201
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Tochio N, Umehara T, Munemasa Y, Suzuki T, Sato S, Tsuda K, Koshiba S, Kigawa T, Nagai R, Yokoyama S. Solution structure of histone chaperone ANP32B: interaction with core histones H3-H4 through its acidic concave domain. J Mol Biol 2010; 401:97-114. [PMID: 20538007 DOI: 10.1016/j.jmb.2010.06.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2010] [Revised: 05/27/2010] [Accepted: 06/01/2010] [Indexed: 01/08/2023]
Abstract
Eukaryotic gene expression is regulated by histone deposition onto and eviction from nucleosomes, which are mediated by several chromatin-modulating factors. Among them, histone chaperones are key factors that facilitate nucleosome assembly. Acidic nuclear phosphoprotein 32B (ANP32B) belongs to the ANP32 family, which shares N-terminal leucine-rich repeats (LRRs) and a C-terminal variable anionic region. The C-terminal region functions as an inhibitor of histone acetylation, but the functional roles of the LRR domain in chromatin regulation have remained elusive. Here, we report that the LRR domain of ANP32B possesses histone chaperone activity and forms a curved structure with a parallel beta-sheet on the concave side and mostly helical elements on the convex side. Our analyses revealed that the interaction of ANP32B with the core histones H3-H4 occurs on its concave side, and both the acidic and hydrophobic residues that compose the concave surface are critical for histone binding. These results provide a structural framework for understanding the functional mechanisms of acidic histone chaperones.
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Affiliation(s)
- Naoya Tochio
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
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202
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Drané P, Ouararhni K, Depaux A, Shuaib M, Hamiche A. The death-associated protein DAXX is a novel histone chaperone involved in the replication-independent deposition of H3.3. Genes Dev 2010; 24:1253-65. [PMID: 20504901 DOI: 10.1101/gad.566910] [Citation(s) in RCA: 504] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The histone variant H3.3 marks active chromatin by replacing the conventional histone H3.1. In this study, we investigate the detailed mechanism of H3.3 replication-independent deposition. We found that the death domain-associated protein DAXX and the chromatin remodeling factor ATRX (alpha-thalassemia/mental retardation syndrome protein) are specifically associated with the H3.3 deposition machinery. Bacterially expressed DAXX has a marked binding preference for H3.3 and assists the deposition of (H3.3-H4)(2) tetramers on naked DNA, thus showing that DAXX is a H3.3 histone chaperone. In DAXX-depleted cells, a fraction of H3.3 was found associated with the replication-dependent machinery of deposition, suggesting that cells adapt to the depletion. The reintroduced DAXX in these cells colocalizes with H3.3 into the promyelocytic leukemia protein (PML) bodies. Moreover, DAXX associates with pericentric DNA repeats, and modulates the transcription from these repeats through assembly of H3.3 nucleosomes. These findings establish a new link between the PML bodies and the regulation of pericentric DNA repeat chromatin structure. Taken together, our data demonstrate that DAXX functions as a bona fide histone chaperone involved in the replication-independent deposition of H3.3.
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Affiliation(s)
- Pascal Drané
- IGMBC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), Illkirch F-67400, France
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203
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Morillo-Huesca M, Maya D, Muñoz-Centeno MC, Singh RK, Oreal V, Reddy GU, Liang D, Géli V, Gunjan A, Chávez S. FACT prevents the accumulation of free histones evicted from transcribed chromatin and a subsequent cell cycle delay in G1. PLoS Genet 2010; 6:e1000964. [PMID: 20502685 PMCID: PMC2873916 DOI: 10.1371/journal.pgen.1000964] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2009] [Accepted: 04/20/2010] [Indexed: 11/18/2022] Open
Abstract
The FACT complex participates in chromatin assembly and disassembly during transcription elongation. The yeast mutants affected in the SPT16 gene, which encodes one of the FACT subunits, alter the expression of G1 cyclins and exhibit defects in the G1/S transition. Here we show that the dysfunction of chromatin reassembly factors, like FACT or Spt6, down-regulates the expression of the gene encoding the cyclin that modulates the G1 length (CLN3) in START by specifically triggering the repression of its promoter. The G1 delay undergone by spt16 mutants is not mediated by the DNA–damage checkpoint, although the mutation of RAD53, which is otherwise involved in histone degradation, enhances the cell-cycle defects of spt16-197. We reveal how FACT dysfunction triggers an accumulation of free histones evicted from transcribed chromatin. This accumulation is enhanced in a rad53 background and leads to a delay in G1. Consistently, we show that the overexpression of histones in wild-type cells down-regulates CLN3 in START and causes a delay in G1. Our work shows that chromatin reassembly factors are essential players in controlling the free histones potentially released from transcribed chromatin and describes a new cell cycle phenomenon that allows cells to respond to excess histones before starting DNA replication. Lengthy genomic DNA is packed in a highly organized nucleoprotein structure called chromatin, whose basic subunit is the nucleosome which is formed by DNA wrapped around an octamer of proteins called histones. Nucleosomes need to be disassembled to allow DNA transcription by RNA polymerases. An essential factor for the disassembly/reassembly process during DNA transcription is the FACT complex. We investigated a phenotype of yeast FACT mutants, a delay in a specific step of the cell cycle division process immediately prior to starting DNA replication. The dysfunction caused by the FACT mutation causes a downregulation of a gene, CLN3, which controls the length of that specific step of the cell cycle. FACT dysfunction also increases the level of the free histones released from chromatin during transcription, and the phenotype of the Spt16 mutant is enhanced by a second mutation affecting a protein that regulates DNA repair and excess histone degradation. Moreover, we show that the overexpression of histones causes a cell cycle delay before DNA replication in wild-type cells. Our results point out a so-far unknown connection between chromatin dynamics and the regulation of the cell cycle.
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Affiliation(s)
| | - Douglas Maya
- Departamento de Genética, Universidad de Sevilla, Seville, Spain
| | | | - Rakesh Kumar Singh
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida, United States of America
| | - Vincent Oreal
- Laboratoire d'Instabilité Génétique et Cancérogenèse, Institut de Biologie Struturale et Microbiologie, Centre National de la Recherche Scientifique, Marseille, France
| | - Gajjalaiahvari Ugander Reddy
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida, United States of America
| | - Dun Liang
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida, United States of America
| | - Vincent Géli
- Laboratoire d'Instabilité Génétique et Cancérogenèse, Institut de Biologie Struturale et Microbiologie, Centre National de la Recherche Scientifique, Marseille, France
| | - Akash Gunjan
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida, United States of America
| | - Sebastián Chávez
- Departamento de Genética, Universidad de Sevilla, Seville, Spain
- * E-mail: (SC); (MCM-C)
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204
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Akai Y, Adachi N, Hayashi Y, Eitoku M, Sano N, Natsume R, Kudo N, Tanokura M, Senda T, Horikoshi M. Structure of the histone chaperone CIA/ASF1-double bromodomain complex linking histone modifications and site-specific histone eviction. Proc Natl Acad Sci U S A 2010; 107:8153-8. [PMID: 20393127 PMCID: PMC2889523 DOI: 10.1073/pnas.0912509107] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Nucleosomes around the promoter region are disassembled for transcription in response to various signals, such as acetylation and methylation of histones. Although the interactions between histone-acetylation-recognizing bromodomains and factors involved in nucleosome disassembly have been reported, no structural basis connecting histone modifications and nucleosome disassembly has been obtained. Here, we determined at 3.3 A resolution the crystal structure of histone chaperone cell cycle gene 1 (CCG1) interacting factor A/antisilencing function 1 (CIA/ASF1) in complex with the double bromodomain in the CCG1/TAF1/TAF(II)250 subunit of transcription factor IID. Structural, biochemical, and biological studies suggested that interaction between double bromodomain and CIA/ASF1 is required for their colocalization, histone eviction, and pol II entry at active promoter regions. Furthermore, the present crystal structure has characteristics that can connect histone acetylation and CIA/ASF1-mediated histone eviction. These findings suggest that the molecular complex between CIA/ASF1 and the double bromodomain plays a key role in site-specific histone eviction at active promoter regions. The model we propose here is the initial structure-based model of the biological signaling from histone modifications to structural change of the nucleosome (hi-MOST model).
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Affiliation(s)
- Yusuke Akai
- Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
- Protein Structural Information Analysis Team, Japan Biological Informatics Consortium, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Naruhiko Adachi
- Protein Structural Information Analysis Team, Japan Biological Informatics Consortium, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
- Laboratory of Developmental Biology, Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan; and
- Horikoshi Gene Selector Project, Exploratory Research for Advanced Technology, Japan Science and Technology Agency, 5-9-6 Tokodai, Tsukuba, Ibaraki 300-2635, Japan
| | - Yohei Hayashi
- Laboratory of Developmental Biology, Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan; and
| | - Masamitsu Eitoku
- Laboratory of Developmental Biology, Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan; and
| | - Norihiko Sano
- Laboratory of Developmental Biology, Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan; and
| | - Ryo Natsume
- Protein Structural Information Analysis Team, Japan Biological Informatics Consortium, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Norio Kudo
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Masaru Tanokura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Toshiya Senda
- Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Masami Horikoshi
- Laboratory of Developmental Biology, Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan; and
- Horikoshi Gene Selector Project, Exploratory Research for Advanced Technology, Japan Science and Technology Agency, 5-9-6 Tokodai, Tsukuba, Ibaraki 300-2635, Japan
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205
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The histone shuffle: histone chaperones in an energetic dance. Trends Biochem Sci 2010; 35:476-89. [PMID: 20444609 DOI: 10.1016/j.tibs.2010.04.001] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2010] [Revised: 03/30/2010] [Accepted: 04/05/2010] [Indexed: 11/22/2022]
Abstract
Our genetic information is tightly packaged into a rather ingenious nucleoprotein complex called chromatin in a manner that enables it to be rapidly accessed during genomic processes. Formation of the nucleosome, which is the fundamental unit of chromatin, occurs via a stepwise process that is reversed to enable the disassembly of nucleosomes. Histone chaperone proteins have prominent roles in facilitating these processes as well as in replacing old histones with new canonical histones or histone variants during the process of histone exchange. Recent structural, biophysical and biochemical studies have begun to shed light on the molecular mechanisms whereby histone chaperones promote chromatin assembly, disassembly and histone exchange to facilitate DNA replication, repair and transcription.
