1
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Salinas-Pena M, Rebollo E, Jordan A. Imaging analysis of six human histone H1 variants reveals universal enrichment of H1.2, H1.3, and H1.5 at the nuclear periphery and nucleolar H1X presence. eLife 2024; 12:RP91306. [PMID: 38530350 DOI: 10.7554/elife.91306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024] Open
Abstract
Histone H1 participates in chromatin condensation and regulates nuclear processes. Human somatic cells may contain up to seven histone H1 variants, although their functional heterogeneity is not fully understood. Here, we have profiled the differential nuclear distribution of the somatic H1 repertoire in human cells through imaging techniques including super-resolution microscopy. H1 variants exhibit characteristic distribution patterns in both interphase and mitosis. H1.2, H1.3, and H1.5 are universally enriched at the nuclear periphery in all cell lines analyzed and co-localize with compacted DNA. H1.0 shows a less pronounced peripheral localization, with apparent variability among different cell lines. On the other hand, H1.4 and H1X are distributed throughout the nucleus, being H1X universally enriched in high-GC regions and abundant in the nucleoli. Interestingly, H1.4 and H1.0 show a more peripheral distribution in cell lines lacking H1.3 and H1.5. The differential distribution patterns of H1 suggest specific functionalities in organizing lamina-associated domains or nucleolar activity, which is further supported by a distinct response of H1X or phosphorylated H1.4 to the inhibition of ribosomal DNA transcription. Moreover, H1 variants depletion affects chromatin structure in a variant-specific manner. Concretely, H1.2 knock-down, either alone or combined, triggers a global chromatin decompaction. Overall, imaging has allowed us to distinguish H1 variants distribution beyond the segregation in two groups denoted by previous ChIP-Seq determinations. Our results support H1 variants heterogeneity and suggest that variant-specific functionality can be shared between different cell types.
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Affiliation(s)
| | - Elena Rebollo
- Molecular Biology Institute of Barcelona (IBMB-CSIC), Barcelona, Spain
| | - Albert Jordan
- Molecular Biology Institute of Barcelona (IBMB-CSIC), Barcelona, Spain
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2
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Serna-Pujol N, Salinas-Pena M, Mugianesi F, Le Dily F, Marti-Renom MA, Jordan A. Coordinated changes in gene expression, H1 variant distribution and genome 3D conformation in response to H1 depletion. Nucleic Acids Res 2022; 50:3892-3910. [PMID: 35380694 PMCID: PMC9023279 DOI: 10.1093/nar/gkac226] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 03/21/2022] [Accepted: 03/28/2022] [Indexed: 11/12/2022] Open
Abstract
Up to seven members of the histone H1 family may contribute to chromatin compaction and its regulation in human somatic cells. In breast cancer cells, knock-down of multiple H1 variants deregulates many genes, promotes the appearance of genome-wide accessibility sites and triggers an interferon response via activation of heterochromatic repeats. However, how these changes in the expression profile relate to the re-distribution of H1 variants as well as to genome conformational changes have not been yet studied. Here, we combined ChIP-seq of five endogenous H1 variants with Chromosome Conformation Capture analysis in wild-type and H1.2/H1.4 knock-down T47D cells. The results indicate that H1 variants coexist in the genome in two large groups depending on the local GC content and that their distribution is robust with respect to H1 depletion. Despite the small changes in H1 variants distribution, knock-down of H1 translated into more isolated but de-compacted chromatin structures at the scale of topologically associating domains (TADs). Such changes in TAD structure correlated with a coordinated gene expression response of their resident genes. This is the first report describing simultaneous profiling of five endogenous H1 variants and giving functional evidence of genome topology alterations upon H1 depletion in human cancer cells.
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Affiliation(s)
- Núria Serna-Pujol
- Molecular Biology Institute of Barcelona (IBMB-CSIC), Barcelona, 08028 Spain
| | - Mónica Salinas-Pena
- Molecular Biology Institute of Barcelona (IBMB-CSIC), Barcelona, 08028 Spain
| | - Francesca Mugianesi
- CNAG-CRG, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona 08028, Spain
| | - François Le Dily
- Centre for Genomic Regulation, The Barcelona Institute for Science and Technology, Carrer del Doctor Aiguader 88, Barcelona 08003, Spain
| | - Marc A Marti-Renom
- CNAG-CRG, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona 08028, Spain.,Centre for Genomic Regulation, The Barcelona Institute for Science and Technology, Carrer del Doctor Aiguader 88, Barcelona 08003, Spain.,Pompeu Fabra University, Doctor Aiguader 88, Barcelona 08003, Spain.,ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Albert Jordan
- Molecular Biology Institute of Barcelona (IBMB-CSIC), Barcelona, 08028 Spain
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3
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Abstract
In this review, Prendergast and Reinberg discuss the likelihood that the family of histone H1 variants may be key to understanding several fundamental processes in chromatin biology and underscore their particular contributions to distinctly significant chromatin-related processes. Major advances in the chromatin and epigenetics fields have uncovered the importance of core histones, histone variants and their post-translational modifications (PTMs) in modulating chromatin structure. However, an acutely understudied related feature of chromatin structure is the role of linker histone H1. Previous assumptions of the functional redundancy of the 11 nonallelic H1 variants are contrasted by their strong evolutionary conservation, variability in their potential PTMs, and increased reports of their disparate functions, sub-nuclear localizations and unique expression patterns in different cell types. The commonly accepted notion that histone H1 functions solely in chromatin compaction and transcription repression is now being challenged by work from multiple groups. These studies highlight histone H1 variants as underappreciated facets of chromatin dynamics that function independently in various chromatin-based processes. In this review, we present notable findings involving the individual somatic H1 variants of which there are seven, underscoring their particular contributions to distinctly significant chromatin-related processes.
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Affiliation(s)
- Laura Prendergast
- Howard Hughes Medical Institute, New York University Langone Health, New York, New York 10016, USA.,Department of Biochemistry and Molecular Pharmacology, New York University Langone Medical School, New York, New York 10016, USA
| | - Danny Reinberg
- Howard Hughes Medical Institute, New York University Langone Health, New York, New York 10016, USA.,Department of Biochemistry and Molecular Pharmacology, New York University Langone Medical School, New York, New York 10016, USA
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4
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Fernández-Ponce C, Durán-Ruiz MC, Narbona-Sánchez I, Muñoz-Miranda JP, Arbulo-Echevarria MM, Serna-Sanz A, Baumann C, Litrán R, Aguado E, Bloch W, García-Cozar F. Ultrastructural Localization and Molecular Associations of HCV Capsid Protein in Jurkat T Cells. Front Microbiol 2018; 8:2595. [PMID: 29354102 PMCID: PMC5758585 DOI: 10.3389/fmicb.2017.02595] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 12/12/2017] [Indexed: 12/24/2022] Open
Abstract
Hepatitis C virus core protein is a highly basic viral protein that multimerizes with itself to form the viral capsid. When expressed in CD4+ T lymphocytes, it can induce modifications in several essential cellular and biological networks. To shed light on the mechanisms underlying the alterations caused by the viral protein, we have analyzed HCV-core subcellular localization and its associations with host proteins in Jurkat T cells. In order to investigate the intracellular localization of Hepatitis C virus core protein, we have used a lentiviral system to transduce Jurkat T cells and subsequently localize the protein using immunoelectron microscopy techniques. We found that in Jurkat T cells, Hepatitis C virus core protein mostly localizes in the nucleus and specifically in the nucleolus. In addition, we performed pull-down assays combined with Mass Spectrometry Analysis, to identify proteins that associate with Hepatitis C virus core in Jurkat T cells. We found proteins such as NOLC1, PP1γ, ILF3, and C1QBP implicated in localization and/or traffic to the nucleolus. HCV-core associated proteins are implicated in RNA processing and RNA virus infection as well as in functions previously shown to be altered in Hepatitis C virus core expressing CD4+ T cells, such as cell cycle delay, decreased proliferation, and induction of a regulatory phenotype. Thus, in the current work, we show the ultrastructural localization of Hepatitis C virus core and the first profile of HCV core associated proteins in T cells, and we discuss the functions and interconnections of these proteins in molecular networks where relevant biological modifications have been described upon the expression of Hepatitis C virus core protein. Thereby, the current work constitutes a necessary step toward understanding the mechanisms underlying HCV core mediated alterations that had been described in relevant biological processes in CD4+ T cells.
