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Abstract
Eukaryotic replication disrupts each nucleosome as the fork passes, followed by re-assembly of disrupted nucleosomes and incorporation of newly synthesized histones into nucleosomes in the daughter genomes. In this review, we examine this process of replication-coupled nucleosome assembly to understand how characteristic steady state nucleosome landscapes are attained. Recent studies have begun to elucidate mechanisms involved in histone transfer during replication and maturation of the nucleosome landscape after disruption by replication. A fuller understanding of replication-coupled nucleosome assembly will be needed to explain how epigenetic information is replicated at every cell division.
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Affiliation(s)
- Srinivas Ramachandran
- Howard Hughes Medical Institute, Seattle, WA 98109, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Steven Henikoff
- Howard Hughes Medical Institute, Seattle, WA 98109, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Corresponding author. E-mail:
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202
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Snyers L, Zupkovitz G, Almeder M, Fliesser M, Stoisser A, Weipoltshammer K, Schöfer C. Distinct chromatin signature of histone H3 variant H3.3 in human cells. Nucleus 2015; 5:449-61. [PMID: 25482197 PMCID: PMC4164487 DOI: 10.4161/nucl.36229] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Actively transcribed regions of the genome have been found enriched for the histone H3 variant H3.3. This variant is incorporated into nucleosomes throughout the cell cycle whereas the canonical isoforms are predominately deposited in association with replication. In order to obtain a global picture of the deposition pattern at the single cell level we expressed H3.3 in both normal and malignant human cells and analyzed nuclei using conventional and structured illumination imaging (SIM). We found that the distribution pattern of H3.3 in interphase differs from that of the canonical histone H3 variants and this difference is conveyed to mitotic chromosomes which display a distinct H3.3 banding pattern. Histone H3.3 localization positively correlated with markers for transcriptionally active chromatin and, notably, H3.3 was almost completely absent from the inactive X chromosome. Collectively, our data show that histone variant H3.3 occupies distinct intranuclear chromatin domains and that these genomic loci are associated with gene expression.
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Affiliation(s)
- Luc Snyers
- a Department for Cell and Developmental Biology; Medical Imaging Cluster; Medical University of Vienna; Vienna, Austria
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203
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Ricketts MD, Frederick B, Hoff H, Tang Y, Schultz DC, Singh Rai T, Grazia Vizioli M, Adams PD, Marmorstein R. Ubinuclein-1 confers histone H3.3-specific-binding by the HIRA histone chaperone complex. Nat Commun 2015; 6:7711. [PMID: 26159857 PMCID: PMC4510971 DOI: 10.1038/ncomms8711] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 06/01/2015] [Indexed: 01/01/2023] Open
Abstract
Histone chaperones bind specific histones to mediate their storage, eviction or deposition from/or into chromatin. The HIRA histone chaperone complex, composed of HIRA, ubinuclein-1 (UBN1) and CABIN1, cooperates with the histone chaperone ASF1a to mediate H3.3-specific binding and chromatin deposition. Here we demonstrate that the conserved UBN1 Hpc2-related domain (HRD) is a novel H3.3-specific-binding domain. Biochemical and biophysical studies show the UBN1-HRD preferentially binds H3.3/H4 over H3.1/H4. X-ray crystallographic and mutational studies reveal that conserved residues within the UBN1-HRD and H3.3 G90 as key determinants of UBN1–H3.3-binding specificity. Comparison of the structure with the unrelated H3.3-specific chaperone DAXX reveals nearly identical points of contact between the chaperone and histone in the proximity of H3.3 G90, although the mechanism for H3.3 G90 recognition appears to be distinct. This study points to UBN1 as the determinant of H3.3-specific binding and deposition by the HIRA complex. Ubinuclein-1 (UBN1) is a subunit of the HIRA histone chaperone complex that deposits histone H3.3 into chromatin. Here the authors use structural and biochemical studies to show that a conserved domain in UBN1 mediates H3.3-specific binding by the HIRA complex.
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Affiliation(s)
- M Daniel Ricketts
- 1] Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA [2] Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Brian Frederick
- The Wistar Institute, Philadelphia, Pennsylvania, 19104, USA
| | - Henry Hoff
- The Wistar Institute, Philadelphia, Pennsylvania, 19104, USA
| | - Yong Tang
- The Wistar Institute, Philadelphia, Pennsylvania, 19104, USA
| | - David C Schultz
- The Wistar Institute, Philadelphia, Pennsylvania, 19104, USA
| | - Taranjit Singh Rai
- 1] Institute of Cancer Sciences, CR-UK Beatson Labs, University of Glasgow, Glasgow G61 1BD, UK [2] Institute of Biomedical and Environmental Health Research, University of West of Scotland, Paisley PA1 2BE, UK
| | - Maria Grazia Vizioli
- Institute of Cancer Sciences, CR-UK Beatson Labs, University of Glasgow, Glasgow G61 1BD, UK
| | - Peter D Adams
- Institute of Cancer Sciences, CR-UK Beatson Labs, University of Glasgow, Glasgow G61 1BD, UK
| | - Ronen Marmorstein
- 1] Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA [2] Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA [3] Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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204
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Clynes D, Jelinska C, Xella B, Ayyub H, Scott C, Mitson M, Taylor S, Higgs DR, Gibbons RJ. Suppression of the alternative lengthening of telomere pathway by the chromatin remodelling factor ATRX. Nat Commun 2015; 6:7538. [PMID: 26143912 PMCID: PMC4501375 DOI: 10.1038/ncomms8538] [Citation(s) in RCA: 225] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 05/19/2015] [Indexed: 02/08/2023] Open
Abstract
Fifteen per cent of cancers maintain telomere length independently of telomerase by the homologous recombination (HR)-associated alternative lengthening of telomeres (ALT) pathway. A unifying feature of these tumours are mutations in ATRX. Here we show that expression of ectopic ATRX triggers a suppression of the pathway and telomere shortening. Importantly ATRX-mediated ALT suppression is dependent on the histone chaperone DAXX. Re-expression of ATRX is associated with a reduction in replication fork stalling, a known trigger for HR and loss of MRN from telomeres. A G-quadruplex stabilizer partially reverses the effect of ATRX, inferring ATRX may normally facilitate replication through these sequences that, if they persist, promote ALT. We propose that defective telomere chromatinization through loss of ATRX promotes the persistence of aberrant DNA secondary structures, which in turn present a barrier to DNA replication, leading to replication fork stalling, collapse, HR and subsequent recombination-mediated telomere synthesis in ALT cancers. ATRX, a chromatin remodelling factor, is mutated in cancers that maintain telomere length by alternative lengthening of telomeres (ALT). Here, the authors show that ectopic expression of ATRX triggers telomere shortening, ALT suppression and reduced replication fork stalling.
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Affiliation(s)
- David Clynes
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Clare Jelinska
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Barbara Xella
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Helena Ayyub
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Caroline Scott
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Matthew Mitson
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Stephen Taylor
- Computational Biology Research Group, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Douglas R Higgs
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Richard J Gibbons
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
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205
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Point mutations in an epigenetic factor lead to multiple types of bone tumors: role of H3.3 histone variant in bone development and disease. BONEKEY REPORTS 2015; 4:715. [PMID: 26157578 DOI: 10.1038/bonekey.2015.84] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Accepted: 04/24/2015] [Indexed: 12/27/2022]
Abstract
Coordinated post-translational modifications (PTMs) of nucleosomal histones emerge as a key mechanism of gene regulation by defining chromatin configuration. Patterns of histone modifications vary in different cells and constitute core elements of cell-specific epigenomes. Recently, in addition to canonical histone proteins produced during the S phase of cell cycle, several non-canonical histone variants have been identified and shown to express in a DNA replication-independent manner. These histone variants generate diversity in nucleosomal structures and add further complexity to mechanisms of epigenetic regulation. Cell-specific functions of histone variants remain to be determined. Several recent studies reported an association between some point mutations in the non-canonical histone H3.3 and particular types of brain and bone tumors. This suggests a possibility of differential physiological effects of histone variants in different cells and tissues, including bone. In this review, we outline the roles of histone variants and their PTMs in the epigenetic regulation of chromatin structure and discuss possible mechanisms of biological effects of the non-canonical histone mutations found in bone tumors on tumorigenesis in differentiating bone stem cells.
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206
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Annunziato AT. The Fork in the Road: Histone Partitioning During DNA Replication. Genes (Basel) 2015; 6:353-71. [PMID: 26110314 PMCID: PMC4488668 DOI: 10.3390/genes6020353] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 06/15/2015] [Accepted: 06/16/2015] [Indexed: 12/22/2022] Open
Abstract
In the following discussion the distribution of histones at the replication fork is examined, with specific attention paid to the question of H3/H4 tetramer "splitting." After a presentation of early experiments surrounding this topic, more recent contributions are detailed. The implications of these findings with respect to the transmission of histone modifications and epigenetic models are also addressed.
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Affiliation(s)
- Anthony T Annunziato
- Biology Department, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA.
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207
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Falk SJ, Guo LY, Sekulic N, Smoak EM, Mani T, Logsdon GA, Gupta K, Jansen LET, Van Duyne GD, Vinogradov SA, Lampson MA, Black BE. Chromosomes. CENP-C reshapes and stabilizes CENP-A nucleosomes at the centromere. Science 2015; 348:699-703. [PMID: 25954010 DOI: 10.1126/science.1259308] [Citation(s) in RCA: 161] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Inheritance of each chromosome depends upon its centromere. A histone H3 variant, centromere protein A (CENP-A), is essential for epigenetically marking centromere location. We find that CENP-A is quantitatively retained at the centromere upon which it is initially assembled. CENP-C binds to CENP-A nucleosomes and is a prime candidate to stabilize centromeric chromatin. Using purified components, we find that CENP-C reshapes the octameric histone core of CENP-A nucleosomes, rigidifies both surface and internal nucleosome structure, and modulates terminal DNA to match the loose wrap that is found on native CENP-A nucleosomes at functional human centromeres. Thus, CENP-C affects nucleosome shape and dynamics in a manner analogous to allosteric regulation of enzymes. CENP-C depletion leads to rapid removal of CENP-A from centromeres, indicating their collaboration in maintaining centromere identity.