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206
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George EM, Brown DT. Prothymosin alpha is a component of a linker histone chaperone. FEBS Lett 2010; 584:2833-6. [PMID: 20434447 DOI: 10.1016/j.febslet.2010.04.065] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Revised: 04/23/2010] [Accepted: 04/26/2010] [Indexed: 10/19/2022]
Abstract
Linker histone H1 binds with high affinity to naked and nucleosomal DNA in vitro but is rapidly exchanged between chromatin sites in vivo suggesting the involvement of one or more linker histone chaperones. Using permeabilized cells, we demonstrate that the small acidic protein prothymosin alpha (ProTalpha) can facilitate H1 displacement from and deposition onto the native chromatin template. Depletion of ProTalpha levels in vivo by siRNA-mediated mRNA degradation resulted in a decreased rate of exchange of linker histones as assayed by photobleaching techniques. These results indicate that ProTalpha is a component of a linker histone chaperone.
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Affiliation(s)
- Eric M George
- Department of Biochemistry, University of Mississippi Medical Center, Jackson, MS 39216, USA
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207
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Jasencakova Z, Scharf AND, Ask K, Corpet A, Imhof A, Almouzni G, Groth A. Replication stress interferes with histone recycling and predeposition marking of new histones. Mol Cell 2010; 37:736-43. [PMID: 20227376 DOI: 10.1016/j.molcel.2010.01.033] [Citation(s) in RCA: 219] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2009] [Revised: 11/25/2009] [Accepted: 01/25/2010] [Indexed: 12/26/2022]
Abstract
To restore chromatin on new DNA during replication, recycling of histones evicted ahead of the fork is combined with new histone deposition. The Asf1 histone chaperone, which buffers excess histones under stress, is a key player in this process. Yet how histones handled by human Asf1 are modified remains unclear. Here we identify marks on histones H3-H4 bound to Asf1 and changes induced upon replication stress. In S phase, distinct cytosolic and nuclear Asf1b complexes show ubiquitous H4K5K12diAc and heterogeneous H3 marks, including K9me1, K14ac, K18ac, and K56ac. Upon acute replication arrest, the predeposition mark H3K9me1 and modifications typical of chromatin accumulate in Asf1 complexes. In parallel, ssDNA is generated at replication sites, consistent with evicted histones being trapped with Asf1. During recovery, histones stored with Asf1 are rapidly used as replication resumes. This shows that replication stress interferes with predeposition marking and histone recycling with potential impact on epigenetic stability.
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Affiliation(s)
- Zuzana Jasencakova
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
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208
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Delbarre E, Jacobsen BM, Reiner AH, Sørensen AL, Küntziger T, Collas P. Chromatin environment of histone variant H3.3 revealed by quantitative imaging and genome-scale chromatin and DNA immunoprecipitation. Mol Biol Cell 2010; 21:1872-84. [PMID: 20375147 PMCID: PMC2877645 DOI: 10.1091/mbc.e09-09-0839] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Histone variant H3.3 is loaded onto chromatin in a replication-independent manner, but the epigenetic environment of H3.3 is unclear. Quantitative imaging and chromatin immunoprecipitation show that in mesenchymal stem cells H3.3 targets lineage-priming genes with a potential for activation facilitated by a permissive chromatin environment. In contrast to canonical histones, histone variant H3.3 is incorporated into chromatin in a replication-independent manner. Posttranslational modifications of H3.3 have been identified; however, the epigenetic environment of incorporated H3.3 is unclear. We have investigated the genomic distribution of epitope-tagged H3.3 in relation to histone modifications, DNA methylation, and transcription in mesenchymal stem cells. Quantitative imaging at the nucleus level shows that H3.3, relative to replicative H3.2 or canonical H2B, is enriched in chromatin domains marked by histone modifications of active or potentially active genes. Chromatin immunoprecipitation of epitope-tagged H3.3 and array hybridization identified 1649 H3.3-enriched promoters, a fraction of which is coenriched in H3K4me3 alone or together with H3K27me3, whereas H3K9me3 is excluded, corroborating nucleus-level imaging data. H3.3-enriched promoters are predominantly CpG-rich and preferentially DNA methylated, relative to the proportion of methylated RefSeq promoters in the genome. Most but not all H3.3-enriched promoters are transcriptionally active, and coenrichment of H3.3 with repressive H3K27me3 correlates with an enhanced proportion of expressed genes carrying this mark. H3.3-target genes are enriched in mesodermal differentiation and signaling functions. Our data suggest that in mesenchymal stem cells, H3.3 targets lineage-priming genes with a potential for activation facilitated by H3K4me3 in facultative association with H3K27me3.
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Affiliation(s)
- Erwan Delbarre
- Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
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209
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Yin L, Velazquez OC, Liu ZJ. Notch signaling: emerging molecular targets for cancer therapy. Biochem Pharmacol 2010; 80:690-701. [PMID: 20361945 DOI: 10.1016/j.bcp.2010.03.026] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2010] [Revised: 03/23/2010] [Accepted: 03/24/2010] [Indexed: 02/07/2023]
Abstract
The Notch signaling pathway is a highly conserved developmental pathway, which plays a critical role in cell-fate decision, tissue patterning and morphogenesis. There is increasing evidence that this pathway is dysregulated in a variety of malignancies, and can behave as either an oncogene or a tumor suppressor depending upon cell context. This review highlights the current evidence for aberration of the Notch signaling pathway in a wide range of tumors from hematological cancers, such as leukemia and lymphoma through to skin, breast, lung, pancreas, colon and brain tumors. It proposes that the Notch signaling pathway may represent novel therapeutic targets and will be a welcome asset to the cancer therapeutic arena.
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Affiliation(s)
- Ling Yin
- Department of Surgery, Miller School of Medicine, University of Miami, Miami, FL 33136, United States
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210
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Distinct factors control histone variant H3.3 localization at specific genomic regions. Cell 2010; 140:678-91. [PMID: 20211137 DOI: 10.1016/j.cell.2010.01.003] [Citation(s) in RCA: 958] [Impact Index Per Article: 68.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2009] [Revised: 11/23/2009] [Accepted: 12/31/2009] [Indexed: 12/17/2022]
Abstract
The incorporation of histone H3 variants has been implicated in the epigenetic memory of cellular state. Using genome editing with zinc-finger nucleases to tag endogenous H3.3, we report genome-wide profiles of H3 variants in mammalian embryonic stem cells and neuronal precursor cells. Genome-wide patterns of H3.3 are dependent on amino acid sequence and change with cellular differentiation at developmentally regulated loci. The H3.3 chaperone Hira is required for H3.3 enrichment at active and repressed genes. Strikingly, Hira is not essential for localization of H3.3 at telomeres and many transcription factor binding sites. Immunoaffinity purification and mass spectrometry reveal that the proteins Atrx and Daxx associate with H3.3 in a Hira-independent manner. Atrx is required for Hira-independent localization of H3.3 at telomeres and for the repression of telomeric RNA. Our data demonstrate that multiple and distinct factors are responsible for H3.3 localization at specific genomic locations in mammalian cells.
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211
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Andrews AJ, Chen X, Zevin A, Stargell LA, Luger K. The histone chaperone Nap1 promotes nucleosome assembly by eliminating nonnucleosomal histone DNA interactions. Mol Cell 2010; 37:834-42. [PMID: 20347425 PMCID: PMC2880918 DOI: 10.1016/j.molcel.2010.01.037] [Citation(s) in RCA: 188] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2009] [Revised: 12/15/2009] [Accepted: 01/19/2010] [Indexed: 11/27/2022]
Abstract
The organization of the eukaryotic genome into nucleosomes dramatically affects the regulation of gene expression. The delicate balance between transcription and DNA compaction relies heavily on nucleosome dynamics. Surprisingly, little is known about the free energy required to assemble these large macromolecular complexes and maintain them under physiological conditions. Here, we describe the thermodynamic parameters that drive nucleosome formation in vitro. To demonstrate the versatility of our approach, we test the effect of DNA sequence and H3K56 acetylation on nucleosome thermodynamics. Furthermore, our studies reveal the mechanism of action of the histone chaperone nucleosome assembly protein 1 (Nap1). We present evidence for a paradigm in which nucleosome assembly requires the elimination of competing, nonnucleosomal histone-DNA interactions by Nap1. This observation is confirmed in vivo, wherein deletion of the NAP1 gene in yeast results in a significant increase in atypical histone-DNA complexes, as well as in deregulated transcription activation and repression.