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Affiliation(s)
- Cecilia Fernández-Ponce
- Department of Biomedicine, Biotechnology and Public Health, University of Cadiz and Institute of Biomedical Research Cádiz (INIBICA), Cadiz, Spain
| | - Maria C Durán-Ruiz
- Department of Biomedicine, Biotechnology and Public Health, University of Cadiz and Institute of Biomedical Research Cádiz (INIBICA), Cadiz, Spain
| | - Isaac Narbona-Sánchez
- Department of Biomedicine, Biotechnology and Public Health, University of Cadiz and Institute of Biomedical Research Cádiz (INIBICA), Cadiz, Spain
| | - Juan P Muñoz-Miranda
- Department of Biomedicine, Biotechnology and Public Health, University of Cadiz and Institute of Biomedical Research Cádiz (INIBICA), Cadiz, Spain
| | - Mikel M Arbulo-Echevarria
- Department of Biomedicine, Biotechnology and Public Health, University of Cadiz and Institute of Biomedical Research Cádiz (INIBICA), Cadiz, Spain
| | | | | | - Rocío Litrán
- Department of Condensed Matter Physics, University of Cádiz, Puerto Real, Spain
| | - Enrique Aguado
- Department of Biomedicine, Biotechnology and Public Health, University of Cadiz and Institute of Biomedical Research Cádiz (INIBICA), Cadiz, Spain
| | - Wilhelm Bloch
- Department of Molecular and Cellular Sport Medicine, Institute of Cardiovascular Research and Sport Medicine, German Sport University Cologne, Cologne, Germany
| | - Francisco García-Cozar
- Department of Biomedicine, Biotechnology and Public Health, University of Cadiz and Institute of Biomedical Research Cádiz (INIBICA), Cadiz, Spain
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5
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Izzo A, Ziegler-Birling C, Hill PWS, Brondani L, Hajkova P, Torres-Padilla ME, Schneider R. Dynamic changes in H1 subtype composition during epigenetic reprogramming. J Cell Biol 2017; 216:3017-3028. [PMID: 28794128 PMCID: PMC5626532 DOI: 10.1083/jcb.201611012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 05/30/2017] [Accepted: 07/07/2017] [Indexed: 12/13/2022] Open
Abstract
In mammals, the histone H1 family includes five somatic replication-dependent (H1.1–H1.5) and two replication-independent (H1.10 and H1.0) subtypes. Izzo et al. analyze the contributions of all somatic H1 subtypes to the chromatin landscape during reprogramming in preimplantation embryo and primordial germ cell development. In mammals, histone H1 consists of a family of related proteins, including five replication-dependent (H1.1–H1.5) and two replication-independent (H1.10 and H1.0) subtypes, all expressed in somatic cells. To systematically study the expression and function of H1 subtypes, we generated knockin mouse lines in which endogenous H1 subtypes are tagged. We focused on key developmental periods when epigenetic reprogramming occurs: early mouse embryos and primordial germ cell development. We found that dynamic changes in H1 subtype expression and localization are tightly linked with chromatin remodeling and might be crucial for transitions in chromatin structure during reprogramming. Although all somatic H1 subtypes are present in the blastocyst, each stage of preimplantation development is characterized by a different combination of H1 subtypes. Similarly, the relative abundance of somatic H1 subtypes can distinguish male and female chromatin upon sex differentiation in developing germ cells. Overall, our data provide new insights into the chromatin changes underlying epigenetic reprogramming. We suggest that distinct H1 subtypes may mediate the extensive chromatin remodeling occurring during epigenetic reprogramming and that they may be key players in the acquisition of cellular totipotency and the establishment of specific cellular states.
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Affiliation(s)
- Annalisa Izzo
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany.,Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Illkirch, France
| | - Céline Ziegler-Birling
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Illkirch, France
| | - Peter W S Hill
- Hammersmith Hospital Campus, Medical Research Council London Institute of Medical Sciences, London, England, UK.,Institute of Clinical Sciences, Hammersmith Hospital Campus, Imperial College Faculty of Medicine, London, England, UK
| | - Lydia Brondani
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Illkirch, France
| | - Petra Hajkova
- Hammersmith Hospital Campus, Medical Research Council London Institute of Medical Sciences, London, England, UK.,Institute of Clinical Sciences, Hammersmith Hospital Campus, Imperial College Faculty of Medicine, London, England, UK
| | - Maria-Elena Torres-Padilla
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Neuherberg, Germany .,Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Illkirch, France
| | - Robert Schneider
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany .,Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Illkirch, France
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6
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Ichihara-Tanaka K, Kadomatsu K, Kishida S. Temporally and Spatially Regulated Expression of the Linker Histone H1fx During Mouse Development. J Histochem Cytochem 2017; 65:513-530. [PMID: 28766996 DOI: 10.1369/0022155417723914] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The linker histone H1fx is the least characterized member of the H1 family. To investigate the developmental changes of H1fx, we performed an immunohistochemical analysis of its expression pattern from embryos to adult mice. We found that H1fx was highly expressed during gastrulation, and was positive in all embryonic germ layers between E8.5 and E10.5, which mostly overlapped with the expression of the proliferation marker Ki-67. Neural and mesenchyme tissues strongly expressed H1fx at E10.5. H1fx expression began to be restricted at around E12.5. Western blot analysis of brain tissues demonstrated that the total expression level of H1fx gradually decreased with time from E12.5 to adulthood, whereas H1f0 was increased over this period. In adult mice, H1fx was restrictively expressed at the hypothalamus, subventricular zone, subgranular zone, medulla of the adrenal grand, islets of Langerhans, and myenteric plexus. Taken together, these data suggest that H1fx is preferentially expressed in immature embryonic cells and plays some roles in cells with neural properties.
