an ATP-dependent manner, like the yeast SWR1 complex. The DOM-A complex, instead, functions as an ATP-independent histone acetyltransferase complex similar to the yeast NuA4, targeting lysine 12 of histone H4. Our work provides an instructive example of how different evolutionary strategies lead to similar functional separation. In yeast and humans, nucleosome remodeling and histone acetyltransferase complexes originate from gene duplication and paralog specification. Drosophila generates the same diversity by alternative splicing of a single gene.
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Affiliation(s)
- Alessandro Scacchetti
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-UniversityMunichGermany
| | - Tamas Schauer
- Bioinformatics Unit, Biomedical Center, Ludwig-Maximilians-UniversityMunichGermany
| | - Alexander Reim
- Department of Proteomics and Signal Transduction, Max Planck Institute of BiochemistryMunichGermany
| | - Zivkos Apostolou
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-UniversityMunichGermany
| | - Aline Campos Sparr
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-UniversityMunichGermany
| | - Silke Krause
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-UniversityMunichGermany
| | - Patrick Heun
- Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of EdinburghEdinburghUnited Kingdom
| | - Michael Wierer
- Department of Proteomics and Signal Transduction, Max Planck Institute of BiochemistryMunichGermany
| | - Peter B Becker
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-UniversityMunichGermany
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Tang S, Huang X, Wang X, Zhou X, Huang H, Qin L, Tao H, Wang Q, Tao Y. Vital and Distinct Roles of H2A.Z Isoforms in Hepatocellular Carcinoma. Onco Targets Ther 2020; 13:4319-4337. [PMID: 32547065 PMCID: PMC7244249 DOI: 10.2147/ott.s243823] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 04/09/2020] [Indexed: 12/24/2022] Open
Abstract
Purpose H2A.Z is an oncogenic histone variant that is overexpressed in cancers. Two isoforms of H2A.Z, H2AFZ and H2AFV, are identical except for a three-amino acid difference. However, their isoform-specific functions remain unclear in cancer development. Thereby, this study aimed to investigate whether the two isoforms play distinct functions in hepatocarcinogenesis. Materials and Methods Expressions of H2A.Z isoforms in 116 paired hepatocellular cancerous and para-cancerous tissues were detected by employing qPCR. GEO and TCGA databases were used to probe expressions and prognostic value of the two H2A.Z isoforms. A comprehensive meta-analysis was conducted. Furthermore, co-expressed analysis of H2AFZ and H2AFV was performed by using cBioPortal database. H2A.Z binding genes from Chip-seq were intersected with H2A.Z isoforms co-expressed genes to perform functional annotations. Cell proliferation experiments from H2AFZ knockout HepG2 and BEL-7402 cells were implemented. Finally, RNA-seq was applied to analyse alternative splicing in H2AFZ knockout and wild-type cells. Results H2AFZ and H2AFV were both significantly upregulated (P < 0.01) in hepatocellular carcinoma and related to poor prognosis (P < 0.01). The two H2A.Z isoforms played vital roles in cell proliferation. It is also predicted that unique functions of H2AFV contain spindle midzone and microtubule, while H2AFZ is especially associated with RNA export and spliceosome. Further, devoid H2AFZ may restrain liver cancer cell proliferation and cause many alternative splicing events. Conclusion Both H2A.Z isoforms play vital and distinct roles in the occurrence and progression of liver cancer, which may pave a way for novel therapeutic applications for cancers in the future.
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Affiliation(s)
- Shaomei Tang
- The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Xiaoliang Huang
- Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, Guangxi 530021, People's Republic of China
| | - Xi Wang
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Xianguo Zhou
- Department of Research, Guangxi Medical University Cancer Hospital, Nanning, Guangxi 530021, People's Republic of China
| | - Huan Huang
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Liwen Qin
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Hongyu Tao
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Qiuyan Wang
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, People's Republic of China.,Department of Research, Guangxi Medical University Cancer Hospital, Nanning, Guangxi 530021, People's Republic of China.,Guangxi Colleges and Universities Key Laboratory of Biological Molecular Medicine Research, Nanning, Guangxi, People's Republic of China
| | - Yuting Tao
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, People's Republic of China.,Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi, Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning, Guangxi, People's Republic of China
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13
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Cheema MS, Good KV, Kim B, Soufari H, O’Sullivan C, Freeman ME, Stefanelli G, Casas CR, Zengeler KE, Kennedy AJ, Eirin Lopez JM, Howard PL, Zovkic IB, Shabanowitz J, Dryhurst DD, Hunt DF, Mackereth CD, Ausió J. Deciphering the Enigma of the Histone H2A.Z-1/H2A.Z-2 Isoforms: Novel Insights and Remaining Questions. Cells 2020; 9:cells9051167. [PMID: 32397240 PMCID: PMC7290884 DOI: 10.3390/cells9051167] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/21/2020] [Accepted: 04/24/2020] [Indexed: 12/20/2022] Open
Abstract
The replication independent (RI) histone H2A.Z is one of the more extensively studied variant members of the core histone H2A family, which consists of many replication dependent (RD) members. The protein has been shown to be indispensable for survival, and involved in multiple roles from DNA damage to chromosome segregation, replication, and transcription. However, its functional involvement in gene expression is controversial. Moreover, the variant in several groups of metazoan organisms consists of two main isoforms (H2A.Z-1 and H2A.Z-2) that differ in a few (3–6) amino acids. They comprise the main topic of this review, starting from the events that led to their identification, what is currently known about them, followed by further experimental, structural, and functional insight into their roles. Despite their structural differences, a direct correlation to their functional variability remains enigmatic. As all of this is being elucidated, it appears that a strong functional involvement of isoform variability may be connected to development.
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Affiliation(s)
- Manjinder S. Cheema
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada; (M.S.C.); (K.V.G.); (B.K.); (C.O.); (M.E.F.); (P.L.H.); (D.D.D.)
| | - Katrina V. Good
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada; (M.S.C.); (K.V.G.); (B.K.); (C.O.); (M.E.F.); (P.L.H.); (D.D.D.)
| | - Bohyun Kim
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada; (M.S.C.); (K.V.G.); (B.K.); (C.O.); (M.E.F.); (P.L.H.); (D.D.D.)
| | - Heddy Soufari
- Institut Européen de Chimie et Biologie, Univ. Bordeaux, 2 rue Robert Escarpit, F-33607 Pessac, France; (H.S.); (C.D.M.)
- Inserm U1212, CNRS UMR 5320, ARNA Laboratory, Univ. Bordeaux, 146 rue Léo Saignat, F-33076 Bordeaux, France
| | - Connor O’Sullivan
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada; (M.S.C.); (K.V.G.); (B.K.); (C.O.); (M.E.F.); (P.L.H.); (D.D.D.)
| | - Melissa E. Freeman
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada; (M.S.C.); (K.V.G.); (B.K.); (C.O.); (M.E.F.); (P.L.H.); (D.D.D.)
| | - Gilda Stefanelli
- Department of Neurosciences & Mental Health, the Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; (G.S.); (I.B.Z.)
| | - Ciro Rivera Casas
- Environmental Epigenetics Group, Department of Biological Sciences, Florida International UniversityNorth Miami, FL 33181, USA; (C.R.C.); (J.M.E.L.)
| | - Kristine E. Zengeler
- Department of Chemistry and Biochemistry, Bates College, 2 Andrews Road, Lewiston, ME 04240, USA; (K.E.Z.); (A.J.K.)
| | - Andrew J. Kennedy
- Department of Chemistry and Biochemistry, Bates College, 2 Andrews Road, Lewiston, ME 04240, USA; (K.E.Z.); (A.J.K.)
| | - Jose Maria Eirin Lopez
- Environmental Epigenetics Group, Department of Biological Sciences, Florida International UniversityNorth Miami, FL 33181, USA; (C.R.C.); (J.M.E.L.)
| | - Perry L. Howard
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada; (M.S.C.); (K.V.G.); (B.K.); (C.O.); (M.E.F.); (P.L.H.); (D.D.D.)
| | - Iva B. Zovkic
- Department of Neurosciences & Mental Health, the Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; (G.S.); (I.B.Z.)
- Department of Psychology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA; (J.S.); (D.F.H.)
| | - Deanna D. Dryhurst
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada; (M.S.C.); (K.V.G.); (B.K.); (C.O.); (M.E.F.); (P.L.H.); (D.D.D.)
| | - Donald F. Hunt
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA; (J.S.); (D.F.H.)
- Department of Pathology, University of Virginia, Charlottesville, VA 22903, USA
| | - Cameron D. Mackereth
- Institut Européen de Chimie et Biologie, Univ. Bordeaux, 2 rue Robert Escarpit, F-33607 Pessac, France; (H.S.); (C.D.M.)
- Inserm U1212, CNRS UMR 5320, ARNA Laboratory, Univ. Bordeaux, 146 rue Léo Saignat, F-33076 Bordeaux, France
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada; (M.S.C.); (K.V.G.); (B.K.); (C.O.); (M.E.F.); (P.L.H.); (D.D.D.)