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Affiliation(s)
- Andrew J. Andrews
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870
| | - Xu Chen
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870
| | - Alexander Zevin
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870
| | - Laurie A. Stargell
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870
| | - Karolin Luger
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870
- Howard Hughes Medical Institute
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212
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Sakamoto M, Noguchi S, Kawashima S, Okada Y, Enomoto T, Seki M, Horikoshi M. Global analysis of mutual interaction surfaces of nucleosomes with comprehensive point mutants. Genes Cells 2010; 14:1271-330. [PMID: 19903202 DOI: 10.1111/j.1365-2443.2009.01350.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The surfaces of core histones in nucleosome are exposed as required for factor recognition, or buried for histone-DNA and histone-histone interactions. To understand the mechanisms by which nucleosome structure and function are coordinately altered in DNA-mediated reactions, it is essential to define the roles of both exposed and buried residues and their functional relationships. For this purpose, we developed GLASP (GLobal Analysis of Surfaces by Point mutation) and GLAMP (GLobal Analysis of Mutual interaction surfaces of multi-subunit protein complex by Point mutation) strategies, both of which are comprehensive analyses by point mutagenesis of exposed and buried residues in nucleosome, respectively. Four distinct DNA-mediated reactions evaluated by Ty suppression (the Spt(-) phenotype), and sensitivities to 6-azauracil (6AU), hydroxyurea (HU), and methyl methanesulfonate (MMS), require common and different GLAMP residues. Mutated GLAMP residues at the interface between histones H2A and H2B mainly affect the Spt(-) phenotype but not HU and MMS sensitivities. Interestingly, among the mutated GLAMP residues surrounding the histone H3-H3' interface, some equally affect the Spt(-) phenotype, and HU and MMS sensitivities, whereas others differentially affect the Spt(-) phenotype, and HU and MMS sensitivities. Based on these and other results, the functional relationships among chromatin factors and GLASP and GLAMP residues provide insights into nucleosome disassembly/assembly processes in DNA-mediated reactions.
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Affiliation(s)
- Makoto Sakamoto
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan
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213
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Straube K, Blackwell JS, Pemberton LF. Nap1 and Chz1 have Separate Htz1 Nuclear Import and Assembly Functions. Traffic 2010. [DOI: 10.1111/j.1600-0854.2009.001010.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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214
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215
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Shuaib M, Ouararhni K, Dimitrov S, Hamiche A. HJURP binds CENP-A via a highly conserved N-terminal domain and mediates its deposition at centromeres. Proc Natl Acad Sci U S A 2010; 107:1349-54. [PMID: 20080577 PMCID: PMC2824361 DOI: 10.1073/pnas.0913709107] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The human histone H3 variant, CENP-A, replaces the conventional histone H3 in centromeric chromatin and, together with centromere-specific DNA-binding factors, directs the assembly of the kinetochore. We purified the prenucelosomal e-CENP-A complex. We found that HJURP, a member of the complex, was required for cell cycle specific targeting of CENP-A to centromeres. HJURP facilitated efficient deposition of CENP-A/H4 tetramers to naked DNA in vitro. Bacterially expressed HJURP binds at a stoichiometric ratio to the CENP-A/H4 tetramer but not to the H3/H4 tetramer. The binding occurred through a conserved HJURP short N-terminal domain, termed CBD. The novel characteristic identified in vertebrates that we named TLTY box of CBD, was essential for formation of the HJURP-CENP-A/H4 complex. Our data identified HJURP as a vertebrate CENP-A chaperone and dissected its mode of interactions with CENP-A.
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Affiliation(s)
- Muhammad Shuaib
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, the Centre National de la Recherche Scientifique, the Institut National de la Santé et de la Recherche Médicale, Université de Strasbourg, Parc d’innovation, 1 rue Laurent Fries, 67404 Illkirch Cedex, France
| | - Khalid Ouararhni
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, the Centre National de la Recherche Scientifique, the Institut National de la Santé et de la Recherche Médicale, Université de Strasbourg, Parc d’innovation, 1 rue Laurent Fries, 67404 Illkirch Cedex, France
| | - Stefan Dimitrov
- the Institut National de la Santé et de la Recherche Médicale, Université Joseph Fourier—Grenoble 1; Institut Albert Bonniot, U823, Site Santé-BP 170, 38042 Grenoble Cedex 9, France
| | - Ali Hamiche
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, the Centre National de la Recherche Scientifique, the Institut National de la Santé et de la Recherche Médicale, Université de Strasbourg, Parc d’innovation, 1 rue Laurent Fries, 67404 Illkirch Cedex, France
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216
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Sawatsubashi S, Murata T, Lim J, Fujiki R, Ito S, Suzuki E, Tanabe M, Zhao Y, Kimura S, Fujiyama S, Ueda T, Umetsu D, Ito T, Takeyama KI, Kato S. A histone chaperone, DEK, transcriptionally coactivates a nuclear receptor. Genes Dev 2010; 24:159-70. [PMID: 20040570 PMCID: PMC2807351 DOI: 10.1101/gad.1857410] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2009] [Accepted: 11/30/2009] [Indexed: 11/25/2022]
Abstract
Chromatin reorganization is essential for transcriptional control by sequence-specific transcription factors. However, the molecular link between transcriptional control and chromatin reconfiguration remains unclear. By colocalization of the nuclear ecdysone receptor (EcR) on the ecdysone-induced puff in the salivary gland, Drosophila DEK (dDEK) was genetically identified as a coactivator of EcR in both insect cells and intact flies. Biochemical purification and characterization of the complexes containing fly and human DEKs revealed that DEKs serve as histone chaperones via phosphorylation by forming complexes with casein kinase 2. Consistent with the preferential association of the DEK complex with histones enriched in active epigenetic marks, dDEK facilitated H3.3 assembly during puff formation. In some human myeloid leukemia patients, DEK was fused to CAN by chromosomal translocation. This mutation significantly reduced formation of the DEK complex, which is required for histone chaperone activity. Thus, the present study suggests that at least one histone chaperone can be categorized as a type of transcriptional coactivator for nuclear receptors.
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Affiliation(s)
- Shun Sawatsubashi
- Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo 113-0032, Japan
- Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Saitama 332-0012, Japan
| | - Takuya Murata
- Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo 113-0032, Japan
| | - Jinseon Lim
- Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo 113-0032, Japan
| | - Ryoji Fujiki
- Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo 113-0032, Japan
| | - Saya Ito
- Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo 113-0032, Japan
- Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Saitama 332-0012, Japan
| | - Eriko Suzuki
- Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo 113-0032, Japan
- Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Saitama 332-0012, Japan
| | - Masahiko Tanabe
- Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo 113-0032, Japan
- Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Saitama 332-0012, Japan
| | - Yue Zhao
- Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo 113-0032, Japan
| | - Shuhei Kimura
- Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo 113-0032, Japan
| | - Sally Fujiyama
- Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo 113-0032, Japan
- Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Saitama 332-0012, Japan
| | - Takashi Ueda
- Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo 113-0032, Japan
| | - Daiki Umetsu
- Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo 113-0032, Japan
| | - Takashi Ito
- Department of Biochemistry, Nagasaki University School of Medicine, Nagasaki 852-8523, Japan
| | - Ken-ichi Takeyama
- Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo 113-0032, Japan
| | - Shigeaki Kato
- Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo 113-0032, Japan
- Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Saitama 332-0012, Japan
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217
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Bowman A, Ward R, El-Mkami H, Owen-Hughes T, Norman DG. Probing the (H3-H4)2 histone tetramer structure using pulsed EPR spectroscopy combined with site-directed spin labelling. Nucleic Acids Res 2010; 38:695-707. [PMID: 19914933 PMCID: PMC2810997 DOI: 10.1093/nar/gkp1003] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2009] [Revised: 10/06/2009] [Accepted: 10/12/2009] [Indexed: 12/30/2022] Open
Abstract
The (H3-H4)(2) histone tetramer forms the central core of nucleosomes and, as such, plays a prominent role in assembly, disassembly and positioning of nucleosomes. Despite its fundamental role in chromatin, the tetramer has received little structural investigation. Here, through the use of pulsed electron-electron double resonance spectroscopy coupled with site-directed spin labelling, we survey the structure of the tetramer in solution. We find that tetramer is structurally more heterogeneous on its own than when sequestered in the octamer or nucleosome. In particular, while the central region including the H3-H3' interface retains a structure similar to that observed in nucleosomes, other regions such as the H3 alphaN helix display increased structural heterogeneity. Flexibility of the H3 alphaN helix in the free tetramer also illustrates the potential for post-translational modifications to alter the structure of this region and mediate interactions with histone chaperones. The approach described here promises to prove a powerful system for investigating the structure of additional assemblies of histones with other important factors in chromatin assembly/fluidity.