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Affiliation(s)
- Keiko Ichihara-Tanaka
- Department of Health and Nutrition, Faculty of Psychological and Physical Science, Aichi Gakuin University, Aichi, Japan (KI-T).,Department of Biochemistry, Nagoya University Graduate School of Medicine, Nagoya, Japan (KI-T, KK, SK)
| | - Kenji Kadomatsu
- Department of Biochemistry, Nagoya University Graduate School of Medicine, Nagoya, Japan (KI-T, KK, SK)
| | - Satoshi Kishida
- Department of Biochemistry, Nagoya University Graduate School of Medicine, Nagoya, Japan (KI-T, KK, SK)
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7
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Regulation of Cellular Dynamics and Chromosomal Binding Site Preference of Linker Histones H1.0 and H1.X. Mol Cell Biol 2016; 36:2681-2696. [PMID: 27528617 DOI: 10.1128/mcb.00200-16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Accepted: 08/08/2016] [Indexed: 01/01/2023] Open
Abstract
Linker histones play important roles in the genomic organization of mammalian cells. Of the linker histone variants, H1.X shows the most dynamic behavior in the nucleus. Recent research has suggested that the linker histone variants H1.X and H1.0 have different chromosomal binding site preferences. However, it remains unclear how the dynamics and binding site preferences of linker histones are determined. Here, we biochemically demonstrated that the DNA/nucleosome and histone chaperone binding activities of H1.X are significantly lower than those of other linker histones. This explains why H1.X moves more rapidly than other linker histones in vivo Domain swapping between H1.0 and H1.X suggests that the globular domain (GD) and C-terminal domain (CTD) of H1.X independently contribute to the dynamic behavior of H1.X. Our results also suggest that the N-terminal domain (NTD), GD, and CTD cooperatively determine the preferential binding sites, and the contribution of each domain for this determination is different depending on the target genes. We also found that linker histones accumulate in the nucleoli when the nucleosome binding activities of the GDs are weak. Our results contribute to understanding the molecular mechanisms of dynamic behaviors, binding site selection, and localization of linker histones.
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8
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Kowalski A, Pałyga J. Modulation of chromatin function through linker histone H1 variants. Biol Cell 2016; 108:339-356. [PMID: 27412812 DOI: 10.1111/boc.201600007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 07/08/2016] [Accepted: 07/08/2016] [Indexed: 12/30/2022]
Abstract
In this review, the structural aspects of linker H1 histones are presented as a background for characterization of the factors influencing their function in animal and human chromatin. The action of H1 histone variants is largely determined by dynamic alterations of their intrinsically disordered tail domains, posttranslational modifications and allelic diversification. The interdependent effects of these factors can establish dynamic histone H1 states that may affect the organization and function of chromatin regions.
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Affiliation(s)
- Andrzej Kowalski
- Department of Biochemistry and Genetics, Institute of Biology, Jan Kochanowski University, 25-406 Kielce, Poland
| | - Jan Pałyga
- Department of Biochemistry and Genetics, Institute of Biology, Jan Kochanowski University, 25-406 Kielce, Poland
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9
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Pirlot C, Thiry M, Trussart C, Di Valentin E, Piette J, Habraken Y. Melanoma antigen-D2: A nucleolar protein undergoing delocalization during cell cycle and after cellular stress. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:581-95. [DOI: 10.1016/j.bbamcr.2015.12.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 12/11/2015] [Accepted: 12/15/2015] [Indexed: 12/25/2022]
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10
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Abstract
H1T is a linker histone H1 variant that is highly expressed at the primary spermatocyte stage through to the early spermatid stage of spermatogenesis. While the functions of the somatic types of H1 have been extensively investigated, the intracellular role of H1T is unclear. H1 variants specifically expressed in germ cells show low amino acid sequence homology to somatic H1s, which suggests that the functions or target loci of germ cell-specific H1T differ from those of somatic H1s. Here, we describe the target loci and function of H1T. H1T was expressed not only in the testis but also in tumor cell lines, mouse embryonic stem cells (mESCs), and some normal somatic cells. To elucidate the intracellular localization and target loci of H1T, fluorescent immunostaining and ChIP-seq were performed in tumor cells and mESCs. We found that H1T accumulated in nucleoli and predominantly targeted rDNA repeats, which differ from somatic H1 targets. Furthermore, by nuclease sensitivity assay and RT-qPCR, we showed that H1T repressed rDNA transcription by condensing chromatin structure. Imaging analysis indicated that H1T expression affected nucleolar formation. We concluded that H1T plays a role in rDNA transcription, by distinctively targeting rDNA repeats.
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Affiliation(s)
- Ruiko Tani
- a Department of Animal Resource Sciences/Veterinary Medical Sciences , The University of Tokyo , Bunkyo-ku, Tokyo , Japan
| | - Koji Hayakawa
- a Department of Animal Resource Sciences/Veterinary Medical Sciences , The University of Tokyo , Bunkyo-ku, Tokyo , Japan
| | - Satoshi Tanaka
- a Department of Animal Resource Sciences/Veterinary Medical Sciences , The University of Tokyo , Bunkyo-ku, Tokyo , Japan
| | - Kunio Shiota
- a Department of Animal Resource Sciences/Veterinary Medical Sciences , The University of Tokyo , Bunkyo-ku, Tokyo , Japan
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11
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Millán-Ariño L, Izquierdo-Bouldstridge A, Jordan A. Specificities and genomic distribution of somatic mammalian histone H1 subtypes. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:510-9. [DOI: 10.1016/j.bbagrm.2015.10.013] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 10/13/2015] [Accepted: 10/14/2015] [Indexed: 11/15/2022]
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12
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Pan C, Fan Y. Role of H1 linker histones in mammalian development and stem cell differentiation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:496-509. [PMID: 26689747 DOI: 10.1016/j.bbagrm.2015.12.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 12/09/2015] [Accepted: 12/09/2015] [Indexed: 12/19/2022]
Abstract
H1 linker histones are key chromatin architectural proteins facilitating the formation of higher order chromatin structures. The H1 family constitutes the most heterogeneous group of histone proteins, with eleven non-allelic H1 variants in mammals. H1 variants differ in their biochemical properties and exhibit significant sequence divergence from one another, yet most of them are highly conserved during evolution from mouse to human. H1 variants are differentially regulated during development and their cellular compositions undergo dramatic changes in embryogenesis, gametogenesis, tissue maturation and cellular differentiation. As a group, H1 histones are essential for mouse development and proper stem cell differentiation. Here we summarize our current knowledge on the expression and functions of H1 variants in mammalian development and stem cell differentiation. Their diversity, sequence conservation, complex expression and distinct functions suggest that H1s mediate chromatin reprogramming and contribute to the large variations and complexity of chromatin structure and gene expression in the mammalian genome.