- Correspondence: ; Tel.: +1-250-721-8863; Fax: +1-250-721-8855
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14
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An improved functional analysis of linker-mediated complex (iFALC) strategy. Biochem Biophys Res Commun 2020; 526:1164-1169. [PMID: 32327258 DOI: 10.1016/j.bbrc.2020.04.039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 04/10/2020] [Indexed: 11/20/2022]
Abstract
The functional analysis of linker-mediated complex (FALC) strategy that facilitates functional analysis of a common subunit of multi-subunit protein complexes in cells constitutes three steps; (1) a common subunit is fused to a specific subunit via recombinant DNA, (2) mutation is introduced into a portion of the common subunit of the fused protein, and (3) the mutational effect on the fused protein is evaluated by transformation and analysis of multiple appropriate gene knockout yeast strains. Conceptually, the FALC strategy is applicable to any common subunit of multi-subunit protein complexes in any cell type. However, the proximity of two subunits to fuse, preparation of multiple gene knockout cells, and utilization of yeast cells can together prevent the practical and broad usage of the FALC strategy for analyzing all multi-subunit complexes in all cell types. In this study, we analyzed histone H2B as a common subunit of histone H2A/H2B and histone variant H2A.Z/H2B dimers. The FALC strategy was improved in three ways; (i) a long linker (up to 300 amino acids) was used to fuse H2B with H2A.Z in yeast cells, (ii) the effects of the fused H2B-H2A.Z harboring mutation in the H2B portion was evaluated in H2A.Z knockout yeast strains and it was not essential to knockout two copies of H2B genes, and (iii) this occurred even in vertebrate cells possessing a dozen H2B genes. This improved FALC (iFALC) strategy reveals that vertebrate H2B-D68, corresponding to yeast H2B-D71, is critical for chromatin binding of the H2A.Z/H2B dimer, and this is evolutionarily conserved.
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15
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Raja DA, Subramaniam Y, Aggarwal A, Gotherwal V, Babu A, Tanwar J, Motiani RK, Sivasubbu S, Gokhale RS, Natarajan VT. Histone variant dictates fate biasing of neural crest cells to melanocyte lineage. Development 2020; 147:dev.182576. [PMID: 32098766 DOI: 10.1242/dev.182576] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 01/24/2020] [Indexed: 11/20/2022]
Abstract
In the neural crest lineage, progressive fate restriction and stem cell assignment are crucial for both development and regeneration. Whereas fate commitment events have distinct transcriptional footprints, fate biasing is often transitory and metastable, and is thought to be moulded by epigenetic programmes. Therefore, the molecular basis of specification is difficult to define. In this study, we established a role for a histone variant, H2a.z.2, in specification of the melanocyte lineage from multipotent neural crest cells. H2a.z.2 silencing reduces the number of melanocyte precursors in developing zebrafish embryos and from mouse embryonic stem cells in vitro We demonstrate that this histone variant occupies nucleosomes in the promoter of the key melanocyte determinant mitf, and enhances its induction. CRISPR/Cas9-based targeted mutagenesis of this gene in zebrafish drastically reduces adult melanocytes, as well as their regeneration. Thereby, our study establishes the role of a histone variant upstream of the core gene regulatory network in the neural crest lineage. This epigenetic mark is a key determinant of cell fate and facilitates gene activation by external instructive signals, thereby establishing melanocyte fate identity.
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Affiliation(s)
- Desingu Ayyappa Raja
- Pigment Cell Biology Group, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific and Innovative Research, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh, 201002, India
| | - Yogaspoorthi Subramaniam
- Pigment Cell Biology Group, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific and Innovative Research, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh, 201002, India
| | - Ayush Aggarwal
- Pigment Cell Biology Group, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific and Innovative Research, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh, 201002, India
| | - Vishvabandhu Gotherwal
- Pigment Cell Biology Group, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific and Innovative Research, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh, 201002, India
| | - Aswini Babu
- Pigment Cell Biology Group, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Jyoti Tanwar
- Pigment Cell Biology Group, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific and Innovative Research, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh, 201002, India
| | - Rajender K Motiani
- Pigment Cell Biology Group, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Sridhar Sivasubbu
- Pigment Cell Biology Group, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Rajesh S Gokhale
- Pigment Cell Biology Group, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Vivek T Natarajan
- Pigment Cell Biology Group, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India .,Academy of Scientific and Innovative Research, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh, 201002, India
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16
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Lamaa A, Humbert J, Aguirrebengoa M, Cheng X, Nicolas E, Côté J, Trouche D. Integrated analysis of H2A.Z isoforms function reveals a complex interplay in gene regulation. eLife 2020; 9:53375. [PMID: 32109204 PMCID: PMC7048395 DOI: 10.7554/elife.53375] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 02/12/2020] [Indexed: 12/13/2022] Open
Abstract
The H2A.Z histone variant plays major roles in the control of gene expression. In human, H2A.Z is encoded by two genes expressing two isoforms, H2A.Z.1 and H2A.Z.2 differing by three amino acids. Here, we undertook an integrated analysis of their functions in gene expression using endogenously-tagged proteins. RNA-Seq analysis in untransformed cells showed that they can regulate both distinct and overlapping sets of genes positively or negatively in a context-dependent manner. Furthermore, they have similar or antagonistic function depending on genes. H2A.Z.1 and H2A.Z.2 can replace each other at Transcription Start Sites, providing a molecular explanation for this interplay. Mass spectrometry analysis showed that H2A.Z.1 and H2A.Z.2 have specific interactors, which can mediate their functional antagonism. Our data indicate that the balance between H2A.Z.1 and H2A.Z.2 at promoters is critically important to regulate specific gene expression, providing an additional layer of complexity to the control of gene expression by histone variants.
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Affiliation(s)
- Assala Lamaa
- LBCMCP, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Jonathan Humbert
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center and Oncology Division of CHU de Québec-Université Laval Research Center, Quebec, Canada
| | - Marion Aguirrebengoa
- BigA Core Facility, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Xue Cheng
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center and Oncology Division of CHU de Québec-Université Laval Research Center, Quebec, Canada
| | - Estelle Nicolas
- LBCMCP, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center and Oncology Division of CHU de Québec-Université Laval Research Center, Quebec, Canada
| | - Didier Trouche
- LBCMCP, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
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17
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Semer M, Bidon B, Larnicol A, Caliskan G, Catez P, Egly JM, Coin F, Le May N. DNA repair complex licenses acetylation of H2A.Z.1 by KAT2A during transcription. Nat Chem Biol 2019; 15:992-1000. [PMID: 31527837 DOI: 10.1038/s41589-019-0354-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 07/24/2019] [Indexed: 12/11/2022]
Abstract
Post-translational modifications of histone variant H2A.Z accompany gene transactivation, but its modifying enzymes still remain elusive. Here, we reveal a hitherto unknown function of human KAT2A (GCN5) as a histone acetyltransferase (HAT) of H2A.Z at the promoters of a set of transactivated genes. Expression of these genes also depends on the DNA repair complex XPC-RAD23-CEN2. We established that XPC-RAD23-CEN2 interacts both with H2A.Z and KAT2A to drive the recruitment of the HAT at promoters and license H2A.Z acetylation. KAT2A selectively acetylates H2A.Z.1 versus H2A.Z.2 in vitro on several well-defined lysines and we unveiled that alanine-14 in H2A.Z.2 is responsible for inhibiting the activity of KAT2A. Notably, the use of a nonacetylable H2A.Z.1 mutant shows that H2A.Z.1ac recruits the epigenetic reader BRD2 to promote RNA polymerase II recruitment. Our studies identify KAT2A as an H2A.Z.1 HAT in mammals and implicate XPC-RAD23-CEN2 as a transcriptional co-activator licensing the reshaping of the promoter epigenetic landscape.
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Affiliation(s)
- M Semer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Illkirch Cedex, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - B Bidon
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Illkirch Cedex, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - A Larnicol
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Illkirch Cedex, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - G Caliskan
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Illkirch Cedex, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France.,Department of Pharmaceutical Biotechnology, Faculty of pharmacy, Sivas Cumhuriyet University, Sivas, Turkey
| | - P Catez
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Illkirch Cedex, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - J M Egly
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Illkirch Cedex, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - F Coin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Illkirch Cedex, Strasbourg, France. .,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France. .,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France. .,Université de Strasbourg, Illkirch, France.
| | - N Le May
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Illkirch Cedex, Strasbourg, France. .,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France. .,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France. .,Université de Strasbourg, Illkirch, France.