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Affiliation(s)
- Andrew Bowman
- Wellcome Trust Centre for Gene Regulation and Expression, Nucleic Acid Structure Research Group, College of Life Sciences, University of Dundee, Dundee DD1 5EH and School of Physics and Astronomy, University of St Andrews, St Andrews FE2 4KM, UK
| | - Richard Ward
- Wellcome Trust Centre for Gene Regulation and Expression, Nucleic Acid Structure Research Group, College of Life Sciences, University of Dundee, Dundee DD1 5EH and School of Physics and Astronomy, University of St Andrews, St Andrews FE2 4KM, UK
| | - Hassane El-Mkami
- Wellcome Trust Centre for Gene Regulation and Expression, Nucleic Acid Structure Research Group, College of Life Sciences, University of Dundee, Dundee DD1 5EH and School of Physics and Astronomy, University of St Andrews, St Andrews FE2 4KM, UK
| | - Tom Owen-Hughes
- Wellcome Trust Centre for Gene Regulation and Expression, Nucleic Acid Structure Research Group, College of Life Sciences, University of Dundee, Dundee DD1 5EH and School of Physics and Astronomy, University of St Andrews, St Andrews FE2 4KM, UK
| | - David G. Norman
- Wellcome Trust Centre for Gene Regulation and Expression, Nucleic Acid Structure Research Group, College of Life Sciences, University of Dundee, Dundee DD1 5EH and School of Physics and Astronomy, University of St Andrews, St Andrews FE2 4KM, UK
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218
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Pilyugin M, Demmers J, Verrijzer CP, Karch F, Moshkin YM. Phosphorylation-mediated control of histone chaperone ASF1 levels by Tousled-like kinases. PLoS One 2009; 4:e8328. [PMID: 20016786 PMCID: PMC2791443 DOI: 10.1371/journal.pone.0008328] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2009] [Accepted: 11/24/2009] [Indexed: 11/19/2022] Open
Abstract
Histone chaperones are at the hub of a diverse interaction networks integrating a plethora of chromatin modifying activities. Histone H3/H4 chaperone ASF1 is a target for cell-cycle regulated Tousled-like kinases (TLKs) and both proteins cooperate during chromatin replication. However, the precise role of post-translational modification of ASF1 remained unclear. Here, we identify the TLK phosphorylation sites for both Drosophila and human ASF1 proteins. Loss of TLK-mediated phosphorylation triggers hASF1a and dASF1 degradation by proteasome-dependent and independent mechanisms respectively. Consistent with this notion, introduction of phosphorylation-mimicking mutants inhibits hASF1a and dASF1 degradation. Human hASF1b is also targeted for proteasome-dependent degradation, but its stability is not affected by phosphorylation indicating that other mechanisms are likely to be involved in control of hASF1b levels. Together, these results suggest that ASF1 cellular levels are tightly controlled by distinct pathways and provide a molecular mechanism for post-translational regulation of dASF1 and hASF1a by TLK kinases.
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Affiliation(s)
- Maxim Pilyugin
- Department of Zoology and National Research Center Frontiers in Genetics, University of Geneva, Geneva, Switzerland
| | - Jeroen Demmers
- Proteomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - C. Peter Verrijzer
- Department of Biochemistry, Center for Biomedical Genetics, Erasmus University, Rotterdam, The Netherlands
| | - Francois Karch
- Department of Zoology and National Research Center Frontiers in Genetics, University of Geneva, Geneva, Switzerland
- * E-mail: (FK); (YMM)
| | - Yuri M. Moshkin
- Department of Biochemistry, Center for Biomedical Genetics, Erasmus University, Rotterdam, The Netherlands
- * E-mail: (FK); (YMM)
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219
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Straube K, Blackwell JS, Pemberton LF. Nap1 and Chz1 have separate Htz1 nuclear import and assembly functions. TRAFFIC (COPENHAGEN, DENMARK) 2009; 11:185-97. [PMID: 19929865 DOI: 10.1111/j.1600-0854.2009.01010.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We analyzed the nuclear import and regulation of the yeast histone variant Htz1 (H2A.Z), and the role of histone chaperones Nap1 and Chz1 in this process. Copurification suggested that Htz1 and H2B dimerized in the cytoplasm prior to import. Like H2B, Htz1 contained a nuclear localization signal (NLS) in its N-terminus that is recognized by multiple karyopherins (also called importins), indicating multiple transport pathways into the nucleus. However, Kap114 and Kap123 appeared to play the major role in Htz1 import. We also identified a role for Nap1 in the import of Htz1/H2B heterodimers, and Nap1 formed a RanGTP-insensitive import complex with Htz1/H2B and Kap114. Nap1 was necessary for maintaining a soluble pool of Htz1, indicating that its chaperone function may be important for the dynamic exchange of histones within nucleosomes. In contrast, Chz1 was imported by a distinct import pathway, and Chz1 did not appear to interact with Htz1 in the cytoplasm. Genetic analysis indicated that NAP1 has a function in the absence of HTZ1 that is not shared with CHZ1. This provides further evidence that the histone chaperones Nap1 and Chz1 have separate Htz1-dependent and -independent functions.
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Affiliation(s)
- Korinna Straube
- Center for Cell Signaling, Department of Microbiology, University of Virginia Health Sciences Center, University of Virginia, Charlottesville, VA 22908, USA
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220
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Bernad R, Sánchez P, Losada A. Epigenetic specification of centromeres by CENP-A. Exp Cell Res 2009; 315:3233-41. [DOI: 10.1016/j.yexcr.2009.07.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Revised: 07/28/2009] [Accepted: 07/29/2009] [Indexed: 10/20/2022]
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221
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Histone chaperones ASF1 and NAP1 differentially modulate removal of active histone marks by LID-RPD3 complexes during NOTCH silencing. Mol Cell 2009; 35:782-93. [PMID: 19782028 DOI: 10.1016/j.molcel.2009.07.020] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2008] [Revised: 04/16/2009] [Accepted: 07/27/2009] [Indexed: 11/20/2022]
Abstract
Histone chaperones are involved in a variety of chromatin transactions. By a proteomics survey, we identified the interaction networks of histone chaperones ASF1, CAF1, HIRA, and NAP1. Here, we analyzed the cooperation of H3/H4 chaperone ASF1 and H2A/H2B chaperone NAP1 with two closely related silencing complexes: LAF and RLAF. NAP1 binds RPD3 and LID-associated factors (RLAF) comprising histone deacetylase RPD3, histone H3K4 demethylase LID/KDM5, SIN3A, PF1, EMSY, and MRG15. ASF1 binds LAF, a similar complex lacking RPD3. ASF1 and NAP1 link, respectively, LAF and RLAF to the DNA-binding Su(H)/Hairless complex, which targets the E(spl) NOTCH-regulated genes. ASF1 facilitates gene-selective removal of the H3K4me3 mark by LAF but has no effect on H3 deacetylation. NAP1 directs high nucleosome density near E(spl) control elements and mediates both H3 deacetylation and H3K4me3 demethylation by RLAF. We conclude that histone chaperones ASF1 and NAP1 differentially modulate local chromatin structure during gene-selective silencing.
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222
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Jamai A, Puglisi A, Strubin M. Histone chaperone spt16 promotes redeposition of the original h3-h4 histones evicted by elongating RNA polymerase. Mol Cell 2009; 35:377-83. [PMID: 19683500 DOI: 10.1016/j.molcel.2009.07.001] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2008] [Revised: 05/27/2009] [Accepted: 07/08/2009] [Indexed: 11/27/2022]
Abstract
Nucleosomes are surprisingly dynamic structures in vivo, showing transcription-independent exchange of histones H2A-H2B genome-wide and exchange of H3-H4 mainly within the promoters of transcribed genes. In addition, nucleosomes are disrupted in front of and reassembled behind the elongating RNA polymerase. Here we show that inactivation of histone chaperone Spt16 in yeast results in rapid loss of H2B and H3 from transcribed genes but also from inactive genes. In all cases, histone loss is blocked by a transcription inhibitor, indicating a transcription-dependent event. Thus, nucleosomes are efficiently evicted by the polymerase but do not reform in the absence of Spt16. Yet exchange of nucleosomal H2B with free histones occurs normally, and, unexpectedly, incorporation of new H3 increases at all loci tested. This points to Spt16 restoring normal nucleosome structure by redepositing the displaced H3-H4 histones, thereby preventing incorporation of new histones and perhaps changes in histone modification patterns associated with ongoing transcription.
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Affiliation(s)
- Adil Jamai
- Department of Microbiology and Molecular Medicine, University Medical Centre, Geneva, Switzerland
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223
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Crawford NPS, Yang H, Mattaini KR, Hunter KW. The metastasis efficiency modifier ribosomal RNA processing 1 homolog B (RRP1B) is a chromatin-associated factor. J Biol Chem 2009; 284:28660-73. [PMID: 19710015 DOI: 10.1074/jbc.m109.023457] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
There is accumulating evidence for a role of germ line variation in breast cancer metastasis. We have recently identified a novel metastasis susceptibility gene, Rrp1b (ribosomal RNA processing 1 homolog B). Overexpression of Rrp1b in a mouse mammary tumor cell line induces a gene expression signature that predicts survival in breast cancer. Here we extend the analysis of RRP1B function by demonstrating that the Rrp1b activation gene expression signature accurately predicted the outcome in three of four publicly available breast carcinoma gene expression data sets. In addition, we provide insights into the mechanism of RRP1B. Tandem affinity purification demonstrated that RRP1B physically interacts with many nucleosome binding factors, including histone H1X, poly(ADP-ribose) polymerase 1, TRIM28 (tripartite motif-containing 28), and CSDA (cold shock domain protein A). Co-immunofluorescence and co-immunoprecipitation confirmed these interactions and also interactions with heterochromatin protein-1alpha and acetyl-histone H4 lysine 5. Finally, we investigated the effects of ectopic expression of an RRP1B allelic variant previously associated with improved survival in breast cancer. Gene expression analyses demonstrate that, compared with ectopic expression of wild type RRP1B in HeLa cells, the variant RRP1B differentially modulates various transcription factors controlled by TRIM28 and CSDA. These data suggest that RRP1B, a tumor progression and metastasis susceptibility candidate gene, is potentially a dynamic modulator of transcription and chromatin structure.