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Affiliation(s)
- Chenyi Pan
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA; The Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Yuhong Fan
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA; The Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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13
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Parseghian MH. What is the role of histone H1 heterogeneity? A functional model emerges from a 50 year mystery. AIMS BIOPHYSICS 2015; 2:724-772. [PMID: 31289748 PMCID: PMC6615755 DOI: 10.3934/biophy.2015.4.724] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
For the past 50 years, understanding the function of histone H1 heterogeneity has been mired in confusion and contradiction. Part of the reason for this is the lack of a working model that tries to explain the large body of data that has been collected about the H1 subtypes so far. In this review, a global model is described largely based on published data from the author and other researchers over the past 20 years. The intrinsic disorder built into H1 protein structure is discussed to help the reader understand that these histones are multi-conformational and adaptable to interactions with different targets. We discuss the role of each structural section of H1 (as we currently understand it), but we focus on the H1's C-terminal domain and its effect on each subtype's affinity, mobility and compaction of chromatin. We review the multiple ways these characteristics have been measured from circular dichroism to FRAP analysis, which has added to the sometimes contradictory assumptions made about each subtype. Based on a tabulation of these measurements, we then organize the H1 variants according to their ability to condense chromatin and produce nucleosome repeat lengths amenable to that compaction. This subtype variation generates a continuum of different chromatin states allowing for fine regulatory control and some overlap in the event one or two subtypes are lost to mutation. We also review the myriad of disparate observations made about each subtype, both somatic and germline specific ones, that lend support to the proposed model. Finally, to demonstrate its adaptability as new data further refines our understanding of H1 subtypes, we show how the model can be applied to experimental observations of telomeric heterochromatin in aging cells.
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14
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Mayor R, Izquierdo-Bouldstridge A, Millán-Ariño L, Bustillos A, Sampaio C, Luque N, Jordan A. Genome distribution of replication-independent histone H1 variants shows H1.0 associated with nucleolar domains and H1X associated with RNA polymerase II-enriched regions. J Biol Chem 2015; 290:7474-91. [PMID: 25645921 DOI: 10.1074/jbc.m114.617324] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Unlike core histones, the linker histone H1 family is more evolutionarily diverse, and many organisms have multiple H1 variants or subtypes. In mammals, the H1 family includes seven somatic H1 variants; H1.1 to H1.5 are expressed in a replication-dependent manner, whereas H1.0 and H1X are replication-independent. Using ChIP-sequencing data and cell fractionation, we have compared the genomic distribution of H1.0 and H1X in human breast cancer cells, in which we previously observed differential distribution of H1.2 compared with the other subtypes. We have found H1.0 to be enriched at nucleolus-associated DNA repeats and chromatin domains, whereas H1X is associated with coding regions, RNA polymerase II-enriched regions, and hypomethylated CpG islands. Further, H1X accumulates within constitutive or included exons and retained introns and toward the 3' end of expressed genes. Inducible H1X knockdown does not affect cell proliferation but dysregulates a subset of genes related to cell movement and transport. In H1X-depleted cells, the promoters of up-regulated genes are not occupied specifically by this variant, have a lower than average H1 content, and, unexpectedly, do not form an H1 valley upon induction. We conclude that H1 variants are not distributed evenly across the genome and may participate with some specificity in chromatin domain organization or gene regulation.
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Affiliation(s)
- Regina Mayor
- From the Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona, Catalonia 08028 Spain
| | - Andrea Izquierdo-Bouldstridge
- From the Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona, Catalonia 08028 Spain
| | - Lluís Millán-Ariño
- From the Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona, Catalonia 08028 Spain
| | - Alberto Bustillos
- From the Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona, Catalonia 08028 Spain
| | - Cristina Sampaio
- From the Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona, Catalonia 08028 Spain
| | - Neus Luque
- From the Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona, Catalonia 08028 Spain
| | - Albert Jordan
- From the Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona, Catalonia 08028 Spain
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15
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Liu J, Wang H, Ma F, Xu D, Chang Y, Zhang J, Wang J, Zhao M, Lin C, Huang C, Qian H, Zhan Q. MTA1 regulates higher-order chromatin structure and histone H1-chromatin interaction in-vivo. Mol Oncol 2015; 9:218-35. [PMID: 25205035 PMCID: PMC5528677 DOI: 10.1016/j.molonc.2014.08.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 08/04/2014] [Accepted: 08/18/2014] [Indexed: 11/27/2022] Open
Abstract
In the current study, for the first time, we found that metastasis-associated gene 1 (MTA1) was a higher-order chromatin structure organizer that decondenses the interphase chromatin and mitotic chromosomes. MTA1 interacts dynamically with nucleosomes during the cell cycle progression, prominently contributing to the mitotic chromatin/chromosome structure transitions at both prophase and telophase. We showed that the decondensation of interphase chromatin by MTA1 was independent of Mi-2 chromatin remodeling activity. H1 was reported to stabilize the compact higher-order chromatin structure through its interaction with DNA. Our data showed that MTA1 caused a reduced H1-chromatin interaction in-vivo. Moreover, the dynamic MTA1-chromatin interaction in the cell cycle contributed to the periodical H1-chromatin interaction, which in turn modulated chromatin/chromosome transitions. Although MTA1 drove a global decondensation of chromatin structure, it changed the expression of only a small proportion of genes. After MTA1 overexpression, the up-regulated genes were distributed in clusters along with down-regulated genes on chromosomes at parallel frequencies.
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Affiliation(s)
- Jian Liu
- State Key Laboratory of Molecular Oncology, Cancer Institute/Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100021, China; Medical Research Center, Beijing ChaoYang Hospital, Capital Medical University, Beijing 100020, China
| | - Haijuan Wang
- State Key Laboratory of Molecular Oncology, Cancer Institute/Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100021, China
| | - Fei Ma
- Department of Medical Oncology, Cancer Institute/Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, State Key Laboratory of Molecular Oncology, Beijing 100021, China
| | - Dongkui Xu
- Department of Abdominal Surgery, Cancer Institute/Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, State Key Laboratory of Molecular Oncology, Beijing 100021, China
| | - Yanan Chang
- State Key Laboratory of Molecular Oncology, Cancer Institute/Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100021, China
| | - Jinlong Zhang
- State Key Laboratory of Molecular Oncology, Cancer Institute/Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100021, China
| | - Jia Wang
- State Key Laboratory of Molecular Oncology, Cancer Institute/Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100021, China
| | - Mei Zhao
- State Key Laboratory of Molecular Oncology, Cancer Institute/Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100021, China
| | - Chen Lin
- State Key Laboratory of Molecular Oncology, Cancer Institute/Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100021, China
| | - Changzhi Huang
- State Key Laboratory of Molecular Oncology, Cancer Institute/Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100021, China.
| | - Haili Qian
- State Key Laboratory of Molecular Oncology, Cancer Institute/Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100021, China.
| | - Qimin Zhan
- State Key Laboratory of Molecular Oncology, Cancer Institute/Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100021, China.