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18
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Structure-based design of an H2A.Z.1 mutant stabilizing a nucleosome in vitro and in vivo. Biochem Biophys Res Commun 2019; 515:719-724. [DOI: 10.1016/j.bbrc.2019.06.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 06/02/2019] [Indexed: 11/20/2022]
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19
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Shen T, Ji F, Wang Y, Lei X, Zhang D, Jiao J. Brain-specific deletion of histone variant H2A.z results in cortical neurogenesis defects and neurodevelopmental disorder. Nucleic Acids Res 2019; 46:2290-2307. [PMID: 29294103 PMCID: PMC5861433 DOI: 10.1093/nar/gkx1295] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 12/19/2017] [Indexed: 12/14/2022] Open
Abstract
Defects in neurogenesis alter brain circuit formations and may lead to neurodevelopmental disorders such as autism and schizophrenia. Histone H2A.z, a variant of histone H2A, plays critical roles in chromatin structure and epigenetic regulation, but its function and mechanism in brain development remain largely unknown. Here, we find that the deletion of H2A.z results in enhanced proliferation of neural progenitors but reduced neuronal differentiation. In addition, neurons in H2A.z knockout mice exhibit abnormal dendrites during brain development. Furthermore, H2A.zcKO mice exhibit serial behavioral deficits, such as decreased exploratory activity and impaired learning and memory. Mechanistically, H2A.z regulates embryonic neurogenesis by targeting Nkx2–4 through interaction with Setd2, thereby promoting H3K36me3 modification to activate the transcription of Nkx2–4. Furthermore, enforced expression of Nkx2–4 can rescue the defective neurogenesis in the H2A.z-knockdown embryonic brain. Together, our findings implicate the epigenetic regulation by H2A.z in embryonic neurogenesis and provide a framework for understanding how disruption in the H2A.z gene may contribute to neurological disorders.
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Affiliation(s)
- Tianjin Shen
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fen Ji
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuanyuan Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuepei Lei
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dongming Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianwei Jiao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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20
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Giaimo BD, Ferrante F, Herchenröther A, Hake SB, Borggrefe T. The histone variant H2A.Z in gene regulation. Epigenetics Chromatin 2019; 12:37. [PMID: 31200754 PMCID: PMC6570943 DOI: 10.1186/s13072-019-0274-9] [Citation(s) in RCA: 173] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 04/23/2019] [Indexed: 01/04/2023] Open
Abstract
The histone variant H2A.Z is involved in several processes such as transcriptional control, DNA repair, regulation of centromeric heterochromatin and, not surprisingly, is implicated in diseases such as cancer. Here, we review the recent developments on H2A.Z focusing on its role in transcriptional activation and repression. H2A.Z, as a replication-independent histone, has been studied in several model organisms and inducible mammalian model systems. Its loading machinery and several modifying enzymes have been recently identified, and some of the long-standing discrepancies in transcriptional activation and/or repression are about to be resolved. The buffering functions of H2A.Z, as supported by genome-wide localization and analyzed in several dynamic systems, are an excellent example of transcriptional control. Posttranslational modifications such as acetylation and ubiquitination of H2A.Z, as well as its specific binding partners, are in our view central players in the control of gene expression. Understanding the key-mechanisms in either turnover or stabilization of H2A.Z-containing nucleosomes as well as defining the H2A.Z interactome will pave the way for therapeutic applications in the future.
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Affiliation(s)
| | - Francesca Ferrante
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392, Giessen, Germany
| | - Andreas Herchenröther
- Institute for Genetics, University of Giessen, Heinrich-Buff-Ring 58-62, 35392, Giessen, Germany
| | - Sandra B Hake
- Institute for Genetics, University of Giessen, Heinrich-Buff-Ring 58-62, 35392, Giessen, Germany
| | - Tilman Borggrefe
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392, Giessen, Germany.
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21
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Gretzinger TL, Tyagi M, Fontaine CJ, Cheema MS, González-Perez M, Freeman ME, Christie BR, Ausió J. Fetal alcohol spectrum disorder (FASD) affects the hippocampal levels of histone variant H2A.Z-2. Biochem Cell Biol 2019; 97:431-436. [PMID: 30605356 DOI: 10.1139/bcb-2018-0240] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Fetal alcohol spectrum disorder (FASD) is caused by prenatal exposure to ethanol and has been linked to neurodevelopmental impairments. Alcohol has the potential to alter some of the epigenetic components that play a critical role during development. Previous studies have provided evidence that prenatal exposure to ethanol results in abnormal epigenetic patterns (i.e., hypomethylation) of the genome. The aim of this study was to determine how prenatal exposure to ethanol in rats affects the hippocampal levels of expression of two important brain epigenetic transcriptional regulators involved in synaptic plasticity and memory consolidation: methyl CpG-binding protein 2 (MeCP2) and histone variant H2A.Z. Unexpectedly, under the conditions used in this work we were not able to detect any changes in MeCP2. Interestingly, however, we observed a significant decrease in H2A.Z, accompanied by its chromatin redistribution in both female and male FASD rat pups. Moreover, the data from reverse-transcription qPCR later confirmed that this decrease in H2A.Z is mainly due to down-regulation of its H2A.Z-2 isoform gene expression. Altogether, these data provide strong evidence that prenatal exposure to ethanol alters histone variant H2A.Z during neurogenesis of rat hippocampus.
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Affiliation(s)
- Taylor L Gretzinger
- a Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada
| | - Monica Tyagi
- a Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada
| | - Christine J Fontaine
- b Division of Medical Sciences and Neuroscience Graduate Program, University of Victoria, Victoria, British Columbia, Canada
| | - Manjinder S Cheema
- a Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada
| | - María González-Perez
- a Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada
| | - Melissa E Freeman
- a Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada
| | - Brian R Christie
- b Division of Medical Sciences and Neuroscience Graduate Program, University of Victoria, Victoria, British Columbia, Canada
| | - Juan Ausió
- a Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada
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22
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Tyagi M, Cheema MS, Dryhurst D, Eskiw CH, Ausió J. Metformin alters H2A.Z dynamics and regulates androgen dependent prostate cancer progression. Oncotarget 2018; 9:37054-37068. [PMID: 30651935 PMCID: PMC6319340 DOI: 10.18632/oncotarget.26457] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 11/05/2018] [Indexed: 12/13/2022] Open
Abstract
Epigenetic mechanisms involved in prostate cancer include hypermethylation of tumor suppressor genes, general hypomethylation of the genome, and alterations in histone posttranslational modifications (PTMs). In addition, over expression of the histone variant H2A.Z as well as deregulated expression of Polycomb group proteins including EZH2 have been well-documented. Recent evidence supports a role for metformin in prostate cancer (PCa) treatment. However, the mechanism of action of metformin in PCa is poorly understood. We provide data showing that metformin epigenetically targets PCa by altering the levels and gene binding dynamics of histone variant H2A.Z. Moreover, we show that the increase in H2A.Z upon metformin treatment occurs preferentially due to H2A.Z.1 isoform. Chromatin immunoprecipitation (ChIP)-RT PCR analysis indicates that metformin treatment results in an increased H2A.Z occupancy on the androgen receptor (AR) and AR-regulated genes that is more prominent in the androgen dependent AR positive LNCaP cells. Repression of H2A.Z.1 gene by siRNA-mediated knock down identified this H2A.Z isoform to be responsible. Based on preliminary data with an EZH2-specific inhibitor, we suggest that the effects of metformin on the early stages of PCa may involve both EZH2 and H2A.Z through the alteration of different molecular pathways.
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Affiliation(s)
- Monica Tyagi
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Manjinder S. Cheema
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | | | - Christopher H. Eskiw
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
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23
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Gas41 links histone acetylation to H2A.Z deposition and maintenance of embryonic stem cell identity. Cell Discov 2018; 4:28. [PMID: 29900004 PMCID: PMC5995911 DOI: 10.1038/s41421-018-0027-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 03/22/2018] [Accepted: 03/23/2018] [Indexed: 01/07/2023] Open
Abstract
The histone variant H2A.Z is essential for maintaining embryonic stem cell (ESC) identity in part by keeping developmental genes in a poised bivalent state. However, how H2A.Z is deposited into the bivalent domains remains unknown. In mammals, two chromatin remodeling complexes, Tip60/p400 and SRCAP, exchange the canonical histone H2A for H2A.Z in the chromatin. Here we show that Glioma Amplified Sequence 41 (Gas41), a shared subunit of the two H2A.Z-depositing complexes, functions as a reader of histone lysine acetylation and recruits Tip60/p400 and SRCAP to deposit H2A.Z into specific chromatin regions including bivalent domains. The YEATS domain of Gas41 bound to acetylated histone H3K27 and H3K14 both in vitro and in cells. The crystal structure of the Gas41 YEATS domain in complex with the H3K27ac peptide revealed that, similar to the AF9 and ENL YEATS domains, Gas41 YEATS forms a serine-lined aromatic cage for acetyllysine recognition. Consistently, mutations in the aromatic residues of the Gas41 YEATS domain abrogated the interaction. In mouse ESCs, knockdown of Gas41 led to flattened morphology of ESC colonies, as the result of derepression of differentiation genes. Importantly, the abnormal morphology was rescued by expressing wild-type Gas41, but not the YEATS domain mutated counterpart that does not recognize histone acetylation. Mechanically, we found that Gas41 depletion led to reduction of H2A.Z levels and a concomitant reduction of H3K27me3 levels on bivalent domains. Together, our study reveals an essential role of the Gas41 YEATS domain in linking histone acetylation to H2A.Z deposition and maintenance of ESC identity.