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Affiliation(s)
- Nigel P S Crawford
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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224
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Dunleavy EM, Roche D, Tagami H, Lacoste N, Ray-Gallet D, Nakamura Y, Daigo Y, Nakatani Y, Almouzni-Pettinotti G. HJURP is a cell-cycle-dependent maintenance and deposition factor of CENP-A at centromeres. Cell 2009; 137:485-97. [PMID: 19410545 DOI: 10.1016/j.cell.2009.02.040] [Citation(s) in RCA: 486] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2008] [Revised: 11/12/2008] [Accepted: 02/20/2009] [Indexed: 01/19/2023]
Abstract
The histone H3 variant CenH3, called CENP-A in humans, is central in centromeric chromatin to ensure proper chromosome segregation. In the absence of an underlying DNA sequence, it is still unclear how CENP-A deposition at centromeres is determined. Here, we purified non-nucleosomal CENP-A complexes to identify direct CENP-A partners involved in such a mechanism and identified HJURP. HJURP was not detected in H3.1- or H3.3-containing complexes, indicating its specificity for CENP-A. HJURP centromeric localization is cell cycle regulated, and its transient appearance at the centromere coincides precisely with the proposed time window for new CENP-A deposition. Furthermore, HJURP downregulation leads to a major reduction in CENP-A at centromeres and impairs deposition of newly synthesized CENP-A, causing mitotic defects. We conclude that HJURP is a key factor for CENP-A deposition and maintenance at centromeres.
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Affiliation(s)
- Elaine M Dunleavy
- Laboratory of Nuclear Dynamics and Genome Plasticity, UMR CNRS/Institut Curie, Paris, France
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225
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Fillingham J, Kainth P, Lambert JP, van Bakel H, Tsui K, Peña-Castillo L, Nislow C, Figeys D, Hughes TR, Greenblatt J, Andrews BJ. Two-Color Cell Array Screen Reveals Interdependent Roles for Histone Chaperones and a Chromatin Boundary Regulator in Histone Gene Repression. Mol Cell 2009; 35:340-51. [DOI: 10.1016/j.molcel.2009.06.023] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2009] [Revised: 05/12/2009] [Accepted: 06/08/2009] [Indexed: 01/01/2023]
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226
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Liu Z, Zhu Y, Gao J, Yu F, Dong A, Shen WH. Molecular and reverse genetic characterization of NUCLEOSOME ASSEMBLY PROTEIN1 (NAP1) genes unravels their function in transcription and nucleotide excision repair in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2009; 59:27-38. [PMID: 19228338 DOI: 10.1111/j.1365-313x.2009.03844.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Compared with the well-studied biochemical function of NUCLEOSOME ASSEMBLY PROTEIN1 (NAP1) as a histone chaperone in nucleosome assembly/disassembly, the physiological roles of NAP1 remain largely uncharacterized. Here, we define the NAP1 gene family members in Arabidopsis, examine their molecular properties, and use reverse genetics to characterize their biological roles. We show that the four AtNAP1-group proteins can form homodimers and heterodimers, can bind histone H2A, and are localized abundantly in the cytoplasm and weakly in the nucleus at steady state. AtNAP1;4 differs from the others by showing inhibitor-sensitive nucleocytoplasmic shuttling and tissue-specific expression, restricted to root segments and pollen grains. The other three AtNAP1 genes are ubiquitously expressed in plants and the AtNAP1;3 protein is detected as the major isoform in seedlings. We show that disruption of the AtNAP1-group genes does not affect normal plant growth under our laboratory conditions. Interestingly, two allelic triple mutants, Atnap1;1-1 Atnap1;2-1 Atnap1;3-1 and Atnap1;1-1 Atnap1;2-1 Atnap1;3-2, exhibit perturbed genome transcription, and show hypersensitivity to DNA damage caused by UV-C irradiation. We show that AtNAP1;3 binds chromatin, with enrichment at some genes involved in the nucleotide excision repair (NER) pathway, and that the expression of these genes is downregulated in the triple mutants. Taken together, our results highlight conserved and isoform-specific properties of AtNAP1 proteins, and unravel their function in the NER pathway of DNA damage repair.
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Affiliation(s)
- Ziqiang Liu
- State Key Laboratory of Genetic Engineering, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, PR China
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227
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Shen WH, Xu L. Chromatin remodeling in stem cell maintenance in Arabidopsis thaliana. MOLECULAR PLANT 2009; 2:600-609. [PMID: 19825642 DOI: 10.1093/mp/ssp022] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Pluripotent stem cells are able to both self-renew and generate undifferentiated cells for the formation of new tissues and organs. In higher plants, stem cells found in the shoot apical meristem (SAM) and the root apical meristem (RAM) are origins of organogenesis occurring post-embryonically. It is important to understand how the regulation of stem cell fate is coordinated to enable the meristem to constantly generate different types of lateral organs. Much knowledge has accumulated on specific transcription factors controlling SAM and RAM activity. Here, we review recent evidences for a role of chromatin remodeling in the maintenance of stable expression states of transcription factor genes and the control of stem cell activity in Arabidopsis.
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Affiliation(s)
- Wen-Hui Shen
- Institut de Biologie Moléculaire des Plantes (IBMP) du CNRS, Université de Strasbourg (UdS), 12 rue du Général Zimmer, 67084 Strasbourg Cédex, France.
| | - Lin Xu
- Institut de Biologie Moléculaire des Plantes (IBMP) du CNRS, Université de Strasbourg (UdS), 12 rue du Général Zimmer, 67084 Strasbourg Cédex, France; National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
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228
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FACT and Asf1 regulate nucleosome dynamics and coactivator binding at the HO promoter. Mol Cell 2009; 34:405-15. [PMID: 19481521 DOI: 10.1016/j.molcel.2009.04.010] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2008] [Revised: 02/10/2009] [Accepted: 04/09/2009] [Indexed: 11/23/2022]
Abstract
Transcriptional activators and coactivators overcome repression by chromatin, but regulation of chromatin disassembly and coactivator binding to promoters is poorly understood. Activation of the yeast HO gene follows the sequential binding of both sequence-specific DNA-binding proteins and coactivators during the cell cycle. Here, we show that the nucleosome disassembly occurs in waves both along the length of the promoter and during the cell cycle. Different chromatin modifiers are required for chromatin disassembly at different regions of the promoter, with Swi/Snf, the FACT chromatin reorganizer, and the Asf1 histone chaperone each required for nucleosome eviction at distinct promoter regions. FACT and Asf1 both bind to upstream elements of the HO promoter well before the gene is transcribed. The Swi/Snf, SAGA, and Mediator coactivators bind first to the far upstream promoter region and subsequently to a promoter proximal region, and FACT and Asf1 are both required for this coactivator re-recruitment.
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229
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Gill J, Yogavel M, Kumar A, Belrhali H, Jain SK, Rug M, Brown M, Maier AG, Sharma A. Crystal structure of malaria parasite nucleosome assembly protein: distinct modes of protein localization and histone recognition. J Biol Chem 2009; 284:10076-87. [PMID: 19176479 PMCID: PMC2665062 DOI: 10.1074/jbc.m808633200] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2008] [Revised: 01/09/2009] [Indexed: 01/08/2023] Open
Abstract
Nucleosome assembly proteins (NAPs) are histone chaperones that are essential for the transfer and incorporation of histones into nucleosomes. NAPs participate in assembly and disassembly of nucleosomes and in chromatin structure organization. Human malaria parasite Plasmodium falciparum contains two nucleosome assembly proteins termed PfNapL and PfNapS. To gain structural insights into the mechanism of NAPs, we have determined and analyzed the crystal structure of PfNapL at 2.3 A resolution. PfNapL, an ortholog of eukaryotic NAPs, is dimeric in nature and adopts a characteristic fold seen previously for yeast NAP-1 and Vps75 and for human SET/TAF-1b (beta)/INHAT. The PfNapL monomer is comprised of domain I, containing a dimerization alpha-helix, and a domain II, composed of alpha-helices and a beta-subdomain. Structural comparisons reveal that the "accessory domain," which is inserted between the domain I and domain II in yeast NAP-1 and other eukaryotic NAPs, is surprisingly absent in PfNapL. Expression of green fluorescent protein-tagged PfNapL confirmed its exclusive localization to the parasite cytoplasm. Attempts to disrupt the PfNapL gene were not successful, indicating its essential role for the malaria parasite. A detailed analysis of PfNapL structure suggests unique histone binding properties. The crucial structural differences observed between parasite and yeast NAPs shed light on possible new modes of histone recognition by nucleosome assembly proteins.