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Affiliation(s)
- Samantha J Falk
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Graduate Program in Cell and Molecular Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lucie Y Guo
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Graduate Program in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nikolina Sekulic
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Evan M Smoak
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Graduate Program in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Tomoyasu Mani
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Graduate Program in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Glennis A Logsdon
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Graduate Program in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kushol Gupta
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Gregory D Van Duyne
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Graduate Program in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sergei A Vinogradov
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Graduate Program in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael A Lampson
- Graduate Program in Cell and Molecular Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Graduate Program in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ben E Black
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Graduate Program in Cell and Molecular Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Graduate Program in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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208
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Saade E, Pirozhkova I, Aimbetov R, Lipinski M, Ogryzko V. Molecular turnover, the H3.3 dilemma and organismal aging (hypothesis). Aging Cell 2015; 14:322-33. [PMID: 25720734 PMCID: PMC4406661 DOI: 10.1111/acel.12332] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/28/2015] [Indexed: 12/22/2022] Open
Abstract
The H3.3 histone variant has been a subject of increasing interest in the field of chromatin studies due to its two distinguishing features. First, its incorporation into chromatin is replication independent unlike the replication-coupled deposition of its canonical counterparts H3.1/2. Second, H3.3 has been consistently associated with an active state of chromatin. In accordance, this histone variant should be expected to be causally involved in the regulation of gene expression, or more generally, its incorporation should have downstream consequences for the structure and function of chromatin. This, however, leads to an apparent paradox: In cells that slowly replicate in the organism, H3.3 will accumulate with time, opening the way to aberrant effects on heterochromatin. Here, we review the indications that H3.3 is expected both to be incorporated in the heterochromatin of slowly replicating cells and to retain its functional downstream effects. Implications for organismal aging are discussed.
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Affiliation(s)
- Evelyne Saade
- Faculty of Public Health Lebanese University LU Beirut Lebanon
| | - Iryna Pirozhkova
- Institute Gustave Roussy University Paris SUD 114, rue Edouard Vaillant Villejuif 94805France
| | - Rakhan Aimbetov
- Institute Gustave Roussy University Paris SUD 114, rue Edouard Vaillant Villejuif 94805France
| | - Marc Lipinski
- Institute Gustave Roussy University Paris SUD 114, rue Edouard Vaillant Villejuif 94805France
| | - Vasily Ogryzko
- Institute Gustave Roussy University Paris SUD 114, rue Edouard Vaillant Villejuif 94805France
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209
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Brachet E, Béneut C, Serrentino ME, Borde V. The CAF-1 and Hir Histone Chaperones Associate with Sites of Meiotic Double-Strand Breaks in Budding Yeast. PLoS One 2015; 10:e0125965. [PMID: 25938567 PMCID: PMC4418760 DOI: 10.1371/journal.pone.0125965] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 03/27/2015] [Indexed: 11/22/2022] Open
Abstract
In the meiotic prophase, programmed DNA double-strand breaks (DSB) are introduced along chromosomes to promote homolog pairing and recombination. Although meiotic DSBs usually occur in nucleosome-depleted, accessible regions of chromatin, their repair by homologous recombination takes place in a nucleosomal environment. Nucleosomes may represent an obstacle for the recombination machinery and their timely eviction and reincorporation into chromatin may influence the outcome of recombination, for instance by stabilizing recombination intermediates. Here we show in budding yeast that nucleosomes flanking a meiotic DSB are transiently lost during recombination, and that specific histone H3 chaperones, CAF-1 and Hir, are mobilized at meiotic DSBs. However, the absence of these chaperones has no effect on meiotic recombination, suggesting that timely histone reincorporation following their eviction has no influence on the recombination outcome, or that redundant pathways are activated. This study is the first example of the involvement of histone H3 chaperones at naturally occurring, developmentally programmed DNA double-strand breaks.
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Affiliation(s)
- Elsa Brachet
- Institut Curie, Centre de Recherche, Paris, France
- CNRS, UMR 3664, Paris, France
| | - Claire Béneut
- Institut Curie, Centre de Recherche, Paris, France
- CNRS, UMR 3664, Paris, France
| | | | - Valérie Borde
- Institut Curie, Centre de Recherche, Paris, France
- CNRS, UMR 3664, Paris, France
- * E-mail:
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210
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Lund EG, Collas P, Delbarre E. Transcription outcome of promoters enriched in histone variant H3.3 defined by positioning of H3.3 and local chromatin marks. Biochem Biophys Res Commun 2015; 460:348-53. [PMID: 25783056 DOI: 10.1016/j.bbrc.2015.03.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2015] [Accepted: 03/08/2015] [Indexed: 10/23/2022]
Abstract
Replication-independent histone variant H3.3 is incorporated into distinct genomic regions including promoters. However topology of promoter-associated H3.3 in relation to chromatin modifications and transcriptional outcome is not known, providing no insight on any distinction between H3.3-containing active and inactive promoters. Here, we report algorithms providing information on gene expression status as a function of density and position of multiple chromatin marks on promoters. We identify a relationship between promoter enrichment in epitope-tagged H3.3 or its canonical isoform H3.2 and corresponding transcriptional outcomes, as a function of sub-promoter positioning of DNA methylation and H3K4me3, H3K9me3 and H3K27me3. We identify a low-frequency configuration of H3.3 and H3K9me3 co-occupancy associated with transcriptional activity, while H3.3 and H3K27me3 promoters are invariably inactive. We unveil H3.3 and DNA methylated promoters whose transcription outcome depends on H3.3 sub-promoter positioning. Our results indicate how spatially restricted positioning of H3.3 may add another layer of transcription regulation.
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Affiliation(s)
- Eivind G Lund
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0317 Oslo, Norway
| | - Philippe Collas
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0317 Oslo, Norway
| | - Erwan Delbarre
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0317 Oslo, Norway.
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211
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Won KJ, Choi I, LeRoy G, Zee BM, Sidoli S, Gonzales-Cope M, Garcia BA. Proteogenomics analysis reveals specific genomic orientations of distal regulatory regions composed by non-canonical histone variants. Epigenetics Chromatin 2015; 8:13. [PMID: 25878728 PMCID: PMC4397702 DOI: 10.1186/s13072-015-0005-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 03/19/2015] [Indexed: 01/05/2023] Open
Abstract
Background Histone variants play further important roles in DNA packaging and controlling gene expression. However, our understanding about their composition and their functions is limited. Results Integrating proteomic and genomic approaches, we performed a comprehensive analysis of the epigenetic landscapes containing the four histone variants H3.1, H3.3, H2A.Z, and macroH2A. These histones were FLAG-tagged in HeLa cells and purified using chromatin immunoprecipitation (ChIP). By adopting ChIP followed by mass spectrometry (ChIP-MS), we quantified histone post-translational modifications (PTMs) and histone variant nucleosomal ratios in highly purified mononucleosomes. Subsequent ChIP followed by next-generation sequencing (ChIP-seq) was used to map the genome-wide localization of the analyzed histone variants and define their chromatin domains. Finally, we included in our study large datasets contained in the ENCODE database. We newly identified a group of regulatory regions enriched in H3.1 and the histone variant associated with repressive marks macroH2A. Systematic analysis identified both symmetric and asymmetric patterns of histone variant occupancies at intergenic regulatory regions. Strikingly, these directional patterns were associated with RNA polymerase II (PolII). These asymmetric patterns correlated with the enhancer activities measured using global run-on sequencing (GRO-seq) data. Conclusions Our studies show that H2A.Z and H3.3 delineate the orientation of transcription at enhancers as observed at promoters. We also showed that enhancers with skewed histone variant patterns well facilitate enhancer activity. Collectively, our study indicates that histone variants are deposited at regulatory regions to assist gene regulation. Electronic supplementary material The online version of this article (doi:10.1186/s13072-015-0005-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kyoung-Jae Won
- The Institute for Diabetes, Obesity, and Metabolism, Philadelphia, PA 19104 USA.,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Inchan Choi
- The Institute for Diabetes, Obesity, and Metabolism, Philadelphia, PA 19104 USA.,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA.,Department of Agricultural Biotechnology, National Academy of Agricultural Science, 370 Nongsaengmyeong-ro, Wansan-gu, Jeonju-si, Jeollabuk-do 560-500 South Korea
| | - Gary LeRoy
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544 USA
| | - Barry M Zee
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544 USA.,Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Simone Sidoli
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Michelle Gonzales-Cope
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544 USA.,Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Benjamin A Garcia
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
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212
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Mouysset J, Gilberto S, Meier MG, Lampert F, Belwal M, Meraldi P, Peter M. CRL4(RBBP7) is required for efficient CENP-A deposition at centromeres. J Cell Sci 2015; 128:1732-45. [PMID: 25795299 DOI: 10.1242/jcs.162305] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Accepted: 03/13/2015] [Indexed: 12/15/2022] Open
Abstract
The mitotic spindle drives chromosome movement during mitosis and attaches to chromosomes at dedicated genomic loci named centromeres. Centromeres are epigenetically specified by their histone composition, namely the presence of the histone H3 variant CENP-A, which is regulated during the cell cycle by its dynamic expression and localization. Here, we combined biochemical methods and quantitative imaging approaches to investigate a new function of CUL4-RING E3 ubiquitin ligases (CRL4) in regulating CENP-A dynamics. We found that the core components CUL4 and DDB1 are required for centromeric loading of CENP-A, but do not influence CENP-A maintenance or pre-nucleosomal CENP-A levels. Interestingly, we identified RBBP7 as a substrate-specific CRL4 adaptor required for this process, in addition to its role in binding and stabilizing soluble CENP-A. Our data thus suggest that the CRL4 complex containing RBBP7 (CRL4(RBBP7)) might regulate mitosis by promoting ubiquitin-dependent loading of newly synthesized CENP-A during the G1 phase of the cell cycle.
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Affiliation(s)
- Julien Mouysset
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland
| | - Samuel Gilberto
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland
| | - Michelle G Meier
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland Department of Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Fabienne Lampert
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland
| | - Mukta Belwal
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland
| | - Patrick Meraldi
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland Department of Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Matthias Peter
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland
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213
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Kallappagoudar S, Yadav RK, Lowe BR, Partridge JF. Histone H3 mutations--a special role for H3.3 in tumorigenesis? Chromosoma 2015; 124:177-89. [PMID: 25773741 PMCID: PMC4446520 DOI: 10.1007/s00412-015-0510-4] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 02/19/2015] [Accepted: 02/26/2015] [Indexed: 12/31/2022]
Abstract
Brain tumors are the most common solid tumors in children. Pediatric high-grade glioma (HGG) accounts for ∼8–12 % of these brain tumors and is a devastating disease as 70–90 % of patients die within 2 years of diagnosis. The failure to advance therapy for these children over the last 30 years is largely due to limited knowledge of the molecular basis for these tumors and a lack of disease models. Recently, sequencing of tumor cells revealed that histone H3 is frequently mutated in pediatric HGG, with up to 78 % of diffuse intrinsic pontine gliomas (DIPGs) carrying K27M and 36 % of non-brainstem gliomas carrying either K27M or G34R/V mutations. Although mutations in many chromatin modifiers have been identified in cancer, this was the first demonstration that histone mutations may be drivers of disease. Subsequent studies have identified high-frequency mutation of histone H3 to K36M in chondroblastomas and to G34W/L in giant cell tumors of bone, which are diseases of adolescents and young adults. Interestingly, the G34 mutations, the K36M mutations, and the majority of K27M mutations occur in genes encoding the replacement histone H3.3. Here, we review the peculiar characteristics of histone H3.3 and use this information as a backdrop to highlight current thinking about how the identified mutations may contribute to disease development.