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16
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Biterge B, Schneider R. Histone variants: key players of chromatin. Cell Tissue Res 2014; 356:457-66. [PMID: 24781148 DOI: 10.1007/s00441-014-1862-4] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 02/27/2014] [Indexed: 01/01/2023]
Abstract
Histones are fundamental structural components of chromatin. Eukaryotic DNA is wound around an octamer of the core histones H2A, H2B, H3, and H4. Binding of linker histone H1 promotes higher order chromatin organization. In addition to their structural role, histones impact chromatin function and dynamics by, e.g., post-translational histone modifications or the presence of specific histone variants. Histone variants exhibit differential expression timings (DNA replication-independent) and mRNA characteristics compared to canonical histones. Replacement of canonical histones with histone variants can affect nucleosome stability and help to create functionally distinct chromatin domains. In line with this, several histone variants have been implicated in the regulation of cellular processes such as DNA repair and transcriptional activity. In this review, we focus on recent progress in the study of core histone variants H2A.X, H2A.Z, macroH2A, H3.3, and CENP-A, as well as linker histone H1 variants, their functions and their links to development and disease.
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Affiliation(s)
- Burcu Biterge
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS UMR 7104, INSERM U 964, Université de Strasbourg, 67404, Illkirch, France
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17
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Prévost M, Chamousset D, Nasa I, Freele E, Morrice N, Moorhead G, Trinkle-Mulcahy L. Quantitative fragmentome mapping reveals novel, domain-specific partners for the modular protein RepoMan (recruits PP1 onto mitotic chromatin at anaphase). Mol Cell Proteomics 2013; 12:1468-86. [PMID: 23362328 DOI: 10.1074/mcp.m112.023291] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
RepoMan is a protein phosphatase 1 (PP1) regulatory subunit that targets the phosphatase to key substrates throughout the cell cycle. Most work to date has focused on the mitotic roles of RepoMan/PP1, although equally important interphase role(s) have been demonstrated. Initial mapping of the interactome of nuclear RepoMan, both endogenous and tagged, was complicated by various factors, including antibody cross-reactivity and low sensitivity of the detection of chromatin-associated partners above the high background of proteins that bind nonspecifically to affinity matrices. We therefore adapted the powerful combination of fluorescence imaging with labeling-based quantitative proteomics to map the "fragmentomes" of specific regions of RepoMan. These regions demonstrate distinct localization patterns and turnover dynamics that reflect underlying binding events. The increased sensitivity and signal-to-noise ratio provided by this unique approach facilitated identification of a large number of novel RepoMan interactors, several of which were rigorously validated in follow-up experiments, including the association of RepoMan/PP1 with a specific PP2A-B56γ complex, interaction with ribosomal proteins and import factors involved in their nucleocytoplasmic transport and interaction with proteins involved in the response to DNA damage. This same strategy can be used to investigate the cellular roles of other modular proteins.
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Affiliation(s)
- Michèle Prévost
- Department of Cellular and Molecular Medicine and Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
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18
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Leljak Levanić D, Horvat T, Martinčić J, Bauer N. A novel bipartite nuclear localization signal guides BPM1 protein to nucleolus suggesting its Cullin3 independent function. PLoS One 2012; 7:e51184. [PMID: 23251450 PMCID: PMC3519589 DOI: 10.1371/journal.pone.0051184] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Accepted: 10/31/2012] [Indexed: 01/12/2023] Open
Abstract
BPM1 belongs to the MATH-BTB family of proteins, which act as substrate-binding adaptors for the Cullin3-based E3 ubiquitin ligase. MATH-BTB proteins associate with Cullin3 via the BTB domain and with the substrate protein via the MATH domain. Few BPM1-interacting proteins with different functions are recognized, however, specific roles of BPM1, depending on its cellular localization have not been studied so far. Here, we found a novel bipartite nuclear localization signal at the C-terminus of the BPM1 protein, responsible for its nuclear and nucleolar localization and sufficient to drive the green fluorescent protein and cytoplasmic BPM4 protein into the nucleus. Co-localization analysis in live Nicotiana tabacum BY2 cells indicates a Cullin3 independent function since BPM1 localization is predominantly nucleolar and thus devoid of Cullin3. Treatment of BY2 cells with the proteasome inhibitor MG132 blocks BPM1 and Cullin3 degradation, suggesting turnover of both proteins through the ubiquitin-proteasome pathway. Possible roles of BPM1 in relation to its in vivo localization are discussed.
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Affiliation(s)
- Dunja Leljak Levanić
- Department of Molecular Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Tomislav Horvat
- Department of Molecular Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Jelena Martinčić
- Department of Molecular Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Nataša Bauer
- Department of Molecular Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
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19
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Nucleophosmin is essential for c-Myc nucleolar localization and c-Myc-mediated rDNA transcription. Oncogene 2012; 32:1988-94. [PMID: 22665062 DOI: 10.1038/onc.2012.227] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The transcription factor c-Myc has a critical role in cell proliferation and growth. The control of ribosome biogenesis by c-Myc through the regulation of transcription mediated by all three RNA polymerases is essential for c-Myc-driven proliferation. Specifically, in the nucleolus, c-Myc has been shown to be recruited to ribosomal DNA and activate RNA polymerase (pol) I-mediated transcription of ribosomal RNA (rRNA) genes. In addition, c-Myc accumulates in nucleoli upon inhibition of the proteasome, suggesting nucleolar localization also has a role in c-Myc proteolysis. Nucleophosmin (NPM), a predominantly nucleolar protein, is also critical in ribosome biogenesis and, like c-Myc, is found overexpressed in many types of tumors. Previously, we demonstrated that NPM directly interacts with c-Myc and controls c-Myc-induced hyperproliferation and transformation. Here, we show that NPM is necessary for the localization of c-Myc protein to nucleoli, whereas c-Myc nucleolar localization is independent of p53, Mdm2 and ARF. Conversely, high transient NPM expression enhances c-Myc nucleolar localization, leading to increased c-Myc proteolysis. In addition, NPM is necessary for the ability of c-Myc to induce rRNA synthesis in the nucleolus, and constitutive NPM overexpression stimulates c-Myc-mediated rRNA synthesis. Taken together, these results demonstrate an essential role for NPM in c-Myc nucleolar localization and c-Myc-mediated rDNA transcription.
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20
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Medrzycki M, Zhang Y, McDonald JF, Fan Y. Profiling of linker histone variants in ovarian cancer. FRONT BIOSCI-LANDMRK 2012; 17:396-406. [PMID: 22201751 DOI: 10.2741/3934] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
H1 linker histones play a key role in facilitating higher order chromatin folding. Emerging evidence suggests that H1 and its multiple variants are important epigenetic factors in modulating chromatin function and gene expression. Ovarian cancer is a devastating disease, ranking the fifth leading cause of all women cancer death due to its poor prognosis and difficulty in early diagnosis. Although epigenetic alterations in ovarian cancers are being appreciated in general, the role of H1 has not been explored. Here, using quantitative RT-PCR assays, we systematically examined the expression of 7 H1 genes in 33 human epithelial ovarian tumors. Whereas the expression of H1.3 was markedly increased, the expression of H10, H1.1, H1.4 and H1x were significantly reduced in malignant adenocarcinomas compared with benign adenomas. Strikingly, ovarian adenocarcinomas and adenomas exhibited characteristic expression patterns, and expression profiling of 7 H1 genes in tumor samples discriminated adenocarcinomas vs. adenomas with high accuracy. These findings indicate that the expression of H1 variants is exquisitely regulated and may serve as potential epigenetic biomarkers for ovarian cancer.