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24
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Fukuto A, Ikura M, Ikura T, Sun J, Horikoshi Y, Shima H, Igarashi K, Kusakabe M, Harata M, Horikoshi N, Kurumizaka H, Kiuchi Y, Tashiro S. SUMO modification system facilitates the exchange of histone variant H2A.Z-2 at DNA damage sites. Nucleus 2017; 9:87-94. [PMID: 29095668 PMCID: PMC5973225 DOI: 10.1080/19491034.2017.1395543] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Histone exchange and histone post-translational modifications play important roles in the regulation of DNA metabolism, by re-organizing the chromatin configuration. We previously demonstrated that the histone variant H2A.Z-2 is rapidly exchanged at damaged sites after DNA double strand break induction in human cells. In yeast, the small ubiquitin-like modifier (SUMO) modification of H2A.Z is involved in the DNA damage response. However, whether the SUMO modification regulates the exchange of human H2A.Z-2 at DNA damage sites remains unclear. Here, we show that H2A.Z-2 is SUMOylated in a damage-dependent manner, and the SUMOylation of H2A.Z-2 is suppressed by the depletion of the SUMO E3 ligase, PIAS4. Moreover, PIAS4 depletion represses the incorporation and eviction of H2A.Z-2 at damaged sites. These findings demonstrate that the PIAS4-mediated SUMOylation regulates the exchange of H2A.Z-2 at DNA damage sites.
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Affiliation(s)
- Atsuhiko Fukuto
- a Department of Cellular Biology , Research Institute for Radiation Biology and Medicine, Hiroshima University , Hiroshima , Japan.,b Department of Ophthalmology and Visual Science , Graduate School of Biomedical Sciences, Hiroshima University , Hiroshima , Japan
| | - Masae Ikura
- c Laboratory of Chromatin Regulatory Network, Department of Mutagenesis , Radiation Biology Center, Kyoto University , Kyoto , Japan
| | - Tsuyoshi Ikura
- c Laboratory of Chromatin Regulatory Network, Department of Mutagenesis , Radiation Biology Center, Kyoto University , Kyoto , Japan
| | - Jiying Sun
- a Department of Cellular Biology , Research Institute for Radiation Biology and Medicine, Hiroshima University , Hiroshima , Japan
| | - Yasunori Horikoshi
- a Department of Cellular Biology , Research Institute for Radiation Biology and Medicine, Hiroshima University , Hiroshima , Japan
| | - Hiroki Shima
- d Department of Biochemistry , Tohoku University Graduate School of Medicine , Sendai , Miyagi , Japan
| | - Kazuhiko Igarashi
- d Department of Biochemistry , Tohoku University Graduate School of Medicine , Sendai , Miyagi , Japan
| | - Masayuki Kusakabe
- e Laboratory of Molecular Biology, Graduate School of Agricultural Science , Tohoku University , Sendai , Miyagi , Japan
| | - Masahiko Harata
- e Laboratory of Molecular Biology, Graduate School of Agricultural Science , Tohoku University , Sendai , Miyagi , Japan
| | - Naoki Horikoshi
- f Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering , Waseda University, Shinjukuku , Tokyo , Japan.,g Present address; Department of Structural Biology, School of Medicine , Stanford University , Stanford , CA , USA
| | - Hitoshi Kurumizaka
- f Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering , Waseda University, Shinjukuku , Tokyo , Japan
| | - Yoshiaki Kiuchi
- b Department of Ophthalmology and Visual Science , Graduate School of Biomedical Sciences, Hiroshima University , Hiroshima , Japan
| | - Satoshi Tashiro
- a Department of Cellular Biology , Research Institute for Radiation Biology and Medicine, Hiroshima University , Hiroshima , Japan
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25
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Histone Hypervariants H2A.Z.1 and H2A.Z.2 Play Independent and Context-Specific Roles in Neuronal Activity-Induced Transcription of Arc/Arg3.1 and Other Immediate Early Genes. eNeuro 2017; 4:eN-NWR-0040-17. [PMID: 28856239 PMCID: PMC5569379 DOI: 10.1523/eneuro.0040-17.2017] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 08/07/2017] [Accepted: 08/09/2017] [Indexed: 12/21/2022] Open
Abstract
The histone variant H2A.Z is an essential and conserved regulator of eukaryotic gene transcription. However, the exact role of this histone in the transcriptional process remains perplexing. In vertebrates, H2A.Z has two hypervariants, H2A.Z.1 and H2A.Z.2, that have almost identical sequences except for three amino acid residues. Due to such similarity, functional specificity of these hypervariants in neurobiological processes, if any, remain largely unknown. In this study with dissociated rat cortical neurons, we asked if H2A.Z hypervariants have distinct functions in regulating basal and activity-induced gene transcription. Hypervariant-specific RNAi and microarray analyses revealed that H2A.Z.1 and H2A.Z.2 regulate basal expression of largely nonoverlapping gene sets, including genes that code for several synaptic proteins. In response to neuronal activity, rapid transcription of our model gene Arc is impaired by depletion of H2A.Z.2, but not H2A.Z.1. This impairment is partially rescued by codepletion of the H2A.Z chaperone, ANP32E. In contrast, under a different context (after 48 h of tetrodotoxin, TTX), rapid transcription of Arc is impaired by depletion of either hypervariant. Such context-dependent roles of H2A.Z hypervariants, as revealed by our multiplexed gene expression assays, are also evident with several other immediate early genes, where regulatory roles of these hypervariants vary from gene to gene under different conditions. Together, our data suggest that H2A.Z hypervariants have context-specific roles that complement each other to mediate activity-induced neuronal gene transcription.
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26
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El Kennani S, Adrait A, Shaytan AK, Khochbin S, Bruley C, Panchenko AR, Landsman D, Pflieger D, Govin J. MS_HistoneDB, a manually curated resource for proteomic analysis of human and mouse histones. Epigenetics Chromatin 2017; 10:2. [PMID: 28096900 PMCID: PMC5223428 DOI: 10.1186/s13072-016-0109-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 12/14/2016] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Histones and histone variants are essential components of the nuclear chromatin. While mass spectrometry has opened a large window to their characterization and functional studies, their identification from proteomic data remains challenging. Indeed, the current interpretation of mass spectrometry data relies on public databases which are either not exhaustive (Swiss-Prot) or contain many redundant entries (UniProtKB or NCBI). Currently, no protein database is ideally suited for the analysis of histones and the complex array of mammalian histone variants. RESULTS We propose two proteomics-oriented manually curated databases for mouse and human histone variants. We manually curated >1700 gene, transcript and protein entries to produce a non-redundant list of 83 mouse and 85 human histones. These entries were annotated in accordance with the current nomenclature and unified with the "HistoneDB2.0 with Variants" database. This resource is provided in a format that can be directly read by programs used for mass spectrometry data interpretation. In addition, it was used to interpret mass spectrometry data acquired on histones extracted from mouse testis. Several histone variants, which had so far only been inferred by homology or detected at the RNA level, were detected by mass spectrometry, confirming the existence of their protein form. CONCLUSIONS Mouse and human histone entries were collected from different databases and subsequently curated to produce a non-redundant protein-centric resource, MS_HistoneDB. It is dedicated to the proteomic study of histones in mouse and human and will hopefully facilitate the identification and functional study of histone variants.