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Affiliation(s)
- Jasmita Gill
- Structural and Computational Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Road, New Delhi 110067, India
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230
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Karetsou Z, Emmanouilidou A, Sanidas I, Liokatis S, Nikolakaki E, Politou AS, Papamarcaki T. Identification of distinct SET/TAF-Ibeta domains required for core histone binding and quantitative characterisation of the interaction. BMC BIOCHEMISTRY 2009; 10:10. [PMID: 19358706 PMCID: PMC2676315 DOI: 10.1186/1471-2091-10-10] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2008] [Accepted: 04/09/2009] [Indexed: 11/10/2022]
Abstract
BACKGROUND The assembly of nucleosomes to higher-order chromatin structures is finely tuned by the relative affinities of histones for chaperones and nucleosomal binding sites. The myeloid leukaemia protein SET/TAF-Ibeta belongs to the NAP1 family of histone chaperones and participates in several chromatin-based mechanisms, such as chromatin assembly, nucleosome reorganisation and transcriptional activation. To better understand the histone chaperone function of SET/TAF-Ibeta, we designed several SET/TAF-Ibeta truncations, examined their structural integrity by circular Dichroism and assessed qualitatively and quantitatively the histone binding properties of wild-type protein and mutant forms using GST-pull down experiments and fluorescence spectroscopy-based binding assays. RESULTS Wild type SET/TAF-Ibeta binds to histones H2B and H3 with Kd values of 2.87 and 0.15 microM, respectively. The preferential binding of SET/TAF-Ibeta to histone H3 is mediated by its central region and the globular part of H3. On the contrary, the acidic C-terminal tail and the amino-terminal dimerisation domain of SET/TAF-Ibeta, as well as the H3 amino-terminal tail, are dispensable for this interaction. CONCLUSION This type of analysis allowed us to assess the relative affinities of SET/TAF-Ibeta for different histones and identify the domains of the protein required for effective histone recognition. Our findings are consistent with recent structural studies of SET/TAF-Ibeta and can be valuable to understand the role of SET/TAF-Ibeta in chromatin function.
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Affiliation(s)
- Zoe Karetsou
- Laboratory of Biological Chemistry, Medical School, University of Ioannina, 451 10 Ioannina, Greece.
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231
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Probst AV, Dunleavy E, Almouzni G. Epigenetic inheritance during the cell cycle. Nat Rev Mol Cell Biol 2009; 10:192-206. [PMID: 19234478 DOI: 10.1038/nrm2640] [Citation(s) in RCA: 559] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Studies that concern the mechanism of DNA replication have provided a major framework for understanding genetic transmission through multiple cell cycles. Recent work has begun to gain insight into possible means to ensure the stable transmission of information beyond just DNA, and has led to the concept of epigenetic inheritance. Considering chromatin-based information, key candidates have arisen as epigenetic marks, including DNA and histone modifications, histone variants, non-histone chromatin proteins, nuclear RNA as well as higher-order chromatin organization. Understanding the dynamics and stability of these marks through the cell cycle is crucial in maintaining a given chromatin state.
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Affiliation(s)
- Aline V Probst
- Laboratory of Nuclear Dynamics and Genome Plasticity, UMR218 Centre National de la Recherche Scientifique/Institut Curie, 26, rue d'Ulm, 75231 Paris Cedex 05, France
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232
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Abstract
Rtt109 is a histone acetyltransferase that requires a histone chaperone for the acetylation of histone 3 at lysine 56 (H3K56). Rtt109 forms a complex with the chaperone Vps75 in vivo and is implicated in DNA replication and repair. Here we show that both Rtt109 and Vps75 bind histones with high affinity, but only the complex is efficient for catalysis. The C-terminal acidic domain of Vps75 contributes to activation of Rtt109 and is necessary for in vivo functionality of Vps75, but it is not required for interaction with either Rtt109 or histones. We demonstrate that Vps75 is a structural homolog of yeast Nap1 by solving its crystal structure. Nap1 and Vps75 interact with histones and Rtt109 with comparable affinities. However, only Vps75 stimulates Rtt109 enzymatic activity. Our data highlight the functional specificity of Vps75 in Rtt109 activation.
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233
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Berndsen CE, Tsubota T, Lindner SE, Lee S, Holton JM, Kaufman PD, Keck JL, Denu JM. Molecular functions of the histone acetyltransferase chaperone complex Rtt109-Vps75. Nat Struct Mol Biol 2009; 15:948-56. [PMID: 19172748 PMCID: PMC2678805 DOI: 10.1038/nsmb.1459] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Histone acetylation and nucleosome remodeling regulate DNA damage repair, replication and transcription. Rtt109, a recently discovered histone acetyltransferase (HAT) from Saccharomyces cerevisiae, functions with the histone chaperone Asf1 to acetylate lysine K56 on histone H3 (H3K56), a modification associated with newly synthesized histones. In vitro analysis of Rtt109 revealed that Vps75, a Nap1 family histone chaperone, could also stimulate Rtt109-dependent acetylation of H3K56. However, the molecular function of the Rtt109-Vps75 complex remains elusive. Here we have probed the molecular functions of Vps75 and the Rtt109-Vps75 complex through biochemical, structural and genetic means. We find that Vps75 stimulates the kcat of histone acetylation by ∼100-fold relative to Rtt109 alone and enhances acetylation of K9 in the H3 histone tail. Consistent with the In vitro evidence, cells lacking Vps75 showed a substantial reduction (60%) in H3K9 acetylation during S phase. X-ray structural, biochemical and genetic analyses of Vps75 indicate a unique, structurally dynamic Nap1-like fold that suggests a potential mechanism of Vps75-dependent activation of Rtt109. Together, these data provide evidence for a multifunctional HAT-chaperone complex that acetylates histone H3 and deposits H3-H4 onto DNA, linking histone modification and nucleosome assembly.
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Affiliation(s)
- Christopher E Berndsen
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, 1300 University Avenue, Madison, Wisconsin 53706, USA
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234
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Williams JS, Hayashi T, Yanagida M, Russell P. Fission yeast Scm3 mediates stable assembly of Cnp1/CENP-A into centromeric chromatin. Mol Cell 2009; 33:287-98. [PMID: 19217403 PMCID: PMC2677390 DOI: 10.1016/j.molcel.2009.01.017] [Citation(s) in RCA: 165] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2008] [Revised: 10/13/2008] [Accepted: 01/27/2009] [Indexed: 11/17/2022]
Abstract
Mis16 and Mis18 are subunits of a protein complex required for incorporation of the histone H3 variant CenH3 (Cnp1/CENP-A) into centromeric chromatin in Schizosaccharomyces pombe and mammals. How the Mis16-Mis18 complex performs this function is unknown. Here, we report that the Mis16-Mis18 complex is required for centromere localization of Scm3(Sp), a Cnp1-binding protein related to Saccharomyces cerevisiae Scm3. Scm3(Sp) is required for centromeric localization of Cnp1, while Scm3(Sp) localizes at centromeres independently of Cnp1. Like the Mis16-Mis18 complex but unlike Cnp1, Scm3(Sp) dissociates from centromeres during mitosis. Inactivation of Scm3(Sp) or Mis18 increases centromere localization of histones H3 and H2A/H2B, which are largely absent from centromeres in wild-type cells. Whereas S. cerevisiae Scm3 is proposed to replace histone H2A/H2B in centromeric nucleosomes, the dynamic behavior of S. pombe Scm3 suggests that it acts as a Cnp1 assembly/maintenance factor that directly mediates the stable deposition of Cnp1 into centromeric chromatin.
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Affiliation(s)
- Jessica S. Williams
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 90237, USA
| | - Takeshi Hayashi
- CREST Research Program, Japan Science and Technology Corporation, Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan
| | - Mitsuhiro Yanagida
- CREST Research Program, Japan Science and Technology Corporation, Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan
| | - Paul Russell
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 90237, USA
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California 90237, USA
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235
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Evidence for gene-specific rather than transcription rate-dependent histone H3 exchange in yeast coding regions. PLoS Comput Biol 2009; 5:e1000282. [PMID: 19197343 PMCID: PMC2625437 DOI: 10.1371/journal.pcbi.1000282] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2008] [Accepted: 12/17/2008] [Indexed: 01/14/2023] Open
Abstract
In eukaryotic organisms, histones are dynamically exchanged independently of DNA replication. Recent reports show that different coding regions differ in their amount of replication-independent histone H3 exchange. The current paradigm is that this histone exchange variability among coding regions is a consequence of transcription rate. Here we put forward the idea that this variability might be also modulated in a gene-specific manner independently of transcription rate. To that end, we study transcription rate–independent replication-independent coding region histone H3 exchange. We term such events relative exchange. Our genome-wide analysis shows conclusively that in yeast, relative exchange is a novel consistent feature of coding regions. Outside of replication, each coding region has a characteristic pattern of histone H3 exchange that is either higher or lower than what was expected by its RNAPII transcription rate alone. Histone H3 exchange in coding regions might be a way to add or remove certain histone modifications that are important for transcription elongation. Therefore, our results that gene-specific coding region histone H3 exchange is decoupled from transcription rate might hint at a new epigenetic mechanism of transcription regulation. During nucleosome disassembly and reassembly, evicted histones are exchanged with newly synthesized histones. Histone exchange occurs in several DNA metabolism processes, including replication, transcription, and repair. Recent reports from several labs show that replication-independent histone H3 exchange in yeast coding regions is tightly correlated with transcription rate. We have computationally shown that histone exchange variability among genes is not only a consequence of transcription rate. Instead, each coding region has a characteristic amount of replication-independent histone exchange, even when excluding the confounding effect of transcription rate. We show that this transcription rate–independent exchange, referred to as relative exchange, is a reproducible and consistent feature of the entire coding region and cannot be explained by regional effects. Next, we characterize the relations between relative exchange and a variety of histone H3 modifications, as well as the histone chaperone Asf1. Taken together, our analysis shows that gene-specific replication-independent histone H3 exchange in coding regions is mediated independently of transcription rate, thus constituting a new mechanism in epigenetic transcription regulation.