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Affiliation(s)
- Magdalena Medrzycki
- School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30332, USA
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21
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Kar B, Liu B, Zhou Z, Lam YW. Quantitative nucleolar proteomics reveals nuclear re-organization during stress- induced senescence in mouse fibroblast. BMC Cell Biol 2011; 12:33. [PMID: 21835027 PMCID: PMC3163619 DOI: 10.1186/1471-2121-12-33] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Accepted: 08/11/2011] [Indexed: 12/21/2022] Open
Abstract
Background Nucleolus is the most prominent mammalian organelle within the nucleus which is also the site for ribosomal biogenesis. There have been many reports indicating the involvement of nucleolus in the process of aging. Several proteins related to aging have been shown to localize in the nucleolus, which suggests the role of this organelle in senescence. Results In this study, we used quantitative mass spectrometry to map the flux of proteins into and out of the nucleolus during the induction of senescence in cultured mammalian cells. Changes in the abundance of 344 nucleolar proteins in sodium butyrate-induced senescence in NIH3T3 cells were studied by SILAC (stable isotope labeling by amino acids in cell culture)-based mass spectrometry. Biochemically, we have validated the proteomic results and confirmed that B23 (nucleophosmin) protein was down-regulated, while poly (ADP-ribose) polymerase (PARP) and nuclear DNA helicase II (NDH II/DHX9/RHA) were up-regulated in the nucleolus upon treatment with sodium butyrate. Accumulation of chromatin in the nucleolus was also observed, by both proteomics and microscopy, in sodium butyrate-treated cells. Similar observations were found in other models of senescence, namely, in mitoxantrone- (MTX) treated cells and primary fibroblasts from the Lamin A knockout mice. Conclusion Our data indicate an extensive nuclear organization during senescence and suggest that the redistribution of B23 protein and chromatin can be used as an important marker for senescence.
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Affiliation(s)
- Bishnupriya Kar
- Department of Biology and Chemistry, City University of Hong Kong, 88 Tat Chee Avenue, Hong Kong.
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22
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Gu Z, Zhou L, Gao S, Wang Z. Nuclear transport signals control cellular localization and function of androgen receptor cofactor p44/WDR77. PLoS One 2011; 6:e22395. [PMID: 21789256 PMCID: PMC3137635 DOI: 10.1371/journal.pone.0022395] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Accepted: 06/20/2011] [Indexed: 12/26/2022] Open
Abstract
The androgen receptor (AR) cofactor p44/WDR77, which regulates expression of a set of androgen target genes, is required for differentiation of prostate epithelium. Aberrant localization of p44/WDR77 in the cytoplasm is associated with prostate tumorigenesis. Here, we describe studies that used the mouse prostate and human prostate cancer cells as model systems to investigate signals that control subcellular localization of p44/WDR77. We observed distinct subcellular location of p44/WDR77 during prostate development. p44/WDR77 localizes in the cytoplasm at the early stage of prostate development, when prostate epithelial cells are rapidly proliferating, and in the nucleus in adult prostate, when epithelial cells are fully differentiated. Subcellular localization assays designed to span the entire open-reading frame of p44/WDR77 protein revealed the presence of two nuclear exclusion signal (NES) and three nuclear localization signal (NLS) sequences in the p44/WDR77 protein. Site-directed mutagenesis of critical residues within an NLS led to loss of nuclear localization and transcriptional activity of p44/WDR77, suggesting that nuclear localization of p44/WDR77 is essential for its function as a transcriptional cofactor for AR. Three identified NLS were not functional in AR-positive prostate cancer (LNCaP and 22RV1) cells, which led to localization of p44/WDR77 in cytoplasm. The function of NLS in LNCaP cells could be restored by factor(s) from Cos 7 or PC3 cells. Mass spectrometric (MALDI-TOF/TOF) analysis identified proteins associated with an NLS and an NES in prostate cancer cells. These results provide a basis for understanding subcellular transport of p44/WDR77 during prostate development and tumorigenesis.
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Affiliation(s)
- Zhongping Gu
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Liran Zhou
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Shen Gao
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Zhengxin Wang
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- * E-mail:
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23
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Sharma K, Åkerström S, Sharma AK, Chow VTK, Teow S, Abrenica B, Booth SA, Booth TF, Mirazimi A, Lal SK. SARS-CoV 9b protein diffuses into nucleus, undergoes active Crm1 mediated nucleocytoplasmic export and triggers apoptosis when retained in the nucleus. PLoS One 2011; 6:e19436. [PMID: 21637748 PMCID: PMC3103500 DOI: 10.1371/journal.pone.0019436] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Accepted: 04/06/2011] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND 9b is an accessory protein of the SARS-CoV. It is a small protein of 98 amino acids and its structure has been solved recently. 9b is known to localize in the extra-nuclear region and has been postulated to possess a nuclear export signal (NES), however the role of NES in 9b functioning is not well understood. PRINCIPAL FINDINGS/METHODOLOGY In this report, we demonstrate that 9b in the absence of any nuclear localization signal (NLS) enters the nucleus by passive transport. Using various cell cycle inhibitors, we have shown that the nuclear entry of 9b is independent of the cell cycle. Further, we found that 9b interacts with the cellular protein Crm1 and gets exported out of the nucleus using an active NES. We have also revealed that this NES activity influences the half-life of 9b and affects host cell death. We found that an export signal deficient SARS-CoV 9b protein induces apoptosis in transiently transfected cells and showed elevated caspase-3 activity. CONCLUSION/SIGNIFICANCE Here, we showed that nuclear shuttling of 9b and its interaction with Crm1 are essential for the proper degradation of 9b and blocking the nuclear export of this protein induces apoptosis. This phenomenon may be critical in providing a novel role to the 9b accessory protein of SARS-CoV.
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Affiliation(s)
- Kulbhushan Sharma
- Virology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Sara Åkerström
- Swedish Institute for Communicable Disease Control, Solna, Sweden
| | - Anuj Kumar Sharma
- The School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Vincent T. K. Chow
- The YLL School of Medicine, National University of Singapore, Kent Ridge, Singapore, Singapore
| | - Shumein Teow
- The National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Bernard Abrenica
- The National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Stephanie A. Booth
- The National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- The Department of Medical Microbiology, University of Manitoba, Basic Medical Sciences Building, Winnipeg, Canada
| | - Timothy F. Booth
- The National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- The Department of Medical Microbiology, University of Manitoba, Basic Medical Sciences Building, Winnipeg, Canada
| | - Ali Mirazimi
- Swedish Institute for Communicable Disease Control, Solna, Sweden
| | - Sunil K. Lal
- Virology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
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24
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Gadad SS, Senapati P, Syed SH, Rajan RE, Shandilya J, Swaminathan V, Chatterjee S, Colombo E, Dimitrov S, Pelicci PG, Ranga U, Kundu TK. The multifunctional protein nucleophosmin (NPM1) is a human linker histone H1 chaperone. Biochemistry 2011; 50:2780-9. [PMID: 21425800 DOI: 10.1021/bi101835j] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Linker histone H1 plays an essential role in chromatin organization. Proper deposition of linker histone H1 as well as its removal is essential for chromatin dynamics and function. Linker histone chaperones perform this important task during chromatin assembly and other DNA-templated phenomena in the cell. Our in vitro data show that the multifunctional histone chaperone NPM1 interacts with linker histone H1 through its first acidic stretch (residues 120-132). Association of NPM1 with linker histone H1 was also observed in cells in culture. NPM1 exhibited remarkable linker histone H1 chaperone activity, as it was able to efficiently deposit histone H1 onto dinucleosomal templates. Overexpression of NPM1 reduced the histone H1 occupancy on the chromatinized template of HIV-1 LTR in TZM-bl cells, which led to enhanced Tat-mediated transactivation. These data identify NPM1 as an important member of the linker histone chaperone family in humans.