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Affiliation(s)
- Sara El Kennani
- INSERM, U1038, CEA, BIG FR CNRS 3425-BGE, Université Grenoble Alpes, Grenoble, France
| | - Annie Adrait
- INSERM, U1038, CEA, BIG FR CNRS 3425-BGE, Université Grenoble Alpes, Grenoble, France
| | - Alexey K Shaytan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894 USA
| | - Saadi Khochbin
- CNRS UMR 5309 INSERM U1209, Institute of Advanced Biosciences, Université Grenoble Alpes, Grenoble, France
| | - Christophe Bruley
- INSERM, U1038, CEA, BIG FR CNRS 3425-BGE, Université Grenoble Alpes, Grenoble, France
| | - Anna R Panchenko
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894 USA
| | - David Landsman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894 USA
| | - Delphine Pflieger
- INSERM, U1038, CEA, BIG FR CNRS 3425-BGE, Université Grenoble Alpes, Grenoble, France
| | - Jérôme Govin
- INSERM, U1038, CEA, BIG FR CNRS 3425-BGE, Université Grenoble Alpes, Grenoble, France
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27
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Rivera-Casas C, González-Romero R, Vizoso-Vazquez Á, Cheema MS, Cerdán ME, Méndez J, Ausió J, Eirin-Lopez JM. Characterization of mussel H2A.Z.2: a new H2A.Z variant preferentially expressed in germinal tissues from Mytilus. Biochem Cell Biol 2016; 94:480-490. [DOI: 10.1139/bcb-2016-0056] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Histones are the fundamental constituents of the eukaryotic chromatin, facilitating the physical organization of DNA in chromosomes and participating in the regulation of its metabolism. The H2A family displays the largest number of variants among core histones, including the renowned H2A.X, macroH2A, H2A.B (Bbd), and H2A.Z. This latter variant is especially interesting because of its regulatory role and its differentiation into 2 functionally divergent variants (H2A.Z.1 and H2A.Z.2), further specializing the structure and function of vertebrate chromatin. In the present work we describe, for the first time, the presence of a second H2A.Z variant (H2A.Z.2) in the genome of a non-vertebrate animal, the mussel Mytilus. The molecular and evolutionary characterization of mussel H2A.Z.1 and H2A.Z.2 histones is consistent with their functional specialization, supported on sequence divergence at promoter and coding regions as well as on varying gene expression patterns. More precisely, the expression of H2A.Z.2 transcripts in gonadal tissue and its potential upregulation in response to genotoxic stress might be mirroring the specialization of this variant in DNA repair. Overall, the findings presented in this work complement recent reports describing the widespread presence of other histone variants across eukaryotes, supporting an ancestral origin and conserved role for histone variants in chromatin.
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Affiliation(s)
- Ciro Rivera-Casas
- Chromatin Structure and Evolution (Chromevol) Group, Department of Biological Sciences, Florida International University, North Miami, FL 33181, USA
| | - Rodrigo González-Romero
- Chromatin Structure and Evolution (Chromevol) Group, Department of Biological Sciences, Florida International University, North Miami, FL 33181, USA
| | - Ángel Vizoso-Vazquez
- Exprela Group, Department of Cellular and Molecular Biology, University of A Coruña, A Coruña E15071, Spain
| | - Manjinder S. Cheema
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada
| | - M. Esperanza Cerdán
- Exprela Group, Department of Cellular and Molecular Biology, University of A Coruña, A Coruña E15071, Spain
| | - Josefina Méndez
- Xenomar Group, Department of Cellular and Molecular Biology, University of A Coruña, A Coruña E15071, Spain
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada
| | - Jose M. Eirin-Lopez
- Chromatin Structure and Evolution (Chromevol) Group, Department of Biological Sciences, Florida International University, North Miami, FL 33181, USA
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Kusakabe M, Oku H, Matsuda R, Hori T, Muto A, Igarashi K, Fukagawa T, Harata M. Genetic complementation analysis showed distinct contributions of the N-terminal tail of H2A.Z to epigenetic regulations. Genes Cells 2016; 21:122-35. [DOI: 10.1111/gtc.12327] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 11/18/2015] [Indexed: 12/30/2022]
Affiliation(s)
- Masayuki Kusakabe
- Laboratory of Molecular Biology; Graduate School of Agricultural Science; Tohoku University; Tsutsumidori-amamiyamachi 1-1 Aoba-ku Sendai 981-8555 Japan
| | - Hiroyuki Oku
- Laboratory of Molecular Biology; Graduate School of Agricultural Science; Tohoku University; Tsutsumidori-amamiyamachi 1-1 Aoba-ku Sendai 981-8555 Japan
| | - Ryo Matsuda
- Laboratory of Molecular Biology; Graduate School of Agricultural Science; Tohoku University; Tsutsumidori-amamiyamachi 1-1 Aoba-ku Sendai 981-8555 Japan
| | - Tetsuya Hori
- Graduate School of Frontier Biosciences; Osaka University; Yamadaoka 1-3 Suita Osaka 565-0871 Japan
| | - Akihiko Muto
- Department of Biochemistry; Graduate School of Medicine; Tohoku University; Seiryo-cho 2-1 Aoba-ku Sendai 980-8575 Japan
| | - Kazuhiko Igarashi
- Department of Biochemistry; Graduate School of Medicine; Tohoku University; Seiryo-cho 2-1 Aoba-ku Sendai 980-8575 Japan
| | - Tatsuo Fukagawa
- Graduate School of Frontier Biosciences; Osaka University; Yamadaoka 1-3 Suita Osaka 565-0871 Japan
| | - Masahiko Harata
- Laboratory of Molecular Biology; Graduate School of Agricultural Science; Tohoku University; Tsutsumidori-amamiyamachi 1-1 Aoba-ku Sendai 981-8555 Japan
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29
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The actin family protein ARP6 contributes to the structure and the function of the nucleolus. Biochem Biophys Res Commun 2015; 464:554-60. [PMID: 26164235 DOI: 10.1016/j.bbrc.2015.07.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 07/01/2015] [Indexed: 12/22/2022]
Abstract
The actin family members, consisting of actin and actin-related proteins (ARPs), are essential components of chromatin remodeling complexes. ARP6, one of the nuclear ARPs, is part of the Snf-2-related CREB-binding protein activator protein (SRCAP) chromatin remodeling complex, which promotes the deposition of the histone variant H2A.Z into the chromatin. In this study, we showed that ARP6 influences the structure and the function of the nucleolus. ARP6 is localized in the central region of the nucleolus, and its knockdown induced a morphological change in the nucleolus. We also found that in the presence of high concentrations of glucose ARP6 contributed to the maintenance of active ribosomal DNA (rDNA) transcription by placing H2A.Z into the chromatin. In contrast, under starvation, ARP6 was required for cell survival through the repression of rDNA transcription independently of H2A.Z. These findings reveal novel pleiotropic roles for the actin family in nuclear organization and metabolic homeostasis.
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30
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Vardabasso C, Gaspar-Maia A, Hasson D, Pünzeler S, Valle-Garcia D, Straub T, Keilhauer EC, Strub T, Dong J, Panda T, Chung CY, Yao JL, Singh R, Segura MF, Fontanals-Cirera B, Verma A, Mann M, Hernando E, Hake SB, Bernstein E. Histone Variant H2A.Z.2 Mediates Proliferation and Drug Sensitivity of Malignant Melanoma. Mol Cell 2015; 59:75-88. [PMID: 26051178 DOI: 10.1016/j.molcel.2015.05.009] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 03/24/2015] [Accepted: 04/30/2015] [Indexed: 01/19/2023]
Abstract
Histone variants are emerging as key regulatory molecules in cancer. We report a unique role for the H2A.Z isoform H2A.Z.2 as a driver of malignant melanoma. H2A.Z.2 is highly expressed in metastatic melanoma, correlates with decreased patient survival, and is required for cellular proliferation. Our integrated genomic analyses reveal that H2A.Z.2 controls the transcriptional output of E2F target genes in melanoma cells. These genes are highly expressed and display a distinct signature of H2A.Z occupancy. We identify BRD2 as an H2A.Z-interacting protein, levels of which are also elevated in melanoma. We further demonstrate that H2A.Z.2-regulated genes are bound by BRD2 and E2F1 in an H2A.Z.2-dependent manner. Importantly, H2A.Z.2 deficiency sensitizes melanoma cells to chemotherapy and targeted therapies. Collectively, our findings implicate H2A.Z.2 as a mediator of cell proliferation and drug sensitivity in malignant melanoma, holding translational potential for novel therapeutic strategies.
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Affiliation(s)
- Chiara Vardabasso
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alexandre Gaspar-Maia
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dan Hasson
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sebastian Pünzeler
- Center for Integrated Protein Science Munich and Department of Molecular Biology, Adolf-Butenandt Institute, Ludwig-Maximilians University, 80336 Munich, Germany
| | - David Valle-Garcia
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Molecular Genetics Department, Institute for Cellular Physiology, National Autonomous University of Mexico, 04510 Mexico City, Mexico
| | - Tobias Straub
- Center for Integrated Protein Science Munich and Department of Molecular Biology, Adolf-Butenandt Institute, Ludwig-Maximilians University, 80336 Munich, Germany
| | - Eva C Keilhauer
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Thomas Strub
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Joanna Dong
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Taniya Panda
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Chi-Yeh Chung
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jonathan L Yao
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Rajendra Singh
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Miguel F Segura
- Department of Pathology and Interdisciplinary Melanoma Cooperative Group, New York University Langone Medical Center, New York, NY 10016, USA
| | - Barbara Fontanals-Cirera
- Department of Pathology and Interdisciplinary Melanoma Cooperative Group, New York University Langone Medical Center, New York, NY 10016, USA
| | - Amit Verma
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Eva Hernando
- Department of Pathology and Interdisciplinary Melanoma Cooperative Group, New York University Langone Medical Center, New York, NY 10016, USA
| | - Sandra B Hake
- Center for Integrated Protein Science Munich and Department of Molecular Biology, Adolf-Butenandt Institute, Ludwig-Maximilians University, 80336 Munich, Germany.
| | - Emily Bernstein
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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31
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Abstract
Histone variant exchange is a novel epigenetic regulator of cognition. We speculate that H2A.Z, a variant of canonical histone H2A, exerts unique effects on transcription during distinct stages of memory formation, ultimately acting to maintain memory of previous transcriptional states and poise genes for re-activation. Hippocampus-dependent memory formation is initiated by transient expression of memory-related genes, which support the storage of recently acquired memories. Soon after, memories undergo systems consolidation, which transfers memories from the hippocampus to the cortex for long-term storage, and requires ongoing re-activation of memory-related genes. We speculate that learning-induced H2A.Z eviction from nucleosomes initially contributes to stimulus-induced transcriptional induction needed for the initial process of memory consolidation. During systems consolidation, we speculate that delayed incorporation of H2A.Z into nucleosomes of memory-related genes in the cortex is needed to poise genes for rapid re-activation, thus supporting the long-term process of memory stabilization.