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Affiliation(s)
- Satish Kallappagoudar
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
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214
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Duc C, Benoit M, Le Goff S, Simon L, Poulet A, Cotterell S, Tatout C, Probst AV. The histone chaperone complex HIR maintains nucleosome occupancy and counterbalances impaired histone deposition in CAF-1 complex mutants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 81:707-22. [PMID: 25600486 DOI: 10.1111/tpj.12758] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 11/21/2014] [Accepted: 12/23/2014] [Indexed: 05/09/2023]
Abstract
Chromatin organization is essential for coordinated gene expression, genome stability, and inheritance of epigenetic information. The main components involved in chromatin assembly are specific complexes such as Chromatin Assembly Factor 1 (CAF-1) and Histone Regulator (HIR), which deposit histones in a DNA synthesis-dependent or -independent manner, respectively. Here, we characterize the role of the plant orthologs Histone Regulator A (HIRA), Ubinuclein (UBN) and Calcineurin Binding protein 1 (CABIN1), which constitute the HIR complex. Arabidopsis loss-of-function mutants for the various subunits of the complex are viable, but hira mutants show reduced fertility. We show that loss of HIRA reduces extractable histone H3 protein levels and decreases nucleosome occupancy at both actively transcribed genes and heterochromatic regions. Concomitantly, HIRA contributes to maintenance of silencing of pericentromeric repeats and certain transposons. A genetic analysis based on crosses between mutants deficient in subunits of the CAF-1 and HIR complexes showed that simultaneous loss of both the CAF-1 and HIR histone H3 chaperone complexes severely affects plant survival, growth and reproductive development. Our results suggest that HIRA partially rescues impaired histone deposition in fas mutants to preserve nucleosome occupancy, implying plasticity in histone variant interaction and deposition.
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Affiliation(s)
- Céline Duc
- Génétique, Reproduction et Développement, CNRS UMR 6293, Clermont Université, INSERM U1103, 24 Avenue des Landais, BP 80026, Aubière Cedex, 63171, France
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215
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Cancer genomics: why rare is valuable. J Mol Med (Berl) 2015; 93:369-81. [PMID: 25676695 PMCID: PMC4366545 DOI: 10.1007/s00109-015-1260-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 12/26/2014] [Accepted: 01/29/2015] [Indexed: 02/07/2023]
Abstract
Rare conditions are sometimes ignored in biomedical research because of difficulties in obtaining specimens and limited interest from fund raisers. However, the study of rare diseases such as unusual cancers has again and again led to breakthroughs in our understanding of more common diseases. It is therefore unsurprising that with the development and accessibility of next-generation sequencing, much has been learnt from studying cancers that are rare and in particular those with uniform biological and clinical behavior. Herein, we describe how shotgun sequencing of cancers such as granulosa cell tumor, endometrial stromal sarcoma, epithelioid hemangioendothelioma, ameloblastoma, small-cell carcinoma of the ovary, clear-cell carcinoma of the ovary, nonepithelial ovarian tumors, chondroblastoma, and giant cell tumor of the bone has led to rapidly translatable discoveries in diagnostics and tumor taxonomies, as well as providing insights into cancer biology.
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216
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Chen WY, Shih HT, Liu KY, Shih ZS, Chen LK, Tsai TH, Chen MJ, Liu H, Tan BCM, Chen CY, Lee HH, Loppin B, Aït-Ahmed O, Wu JT. Intellectual disability-associated dBRWD3 regulates gene expression through inhibition of HIRA/YEM-mediated chromatin deposition of histone H3.3. EMBO Rep 2015; 16:528-38. [PMID: 25666827 DOI: 10.15252/embr.201439092] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 01/16/2015] [Indexed: 12/28/2022] Open
Abstract
Many causal mutations of intellectual disability have been found in genes involved in epigenetic regulations. Replication-independent deposition of the histone H3.3 variant by the HIRA complex is a prominent nucleosome replacement mechanism affecting gene transcription, especially in postmitotic neurons. However, how HIRA-mediated H3.3 deposition is regulated in these cells remains unclear. Here, we report that dBRWD3, the Drosophila ortholog of the intellectual disability gene BRWD3, regulates gene expression through H3.3, HIRA, and its associated chaperone Yemanuclein (YEM), the fly ortholog of mammalian Ubinuclein1. In dBRWD3 mutants, increased H3.3 levels disrupt gene expression, dendritic morphogenesis, and sensory organ differentiation. Inactivation of yem or H3.3 remarkably suppresses the global transcriptome changes and various developmental defects caused by dBRWD3 mutations. Our work thus establishes a previously unknown negative regulation of H3.3 and advances our understanding of BRWD3-dependent intellectual disability.
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Affiliation(s)
- Wei-Yu Chen
- Institute of Molecular Medicine College of Medicine National Taiwan University, Taipei, Taiwan
| | - Hsueh-Tzu Shih
- Institute of Molecular Medicine College of Medicine National Taiwan University, Taipei, Taiwan
| | - Kwei-Yan Liu
- Institute of Molecular Medicine College of Medicine National Taiwan University, Taipei, Taiwan
| | - Zong-Siou Shih
- Institute of Molecular Medicine College of Medicine National Taiwan University, Taipei, Taiwan
| | - Li-Kai Chen
- Institute of Molecular Medicine College of Medicine National Taiwan University, Taipei, Taiwan
| | - Tsung-Han Tsai
- Institute of Molecular Medicine College of Medicine National Taiwan University, Taipei, Taiwan
| | - Mei-Ju Chen
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
| | - Hsuan Liu
- Department of Cell and Molecular Biology, College of Medicine Chang Gung University, Tao-Yuan, Taiwan Molecular Medicine Research Center Chang Gung University, Tao-Yuan, Taiwan
| | - Bertrand Chin-Ming Tan
- Molecular Medicine Research Center Chang Gung University, Tao-Yuan, Taiwan Department of Biomedical Sciences and Graduate Institute of Biomedical Sciences, College of Medicine Chang Gung University, Tao-Yuan, Taiwan
| | - Chien-Yu Chen
- Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei, Taiwan
| | - Hsiu-Hsiang Lee
- Institute of Molecular Medicine College of Medicine National Taiwan University, Taipei, Taiwan
| | - Benjamin Loppin
- Centre de Génétique et de Physiologie Moléculaire et Cellulaire CNRS UMR5534 Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Ounissa Aït-Ahmed
- Institute of Regenerative medicine and Biotherapy (IRMB) Inserm U1203 Saint-Eloi Hospital, CHRU Montpellier, France
| | - June-Tai Wu
- Institute of Molecular Medicine College of Medicine National Taiwan University, Taipei, Taiwan Department of Dermatology, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan Research Center for Developmental Biology and Regenerative Medicine National Taiwan University, Taipei, Taiwan
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217
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Histone exchange, chromatin structure and the regulation of transcription. Nat Rev Mol Cell Biol 2015; 16:178-89. [DOI: 10.1038/nrm3941] [Citation(s) in RCA: 650] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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218
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Gurard-Levin ZA, Quivy JP, Almouzni G. Histone chaperones: assisting histone traffic and nucleosome dynamics. Annu Rev Biochem 2015; 83:487-517. [PMID: 24905786 DOI: 10.1146/annurev-biochem-060713-035536] [Citation(s) in RCA: 229] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The functional organization of eukaryotic DNA into chromatin uses histones as components of its building block, the nucleosome. Histone chaperones, which are proteins that escort histones throughout their cellular life, are key actors in all facets of histone metabolism; they regulate the supply and dynamics of histones at chromatin for its assembly and disassembly. Histone chaperones can also participate in the distribution of histone variants, thereby defining distinct chromatin landscapes of importance for genome function, stability, and cell identity. Here, we discuss our current knowledge of the known histone chaperones and their histone partners, focusing on histone H3 and its variants. We then place them into an escort network that distributes these histones in various deposition pathways. Through their distinct interfaces, we show how they affect dynamics during DNA replication, DNA damage, and transcription, and how they maintain genome integrity. Finally, we discuss the importance of histone chaperones during development and describe how misregulation of the histone flow can link to disease.
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Affiliation(s)
- Zachary A Gurard-Levin
- Institut Curie, Centre de Recherche; CNRS UMR 3664; Equipe Labellisée, Ligue contre le Cancer; and Université Pierre et Marie Curie, Paris F-75248, France;
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219
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Horard B, Loppin B. Histone storage and deposition in the early Drosophila embryo. Chromosoma 2015; 124:163-75. [PMID: 25563491 DOI: 10.1007/s00412-014-0504-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 12/17/2014] [Accepted: 12/18/2014] [Indexed: 12/18/2022]
Abstract
Drosophila development initiates with the formation of a diploid zygote followed by the rapid division of embryonic nuclei. This syncytial phase of development occurs almost entirely under maternal control and ends when the blastoderm embryo cellularizes and activates its zygotic genome. The biosynthesis and storage of histones in quantity sufficient for chromatin assembly of several thousands of genome copies represent a unique challenge for the developing embryo. In this article, we have reviewed our current understanding of the mechanisms involved in the production, storage, and deposition of histones in the fertilized egg and during the exponential amplification of cleavage nuclei.
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Affiliation(s)
- Béatrice Horard
- Centre de Génétique et de Physiologie Moléculaire et Cellulaire-CNRS UMR5534, Université Claude Bernard Lyon 1, University of Lyon, 69100, Villeurbanne, France
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220
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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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221
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Histone Variants and Reprogramming in Early Development. EPIGENETIC MECHANISMS IN CELLULAR REPROGRAMMING 2015. [DOI: 10.1007/978-3-642-31974-7_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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222
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Adam S, Dabin J, Bai SK, Polo SE. Imaging local deposition of newly synthesized histones in UVC-damaged chromatin. Methods Mol Biol 2015; 1288:337-47. [PMID: 25827889 DOI: 10.1007/978-1-4939-2474-5_19] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
DNA damage not only jeopardizes genome integrity but also challenges the well-organized association of DNA with histone proteins into chromatin, which is key for regulating gene expression and cell functions. The extent to which the original chromatin structure is altered after repair of DNA lesions is thus a critical issue. Dissecting histone dynamics at sites of DNA damage has provided mechanistic insights into chromatin plasticity in response to genotoxic stress. Here, we present an experimental protocol for visualizing the deposition of newly synthesized histone H3 variants at sites of UVC damage in human cells that couples SNAP-tag based labeling of new histones with local UVC irradiation of cells through micropore filters.
