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Bernstein E, Hake SB. The nucleosome: a little variation goes a long wayThis paper is one of a selection of papers published in this Special Issue, entitled 27th International West Coast Chromatin and Chromosome Conference, and has undergone the Journal's usual peer review process. Biochem Cell Biol 2006; 84:505-17. [PMID: 16936823 DOI: 10.1139/o06-085] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Changes in the overall structure of chromatin are essential for the proper regulation of cellular processes, including gene activation and silencing, DNA repair, chromosome segregation during mitosis and meiosis, X chromosome inactivation in female mammals, and chromatin compaction during apoptosis. Such alterations of the chromatin template occur through at least 3 interrelated mechanisms: post-translational modifications of histones, ATP-dependent chromatin remodeling, and the incorporation (or replacement) of specialized histone variants into chromatin. Of these mechanisms, the exchange of variants into and out of chromatin is the least well understood. However, the exchange of conventional histones for variant histones has distinct and profound consequences within the cell. This review focuses on the growing number of mammalian histone variants, their particular biological functions and unique features, and how they may affect the structure of the nucleosome. We propose that a given nucleosome might not consist of heterotypic variants, but rather, that only specific histone variants come together to form a homotypic nucleosome, a hypothesis that we refer to as the nucleosome code. Such nucleosomes might in turn participate in marking specific chromatin domains that may contribute to epigenetic inheritance.
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Affiliation(s)
- Emily Bernstein
- Laboratory of Chromatin Biology, The Rockefeller University, Box 78, 1230 York Avenue, NY, NY 10021, USA
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102
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Valley CM, Pertz LM, Balakumaran BS, Willard HF. Chromosome-wide, allele-specific analysis of the histone code on the human X chromosome. Hum Mol Genet 2006; 15:2335-47. [PMID: 16787966 DOI: 10.1093/hmg/ddl159] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Variation in the composition of chromatin has been proposed to generate a 'histone code' that epigenetically regulates gene expression in a variety of eukaryotic systems. As a result of the process of X chromosome inactivation, chromatinon the mammalian inactive X chromosome (Xi) is marked by several modifications, including histone hypoacetylation, trimethylation of lysine 9 on histone H3 (H3TrimK9) and substitution of core histone H2A with the histone variant MacroH2A. H3TrimK9 is a well-studied marker for heterochromatin in many organisms, but the distribution and function of MacroH2A are less clear. Cytologically, the Xi in human cells comprises alternating and largely non-overlapping approximately 10-15 Mb domains marked by MacroH2A and H3TrimK9. To examine the genomic deposition of MacroH2A, H3TrimK9 and acetylated histone H4 modifications on the Xi at higher resolution, we used chromatin immunoprecipitation in combination with a SNP-based assay to distinguish the Xi and active X (Xa) in a diploid female cell line and to determine quantitatively the relative enrichment of these histone code elements on the Xi relative to the Xa. Although we found a majority of sites were enriched for either MacroH2A or H3TrimK9 in a manner consistent with the cytological appearance of the Xi, a range of different histone code types were detected at different sites along the X. These findings suggest that the nature of the heterochromatin histone code associated with X inactivation may be more heterogeneous than previously thought and imply that gene silencing can be achieved by a variety of different epigenetic mechanisms whose genomic, evolutionary or developmental basis is now amenable to investigation.
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Affiliation(s)
- Cory M Valley
- Institute for Genome Sciences & Policy, Duke University, Durham, NC 27708, USA
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103
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Angelov D, Bondarenko VA, Almagro S, Menoni H, Mongélard F, Hans F, Mietton F, Studitsky VM, Hamiche A, Dimitrov S, Bouvet P. Nucleolin is a histone chaperone with FACT-like activity and assists remodeling of nucleosomes. EMBO J 2006; 25:1669-79. [PMID: 16601700 PMCID: PMC1440837 DOI: 10.1038/sj.emboj.7601046] [Citation(s) in RCA: 189] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2005] [Accepted: 02/21/2006] [Indexed: 11/09/2022] Open
Abstract
Remodeling machines play an essential role in the control of gene expression, but how their activity is regulated is not known. Here we report that the nuclear protein nucleolin possesses a histone chaperone activity and that this factor greatly enhances the activity of the chromatin remodeling machineries SWI/SNF and ACF. Interestingly, nucleolin is able to induce the remodeling by SWI/SNF of macroH2A, but not of H2ABbd nucleosomes, which are otherwise resistant to remodeling. This new histone chaperone promotes the destabilization of the histone octamer, helping the dissociation of a H2A-H2B dimer, and stimulates the SWI/SNF-mediated transfer of H2A-H2B dimers. Furthermore, nucleolin facilitates transcription through the nucleosome, which is reminiscent of the activity of the FACT complex. This work defines new functions for histone chaperones in chromatin remodeling and regulation of transcription and explains how nucleolin could act on transcription.
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Affiliation(s)
- Dimitar Angelov
- Ecole Normale Supérieure de Lyon, CNRS-UMR 5161/INRA 1237/IFR128 Biosciences, Lyon-Gerland, France
- Laboratoire Joliot-Curie, Lyon, France
| | - Vladimir A Bondarenko
- Department of Pharmacology, University of Medicine and Dentistry of New Jersey, Piscataway, NJ, USA
| | - Sébastien Almagro
- Ecole Normale Supérieure de Lyon, CNRS-UMR 5161/INRA 1237/IFR128 Biosciences, Lyon-Gerland, France
- Laboratoire Joliot-Curie, Lyon, France
| | - Hervé Menoni
- Ecole Normale Supérieure de Lyon, CNRS-UMR 5161/INRA 1237/IFR128 Biosciences, Lyon-Gerland, France
- Laboratoire Joliot-Curie, Lyon, France
| | - Fabien Mongélard
- Ecole Normale Supérieure de Lyon, CNRS-UMR 5161/INRA 1237/IFR128 Biosciences, Lyon-Gerland, France
- Laboratoire Joliot-Curie, Lyon, France
| | - Fabienne Hans
- Institut Albert Bonniot, INSERM U309, La Tronche Cedex, France
| | - Flore Mietton
- Institut Albert Bonniot, INSERM U309, La Tronche Cedex, France
| | - Vasily M Studitsky
- Department of Pharmacology, University of Medicine and Dentistry of New Jersey, Piscataway, NJ, USA
| | - Ali Hamiche
- Institut André Lwoff, CNRS UPR 9079, Villejuif, France
| | - Stefan Dimitrov
- Laboratoire Joliot-Curie, Lyon, France
- Institut Albert Bonniot, INSERM U309, La Tronche Cedex, France
| | - Philippe Bouvet
- Ecole Normale Supérieure de Lyon, CNRS-UMR 5161/INRA 1237/IFR128 Biosciences, Lyon-Gerland, France
- Laboratoire Joliot-Curie, Lyon, France
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