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Affiliation(s)
- Iva B Zovkic
- Department of Psychology, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Brandon J Walters
- Department of Neuroscience and Mental Health, The Hospital for Sick Children, Toronto, ON, Canada
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Law C, Cheung P. Expression of Non-acetylatable H2A.Z in Myoblast Cells Blocks Myoblast Differentiation through Disruption of MyoD Expression. J Biol Chem 2015; 290:13234-49. [PMID: 25839232 DOI: 10.1074/jbc.m114.595462] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Indexed: 11/06/2022] Open
Abstract
H2A.Z is a histone H2A variant that is essential for viability in Tetrahymena and Drosophila and also during embryonic development of mice. Although implicated in diverse cellular processes, including transcriptional regulation, chromosome segregation, and heterochromatin formation, its essential function in cells remains unknown. Cellular differentiation is part of the developmental process of multicellular organisms. To elucidate the roles of H2A.Z and H2A.Z acetylation in cellular differentiation, we examined the effects of expressing wild type (WT) or a non-acetylatable form of H2A.Z in the growth and differentiation of the myoblast C2C12 cell line. Ectopic expression of wild type or mutant H2A.Z resulted in distinct phenotypes in the differentiation of the C2C12 cells and the formation of myotubes. Most strikingly, expression of the H2A.Z non-acetylatable mutant (H2A.Z-Ac-mut) resulted in a complete block of myoblast differentiation. We determined that this phenotype is caused by a loss of MyoD expression in the Ac-mut-expressing cells prior to and after induction of differentiation. Moreover, chromatin accessibility assays showed that the promoter region of MyoD is less accessible in the differentiation-defective cells. Altogether, these new findings show that expression of the Ac-mut form of H2A.Z resulted in a dominant phenotype that blocked differentiation due to chromatin changes at the MyoD promoter.
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Affiliation(s)
- Cindy Law
- From the Department of Medical Biophysics, University of Toronto, Ontario M5G 1L7, Canada and
| | - Peter Cheung
- From the Department of Medical Biophysics, University of Toronto, Ontario M5G 1L7, Canada and the Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada
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Abstract
Genetic and epigenetic changes are at the root of all cancers. The epigenetic component involves alterations of the post-synthetic modifications of DNA (methylation) and histones (histone posttranslational modifications, PTMs) as well as of those of their molecular "writers," "readers," and "erasers." Noncoding RNAs (ncRNA) can also play a role. Here, we focus on the involvement of histone alterations in cancer, in particular that of the histone variant H2A.Z in the etiology of prostate cancer. The structural mechanisms putatively responsible for the contribution of H2A.Z to oncogenic gene expression programs are first described, followed by what is currently known about the involvement of this histone variant in the regulation of androgen receptor regulated gene expression. The implications of this and their relevance to oncogene deregulation in different stages of prostate cancer, including the progression toward androgen independence, are discussed. This review underscores the increasing awareness of the epigenetic contribution of histone variants to oncogenic progression.
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Affiliation(s)
- Deanna Dryhurst
- Department of Biochemistry and Microbiology, University of Victoria, Petch building, 258a, Victoria, British Columbia Canada V8W 3P6
- ImmunoPrecise Antibodies Ltd., 3204-4464 Markham St., Victoria, British Columbia Canada V8Z 7X8
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Petch building, 258a, Victoria, British Columbia Canada V8W 3P6
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Abstract
Histones package and compact DNA by assembling into nucleosome core particles. Most histones are synthesized at S phase for rapid deposition behind replication forks. In addition, the replacement of histones deposited during S phase by variants that can be deposited independently of replication provide the most fundamental level of chromatin differentiation. Alternative mechanisms for depositing different variants can potentially establish and maintain epigenetic states. Variants have also evolved crucial roles in chromosome segregation, transcriptional regulation, DNA repair, and other processes. Investigations into the evolution, structure, and metabolism of histone variants provide a foundation for understanding the participation of chromatin in important cellular processes and in epigenetic memory.
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Affiliation(s)
- Steven Henikoff
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109-1024
| | - M Mitchell Smith
- Department of Microbiology, University of Virginia, Charlottesville, Virginia 22908
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Nishibuchi I, Suzuki H, Kinomura A, Sun J, Liu NA, Horikoshi Y, Shima H, Kusakabe M, Harata M, Fukagawa T, Ikura T, Ishida T, Nagata Y, Tashiro S. Reorganization of damaged chromatin by the exchange of histone variant H2A.Z-2. Int J Radiat Oncol Biol Phys 2014; 89:736-44. [PMID: 24969791 DOI: 10.1016/j.ijrobp.2014.03.031] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Revised: 03/13/2014] [Accepted: 03/19/2014] [Indexed: 01/08/2023]
Abstract
PURPOSE The reorganization of damaged chromatin plays an important role in the regulation of the DNA damage response. A recent study revealed the presence of 2 vertebrate H2A.Z isoforms, H2A.Z-1 and H2A.Z-2. However, the roles of the vertebrate H2A.Z isoforms are still unclear. Thus, in this study we examined the roles of the vertebrate H2A.Z isoforms in chromatin reorganization after the induction of DNA double-strand breaks (DSBs). METHODS AND MATERIALS To examine the dynamics of H2A.Z isoforms at damaged sites, we constructed GM0637 cells stably expressing each of the green fluorescent protein (GFP)-labeled H2A.Z isoforms, and performed fluorescence recovery after photobleaching (FRAP) analysis and inverted FRAP analysis in combination with microirradiation. Immunofluorescence staining using an anti-RAD51 antibody was performed to study the kinetics of RAD51 foci formation after 2-Gy irradiation of wild-type (WT), H2A.Z-1- and H2A.Z-2-deficient DT40 cells. Colony-forming assays were also performed to compare the survival rates of WT, H2A.Z-1-, and H2A.Z-2-deficient DT40 cells with control, and H2A.Z-1- and H2A.Z-2-depleted U2OS cells after irradiation. RESULTS FRAP analysis revealed that H2A.Z-2 was incorporated into damaged chromatin just after the induction of DSBs, whereas H2A.Z-1 remained essentially unchanged. Inverted FRAP analysis showed that H2A.Z-2 was released from damaged chromatin. These findings indicated that H2A.Z-2 was exchanged at DSB sites immediately after the induction of DSBs. RAD51 focus formation after ionizing irradiation was disturbed in H2A.Z-2-deficient DT40 cells but not in H2A.Z-1-deficient cells. The survival rate of H2A.Z-2-deficient cells after irradiation was lower than those of WT and H2A.Z-1- DT40 cells. Similar to DT40 cells, H2A.Z-2-depleted U2OS cells were also radiation-sensitive compared to control and H2A.Z-1-depleted cells. CONCLUSIONS We found that vertebrate H2A.Z-2 is involved in the regulation of the DNA damage response at a very early stage, via the damaged chromatin reorganization required for RAD51 focus formation.
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Affiliation(s)
- Ikuno Nishibuchi
- Department of Cellular Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan; Department of Radiation Oncology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan; Department of Radiation Oncology, Hiroshima Prefectural Hospital, Hiroshima, Japan
| | - Hidekazu Suzuki
- Department of Cellular Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Aiko Kinomura
- Department of Cellular Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Jiying Sun
- Department of Cellular Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Ning-Ang Liu
- Department of Cellular Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Yasunori Horikoshi
- Department of Cellular Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan; Research Center for Mathematics of Chromatin Live Dynamics, Hiroshima University, Hiroshima, Japan
| | - Hiroki Shima
- Department of Biochemistry, Graduate School of Medical Sciences, Tohoku University, Sendai, Japan
| | - Masayuki Kusakabe
- Laboratory of Molecular Biology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Masahiko Harata
- Laboratory of Molecular Biology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Tatsuo Fukagawa
- Department of Molecular Genetics, National Institute of Genetics and The Graduate University for Advanced Studies, Mishima, Japan
| | - Tsuyoshi Ikura
- Laboratory of Chromatin Regulatory Network, Department of Mutagenesis, Radiation Biology Center, Kyoto University, Kyoto, Japan
| | - Takafumi Ishida
- Department of Cardiovascular Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Yasushi Nagata
- Department of Radiation Oncology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Satoshi Tashiro
- Department of Cellular Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan; Research Center for Mathematics of Chromatin Live Dynamics, Hiroshima University, Hiroshima, Japan.