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Affiliation(s)
- Salomé Adam
- Epigenetics and Cell Fate Centre, UMR7216 CNRS/Paris Diderot University, Bâtiment Lamarck (4ème étage) Case 7042, 35 rue Hélène Brion, Paris, 75205, France
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223
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Ha M, Kraushaar DC, Zhao K. Genome-wide analysis of H3.3 dissociation reveals high nucleosome turnover at distal regulatory regions of embryonic stem cells. Epigenetics Chromatin 2014; 7:38. [PMID: 25598842 PMCID: PMC4297464 DOI: 10.1186/1756-8935-7-38] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 11/27/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The histone variant H3.3 plays a critical role in maintaining the pluripotency of embryonic stem cells (ESCs) by regulating gene expression programs important for lineage specification. H3.3 is deposited by various chaperones at regulatory sites, gene bodies, and certain heterochromatic sites such as telomeres and centromeres. Using Tet-inhibited expression of epitope-tagged H3.3 combined with ChIP-Seq we undertook genome-wide measurements of H3.3 dissociation rates across the ESC genome and examined the relationship between H3.3-nucleosome turnover and ESC-specific transcription factors, chromatin modifiers, and epigenetic marks. RESULTS Our comprehensive analysis of H3.3 dissociation rates revealed distinct H3.3 dissociation dynamics at various functional chromatin domains. At transcription start sites, H3.3 dissociates rapidly with the highest rate at nucleosome-depleted regions (NDRs) just upstream of Pol II binding, followed by low H3.3 dissociation rates across gene bodies. H3.3 turnover at transcription start sites, gene bodies, and transcription end sites was positively correlated with transcriptional activity. H3.3 is found decorated with various histone modifications that regulate transcription and maintain chromatin integrity. We find greatly varying H3.3 dissociation rates across various histone modification domains: high dissociation rates at active histone marks and low dissociation rates at heterochromatic marks. Well- defined zones of high H3.3-nucleosome turnover were detected at binding sites of ESC-specific pluripotency factors and chromatin remodelers, suggesting an important role for H3.3 in facilitating protein binding. Among transcription factor binding sites we detected higher H3.3 turnover at distal cis-acting sites compared to proximal genic transcription factor binding sites. Our results imply that fast H3.3 dissociation is a hallmark of interactions between DNA and transcriptional regulators. CONCLUSION Our study demonstrates that H3.3 turnover and nucleosome stability vary greatly across the chromatin landscape of embryonic stem cells. The presence of high H3.3 turnover at RNA Pol II binding sites at extragenic regions as well as at transcription start and end sites of genes, suggests a specific role for H3.3 in transcriptional initiation and termination. On the other hand, the presence of well-defined zones of high H3.3 dissociation at transcription factor and chromatin remodeler binding sites point to a broader role in facilitating accessibility.
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Affiliation(s)
- Misook Ha
- Samsung Advanced Institute of Technology, Samsung Electronics Corporation, Yongin-Si, 446-712 Gyeonggi-Do South Korea
| | - Daniel C Kraushaar
- Systems Biology Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892 USA
| | - Keji Zhao
- Systems Biology Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892 USA
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224
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Rai TS, Cole JJ, Nelson DM, Dikovskaya D, Faller WJ, Vizioli MG, Hewitt RN, Anannya O, McBryan T, Manoharan I, van Tuyn J, Morrice N, Pchelintsev NA, Ivanov A, Brock C, Drotar ME, Nixon C, Clark W, Sansom OJ, Anderson KI, King A, Blyth K, Adams PD. HIRA orchestrates a dynamic chromatin landscape in senescence and is required for suppression of neoplasia. Genes Dev 2014; 28:2712-25. [PMID: 25512559 PMCID: PMC4265675 DOI: 10.1101/gad.247528.114] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Accepted: 11/04/2014] [Indexed: 01/06/2023]
Abstract
Cellular senescence is a stable proliferation arrest that suppresses tumorigenesis. Cellular senescence and associated tumor suppression depend on control of chromatin. Histone chaperone HIRA deposits variant histone H3.3 and histone H4 into chromatin in a DNA replication-independent manner. Appropriately for a DNA replication-independent chaperone, HIRA is involved in control of chromatin in nonproliferating senescent cells, although its role is poorly defined. Here, we show that nonproliferating senescent cells express and incorporate histone H3.3 and other canonical core histones into a dynamic chromatin landscape. Expression of canonical histones is linked to alternative mRNA splicing to eliminate signals that confer mRNA instability in nonproliferating cells. Deposition of newly synthesized histones H3.3 and H4 into chromatin of senescent cells depends on HIRA. HIRA and newly deposited H3.3 colocalize at promoters of expressed genes, partially redistributing between proliferating and senescent cells to parallel changes in expression. In senescent cells, but not proliferating cells, promoters of active genes are exceptionally enriched in H4K16ac, and HIRA is required for retention of H4K16ac. HIRA is also required for retention of H4K16ac in vivo and suppression of oncogene-induced neoplasia. These results show that HIRA controls a specialized, dynamic H4K16ac-decorated chromatin landscape in senescent cells and enforces tumor suppression.
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Affiliation(s)
- Taranjit Singh Rai
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom; Institute of Biomedical and Environmental Health Research, University of West of Scotland, Paisley PA1 2BE, United Kingdom
| | - John J Cole
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom
| | - David M Nelson
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom
| | - Dina Dikovskaya
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom
| | - William J Faller
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom
| | - Maria Grazia Vizioli
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom
| | - Rachael N Hewitt
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom
| | - Orchi Anannya
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom
| | - Tony McBryan
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom
| | - Indrani Manoharan
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom
| | - John van Tuyn
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom
| | - Nicholas Morrice
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom
| | - Nikolay A Pchelintsev
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom
| | - Andre Ivanov
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom
| | - Claire Brock
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom
| | - Mark E Drotar
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom
| | - Colin Nixon
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom
| | - William Clark
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom
| | - Owen J Sansom
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom
| | - Kurt I Anderson
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom
| | - Ayala King
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom
| | - Karen Blyth
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom
| | - Peter D Adams
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom;
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225
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Transcribing through the nucleosome. Trends Biochem Sci 2014; 39:577-86. [DOI: 10.1016/j.tibs.2014.10.004] [Citation(s) in RCA: 125] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 10/06/2014] [Accepted: 10/07/2014] [Indexed: 11/20/2022]
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226
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Abstract
The building block of chromatin is nucleosome, which consists of 146 base pairs of DNA wrapped around a histone octamer composed of two copies of histone H2A, H2B, H3, and H4. Significantly, the somatic missense mutations of the histone H3 variant, H3.3, are associated with childhood and young-adult tumors, such as pediatric high-grade astrocytomas, as well as chondroblastoma and giant-cell tumors of the bone. The mechanisms by which these histone mutations cause cancer are by and large unclear. Interestingly, two recent studies identified BS69/ZMYND11, which was proposed to be a candidate tumor suppressor, as a specific reader for a modified form of H3.3 (H3.3K36me3). Importantly, some H3.3 cancer mutations are predicted to abrogate the H3.3K36me3/BS69 interaction, suggesting that this interaction may play an important role in tumor suppression. These new findings also raise the question of whether H3.3 cancer mutations may lead to the disruption and/or gain of interactions of additional cellular factors that contribute to tumorigenesis.
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227
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Montes de Oca R, Gurard-Levin ZA, Berger F, Rehman H, Martel E, Corpet A, de Koning L, Vassias I, Wilson LOW, Meseure D, Reyal F, Savignoni A, Asselain B, Sastre-Garau X, Almouzni G. The histone chaperone HJURP is a new independent prognostic marker for luminal A breast carcinoma. Mol Oncol 2014; 9:657-74. [PMID: 25497280 DOI: 10.1016/j.molonc.2014.11.002] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 11/12/2014] [Accepted: 11/12/2014] [Indexed: 10/24/2022] Open
Abstract
BACKGROUND Breast cancer is a heterogeneous disease with different molecular subtypes that have varying responses to therapy. An ongoing challenge in breast cancer research is to distinguish high-risk patients from good prognosis patients. This is particularly difficult in the low-grade, ER-positive luminal A tumors, where robust diagnostic tools to aid clinical treatment decisions are lacking. Recent data implicating chromatin regulators in cancer initiation and progression offers a promising avenue to develop new tools to help guide clinical decisions. METHODS Here we exploit a published transcriptome dataset and an independent validation cohort to correlate the mRNA expression of selected chromatin regulators with respect to the four intrinsic breast cancer molecular subtypes. We then perform univariate and multivariate analyses to compare the prognostic value of a panel of chromatin regulators to Ki67, a currently utilized proliferation marker. RESULTS Unsupervised hierarchical clustering revealed a gene cluster containing several histone chaperones and histone variants highly-expressed in the proliferative subtypes (basal-like, HER2-positive, luminal B) but not in the luminal A subtype. Several chromatin regulators, including the histone chaperones CAF-1 (subunits p150 and p60), ASF1b, and HJURP, and the centromeric histone variant CENP-A, associated with local and metastatic relapse and poor patient outcome. Importantly, we find that HJURP can discriminate favorable and unfavorable outcome within the luminal A subtype, outperforming the currently utilized proliferation marker Ki67, as an independent prognostic marker for luminal A patients. CONCLUSIONS The integration of chromatin regulators as clinical biomarkers, in particular the histone chaperone HJURP, will help guide patient substratification and treatment options for low-risk luminal A breast carcinoma patients.