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236
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Groth A. Replicating chromatin: a tale of histonesThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB’s 51st Annual Meeting – Epigenetics and Chromatin Dynamics, and has undergone the Journal’s usual peer review process. Biochem Cell Biol 2009; 87:51-63. [DOI: 10.1139/o08-102] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Chromatin serves structural and functional roles crucial for genome stability and correct gene expression. This organization must be reproduced on daughter strands during replication to maintain proper overlay of epigenetic fabric onto genetic sequence. Nucleosomes constitute the structural framework of chromatin and carry information to specify higher-order organization and gene expression. When replication forks traverse the chromosomes, nucleosomes are transiently disrupted, allowing the replication machinery to gain access to DNA. Histone recycling, together with new deposition, ensures reassembly on nascent DNA strands. The aim of this review is to discuss how histones — new and old — are handled at the replication fork, highlighting new mechanistic insights and revisiting old paradigms.
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Affiliation(s)
- Anja Groth
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark (e-mail: )
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237
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Chromatin assembly factors Asf1 and CAF-1 have overlapping roles in deactivating the DNA damage checkpoint when DNA repair is complete. Proc Natl Acad Sci U S A 2009; 106:1151-6. [PMID: 19164567 DOI: 10.1073/pnas.0812578106] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In response to a DNA double-strand break (DSB), chromatin is rapidly modified by the damage dependent checkpoint kinases. Also, disassembly of chromatin occurs at the break site. The damage-induced modification of chromatin structure is involved in the maintenance of the checkpoint. However, it has not been determined how chromatin is restored to its undamaged state when DSB repair is complete. Here, we show the involvement of two chromatin assembly factors (CAFs), Asf1 and CAF-1, in turning off the DNA damage checkpoint in budding yeast. DSB repair or formation of gamma-H2AX does not depend on either the CAF-1 protein, Cac1, or Asf1. Absence of these proteins does not impair the ability of cells to resume cell cycle progression in the presence of an unrepaired DSB (adaptation). However, recovery from cell cycle checkpoint arrest when the DSB is repaired by gene conversion is substantially defective in the absence of both CAF-1 and Asf1, whereas deleting CAC1 or ASF1 individually had little effect. We suggest that CAF-1 and Asf1 function redundantly to deactivate the checkpoint by restoring chromatin structure on the completion of DSB repair.
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238
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Cummings WJ, Bednarski DW, Maizels N. Genetic variation stimulated by epigenetic modification. PLoS One 2008; 3:e4075. [PMID: 19115012 PMCID: PMC2605549 DOI: 10.1371/journal.pone.0004075] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2008] [Accepted: 11/30/2008] [Indexed: 11/19/2022] Open
Abstract
Homologous recombination is essential for maintaining genomic integrity. A common repair mechanism, it uses a homologous or homeologous donor as a template for repair of a damaged target gene. Such repair must be regulated, both to identify appropriate donors for repair, and to avoid excess or inappropriate recombination. We show that modifications of donor chromatin structure can promote homology-directed repair. These experiments demonstrate that either the activator VP16 or the histone chaperone, HIRA, accelerated gene conversion approximately 10-fold when tethered within the donor array for Ig gene conversion in the chicken B cell line DT40. VP16 greatly increased levels of acetylated histones H3 and H4, while tethered HIRA did not affect histone acetylation, but caused an increase in local nucleosome density and levels of histone H3.3. Thus, epigenetic modification can stimulate genetic variation. The evidence that distinct activating modifications can promote similar functional outcomes suggests that a variety of chromatin changes may regulate homologous recombination, and that disregulation of epigenetic marks may have deleterious genetic consequences.
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Affiliation(s)
- W. Jason Cummings
- Department of Immunology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - David W. Bednarski
- Department of Immunology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Nancy Maizels
- Department of Immunology, University of Washington School of Medicine, Seattle, Washington, United States of America
- Department of Biochemistry, University of Washington School of Medicine, Seattle, Washington, United States of America
- * E-mail:
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239
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CAF-1 is required for efficient replication of euchromatic DNA in Drosophila larval endocycling cells. Chromosoma 2008; 118:235-48. [PMID: 19066929 DOI: 10.1007/s00412-008-0192-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2008] [Revised: 10/27/2008] [Accepted: 10/28/2008] [Indexed: 01/04/2023]
Abstract
The endocycle constitutes an effective strategy for cell growth during development. In contrast to the mitotic cycle, it consists of multiple S-phases with no intervening mitosis and lacks a checkpoint ensuring the replication of the entire genome. Here, we report an essential requirement of chromatin assembly factor-1 (CAF-1) for Drosophila larval endocycles. This complex promotes histone H3-H4 deposition onto newly synthesised DNA in vitro. In metazoans, the depletion of its large subunit leads to the rapid accumulation of cells in S-phase. However, whether this slower S-phase progression results from the activation of cell cycle checkpoints or whether it reflects a more direct requirement of CAF-1 for efficient replication in vivo is still debated. Here, we show that, strikingly, Drosophila larval endocycling cells depleted for the CAF-1 large subunit exhibit normal dynamics of progression through endocycles, although accumulating defects, such as perturbation of nucleosomal organisation, reduction of the replication efficiency of euchromatic DNA and accumulation of DNA damage. Given that the endocycle lacks a checkpoint ensuring the replication of the entire genome, the biological context of Drosophila larval development offered a unique opportunity to highlight the requirement of CAF-1 for chromatin organisation and efficient replication processes in vivo, independently of checkpoint activation.
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240
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Andrews AJ, Downing G, Brown K, Park YJ, Luger K. A thermodynamic model for Nap1-histone interactions. J Biol Chem 2008; 283:32412-8. [PMID: 18728017 PMCID: PMC2583301 DOI: 10.1074/jbc.m805918200] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2008] [Revised: 08/25/2008] [Indexed: 11/25/2022] Open
Abstract
The yeast nucleosome assembly protein 1 (yNap1) plays a role in chromatin maintenance by facilitating histone exchange as well as nucleosome assembly and disassembly. It has been suggested that yNap1 carries out these functions by regulating the concentration of free histones. Therefore, a quantitative understanding of yNap1-histone interactions also provides information on the thermodynamics of chromatin. We have developed quantitative methods to study the affinity of yNap1 for histones. We show that yNap1 binds H2A/H2B and H3/H4 histone complexes with low nm affinity, and that each yNap1 dimer binds two histone fold dimers. The yNap1 tails contribute synergistically to histone binding while the histone tails have a slightly repressive effect on binding. The (H3/H4)(2) tetramer binds DNA with higher affinity than it binds yNap1.
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Affiliation(s)
- Andrew J Andrews
- Howard Hughes Medical Institute and Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, USA
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241
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Making copies of chromatin: the challenge of nucleosomal organization and epigenetic information. Trends Cell Biol 2008; 19:29-41. [PMID: 19027300 DOI: 10.1016/j.tcb.2008.10.002] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2008] [Revised: 10/22/2008] [Accepted: 10/23/2008] [Indexed: 12/18/2022]
Abstract
Understanding the basic mechanisms underlying chromatin dynamics during DNA replication in eukaryotic cells is of fundamental importance. Beyond DNA compaction, chromatin organization represents a means to regulate genome function. Thus, the inheritance and maintenance of the DNA sequence, along with its organization into chromatin, is central for eukaryotic life. To orchestrate DNA replication in the context of chromatin is a challenge, both in terms of accessibility to the compact structures and maintenance of chromatin organization. To meet the challenge of maintenance, cells have evolved efficient nucleosome dynamics involving assembly pathways and chromatin maturation mechanisms that restore chromatin organization in the wake of DNA replication. In this review, we describe our current knowledge concerning how these pathways operate at the nucleosomal level and highlight the key players, such as histone chaperones, chromatin remodelers or modifiers, involved in the process of chromatin duplication. Major advances have been made recently concerning de novo nucleosome assembly and our understanding of its coordination with recycling of parental histones is progressing. Insights into the transmission of chromatin-based information during replication have important implications in the field of epigenetics to fully comprehend how the epigenetic landscape might, or at times might not, be stably maintained in the face of dramatic changes in chromatin structure.
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242
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Marzluff WF, Wagner EJ, Duronio RJ. Metabolism and regulation of canonical histone mRNAs: life without a poly(A) tail. Nat Rev Genet 2008; 9:843-54. [PMID: 18927579 DOI: 10.1038/nrg2438] [Citation(s) in RCA: 540] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The canonical histone proteins are encoded by replication-dependent genes and must rapidly reach high levels of expression during S phase. In metazoans the genes that encode these proteins produce mRNAs that, instead of being polyadenylated, contain a unique 3' end structure. By contrast, the synthesis of the variant, replication-independent histones, which are encoded by polyadenylated mRNAs, persists outside of S phase. Accurate positioning of both histone types in chromatin is essential for proper transcriptional regulation, the demarcation of heterochromatic boundaries and the epigenetic inheritance of gene expression patterns. Recent results suggest that the coordinated synthesis of replication-dependent and variant histone mRNAs is achieved by signals that affect formation of the 3' end of the replication-dependent histone mRNAs.
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Affiliation(s)
- William F Marzluff
- Program in Molecular Biology and Biotechnology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.
