1
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Gao E, Brown JAR, Jung S, Howe LJ. A fluorescent assay for cryptic transcription in Saccharomyces cerevisiae reveals novel insights into factors that stabilize chromatin structure on newly replicated DNA. Genetics 2024; 226:iyae016. [PMID: 38407959 PMCID: PMC10990430 DOI: 10.1093/genetics/iyae016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 01/12/2024] [Indexed: 02/27/2024] Open
Abstract
The disruption of chromatin structure can result in transcription initiation from cryptic promoters within gene bodies. While the passage of RNA polymerase II is a well-characterized chromatin-disrupting force, numerous factors, including histone chaperones, normally stabilize chromatin on transcribed genes, thereby repressing cryptic transcription. DNA replication, which employs a partially overlapping set of histone chaperones, is also inherently disruptive to chromatin, but a role for DNA replication in cryptic transcription has never been examined. In this study, we tested the hypothesis that, in the absence of chromatin-stabilizing factors, DNA replication can promote cryptic transcription in Saccharomyces cerevisiae. Using a novel fluorescent reporter assay, we show that multiple factors, including Asf1, CAF-1, Rtt106, Spt6, and FACT, block transcription from a cryptic promoter, but are entirely or partially dispensable in G1-arrested cells, suggesting a requirement for DNA replication in chromatin disruption. Collectively, these results demonstrate that transcription fidelity is dependent on numerous factors that function to assemble chromatin on nascent DNA.
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Affiliation(s)
- Ellia Gao
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Joshua A R Brown
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Stephanie Jung
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - LeAnn J Howe
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
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2
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Saredi G, Carelli FN, Rolland SGM, Furlan G, Piquet S, Appert A, Sanchez-Pulido L, Price JL, Alcon P, Lampersberger L, Déclais AC, Ramakrishna NB, Toth R, Macartney T, Alabert C, Ponting CP, Polo SE, Miska EA, Gartner A, Ahringer J, Rouse J. The histone chaperone SPT2 regulates chromatin structure and function in Metazoa. Nat Struct Mol Biol 2024; 31:523-535. [PMID: 38238586 PMCID: PMC7615752 DOI: 10.1038/s41594-023-01204-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 12/14/2023] [Indexed: 02/15/2024]
Abstract
Histone chaperones control nucleosome density and chromatin structure. In yeast, the H3-H4 chaperone Spt2 controls histone deposition at active genes but its roles in metazoan chromatin structure and organismal physiology are not known. Here we identify the Caenorhabditis elegans ortholog of SPT2 (CeSPT-2) and show that its ability to bind histones H3-H4 is important for germline development and transgenerational epigenetic gene silencing, and that spt-2 null mutants display signatures of a global stress response. Genome-wide profiling showed that CeSPT-2 binds to a range of highly expressed genes, and we find that spt-2 mutants have increased chromatin accessibility at a subset of these loci. We also show that SPT2 influences chromatin structure and controls the levels of soluble and chromatin-bound H3.3 in human cells. Our work reveals roles for SPT2 in controlling chromatin structure and function in Metazoa.
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Affiliation(s)
- Giulia Saredi
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK.
| | - Francesco N Carelli
- Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Stéphane G M Rolland
- IBS Centre for Genomic Integrity at Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Giulia Furlan
- Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Transine Therapeutics, Babraham Hall, Cambridge, UK
| | - Sandra Piquet
- Laboratory of Epigenome Integrity, Epigenetics and Cell Fate Centre, UMR 7216 CNRS - Université Paris Cité, Paris, France
| | - Alex Appert
- Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Luis Sanchez-Pulido
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Jonathan L Price
- Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Pablo Alcon
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Lisa Lampersberger
- Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Maxion Therapeutics, Unity Campus, Cambridge, UK
| | - Anne-Cécile Déclais
- Molecular Cell and Developmental Biology Division, School of Life Sciences, University of Dundee, Dundee, UK
| | - Navin B Ramakrishna
- Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Rachel Toth
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Thomas Macartney
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Constance Alabert
- Molecular Cell and Developmental Biology Division, School of Life Sciences, University of Dundee, Dundee, UK
| | - Chris P Ponting
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Sophie E Polo
- Laboratory of Epigenome Integrity, Epigenetics and Cell Fate Centre, UMR 7216 CNRS - Université Paris Cité, Paris, France
| | - Eric A Miska
- Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Anton Gartner
- IBS Centre for Genomic Integrity at Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Julie Ahringer
- Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - John Rouse
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK.