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Affiliation(s)
- Rocío Montes de Oca
- Institut Curie, Centre de Recherche, Paris F-75248, France; CNRS, UMR3664, Paris F-75248, France; Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris F-75248, France; UPMC, UMR3664, Paris F-75248, France; Sorbonne University, PSL*, France.
| | - Zachary A Gurard-Levin
- Institut Curie, Centre de Recherche, Paris F-75248, France; CNRS, UMR3664, Paris F-75248, France; Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris F-75248, France; UPMC, UMR3664, Paris F-75248, France; Sorbonne University, PSL*, France.
| | - Frédérique Berger
- Sorbonne University, PSL*, France; Institut Curie, U900, Paris F-75248, France; INSERM, U900, Mines Paris-Tech, Paris F-75248, France; Institut Curie, Department of Biostatistics, Paris F-75248, France.
| | - Haniya Rehman
- Institut Curie, Centre de Recherche, Paris F-75248, France; CNRS, UMR3664, Paris F-75248, France; Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris F-75248, France; UPMC, UMR3664, Paris F-75248, France; Sorbonne University, PSL*, France.
| | - Elise Martel
- Institut Curie, Investigative Pathology Platform, Paris F-75248, France.
| | - Armelle Corpet
- Institut Curie, Centre de Recherche, Paris F-75248, France; CNRS, UMR3664, Paris F-75248, France; Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris F-75248, France; UPMC, UMR3664, Paris F-75248, France; Sorbonne University, PSL*, France.
| | - Leanne de Koning
- Institut Curie, Centre de Recherche, Paris F-75248, France; CNRS, UMR3664, Paris F-75248, France; Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris F-75248, France; UPMC, UMR3664, Paris F-75248, France; Sorbonne University, PSL*, France.
| | - Isabelle Vassias
- Institut Curie, Centre de Recherche, Paris F-75248, France; CNRS, UMR3664, Paris F-75248, France; Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris F-75248, France; UPMC, UMR3664, Paris F-75248, France; Sorbonne University, PSL*, France.
| | - Laurence O W Wilson
- Institut Curie, Centre de Recherche, Paris F-75248, France; CNRS, UMR3664, Paris F-75248, France; Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris F-75248, France; UPMC, UMR3664, Paris F-75248, France; Sorbonne University, PSL*, France.
| | - Didier Meseure
- Institut Curie, Investigative Pathology Platform, Paris F-75248, France.
| | - Fabien Reyal
- Institut Curie, Department of Surgery, Paris F-75248, France.
| | - Alexia Savignoni
- Institut Curie, U900, Paris F-75248, France; INSERM, U900, Mines Paris-Tech, Paris F-75248, France; Institut Curie, Department of Biostatistics, Paris F-75248, France.
| | - Bernard Asselain
- Institut Curie, U900, Paris F-75248, France; INSERM, U900, Mines Paris-Tech, Paris F-75248, France; Institut Curie, Department of Biostatistics, Paris F-75248, France.
| | | | - Geneviève Almouzni
- Institut Curie, Centre de Recherche, Paris F-75248, France; CNRS, UMR3664, Paris F-75248, France; Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris F-75248, France; UPMC, UMR3664, Paris F-75248, France; Sorbonne University, PSL*, France.
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228
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Waidmann S, Kusenda B, Mayerhofer J, Mechtler K, Jonak C. A DEK domain-containing protein modulates chromatin structure and function in Arabidopsis. THE PLANT CELL 2014; 26:4328-44. [PMID: 25387881 PMCID: PMC4277211 DOI: 10.1105/tpc.114.129254] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 10/01/2014] [Accepted: 10/22/2014] [Indexed: 05/19/2023]
Abstract
Chromatin is a major determinant in the regulation of virtually all DNA-dependent processes. Chromatin architectural proteins interact with nucleosomes to modulate chromatin accessibility and higher-order chromatin structure. The evolutionarily conserved DEK domain-containing protein is implicated in important chromatin-related processes in animals, but little is known about its DNA targets and protein interaction partners. In plants, the role of DEK has remained elusive. In this work, we identified DEK3 as a chromatin-associated protein in Arabidopsis thaliana. DEK3 specifically binds histones H3 and H4. Purification of other proteins associated with nuclear DEK3 also established DNA topoisomerase 1α and proteins of the cohesion complex as in vivo interaction partners. Genome-wide mapping of DEK3 binding sites by chromatin immunoprecipitation followed by deep sequencing revealed enrichment of DEK3 at protein-coding genes throughout the genome. Using DEK3 knockout and overexpressor lines, we show that DEK3 affects nucleosome occupancy and chromatin accessibility and modulates the expression of DEK3 target genes. Furthermore, functional levels of DEK3 are crucial for stress tolerance. Overall, data indicate that DEK3 contributes to modulation of Arabidopsis chromatin structure and function.
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Affiliation(s)
- Sascha Waidmann
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
| | - Branislav Kusenda
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
| | - Juliane Mayerhofer
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
| | - Karl Mechtler
- Research Institute of Molecular Pathology, Vienna Biocenter, 1030 Vienna, Austria
| | - Claudia Jonak
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
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229
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Weth O, Paprotka C, Günther K, Schulte A, Baierl M, Leers J, Galjart N, Renkawitz R. CTCF induces histone variant incorporation, erases the H3K27me3 histone mark and opens chromatin. Nucleic Acids Res 2014; 42:11941-51. [PMID: 25294833 PMCID: PMC4231773 DOI: 10.1093/nar/gku937] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 09/22/2014] [Accepted: 09/24/2014] [Indexed: 12/21/2022] Open
Abstract
Insulators functionally separate active chromatin domains from inactive ones. The insulator factor, CTCF, has been found to bind to boundaries and to mediate insulator function. CTCF binding sites are depleted for the histone modification H3K27me3 and are enriched for the histone variant H3.3. In order to determine whether demethylation of H3K27me3 and H3.3 incorporation are a requirement for CTCF binding at domain boundaries or whether CTCF causes these changes, we made use of the LacI DNA binding domain to control CTCF binding by the Lac inducer IPTG. Here we show that, in contrast to the related factor CTCFL, the N-terminus plus zinc finger domain of CTCF is sufficient to open compact chromatin rapidly. This is preceded by incorporation of the histone variant H3.3, which thereby removes the H3K27me3 mark. This demonstrates the causal role for CTCF in generating the chromatin features found at insulators. Thereby, spreading of a histone modification from one domain through the insulator into the neighbouring domain is inhibited.
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Affiliation(s)
- Oliver Weth
- Institute for Genetics, Justus-Liebig-University, 35392 Giessen, Germany
| | - Christine Paprotka
- Institute for Genetics, Justus-Liebig-University, 35392 Giessen, Germany
| | - Katharina Günther
- Institute for Genetics, Justus-Liebig-University, 35392 Giessen, Germany
| | - Astrid Schulte
- Institute for Genetics, Justus-Liebig-University, 35392 Giessen, Germany
| | - Manuel Baierl
- Institute for Genetics, Justus-Liebig-University, 35392 Giessen, Germany
| | - Joerg Leers
- Institute for Genetics, Justus-Liebig-University, 35392 Giessen, Germany
| | - Niels Galjart
- Department of Cell Biology and Genetics, Erasmus MC, 3000 CA Rotterdam, The Netherlands
| | - Rainer Renkawitz
- Institute for Genetics, Justus-Liebig-University, 35392 Giessen, Germany
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230
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Filipescu D, Müller S, Almouzni G. Histone H3 Variants and Their Chaperones During Development and Disease: Contributing to Epigenetic Control. Annu Rev Cell Dev Biol 2014; 30:615-46. [DOI: 10.1146/annurev-cellbio-100913-013311] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Dan Filipescu
- Institut Curie, Centre de Recherche, Paris, F-75248 France; , ,
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231
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Ivanauskiene K, Delbarre E, McGhie JD, Küntziger T, Wong LH, Collas P. The PML-associated protein DEK regulates the balance of H3.3 loading on chromatin and is important for telomere integrity. Genome Res 2014; 24:1584-94. [PMID: 25049225 PMCID: PMC4199371 DOI: 10.1101/gr.173831.114] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 07/18/2014] [Indexed: 12/24/2022]
Abstract
Histone variant H3.3 is deposited in chromatin at active sites, telomeres, and pericentric heterochromatin by distinct chaperones, but the mechanisms of regulation and coordination of chaperone-mediated H3.3 loading remain largely unknown. We show here that the chromatin-associated oncoprotein DEK regulates differential HIRA- and DAAX/ATRX-dependent distribution of H3.3 on chromosomes in somatic cells and embryonic stem cells. Live cell imaging studies show that nonnucleosomal H3.3 normally destined to PML nuclear bodies is re-routed to chromatin after depletion of DEK. This results in HIRA-dependent widespread chromatin deposition of H3.3 and H3.3 incorporation in the foci of heterochromatin in a process requiring the DAXX/ATRX complex. In embryonic stem cells, loss of DEK leads to displacement of PML bodies and ATRX from telomeres, redistribution of H3.3 from telomeres to chromosome arms and pericentric heterochromatin, induction of a fragile telomere phenotype, and telomere dysfunction. Our results indicate that DEK is required for proper loading of ATRX and H3.3 on telomeres and for telomeric chromatin architecture. We propose that DEK acts as a "gatekeeper" of chromatin, controlling chromatin integrity by restricting broad access to H3.3 by dedicated chaperones. Our results also suggest that telomere stability relies on mechanisms ensuring proper histone supply and routing.
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Affiliation(s)
- Kristina Ivanauskiene
- Stem Cell Epigenetics Laboratory, Institute of Basic Medical Sciences, Faculty of Medicine, and Norwegian Center for Stem Cell Research, University of Oslo, 0317 Oslo, Norway
| | - Erwan Delbarre
- Stem Cell Epigenetics Laboratory, Institute of Basic Medical Sciences, Faculty of Medicine, and Norwegian Center for Stem Cell Research, University of Oslo, 0317 Oslo, Norway
| | - James D McGhie
- Epigenetics and Chromatin (EpiC) Research, Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Thomas Küntziger
- Stem Cell Epigenetics Laboratory, Institute of Basic Medical Sciences, Faculty of Medicine, and Norwegian Center for Stem Cell Research, University of Oslo, 0317 Oslo, Norway
| | - Lee H Wong
- Epigenetics and Chromatin (EpiC) Research, Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Philippe Collas
- Stem Cell Epigenetics Laboratory, Institute of Basic Medical Sciences, Faculty of Medicine, and Norwegian Center for Stem Cell Research, University of Oslo, 0317 Oslo, Norway;
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232
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Campos EI, Stafford JM, Reinberg D. Epigenetic inheritance: histone bookmarks across generations. Trends Cell Biol 2014; 24:664-74. [PMID: 25242115 DOI: 10.1016/j.tcb.2014.08.004] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Revised: 08/13/2014] [Accepted: 08/14/2014] [Indexed: 12/22/2022]
Abstract
Multiple circuitries ensure that cells respond correctly to the environmental cues within defined cellular programs. There is increasing evidence suggesting that cellular memory for these adaptive processes can be passed on through cell divisions and generations. However, the mechanisms by which this epigenetic information is transferred remain elusive, largely because it requires that such memory survive through gross chromatin remodeling events during DNA replication, mitosis, meiosis, and developmental reprogramming. Elucidating the processes by which epigenetic information survives and is transmitted is a central challenge in biology. In this review, we consider recent advances in understanding mechanisms of epigenetic inheritance with a focus on histone segregation at the replication fork, and how an epigenetic memory may get passed through the paternal lineage.
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Affiliation(s)
- Eric I Campos
- Howard Hughes Medical Institute, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - James M Stafford
- Howard Hughes Medical Institute, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Danny Reinberg
- Howard Hughes Medical Institute, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA.