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Affiliation(s)
- Shrikanth S Gadad
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, India
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25
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Nucleolar localization/retention signal is responsible for transient accumulation of histone H2B in the nucleolus through electrostatic interactions. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2010; 1813:27-38. [PMID: 21095207 DOI: 10.1016/j.bbamcr.2010.11.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Revised: 10/24/2010] [Accepted: 11/10/2010] [Indexed: 11/21/2022]
Abstract
The majority of known nuclear proteins are highly mobile. The molecular mechanisms by which they accumulate inside stable compartments that are not separated from the nucleoplasm by membranes are obscure. The compartmental retention of some proteins is associated with their biological function; however, some protein interactions within distinct nuclear structures may be non-specific. The non-specific retention may lead to the accumulation of proteins in distinct structural domains, even if the protein does not function inside this domain. In this study, we have shown that histone H2B-EGFP initially accumulated in the nucleolus after ectopic expression, and then gradually incorporated into the chromatin to leave only a small amount of nucleolus-bound histone that was revealed by removing chromatin-bound proteins with DNase I treatment. Nucleolar histone H2B had several characteristics: (i) it preferentially bound to granular component of the nucleolus and interacted with RNA or RNA-containing nucleolar components; (ii) it freely exchanged between the nucleolus and nucleoplasm; (iii) it associated with the nuclear matrix; and (iv) it bound to interphase prenuclear bodies that formed after hypotonic treatment. The region in histone H2B that acts as a nucleolar localization/retention signal (NoRS) was identified. This signal overlapped with a nuclear localization signal (NLS), which appears to be the primary function of this region. The NoRS activity of this region was non-specific, but the molecular mechanism was probably similar to the NoRSs of other nucleolar proteins. All known NoRSs are enriched with basic amino acids, and we demonstrated that positively charged motifs (nona-arginine (R9) and nona-lysine (K9)) were sufficient for the nucleolar accumulation of EGFP. Also, the correlation between measured NoRS activity and the predicted charge was observed. Thus, NoRSs appear to achieve their function through electrostatic interactions with the negatively charged components of the nucleolus. Though these interactions are non-specific, the functionally unrelated retention of a protein can increase the probability of its interaction with specific and functionally related binding sites.
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Histone H1 subtypes differentially modulate chromatin condensation without preventing ATP-dependent remodeling by SWI/SNF or NURF. PLoS One 2009; 4:e0007243. [PMID: 19794910 PMCID: PMC2748705 DOI: 10.1371/journal.pone.0007243] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2009] [Accepted: 09/07/2009] [Indexed: 12/16/2022] Open
Abstract
Although ubiquitously present in chromatin, the function of the linker histone subtypes is partly unknown and contradictory studies on their properties have been published. To explore whether the various H1 subtypes have a differential role in the organization and dynamics of chromatin we have incorporated all of the somatic human H1 subtypes into minichromosomes and compared their influence on nucleosome spacing, chromatin compaction and ATP-dependent remodeling. H1 subtypes exhibit different affinities for chromatin and different abilities to promote chromatin condensation, as studied with the Atomic Force Microscope. According to this criterion, H1 subtypes can be classified as weak condensers (H1.1 and H1.2), intermediate condensers (H1.3) and strong condensers (H1.0, H1.4, H1.5 and H1x). The variable C-terminal domain is required for nucleosome spacing by H1.4 and is likely responsible for the chromatin condensation properties of the various subtypes, as shown using chimeras between H1.4 and H1.2. In contrast to previous reports with isolated nucleosomes or linear nucleosomal arrays, linker histones at a ratio of one per nucleosome do not preclude remodeling of minichromosomes by yeast SWI/SNF or Drosophila NURF. We hypothesize that the linker histone subtypes are differential organizers of chromatin, rather than general repressors.
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27
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Orthaus S, Klement K, Happel N, Hoischen C, Diekmann S. Linker histone H1 is present in centromeric chromatin of living human cells next to inner kinetochore proteins. Nucleic Acids Res 2009; 37:3391-406. [PMID: 19336418 PMCID: PMC2691837 DOI: 10.1093/nar/gkp199] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2008] [Revised: 03/09/2009] [Accepted: 03/10/2009] [Indexed: 01/04/2023] Open
Abstract
The vertebrate kinetochore complex assembles at the centromere on alpha-satellite DNA. In humans, alpha-satellite DNA has a repeat length of 171 bp slightly longer than the DNA in the chromatosome containing the linker histone H1. The centromere-binding protein CENP-B binds specifically to alpha-satellite DNA with properties of a centromeric-linker histone. Here, we analysed if linker histone H1 is present at or excluded from centromeric chromatin by CENP-B. By immunostaining we detected the presence, but no enrichment or depletion of five different H1 subtypes at centromeric chromatin. The binding dynamics of H1 at centromeric sites were similar to that at other locations in the genome. These dynamics did not change in CENP-B depleted cells, suggesting that CENP-B and H1 co-exist in centromeric chromatin with no or little functional overlap. By bimolecular fluorescence complementation (BiFC) and Förster resonance energy transfer (FRET), we revealed that the linker histone H1 subtypes H1 degrees and H1.2 bind to centromeric chromatin in interphase nuclei in direct neighbourhood to inner kinetochore proteins.