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243
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Downs JA. Histone H3 K56 acetylation, chromatin assembly, and the DNA damage checkpoint. DNA Repair (Amst) 2008; 7:2020-4. [PMID: 18848648 DOI: 10.1016/j.dnarep.2008.08.016] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2008] [Accepted: 08/27/2008] [Indexed: 01/12/2023]
Abstract
The role of chromatin and its modulation during DNA repair has become increasingly understood in recent years. A number of histone modifications that contribute towards the cellular response to DNA damage have been identified, including the acetylation of histone H3 at lysine 56. H3 K56 acetylation occurs normally during S phase, but persists in the presence of DNA damage. In the absence of this modification, cellular survival following DNA damage is impaired. Two recent reports provide additional insights into how H3 K56 acetylation functions in DNA damage responses. In particular, this modification appears to be important for both normal replication-coupled nucleosome assembly as well as nucleosome assembly at sites of DNA damage following repair.
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Affiliation(s)
- Jessica A Downs
- MRC Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, United Kingdom.
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244
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Abstract
FACT is an essential component of the machinery used by eukaryotic cells both to establish and to overcome the nucleosomal barrier to DNA accessibility, and it does so without hydrolyzing ATP. FACT is a transcription elongation factor, but this review stresses additional roles in DNA replication and initiation of transcription. The widely-held model that FACT functions by displacing an H2A-H2B dimer from a nucleosome is examined, and an alternative proposal is presented in which dimer loss can occur but is a secondary effect of a primary structural change induced by FACT binding which we have called "nucleosome reorganization." The structures of two domains of FACT have been determined and they reveal multiple potential interaction sites. Roles for these binding sites in FACT function and regulation are discussed.
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Affiliation(s)
- Tim Formosa
- University of Utah School of Medicine, Department of Biochemistry, 15 N Medical Drive East RM 4100, Salt Lake City, UT 84112-5650, USA.
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245
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Structure of Vps75 and implications for histone chaperone function. Proc Natl Acad Sci U S A 2008; 105:12206-11. [PMID: 18723682 DOI: 10.1073/pnas.0802393105] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The vacuolar protein sorting 75 (Vps75) histone chaperone participates in chromatin assembly and disassembly at both active and inactive genes through the preferential binding to histone H3-H4. Vps75 is also one of two histone chaperones, along with antisilencing factor 1, that promotes histone H3-Lys-56 acetylation by the regulation of Ty1 transposition protein 109 (Rtt109) histone acetyltransferase. Here, we report the x-ray crystal structure of Vps75 and carry out biochemical studies to characterize its interaction with Rtt109. We find that the Vps75 structure forms a homodimeric "headphone" architecture that includes an extended helical dimerization domain and earmuff domains at opposite ends and sides of the dimerization domain. Despite the similar overall architecture with the yeast nucleosome assembly protein 1 and human SET/TAF-1beta/INHAT histone chaperones, Vps75 shows several unique features including the relative disposition of the earmuff domains to the dimerization domain, characteristics of the earmuff domains, and a pronounced cleft at the center of the Vps75 dimer. These differences appear to correlate with the unique function of Vps75 to interact with Rtt109 for histone acetylation. Our biochemical studies reveal that two surfaces on the earmuff domain of Vps75 participate in Rtt109 interaction with a stoichiometry of 2:1, thus leaving the pronounced central cleft of the Vps75 dimer largely accessible for histone binding. Taken together, our data provide a structural framework for understanding how Vps75 mediates both nucleosome assembly and histone acetylation by Rtt109.
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246
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Zhou Z, Feng H, Hansen DF, Kato H, Luk E, Freedberg DI, Kay LE, Wu C, Bai Y. NMR structure of chaperone Chz1 complexed with histones H2A.Z-H2B. Nat Struct Mol Biol 2008; 15:868-9. [PMID: 18641662 PMCID: PMC2574748 DOI: 10.1038/nsmb.1465] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2008] [Accepted: 06/20/2008] [Indexed: 11/08/2022]
Abstract
The NMR structure of budding yeast chaperone Chz1 complexed with histones H2A.Z-H2B has been determined. Chz1 forms a long irregular chain capped by two short alpha-helices, and uses both positively and negatively charged residues to stabilize the histone dimer. A molecular model that docks Chz1 onto the nucleosome has implications for its potential functions.
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Affiliation(s)
- Zheng Zhou
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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247
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Histone acetyltransferase-1 regulates integrity of cytosolic histone H3-H4 containing complex. Biochem Biophys Res Commun 2008; 373:624-30. [PMID: 18601901 DOI: 10.1016/j.bbrc.2008.06.100] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2008] [Accepted: 06/20/2008] [Indexed: 11/21/2022]
Abstract
Amounts of soluble histones in cells are tightly regulated to ensure supplying them for the newly synthesized DNA and preventing the toxic effect of excess histones. Prior to incorporation into chromatin, newly synthesized histones H3 and H4 are highly acetylated in pre-deposition complex, wherein H4 is di-acetylated at Lys-5 and Lys-12 residues by histone acetyltransferase-1 (Hat1), but their role in histone metabolism is still unclear. Here, using chicken DT 40 cytosolic extracts, we found that histones H3/H4 and their chaperone Asf1, including RbAp48, a regulatory subunit of Hat1 enzyme, were associated with Hat1. Interestingly, in HAT1-deficient cells, cytosolic histones H3/H4 fractions on sucrose gradient centrifugation, having a sedimentation coefficient of 5-6S in DT40 cells, were shifted to lower molecular mass fractions, with Asf1. Further, sucrose gradient fractionation of semi-purified tagged Asf1-complexes showed the presence of Hat1, RbAp48 and histones H3/H4 at 5-6S fractions in the complexes. These findings suggest the possible involvement of Hat1 in regulating cytosolic H3/H4 pool mediated by Asf1-containing cytosolic H3/H4 pre-deposition complex.
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248
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Abstract
The FACT complex is a conserved cofactor for RNA polymerase II elongation through nucleosomes. FACT bears histone chaperone activity and contributes to chromatin integrity. However, the molecular mechanisms behind FACT function remain elusive. Here we report biochemical, structural, and mutational analyses that identify the peptidase homology domain of the Schizosaccharomyces pombe FACT large subunit Spt16 (Spt16-N) as a binding module for histones H3 and H4. The 2.1-A crystal structure of Spt16-N reveals an aminopeptidase P fold whose enzymatic activity has been lost. Instead, the highly conserved fold directly binds histones H3-H4 through a tight interaction with their globular core domains, as well as with their N-terminal tails. Mutations within a conserved surface pocket in Spt16-N or posttranslational modification of the histone H4 tail reduce interaction in vitro, whereas the globular domains of H3-H4 and the H3 tail bind distinct Spt16-N surfaces. Our analysis suggests that the N-terminal domain of Spt16 may add to the known H2A-H2B chaperone activity of FACT by including a H3-H4 tail and H3-H4 core binding function mediated by the N terminus of Spt16. We suggest that these interactions may aid FACT-mediated nucleosome reorganization events.
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249
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Park YJ, Luger K. Histone chaperones in nucleosome eviction and histone exchange. Curr Opin Struct Biol 2008; 18:282-9. [PMID: 18534842 PMCID: PMC2525571 DOI: 10.1016/j.sbi.2008.04.003] [Citation(s) in RCA: 153] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2008] [Accepted: 04/15/2008] [Indexed: 11/28/2022]
Abstract
The recent two years have led to the realization that histone chaperones contribute to the delicate balance between nucleosome assembly and re-assembly during transcription, and may in fact be involved as much in histone eviction as they are in chromatin assembly. Recent structural studies (in particular, the structure of an Asf1-H3/H4 complex) have suggested mechanisms by which this may be accomplished. The incorporation of various histone variants into nucleosomes has diverse effects on nucleosome structure, stability, and the ability of nucleosomal arrays to condense into chromatin higher order structures. It is likely that these seemingly independent ways to modify chromatin structure are interdependent.
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Affiliation(s)
- Young-Jun Park
- Howard Hughes Medical Institute and Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, United States.
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250
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Chaperone control of the activity and specificity of the histone H3 acetyltransferase Rtt109. Mol Cell Biol 2008; 28:4342-53. [PMID: 18458063 DOI: 10.1128/mcb.00182-08] [Citation(s) in RCA: 152] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Acetylation of Saccharomyces cerevisiae histone H3 on K56 by the histone acetyltransferase (HAT) Rtt109 is important for repairing replication-associated lesions. Rtt109 purifies from yeast in complex with the histone chaperone Vps75, which stabilizes the HAT in vivo. A whole-genome screen to identify genes whose deletions have synthetic genetic interactions with rtt109Delta suggests Rtt109 has functions in addition to DNA repair. We show that in addition to its known H3-K56 acetylation activity, Rtt109 is also an H3-K9 HAT, and we show that Rtt109 and Gcn5 are the only H3-K9 HATs in vivo. Rtt109's H3-K9 acetylation activity in vitro is enhanced strongly by Vps75. Another histone chaperone, Asf1, and Vps75 are both required for acetylation of lysine 9 on H3 (H3-K9ac) in vivo by Rtt109, whereas H3-K56ac in vivo requires only Asf1. Asf1 also physically interacts with the nuclear Hat1/Hat2/Hif1 complex that acetylates H4-K5 and H4-K12. We suggest Asf1 is capable of assembling into chromatin H3-H4 dimers diacetylated on both H4-K5/12 and H3-K9/56.
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