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Horikoshi N, Sato K, Shimada K, Arimura Y, Osakabe A, Tachiwana H, Hayashi-Takanaka Y, Iwasaki W, Kagawa W, Harata M, Kimura H, Kurumizaka H. Structural polymorphism in the L1 loop regions of human H2A.Z.1 and H2A.Z.2. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:2431-9. [PMID: 24311584 PMCID: PMC3852653 DOI: 10.1107/s090744491302252x] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2013] [Accepted: 08/10/2013] [Indexed: 04/26/2023]
Abstract
The histone H2A.Z variant is widely conserved among eukaryotes. Two isoforms, H2A.Z.1 and H2A.Z.2, have been identified in vertebrates and may have distinct functions in cell growth and gene expression. However, no structural differences between H2A.Z.1 and H2A.Z.2 have been reported. In the present study, the crystal structures of nucleosomes containing human H2A.Z.1 and H2A.Z.2 were determined. The structures of the L1 loop regions were found to clearly differ between H2A.Z.1 and H2A.Z.2, although their amino-acid sequences in this region are identical. This structural polymorphism may have been induced by a substitution that evolutionally occurred at the position of amino acid 38 and by the flexible nature of the L1 loops of H2A.Z.1 and H2A.Z.2. It was also found that in living cells nucleosomal H2A.Z.1 exchanges more rapidly than H2A.Z.2. A mutational analysis revealed that the amino-acid difference at position 38 is at least partially responsible for the distinctive dynamics of H2A.Z.1 and H2A.Z.2. These findings provide important new information for understanding the differences in the regulation and functions of H2A.Z.1 and H2A.Z.2 in cells.
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Affiliation(s)
- Naoki Horikoshi
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Koichi Sato
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Keisuke Shimada
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Yasuhiro Arimura
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Akihisa Osakabe
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Hiroaki Tachiwana
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Yoko Hayashi-Takanaka
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Wakana Iwasaki
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
- RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Wataru Kagawa
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
- Program in Chemistry and Life Science, Department of Interdisciplinary Science and Engineering, School of Science and Engineering, Meisei University, 2-1-1 Hodokubo, Hino-shi, Tokyo 191-8506, Japan
| | - Masahiko Harata
- Laboratory of Molecular Biology, Graduate School of Agricultural Science, Tohoku University, Tsutsumidori-Amamiya-machi 1-1, Aoba-ku, Sendai 981-8555, Japan
| | - Hiroshi Kimura
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
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Vardabasso C, Hasson D, Ratnakumar K, Chung CY, Duarte LF, Bernstein E. Histone variants: emerging players in cancer biology. Cell Mol Life Sci 2013; 71:379-404. [PMID: 23652611 DOI: 10.1007/s00018-013-1343-z] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 04/09/2013] [Accepted: 04/11/2013] [Indexed: 01/01/2023]
Abstract
Histone variants are key players in shaping chromatin structure, and, thus, in regulating fundamental cellular processes such as chromosome segregation and gene expression. Emerging evidence points towards a role for histone variants in contributing to tumor progression, and, recently, the first cancer-associated mutation in a histone variant-encoding gene was reported. In addition, genetic alterations of the histone chaperones that specifically regulate chromatin incorporation of histone variants are rapidly being uncovered in numerous cancers. Collectively, these findings implicate histone variants as potential drivers of cancer initiation and/or progression, and, therefore, targeting histone deposition or the chromatin remodeling machinery may be of therapeutic value. Here, we review the mammalian histone variants of the H2A and H3 families in their respective cellular functions, and their involvement in tumor biology.
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Affiliation(s)
- Chiara Vardabasso
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, USA
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Abstract
Chromatin acts as an organizer and indexer of genomic DNA and is a highly dynamic and regulated structure with properties directly related to its constituent parts. Histone variants are abundant components of chromatin that replace canonical histones in a subset of nucleosomes, thereby altering nucleosomal characteristics. The present review focuses on the H2A variant histones, summarizing current knowledge of how H2A variants can introduce chemical and functional heterogeneity into chromatin, the positions that nucleosomes containing H2A variants occupy in eukaryotic genomes, and the regulation of these localization patterns.
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A combination of H2A.Z and H4 acetylation recruits Brd2 to chromatin during transcriptional activation. PLoS Genet 2012; 8:e1003047. [PMID: 23144632 PMCID: PMC3493454 DOI: 10.1371/journal.pgen.1003047] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Accepted: 09/11/2012] [Indexed: 11/19/2022] Open
Abstract
H2A.Z is an essential histone variant that has been implicated to have multiple chromosomal functions. To understand how H2A.Z participates in such diverse activities, we sought to identify downstream effector proteins that are recruited to chromatin via H2A.Z. For this purpose, we developed a nucleosome purification method to isolate H2A.Z-containing nucleosomes from human cells and used mass spectrometry to identify the co-purified nuclear proteins. Through stringent filtering, we identified the top 21 candidates, many of which have conserved structural motifs that bind post-translationally modified histones. We further validated the biological significance of one such candidate, Brd2, which is a double-bromodomain-containing protein known to function in transcriptional activation. We found that Brd2's preference for H2A.Z nucleosomes is mediated through a combination of hyperacetylated H4 on these nucleosomes, as well as additional features on H2A.Z itself. In addition, comparison of nucleosomes containing either H2A.Z-1 or H2A.Z-2 isoforms showed that significantly more Brd2 co-purifies with the former, suggesting these two isoforms engage different downstream effector proteins. Consistent with these biochemical analyses, we found that Brd2 is recruited to AR–regulated genes in an H2A.Z-dependent manner and that chemical inhibition of Brd2 recruitment greatly inhibits AR–regulated gene expression. Taken together, we propose that Brd2 is a key downstream mediator that links H2A.Z and transcriptional activation of AR–regulated genes. Moreover, this study validates the approach of using proteomics to identify nucleosome-interacting proteins in order to elucidate downstream mechanistic functions associated with the histone variant H2A.Z. Within the cell's nucleus, DNA closely associates with histone proteins, forming a structure known as chromatin. Packaging DNA into chromatin allows for efficient storage of the genome, and it also provides an additional means of regulating processes, such as gene expression, that require access to DNA. Two copies each of the four core histones (H2A, H2B, H3, H4) associate with approximately 150 base pairs of DNA to make up the basic unit of chromatin, the nucleosome. In addition to the core histones, variants exist that have specialized functions within chromatin. One such variant is H2A.Z, which is essential for cell viability. Here, we describe an approach by which to characterize proteins that interact with H2A.Z-containing nucleosomes. Our findings reveal that many of the identified proteins may interact with H2A.Z nucleosomes by recognizing specific chemical modifications uniquely present on H2A.Z nucleosomes. One such protein, Brd2, interacted in a manner dependent on recognition of acetylated histone residues that are enriched on H2A.Z nucleosomes. Furthermore, this interaction is required for expression of hormone-responsive genes in prostate cancer cells. By this approach, we uncovered a key mediator linking H2A.Z to transcriptional regulation and found a potentially targetable step to regulate prostate cell proliferation.
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Coleman-Derr D, Zilberman D. Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. PLoS Genet 2012; 8:e1002988. [PMID: 23071449 PMCID: PMC3469445 DOI: 10.1371/journal.pgen.1002988] [Citation(s) in RCA: 258] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2012] [Accepted: 08/10/2012] [Indexed: 01/07/2023] Open
Abstract
The regulation of eukaryotic chromatin relies on interactions between many epigenetic factors, including histone modifications, DNA methylation, and the incorporation of histone variants. H2A.Z, one of the most conserved but enigmatic histone variants that is enriched at the transcriptional start sites of genes, has been implicated in a variety of chromosomal processes. Recently, we reported a genome-wide anticorrelation between H2A.Z and DNA methylation, an epigenetic hallmark of heterochromatin that has also been found in the bodies of active genes in plants and animals. Here, we investigate the basis of this anticorrelation using a novel h2a.z loss-of-function line in Arabidopsis thaliana. Through genome-wide bisulfite sequencing, we demonstrate that loss of H2A.Z in Arabidopsis has only a minor effect on the level or profile of DNA methylation in genes, and we propose that the global anticorrelation between DNA methylation and H2A.Z is primarily caused by the exclusion of H2A.Z from methylated DNA. RNA sequencing and genomic mapping of H2A.Z show that H2A.Z enrichment across gene bodies, rather than at the TSS, is correlated with lower transcription levels and higher measures of gene responsiveness. Loss of H2A.Z causes misregulation of many genes that are disproportionately associated with response to environmental and developmental stimuli. We propose that H2A.Z deposition in gene bodies promotes variability in levels and patterns of gene expression, and that a major function of genic DNA methylation is to exclude H2A.Z from constitutively expressed genes. Eukaryotes package their DNA to fit within the nucleus using well-conserved proteins, called histones, that form the building blocks of nucleosomes, the fundamental units of chromatin. Histone variants are specialized versions of these proteins that change the chromatin landscape by altering the biochemical properties and interacting partners of the nucleosome. H2A.Z, a conserved eukaryotic histone variant, is preferentially enriched at the beginnings of genes, though the significance of this enrichment remains unknown. We and others have shown that H2A.Z is conspicuously absent from methylated DNA across the genome in plants and animals. Typically considered a mark of epigenetic silencing, DNA methylation has more recently been discovered in the bodies of many genes. Here, we present evidence that the genome-wide anticorrelation between DNA methylation and H2A.Z enrichment in Arabidopsis is the result of DNA methylation acting to prevent H2A.Z incorporation. We demonstrate that the presence of H2A.Z within gene bodies is correlated with lower transcription levels and higher variability in expression patterns across tissue types and environmental conditions, and we propose that a major function of gene-body DNA methylation is to exclude H2A.Z from the bodies of highly and constitutively expressed genes.