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Affiliation(s)
- S. Orthaus
- Leibniz-Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena and Department of Molecular Biology, Institute for Biochemistry and Molecular Cell Biology, University Goettingen, Humboldtallee 23, D-37073 Goettingen, Germany
| | - K. Klement
- Leibniz-Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena and Department of Molecular Biology, Institute for Biochemistry and Molecular Cell Biology, University Goettingen, Humboldtallee 23, D-37073 Goettingen, Germany
| | - N. Happel
- Leibniz-Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena and Department of Molecular Biology, Institute for Biochemistry and Molecular Cell Biology, University Goettingen, Humboldtallee 23, D-37073 Goettingen, Germany
| | - C. Hoischen
- Leibniz-Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena and Department of Molecular Biology, Institute for Biochemistry and Molecular Cell Biology, University Goettingen, Humboldtallee 23, D-37073 Goettingen, Germany
| | - S. Diekmann
- Leibniz-Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena and Department of Molecular Biology, Institute for Biochemistry and Molecular Cell Biology, University Goettingen, Humboldtallee 23, D-37073 Goettingen, Germany
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28
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Happel N, Stoldt S, Schmidt B, Doenecke D. M Phase-Specific Phosphorylation of Histone H1.5 at Threonine 10 by GSK-3. J Mol Biol 2009; 386:339-50. [DOI: 10.1016/j.jmb.2008.12.047] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2008] [Revised: 12/15/2008] [Accepted: 12/19/2008] [Indexed: 12/24/2022]
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Warneboldt J, Haller F, Horstmann O, Danner BC, Füzesi L, Doenecke D, Happel N. Histone H1x is highly expressed in human neuroendocrine cells and tumours. BMC Cancer 2008; 8:388. [PMID: 19108733 PMCID: PMC2631592 DOI: 10.1186/1471-2407-8-388] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2008] [Accepted: 12/24/2008] [Indexed: 11/14/2022] Open
Abstract
Background Histone H1x is a ubiquitously expressed member of the H1 histone family. H1 histones, also called linker histones, stabilize compact, higher order structures of chromatin. In addition to their role as structural proteins, they actively regulate gene expression and participate in chromatin-based processes like DNA replication and repair. The epigenetic contribution of H1 histones to these mechanisms makes it conceivable that they also take part in malignant transformation. Methods Based on results of a Blast data base search which revealed an accumulation of expressed sequence tags (ESTs) of H1x in libraries from neuroendocrine tumours (NETs), we evaluated the expression of H1x in NETs from lung and the gastrointestinal tract using immunohistochemisty. Relative protein and mRNA levels of H1x were analysed by Western blot analysis and quantitative real-time RT-PCR, respectively. Since several reports describe a change of the expression level of the replacement subtype H1.0 during tumourigenesis, the analysis of this subtype was included in this study. Results We found an increased expression of H1x but not of H1.0 in NET tissues in comparison to corresponding normal tissues. Even though the analysed NETs were heterogenous regarding their grade of malignancy, all except one showed a considerably higher protein amount of H1x compared with corresponding non-neoplastic tissue. Furthermore, double-labelling of H1x and chromogranin A in sections of pancreas and small intestine revealed that H1x is highly expressed in neuroendocrine cells of these tissues. Conclusion We conclude that the high expression of histone H1x in NETs is probably due to the abundance of this protein in the cells from which these tumours originate.
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Affiliation(s)
- Julia Warneboldt
- Institute for Biochemistry and Molecular Cell Biology, University of Göttingen, Humboldtallee 23, D-37073 Göttingen, Germany.
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Happel N, Doenecke D. Histone H1 and its isoforms: contribution to chromatin structure and function. Gene 2008; 431:1-12. [PMID: 19059319 DOI: 10.1016/j.gene.2008.11.003] [Citation(s) in RCA: 292] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2008] [Revised: 10/31/2008] [Accepted: 11/02/2008] [Indexed: 01/21/2023]
Abstract
The lysine-rich H1 histone family in mammals includes eleven different subtypes, and thus it is the most divergent class of histone proteins. The central globular H1 domain asymmetrically interacts with DNA at the exit or entry end of the nucleosomal core DNA, and the C-terminal domain has a major impact on the linker DNA conformation and chromatin condensation. H1 histones are thus involved in the formation of higher order chromatin structures, and they modulate the accessibility of regulatory proteins, chromatin remodeling factors and histone modification enzymes to their target sites. The major posttranslational modification of H1 histones is phosphorylation, which reaches a peak during G2 and mitosis. Phosphorylation is, however, also involved in the control of DNA replication and it contributes to the regulation of gene expression. Disruption of linker histone genes, initially performed in order to delineate subtype-specific functions, revealed that disruption of one or two H1 subtype genes is quantitatively compensated by an increased expression of other subtypes. This suggests a functional redundancy among H1 subtypes. However, the inactivation of three subtypes and the reduction of the H1 moiety in half finally resulted in a phenotypic effect. On the other hand, studies on the role of particular subtypes at specific developmental stages in lower eukaryotes, but also in vertebrates suggest that specific subtypes of H1 participate in particular systems of gene regulation.
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Affiliation(s)
- Nicole Happel
- Institute of Biochemistry and Molecular Cell Biology, University of Göttingen, Humboldtallee 23, D-37073 Göttingen, Germany
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Abstract
The linker histone H1 binds to the DNA entering and exiting the nucleosomal core particle and has an important role in establishing and maintaining higher order chromatin structures. H1 forms a complex family of related proteins with distinct species, tissue and developmental specificity. In higher eukaryotes all H1 variants have the same general structure, consisting of a central conserved globular domain and less conserved N-terminal and C-terminal tails. These tails are moderately conserved among species, but differ among variants, suggesting a specific function for each H1 variant. Due to compensatory mechanisms and to the lack of proper tools, it has been very difficult to study the biological role of individual variants in chromatin-mediated processes. Our knowledge about H1 variants is indeed limited, and in vitro and in vivo observations have often been contradictory. Therefore, H1 variants were considered to be functionally redundant. However, recent knockout studies and biochemical analyses in different organisms have revealed exciting new insights into the specificity and mechanisms of actions of the H1 family members. Here, we collect and compare the available literature about H1 variants and discuss possible specific roles that challenge the concept of H1 being a mere structural component of chromatin and a general repressor of transcription.
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Affiliation(s)
- Annalisa Izzo
- Max Planck Institute for Immunobiology, Stübeweg 51, D-79108 Freiburg, Germany
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Happel N, Doenecke D, Sekeri-Pataryas KE, Sourlingas TG. H1 histone subtype constitution and phosphorylation state of the ageing cell system of human peripheral blood lymphocytes. Exp Gerontol 2008; 43:184-99. [DOI: 10.1016/j.exger.2007.11.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2007] [Revised: 11/13/2007] [Accepted: 11/27/2007] [Indexed: 11/15/2022]
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Histone H1 of Trypanosoma cruzi is concentrated in the nucleolus region and disperses upon phosphorylation during progression to mitosis. EUKARYOTIC CELL 2008; 7:560-8. [PMID: 18281601 DOI: 10.1128/ec.00460-07] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Phosphorylation of histone H1 is intimately related to the cell cycle progression in higher eukaryotes, reaching maximum levels during mitosis. We have previously shown that in the flagellated protozoan Trypanosoma cruzi, which does not condense chromatin during mitosis, histone H1 is phosphorylated at a single cyclin-dependent kinase site. By using an antibody that recognizes specifically the phosphorylated T. cruzi histone H1 site, we have now confirmed that T. cruzi histone H1 is also phosphorylated in a cell cycle-dependent manner. Differently from core histones, the bulk of nonphosphorylated histone H1 in G(1) and S phases of the cell cycle is concentrated in the central regions of the nucleus, which contains the nucleolus and less densely packed chromatin. When cells pass G(2), histone H1 becomes phosphorylated and starts to diffuse. At the onset of mitosis, histone H1 phosphorylation is maximal and found in the entire nuclear space. As permeabilized parasites preferentially lose phosphorylated histone H1, we conclude that this modification promotes its release from less condensed and nucleolar chromatin after G(2).
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