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233
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Kraushaar DC, Jin W, Maunakea A, Abraham B, Ha M, Zhao K. Genome-wide incorporation dynamics reveal distinct categories of turnover for the histone variant H3.3. Genome Biol 2014; 14:R121. [PMID: 24176123 PMCID: PMC3983652 DOI: 10.1186/gb-2013-14-10-r121] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 10/31/2013] [Indexed: 11/16/2022] Open
Abstract
Background Nucleosomes are present throughout the genome and must be dynamically regulated to accommodate binding of transcription factors and RNA polymerase machineries by various mechanisms. Despite the development of protocols and techniques that have enabled us to map nucleosome occupancy genome-wide, the dynamic properties of nucleosomes remain poorly understood, particularly in mammalian cells. The histone variant H3.3 is incorporated into chromatin independently of DNA replication and requires displacement of existing nucleosomes for its deposition. Here, we measure H3.3 turnover at high resolution in the mammalian genome in order to present a genome-wide characterization of replication-independent H3.3-nucleosome dynamics. Results We developed a system to study the DNA replication-independent turnover of nucleosomes containing the histone variant H3.3 in mammalian cells. By measuring the genome-wide incorporation of H3.3 at different time points following epitope-tagged H3.3 expression, we find three categories of H3.3-nucleosome turnover in vivo: rapid turnover, intermediate turnover and, specifically at telomeres, slow turnover. Our data indicate that H3.3-containing nucleosomes at enhancers and promoters undergo rapid turnover that is associated with active histone modification marks including H3K4me1, H3K4me3, H3K9ac, H3K27ac and the histone variant H2A.Z. The rate of turnover is negatively correlated with H3K27me3 at regulatory regions and with H3K36me3 at gene bodies. Conclusions We have established a reliable approach to measure turnover rates of H3.3-containing nucleosomes on a genome-wide level in mammalian cells. Our results suggest that distinct mechanisms control the dynamics of H3.3 incorporation at functionally different genomic regions.
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234
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Histone H3.3 is required to maintain replication fork progression after UV damage. Curr Biol 2014; 24:2195-2201. [PMID: 25201682 PMCID: PMC4175177 DOI: 10.1016/j.cub.2014.07.077] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 07/11/2014] [Accepted: 07/30/2014] [Indexed: 11/22/2022]
Abstract
Unlike histone H3, which is present only in S phase, the variant histone H3.3 is expressed throughout the cell cycle [1] and is incorporated into chromatin independent of replication [2]. Recently, H3.3 has been implicated in the cellular response to ultraviolet (UV) light [3]. Here, we show that chicken DT40 cells completely lacking H3.3 are hypersensitive to UV light, a defect that epistasis analysis suggests may result from less-effective nucleotide excision repair. Unexpectedly, H3.3-deficient cells also exhibit a substantial defect in maintaining replication fork progression on UV-damaged DNA, which is independent of nucleotide excision repair, demonstrating a clear requirement for H3.3 during S phase. Both the UV hypersensitivity and replication fork slowing are reversed by expression of H3.3 and require the specific residues in the α2 helix that are responsible for H3.3 binding its dedicated chaperones. However, expression of an H3.3 mutant in which serine 31 is replaced with alanine, the equivalent residue in H3.2, restores normal fork progression but not UV resistance, suggesting that H3.3[S31A] may be incorporated at UV-damaged forks but is unable to help cells tolerate UV lesions. Similar behavior was observed with expression of H3.3 carrying mutations at K27 and G34, which have been reported in pediatric brain cancers. We speculate that incorporation of H3.3 during replication may mark sites of lesion bypass and, possibly through an as-yet-unidentified function of the N-terminal tail, facilitate subsequent processing of the damage. We report a vertebrate cell line completely lacking the histone variant H3.3 H3.3-deficient cells are hypersensitive to DNA damage A supply of H3.3 is required to maintain fork progression after UV damage This S phase role requires the distinct chaperone-binding patch of H3.3
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235
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Gurard-Levin ZA, Almouzni G. Histone modifications and a choice of variant: a language that helps the genome express itself. F1000PRIME REPORTS 2014; 6:76. [PMID: 25343033 PMCID: PMC4166940 DOI: 10.12703/p6-76] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covalent post-translational modifications on histones impact chromatin structure and function. Their misfunction, along with perturbations or mutations in genes that regulate their dynamic status, has been observed in several diseases. Thus, targeting histone modifications represents attractive opportunities for therapeutic intervention and biomarker discovery. The best approach to address this challenge is to paint a comprehensive picture integrating the growing number of modifications on individual residues and their combinatorial association, the corresponding modifying enzymes, and effector proteins that bind modifications. Furthermore, how they are imposed in a distinct manner during the cell cycle and on specific histone variants are important dimensions to consider. Firstly, this report highlights innovative technologies used to characterize histone modifications, and the corresponding enzymes and effector proteins. Secondly, we examine the recent progress made in understanding the dynamics and maintenance of histone modifications on distinct variants. We also discuss their roles as potential carriers of epigenetic information. Finally, we provide examples of initiatives to exploit histone modifications in cancer management, with the potential for new therapeutic opportunities.
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Affiliation(s)
- Zachary A. Gurard-Levin
- Institut Curie, Centre de RechercheParis, F-75248France
- CNRS, UMR3664Paris, F-75248France
- Équipe Labellisée Ligue contre le Cancer, UMR3664Paris, F-75248France
- UPMC, UMR3664Paris, F-75248France
- Sorbonne University, PSLParisFrance
| | - Geneviève Almouzni
- Institut Curie, Centre de RechercheParis, F-75248France
- CNRS, UMR3664Paris, F-75248France
- Équipe Labellisée Ligue contre le Cancer, UMR3664Paris, F-75248France
- UPMC, UMR3664Paris, F-75248France
- Sorbonne University, PSLParisFrance
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236
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Transcription factor EKLF (KLF1) recruitment of the histone chaperone HIRA is essential for β-globin gene expression. Proc Natl Acad Sci U S A 2014; 111:13337-42. [PMID: 25197097 DOI: 10.1073/pnas.1405422111] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The binding of chromatin-associated proteins and incorporation of histone variants correlates with alterations in gene expression. These changes have been particularly well analyzed at the mammalian β-globin locus, where transcription factors such as erythroid Krüppel-like factor (EKLF), which is also known as Krüppel-like factor 1 (KLF1), play a coordinating role in establishing the proper chromatin structure and inducing high-level expression of adult β-globin. We had previously shown that EKLF preferentially interacts with histone H3 and that the H3.3 variant is differentially recruited to the β-globin promoter. We now find that a novel interaction between EKLF and the histone cell cycle regulation defective homolog A (HIRA) histone chaperone accounts for these effects. HIRA is not only critical for β-globin expression but is also required for activation of the erythropoietic regulators EKLF and GATA binding protein 1 (GATA1). Our results provide a mechanism by which transcription factor-directed recruitment of a generally expressed histone chaperone can lead to tissue-restricted changes in chromatin components, structure, and transcription at specific genomic sites during differentiation.
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237
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Yuen BTK, Bush KM, Barrilleaux BL, Cotterman R, Knoepfler PS. Histone H3.3 regulates dynamic chromatin states during spermatogenesis. Development 2014; 141:3483-94. [PMID: 25142466 DOI: 10.1242/dev.106450] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The histone variant H3.3 is involved in diverse biological processes, including development, transcriptional memory and transcriptional reprogramming, as well as diseases, including most notably malignant brain tumors. Recently, we developed a knockout mouse model for the H3f3b gene, one of two genes encoding H3.3. Here, we show that targeted disruption of H3f3b results in a number of phenotypic abnormalities, including a reduction in H3.3 histone levels, leading to male infertility, as well as abnormal sperm and testes morphology. Additionally, null germ cell populations at specific stages in spermatogenesis, in particular spermatocytes and spermatogonia, exhibited increased rates of apoptosis. Disruption of H3f3b also altered histone post-translational modifications and gene expression in the testes, with the most prominent changes occurring at genes involved in spermatogenesis. Finally, H3f3b null testes also exhibited abnormal germ cell chromatin reorganization and reduced protamine incorporation. Taken together, our studies indicate a major role for H3.3 in spermatogenesis through regulation of chromatin dynamics.
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Affiliation(s)
- Benjamin T K Yuen
- Department of Cell Biology and Human Anatomy, Shriners Hospital For Children Northern California, Sacramento, CA 95817, USA Genome Center, University of California Davis School of Medicine, Shriners Hospital For Children Northern California, Sacramento, CA 95817, USA Institute of Pediatric Regenerative Medicine, Shriners Hospital For Children Northern California, Sacramento, CA 95817, USA
| | - Kelly M Bush
- Department of Cell Biology and Human Anatomy, Shriners Hospital For Children Northern California, Sacramento, CA 95817, USA Genome Center, University of California Davis School of Medicine, Shriners Hospital For Children Northern California, Sacramento, CA 95817, USA Institute of Pediatric Regenerative Medicine, Shriners Hospital For Children Northern California, Sacramento, CA 95817, USA
| | - Bonnie L Barrilleaux
- Department of Cell Biology and Human Anatomy, Shriners Hospital For Children Northern California, Sacramento, CA 95817, USA Genome Center, University of California Davis School of Medicine, Shriners Hospital For Children Northern California, Sacramento, CA 95817, USA Institute of Pediatric Regenerative Medicine, Shriners Hospital For Children Northern California, Sacramento, CA 95817, USA
| | - Rebecca Cotterman
- Department of Cell Biology and Human Anatomy, Shriners Hospital For Children Northern California, Sacramento, CA 95817, USA Genome Center, University of California Davis School of Medicine, Shriners Hospital For Children Northern California, Sacramento, CA 95817, USA Institute of Pediatric Regenerative Medicine, Shriners Hospital For Children Northern California, Sacramento, CA 95817, USA
| | - Paul S Knoepfler
- Department of Cell Biology and Human Anatomy, Shriners Hospital For Children Northern California, Sacramento, CA 95817, USA Genome Center, University of California Davis School of Medicine, Shriners Hospital For Children Northern California, Sacramento, CA 95817, USA Institute of Pediatric Regenerative Medicine, Shriners Hospital For Children Northern California, Sacramento, CA 95817, USA
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238
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Skene PJ, Henikoff S. Histones push the envelope. Nat Struct Mol Biol 2014; 21:651-2. [PMID: 25093523 DOI: 10.1038/nsmb.2864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Peter J Skene
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Steven Henikoff
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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239
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Engelhorn J, Blanvillain R, Carles CC. Gene activation and cell fate control in plants: a chromatin perspective. Cell Mol Life Sci 2014; 71:3119-37. [PMID: 24714879 PMCID: PMC11113918 DOI: 10.1007/s00018-014-1609-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Revised: 03/10/2014] [Accepted: 03/12/2014] [Indexed: 01/02/2023]
Abstract
In plants, environment-adaptable organogenesis extends throughout the lifespan, and iterative development requires repetitive rounds of activation and repression of several sets of genes. Eukaryotic genome compaction into chromatin forms a physical barrier for transcription; therefore, induction of gene expression requires alteration in chromatin structure. One of the present great challenges in molecular and developmental biology is to understand how chromatin is brought from a repressive to permissive state on specific loci and in a very specific cluster of cells, as well as how this state is further maintained and propagated through time and cell division in a cell lineage. In this review, we report recent discoveries implementing our knowledge on chromatin dynamics that modulate developmental gene expression. We also discuss how new data sets highlight plant specificities, likely reflecting requirement for a highly dynamic chromatin.