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Affiliation(s)
| | - Daniel Zilberman
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
- * E-mail:
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Bönisch C, Hake SB. Histone H2A variants in nucleosomes and chromatin: more or less stable? Nucleic Acids Res 2012; 40:10719-41. [PMID: 23002134 PMCID: PMC3510494 DOI: 10.1093/nar/gks865] [Citation(s) in RCA: 216] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
In eukaryotes, DNA is organized together with histones and non-histone proteins into a highly complex nucleoprotein structure called chromatin, with the nucleosome as its monomeric subunit. Various interconnected mechanisms regulate DNA accessibility, including replacement of canonical histones with specialized histone variants. Histone variant incorporation can lead to profound chromatin structure alterations thereby influencing a multitude of biological processes ranging from transcriptional regulation to genome stability. Among core histones, the H2A family exhibits highest sequence divergence, resulting in the largest number of variants known. Strikingly, H2A variants differ mostly in their C-terminus, including the docking domain, strategically placed at the DNA entry/exit site and implicated in interactions with the (H3–H4)2-tetramer within the nucleosome and in the L1 loop, the interaction interface of H2A–H2B dimers. Moreover, the acidic patch, important for internucleosomal contacts and higher-order chromatin structure, is altered between different H2A variants. Consequently, H2A variant incorporation has the potential to strongly regulate DNA organization on several levels resulting in meaningful biological output. Here, we review experimental evidence pinpointing towards outstanding roles of these highly variable regions of H2A family members, docking domain, L1 loop and acidic patch, and close by discussing their influence on nucleosome and higher-order chromatin structure and stability.
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Affiliation(s)
- Clemens Bönisch
- Department of Molecular Biology, Center for Integrated Protein Science Munich, Adolf-Butenandt-Institute, Ludwig-Maximilians-University Munich, 80336 Munich, Germany.
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Maruyama EO, Hori T, Tanabe H, Kitamura H, Matsuda R, Tone S, Hozak P, Habermann FA, von Hase J, Cremer C, Fukagawa T, Harata M. The actin family member Arp6 and the histone variant H2A.Z are required for spatial positioning of chromatin in chicken cell nuclei. J Cell Sci 2012; 125:3739-43. [PMID: 22573822 DOI: 10.1242/jcs.103903] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The spatial organization of chromatin in the nucleus contributes to genome function and is altered during the differentiation of normal and tumorigenic cells. Although nuclear actin-related proteins (Arps) have roles in the local alteration of chromatin structure, it is unclear whether they are involved in the spatial positioning of chromatin. In the interphase nucleus of vertebrate cells, gene-dense and gene-poor chromosome territories (CTs) are located in the center and periphery, respectively. We analyzed chicken DT40 cells in which Arp6 had been knocked out conditionally, and showed that the radial distribution of CTs was impaired in these knockout cells. Arp6 is an essential component of the SRCAP chromatin remodeling complex, which deposits the histone variant H2A.Z into chromatin. The redistribution of CTs was also observed in H2A.Z-deficient cells for gene-rich microchromosomes, but to lesser extent for gene-poor macrochromosomes. These results indicate that Arp6 and H2A.Z contribute to the radial distribution of CTs through different mechanisms. Microarray analysis suggested that the localization of chromatin to the nuclear periphery per se is insufficient for the repression of most genes.
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Affiliation(s)
- Eri Ohfuchi Maruyama
- Laboratory of Molecular Biology, Graduate School of Agricultural Science, Tohoku University, Tsutsumidori-Amamiyamachi 1-1, Aoba-ku, Sendai 981-8555, Japan
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Dryhurst D, McMullen B, Fazli L, Rennie PS, Ausió J. Histone H2A.Z prepares the prostate specific antigen (PSA) gene for androgen receptor-mediated transcription and is upregulated in a model of prostate cancer progression. Cancer Lett 2011; 315:38-47. [PMID: 22055461 DOI: 10.1016/j.canlet.2011.10.003] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Revised: 10/04/2011] [Accepted: 10/05/2011] [Indexed: 11/28/2022]
Abstract
The histone variant H2A.Z is present at many eukaryotic gene regulatory regions and can affect rates of transcription. Here we show that total H2A.Z and an acetylated form of H2A.Z is mainly present at the prostate specific antigen (PSA) enhancer and promoter in prostate cancer cell lines where the gene is expressed, but the levels decrease during rapid cycles of transcription. Treatment of prostate cancer cells with androgen results in increased H2A.Z levels due to upregulation of the H2A.Z-1, but not the H2A.Z-2 gene. This upregulation is likely the result of increased MYC transcription factor binding that occurs in response to androgen at the H2A.Z-1 promoter. Furthermore, we show that in a LNCaP xenograft model of prostate cancer progression, there is a significant increase of H2A.Z protein in castration resistant LNCaP tumors resulting from increased expression of the H2A.Z-1 gene. While a similar trend was observed in samples from prostate cancer patients, the results were not statistically significant. Nevertheless, there may be a subset of prostate cancers where elevated expression of H2A.Z-1 is indicative of prostate cancer progression to androgen independence.
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Affiliation(s)
- Deanna Dryhurst
- Department of Biochemistry and Microbiology, University of Victoria, BC, Canada.
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Chauhan S, Boyd DD. Regulation of u-PAR gene expression by H2A.Z is modulated by the MEK-ERK/AP-1 pathway. Nucleic Acids Res 2011; 40:600-13. [PMID: 21937508 PMCID: PMC3258129 DOI: 10.1093/nar/gkr725] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The urokinase receptor (u-PAR) which is largely regulated at the transcriptional level has been implicated in tumor progression. In this study, we explored the epigenetic regulation of u-PAR and showed that the histone variant H2A.Z negatively regulates its expression in multiple cell lines. Chromatin immunoprecipitation assays revealed that H2A.Z was enriched at previously characterized u-PAR-regulatory regions (promoter and a downstream enhancer) and dissociates upon activation of gene expression by phorbol ester (PMA). Using specific chemical and dominant negative expression constructs, we show that the MEK–ERK signaling pathway terminating at AP-1 transcription factors intersects with the epigenetic control of u-PAR expression by H2A.Z. Furthermore, we demonstrate that two other AP-1 targets (MMP9 gene and miR-21 microRNA) are also H2A.Z regulated. In conclusion, our work demonstrates that (i) the expression of two genes and a microRNA all implicated in tumor progression are directly regulated by H2A.Z and (ii) MEK–ERK signaling terminating at AP-1 intersects with the epigenetic control of target gene expression by H2A.Z.
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Affiliation(s)
- Santosh Chauhan
- Department of Cancer Biology, MD Anderson Cancer Center, Houston, TX 77030, USA
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Oma Y, Harata M. Actin-related proteins localized in the nucleus: from discovery to novel roles in nuclear organization. Nucleus 2011; 2:38-46. [PMID: 21647298 PMCID: PMC3104808 DOI: 10.4161/nucl.2.1.14510] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Revised: 12/15/2010] [Accepted: 12/17/2010] [Indexed: 12/18/2022] Open
Abstract
The actin family consists of conventional actin and actin-related proteins (ARPs), and the members show moderate similarity and share the same basal structure. Following the finding of various ARPs in the cytoplasm in the 1990s, multiple subfamilies that are localized predominantly in the nucleus were identified. Consistent with these cytological observations, subsequent biochemical analyses revealed the involvement of the nuclear ARPs in ATP-dependent chromatin-remodeling and histone acetyltransferase complexes. In addition to their contribution to chromatin remodeling, recent studies have shown that nuclear ARPs have roles in the organization of the nucleus that are independent of the activity of the above-mentioned complexes. Therefore, nuclear ARPs are recognized as novel key regulators of genome function, and affect not only the remodeling of chromatin but also the spatial arrangement and dynamics of chromatin within the nucleus.
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Affiliation(s)
- Yukako Oma
- Laboratory of Molecular Biology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
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