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Affiliation(s)
- Julia Engelhorn
- Université Grenoble Alpes, UMR5168, 38041, Grenoble, France,
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240
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Nie X, Wang H, Li J, Holec S, Berger F. The HIRA complex that deposits the histone H3.3 is conserved in Arabidopsis and facilitates transcriptional dynamics. Biol Open 2014; 3:794-802. [PMID: 25086063 PMCID: PMC4163656 DOI: 10.1242/bio.20148680] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
In animals, replication-independent incorporation of nucleosomes containing the histone variant H3.3 enables global reprogramming of histone modifications and transcriptional profiles. H3.3 enrichment over gene bodies correlates with gene transcription in animals and plants. In animals, H3.3 is deposited into chromatin by specific protein complexes, including the HIRA complex. H3.3 variants evolved independently and acquired similar properties in animals and plants, questioning how the H3.3 deposition machinery evolved in plants and what are its biological functions. We performed phylogenetic analyses in the plant kingdom and identified in Arabidopsis all orthologs of human genes encoding members of the HIRA complex. Genetic analyses, biochemical data and protein localisation suggest that these proteins form a complex able to interact with H3.3 in Arabidopsis in a manner similar to that described in mammals. In contrast to animals, where HIRA is required for fertilization and early development, loss of function of HIRA in Arabidopsis causes mild phenotypes in the adult plant and does not perturb sexual reproduction and embryogenesis. Rather, HIRA function is required for transcriptional reprogramming during dedifferentiation of plant cells that precedes vegetative propagation and for the appropriate transcription of genes responsive to biotic and abiotic factors. We conclude that the molecular function of the HIRA complex is conserved between plants and animals. Yet plants diversified HIRA functions to enable asexual reproduction and responsiveness to the environment in response to the plant sessile lifestyle.
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Affiliation(s)
- Xin Nie
- Temasek Lifesciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543 Singapore
| | - Haifeng Wang
- Temasek Lifesciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543 Singapore
| | - Jing Li
- Temasek Lifesciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543 Singapore
| | - Sarah Holec
- Temasek Lifesciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore
| | - Frédéric Berger
- Temasek Lifesciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543 Singapore
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241
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Müller S, Montes de Oca R, Lacoste N, Dingli F, Loew D, Almouzni G. Phosphorylation and DNA binding of HJURP determine its centromeric recruitment and function in CenH3(CENP-A) loading. Cell Rep 2014; 8:190-203. [PMID: 25001279 DOI: 10.1016/j.celrep.2014.06.002] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 05/21/2014] [Accepted: 06/01/2014] [Indexed: 01/20/2023] Open
Abstract
Centromeres, epigenetically defined by the presence of the histone H3 variant CenH3, are essential for ensuring proper chromosome segregation. In mammals, centromeric CenH3(CENP-A) deposition requires its dedicated chaperone HJURP and occurs during telophase/early G1. We find that the cell-cycle-dependent recruitment of HJURP to centromeres depends on its timely phosphorylation controlled via cyclin-dependent kinases. A nonphosphorylatable HJURP mutant localizes prematurely to centromeres in S and G2 phase. This unregulated targeting causes a premature loading of CenH3(CENP-A) at centromeres, and cell-cycle delays ensue. Once recruited to centromeres, HJURP functions to promote CenH3(CENP-A) deposition by a mechanism involving a unique DNA-binding domain. With our findings, we propose a model wherein (1) the phosphorylation state of HJURP controls its centromeric recruitment in a cell-cycle-dependent manner, and (2) HJURP binding to DNA is a mechanistic determinant in CenH3(CENP-A) loading.
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Affiliation(s)
- Sebastian Müller
- Institut Curie, Centre de Recherche, Paris 75248, France; CNRS, UMR3664, Paris 75248, France; Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris 75248, France; UPMC, UMR3664, Paris 75248, France; Sorbonne University, Paris 75005, France
| | - Rocio Montes de Oca
- Institut Curie, Centre de Recherche, Paris 75248, France; CNRS, UMR3664, Paris 75248, France; Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris 75248, France; UPMC, UMR3664, Paris 75248, France; Sorbonne University, Paris 75005, France
| | - Nicolas Lacoste
- Institut Curie, Centre de Recherche, Paris 75248, France; CNRS, UMR3664, Paris 75248, France; Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris 75248, France; UPMC, UMR3664, Paris 75248, France; Sorbonne University, Paris 75005, France
| | - Florent Dingli
- Institut Curie, Centre de Recherche, Paris 75248, France; Laboratory of Proteomic Mass Spectrometry, 75248 Paris Cedex 05, France
| | - Damarys Loew
- Institut Curie, Centre de Recherche, Paris 75248, France; Laboratory of Proteomic Mass Spectrometry, 75248 Paris Cedex 05, France
| | - Geneviève Almouzni
- Institut Curie, Centre de Recherche, Paris 75248, France; CNRS, UMR3664, Paris 75248, France; Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris 75248, France; UPMC, UMR3664, Paris 75248, France; Sorbonne University, Paris 75005, France.
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242
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Bošković A, Eid A, Pontabry J, Ishiuchi T, Spiegelhalter C, Raghu Ram EVS, Meshorer E, Torres-Padilla ME. Higher chromatin mobility supports totipotency and precedes pluripotency in vivo. Genes Dev 2014; 28:1042-7. [PMID: 24831699 PMCID: PMC4035533 DOI: 10.1101/gad.238881.114] [Citation(s) in RCA: 123] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Torres-Padilla and colleagues investigate the chromatin-based mechanisms behind the transition from totipotency to pluripotency in the developing mouse embryo. Tracking histone dynamics by FRAP in vivo reveals that core histone mobility decreases as development proceeds, defining different cellular states (totipotency, pluripotency, and differentiation). Strikingly, totipotent cells in vitro display the same high chromatin mobility as totipotent cells in the embryo. The data suggest that changes in chromatin dynamics underlie the transitions in cellular plasticity and that higher chromatin mobility is at the nuclear foundations of totipotency. The fusion of the gametes upon fertilization results in the formation of a totipotent cell. Embryonic chromatin is expected to be able to support a large degree of plasticity. However, whether this plasticity relies on a particular conformation of the embryonic chromatin is unknown. Moreover, whether chromatin plasticity is functionally linked to cellular potency has not been addressed. Here, we adapted fluorescence recovery after photobleaching (FRAP) in the developing mouse embryo and show that mobility of the core histones H2A, H3.1, and H3.2 is unusually high in two-cell stage embryos and decreases as development proceeds. The transition toward pluripotency is accompanied by a decrease in histone mobility, and, upon lineage allocation, pluripotent cells retain higher mobility than the differentiated trophectoderm. Importantly, totipotent two-cell-like embryonic stem cells also display high core histone mobility, implying that reprogramming toward totipotency entails changes in chromatin mobility. Our data suggest that changes in chromatin dynamics underlie the transitions in cellular plasticity and that higher chromatin mobility is at the nuclear foundations of totipotency.
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Affiliation(s)
- Ana Bošković
- CNRS/INSERM U964, Université de Strasbourg, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67404 Illkirch, France
| | - André Eid
- CNRS/INSERM U964, Université de Strasbourg, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67404 Illkirch, France
| | - Julien Pontabry
- CNRS/INSERM U964, Université de Strasbourg, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67404 Illkirch, France
| | - Takashi Ishiuchi
- CNRS/INSERM U964, Université de Strasbourg, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67404 Illkirch, France
| | - Coralie Spiegelhalter
- CNRS/INSERM U964, Université de Strasbourg, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67404 Illkirch, France
| | - Edupuganti V S Raghu Ram
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Eran Meshorer
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Maria-Elena Torres-Padilla
- CNRS/INSERM U964, Université de Strasbourg, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67404 Illkirch, France
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243
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Inoue A, Zhang Y. Nucleosome assembly is required for nuclear pore complex assembly in mouse zygotes. Nat Struct Mol Biol 2014; 21:609-16. [PMID: 24908396 DOI: 10.1038/nsmb.2839] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 05/08/2014] [Indexed: 12/15/2022]
Abstract
Packaging of DNA into nucleosomes not only helps to store genetic information but also creates diverse means for regulating DNA-templated processes. Attempts to reveal additional functions of the nucleosome have been unsuccessful, owing to cell lethality caused by nucleosome deletion. Taking advantage of the mammalian fertilization process, in which sperm DNA assembles into nucleosomes de novo, we generated nucleosome-depleted (ND) paternal pronuclei by depleting maternal histone H3.3 or its chaperone HIRA in mouse zygotes. We found that the ND pronucleus forms a nuclear envelope devoid of nuclear pore complexes (NPCs). Loss of NPCs is accompanied by defective localization of ELYS, a nucleoporin essential for NPC assembly, to the nuclear rim. Interestingly, tethering ELYS to the nuclear rim of the ND nucleus rescues NPC assembly. Our study thus demonstrates that nucleosome assembly is a prerequisite for NPC assembly during paternal pronuclear formation.
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Affiliation(s)
- Azusa Inoue
- 1] Howard Hughes Medical Institute, Boston, Massachusetts, USA. [2] Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA. [3] Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA. [4] Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Yi Zhang
- 1] Howard Hughes Medical Institute, Boston, Massachusetts, USA. [2] Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA. [3] Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA. [4] Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA. [5] Harvard Stem Cell Institute, Boston, Massachusetts, USA
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244
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Boyarchuk E, Filipescu D, Vassias I, Cantaloube S, Almouzni G. The histone variant composition of centromeres is controlled by the pericentric heterochromatin state during the cell cycle. J Cell Sci 2014; 127:3347-59. [PMID: 24906798 DOI: 10.1242/jcs.148189] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Correct chromosome segregation requires a unique chromatin environment at centromeres and in their vicinity. Here, we address how the deposition of canonical H2A and H2A.Z histone variants is controlled at pericentric heterochromatin (PHC). Whereas in euchromatin newly synthesized H2A and H2A.Z are deposited throughout the cell cycle, we reveal two discrete waves of deposition at PHC - during mid to late S phase in a replication-dependent manner for H2A and during G1 phase for H2A.Z. This G1 cell cycle restriction is lost when heterochromatin features are altered, leading to the accumulation of H2A.Z at the domain. Interestingly, compromising PHC integrity also impacts upon neighboring centric chromatin, increasing the amount of centromeric CENP-A without changing the timing of its deposition. We conclude that the higher-order chromatin structure at the pericentric domain influences dynamics at the nucleosomal level within centromeric chromatin. The two different modes of rearrangement of the PHC during the cell cycle provide distinct opportunities to replenish one or the other H2A variant, highlighting PHC integrity as a potential signal to regulate the deposition timing and stoichiometry of histone variants at the centromere.
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Affiliation(s)
- Ekaterina Boyarchuk
- Institut Curie, Centre de Recherche, Paris, 75248 France CNRS, UMR3664, Paris, 75248 France Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris, 75248 France UPMC, UMR3664, Paris, 75248 France Sorbonne University, PSL, 75006 Paris, France
| | - Dan Filipescu
- Institut Curie, Centre de Recherche, Paris, 75248 France CNRS, UMR3664, Paris, 75248 France Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris, 75248 France UPMC, UMR3664, Paris, 75248 France Sorbonne University, PSL, 75006 Paris, France
| | - Isabelle Vassias
- Institut Curie, Centre de Recherche, Paris, 75248 France CNRS, UMR3664, Paris, 75248 France Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris, 75248 France UPMC, UMR3664, Paris, 75248 France Sorbonne University, PSL, 75006 Paris, France
| | - Sylvain Cantaloube
- Institut Curie, Centre de Recherche, Paris, 75248 France CNRS, UMR3664, Paris, 75248 France Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris, 75248 France UPMC, UMR3664, Paris, 75248 France Sorbonne University, PSL, 75006 Paris, France
| | - Geneviève Almouzni
- Institut Curie, Centre de Recherche, Paris, 75248 France CNRS, UMR3664, Paris, 75248 France Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris, 75248 France UPMC, UMR3664, Paris, 75248 France Sorbonne University, PSL, 75006 Paris, France
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245
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Polo SE. Reshaping chromatin after DNA damage: the choreography of histone proteins. J Mol Biol 2014; 427:626-36. [PMID: 24887097 PMCID: PMC5111727 DOI: 10.1016/j.jmb.2014.05.025] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 05/19/2014] [Accepted: 05/21/2014] [Indexed: 01/03/2023]
Abstract
DNA damage signaling and repair machineries operate in a nuclear environment where DNA is wrapped around histone proteins and packaged into chromatin. Understanding how chromatin structure is restored together with the DNA sequence during DNA damage repair has been a topic of intense research. Indeed, chromatin integrity is central to cell functions and identity. However, chromatin shows remarkable plasticity in response to DNA damage. This review presents our current knowledge of chromatin dynamics in the mammalian cell nucleus in response to DNA double strand breaks and UV lesions. I provide an overview of the key players involved in regulating histone dynamics in damaged chromatin regions, focusing on histone chaperones and their concerted action with histone modifiers, chromatin remodelers and repair factors. I also discuss how these dynamics contribute to reshaping chromatin and, by altering the chromatin landscape, may affect the maintenance of epigenetic information.
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Affiliation(s)
- Sophie E Polo
- Epigenetics and Cell Fate Centre, UMR7216 CNRS, Paris Diderot University, 75205 Paris Cedex 13, France.
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246
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Lund E, Oldenburg AR, Collas P. Enriched domain detector: a program for detection of wide genomic enrichment domains robust against local variations. Nucleic Acids Res 2014; 42:e92. [PMID: 24782521 PMCID: PMC4066758 DOI: 10.1093/nar/gku324] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 04/03/2014] [Accepted: 04/07/2014] [Indexed: 12/31/2022] Open
Abstract
Nuclear lamins contact the genome at the nuclear periphery through large domains and are involved in chromatin organization. Among broad peak calling algorithms available to date, none are suited for mapping lamin-genome interactions genome wide. We disclose a novel algorithm, enriched domain detector (EDD), for analysis of broad enrichment domains from chromatin immunoprecipitation (ChIP)-seq data. EDD enables discovery of genomic domains interacting with broadly distributed proteins, such as A- and B-type lamins affinity isolated by ChIP. The advantages of EDD over existing broad peak callers are sensitivity to domain width rather than enrichment strength at a particular site, and robustness against local variations.
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Affiliation(s)
- Eivind Lund
- Stem Cell Epigenetics Laboratory, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, and Norwegian Center for Stem Cell Research, PO Box 1112 Blindern, 0317 Oslo, Norway
| | - Anja R Oldenburg
- Stem Cell Epigenetics Laboratory, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, and Norwegian Center for Stem Cell Research, PO Box 1112 Blindern, 0317 Oslo, Norway
| | - Philippe Collas
- Stem Cell Epigenetics Laboratory, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, and Norwegian Center for Stem Cell Research, PO Box 1112 Blindern, 0317 Oslo, Norway
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247
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Chromatin maintenance and dynamics in senescence: a spotlight on SAHF formation and the epigenome of senescent cells. Chromosoma 2014; 123:423-36. [PMID: 24861957 DOI: 10.1007/s00412-014-0469-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 05/09/2014] [Accepted: 05/09/2014] [Indexed: 01/28/2023]
Abstract
Senescence is a stable proliferation arrest characterized by profound changes in cellular morphology and metabolism as well as by extensive chromatin reorganization in the nucleus. One particular hallmark of chromatin changes during senescence is the formation of punctate DNA foci in DAPI-stained senescent cells that have been called senescence-associated heterochromatin foci (SAHF). While many advances have been made concerning our understanding of the effectors of senescence, how chromatin is reorganized and maintained in senescent cells has remained largely elusive. Because chromatin structure is inherently dynamic, senescent cells face the challenge of developing chromatin maintenance mechanisms in the absence of DNA replication in order to maintain the senescent phenotype. Here, we summarize and review recent findings shedding light on SAHF composition and formation via spatial repositioning of chromatin, with a specific focus on the role of lamin B1 for this process. In addition, we discuss the physiological implication of SAHF formation, the role of histone variants, and histone chaperones during senescence and also elaborate on the more general changes observed in the epigenome of the senescent cells.
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248
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Abstract
Eukaryotic gene regulation involves a balance between packaging of the genome into nucleosomes and enabling access to regulatory proteins and RNA polymerase. Nucleosomes, consisting of DNA wrapped around a core of histone proteins, are integral components of gene regulation that restrict access to both regulatory sequences and the underlying template. In this review, Weber and Henikoff consider how histone variants and their interacting partners are involved in transcriptional regulation through the creation of unique chromatin states. Eukaryotic gene regulation involves a balance between packaging of the genome into nucleosomes and enabling access to regulatory proteins and RNA polymerase. Nucleosomes are integral components of gene regulation that restrict access to both regulatory sequences and the underlying template. Whereas canonical histones package the newly replicated genome, they can be replaced with histone variants that alter nucleosome structure, stability, dynamics, and, ultimately, DNA accessibility. Here we consider how histone variants and their interacting partners are involved in transcriptional regulation through the creation of unique chromatin states.
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Affiliation(s)
- Christopher M Weber
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
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249
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Mandemaker IK, Vermeulen W, Marteijn JA. Gearing up chromatin: A role for chromatin remodeling during the transcriptional restart upon DNA damage. Nucleus 2014; 5:203-10. [PMID: 24809693 PMCID: PMC4133215 DOI: 10.4161/nucl.29085] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
During transcription, RNA polymerase may encounter DNA lesions, which causes stalling of transcription. To overcome the RNA polymerase blocking lesions, the transcribed strand is repaired by a dedicated repair mechanism, called transcription coupled nucleotide excision repair (TC-NER). After repair is completed, it is essential that transcription restarts. So far, the regulation and exact molecular mechanism of this transcriptional restart upon genotoxic damage has remained elusive. Recently, three different chromatin remodeling factors, HIRA, FACT, and Dot1L, were identified to stimulate transcription restart after DNA damage. These factors either incorporate new histones or establish specific chromatin marks that will gear up the chromatin to subsequently promote transcription recovery. This adds a new layer to the current model of chromatin remodeling necessary for repair and indicates that this specific form of transcription, i.e., the transcriptional restart upon DNA damage, needs specific chromatin remodeling events.
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Affiliation(s)
- Imke K Mandemaker
- Department of Genetics; Erasmus Medical Centre; Rotterdam, the Netherlands
| | - Wim Vermeulen
- Department of Genetics; Erasmus Medical Centre; Rotterdam, the Netherlands
| | - Jurgen A Marteijn
- Department of Genetics; Erasmus Medical Centre; Rotterdam, the Netherlands
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250
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Adam S, Polo SE, Almouzni G. How to restore chromatin structure and function in response to DNA damage--let the chaperones play: delivered on 9 July 2013 at the 38th FEBS Congress in St Petersburg, Russia. FEBS J 2014; 281:2315-23. [PMID: 24673849 DOI: 10.1111/febs.12793] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 03/25/2014] [Indexed: 01/07/2023]
Abstract
Histone deposition onto DNA assisted by specific chaperones forms the chromatin basic unit and serves to package the genome within the cell nucleus. The resulting chromatin organization, often referred to as the epigenome, contributes to a unique transcriptional program that defines cell identity. Importantly, during cellular life, substantial alterations in chromatin structure may arise due to cell stress, including DNA damage, which not only challenges the integrity of the genome but also threatens the epigenome. Considerable efforts have been made to decipher chromatin dynamics in response to genotoxic stress, and to assess how it affects both genome and epigenome stability. Here, we review recent advances in understanding the mechanisms of DNA damage-induced chromatin plasticity in mammalian cells. We focus specifically on the dynamics of histone H3 variants in response to UV irradiation, and highlight the role of their dedicated chaperones in restoring both chromatin structure and function. Finally, we discuss how, in addition to restoring chromatin integrity, the cellular networks that signal and repair DNA damage may also provide a window of opportunity for modulating the information conveyed by chromatin.
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Affiliation(s)
- Salomé Adam
- Institut Curie, Centre de Recherche, Paris, France; Centre National de la Recherche Scientifique, UMR3664, Paris, France; Equipe Labellisée Ligue Contre le Cancer, Paris, France; Institut de Formation Doctorale, University Pierre & Marie Curie, Paris, France; Sorbonne University, PSL*, Paris, France; Epigenetics and Cell Fate Centre, UMR7216, Centre National de la Recherche Scientifique/Paris Diderot University, Paris, France
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