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3
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Robert F, Jeronimo C. Transcription-coupled nucleosome assembly. Trends Biochem Sci 2023; 48:978-992. [PMID: 37657993 DOI: 10.1016/j.tibs.2023.08.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 07/21/2023] [Accepted: 08/04/2023] [Indexed: 09/03/2023]
Abstract
Eukaryotic transcription occurs on chromatin, where RNA polymerase II encounters nucleosomes during elongation. These nucleosomes must unravel for the DNA to enter the active site. However, in most transcribed genes, nucleosomes remain intact due to transcription-coupled chromatin assembly mechanisms. These mechanisms primarily involve the local reassembly of displaced nucleosomes to prevent (epi)genomic instability and the emergence of cryptic transcription. As a fail-safe mechanism, cells can assemble nucleosomes de novo, particularly in highly transcribed genes, but this may result in the loss of epigenetic information. This review examines transcription-coupled chromatin assembly, with an emphasis on studies in yeast and recent structural studies. These studies shed light on how elongation factors and histone chaperones coordinate to enable nucleosome recycling during transcription.
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Affiliation(s)
- François Robert
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada; Département de Médecine, Faculté de Médecine, Université de Montréal, 2900 Boul. Édouard-Montpetit, Montréal, QC H3T 1J4, Canada; Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC H3A 1A3, Canada.
| | - Célia Jeronimo
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
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4
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Pande S, Ghosh DK. Nuclear proteostasis imbalance in laminopathy-associated premature aging diseases. FASEB J 2023; 37:e23116. [PMID: 37498235 DOI: 10.1096/fj.202300878r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/15/2023] [Accepted: 07/13/2023] [Indexed: 07/28/2023]
Abstract
Laminopathies are a group of rare genetic disorders with heterogeneous clinical phenotypes such as premature aging, cardiomyopathy, lipodystrophy, muscular dystrophy, microcephaly, epilepsy, and so on. The cellular phenomena associated with laminopathy invariably show disruption of nucleoskeleton of lamina due to deregulated expression, localization, function, and interaction of mutant lamin proteins. Impaired spatial and temporal tethering of lamin proteins to the lamina or nucleoplasmic aggregation of lamins are the primary molecular events that can trigger nuclear proteotoxicity by modulating differential protein-protein interactions, sequestering quality control proteins, and initiating a cascade of abnormal post-translational modifications. Clearly, laminopathic cells exhibit moderate to high nuclear proteotoxicity, raising the question of whether an imbalance in nuclear proteostasis is involved in laminopathic diseases, particularly in diseases of early aging such as HGPS and laminopathy-associated premature aging. Here, we review nuclear proteostasis and its deregulation in the context of lamin proteins and laminopathies.
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Affiliation(s)
- Shruti Pande
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Debasish Kumar Ghosh
- Enteric Disease Division, Department of Microbiology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
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5
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Carraro M, Hendriks IA, Hammond CM, Solis-Mezarino V, Völker-Albert M, Elsborg JD, Weisser MB, Spanos C, Montoya G, Rappsilber J, Imhof A, Nielsen ML, Groth A. DAXX adds a de novo H3.3K9me3 deposition pathway to the histone chaperone network. Mol Cell 2023; 83:1075-1092.e9. [PMID: 36868228 PMCID: PMC10114496 DOI: 10.1016/j.molcel.2023.02.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 11/29/2022] [Accepted: 02/08/2023] [Indexed: 03/05/2023]
Abstract
A multitude of histone chaperones are required to support histones from their biosynthesis until DNA deposition. They cooperate through the formation of histone co-chaperone complexes, but the crosstalk between nucleosome assembly pathways remains enigmatic. Using exploratory interactomics, we define the interplay between human histone H3-H4 chaperones in the histone chaperone network. We identify previously uncharacterized histone-dependent complexes and predict the structure of the ASF1 and SPT2 co-chaperone complex, expanding the role of ASF1 in histone dynamics. We show that DAXX provides a unique functionality to the histone chaperone network, recruiting histone methyltransferases to promote H3K9me3 catalysis on new histone H3.3-H4 prior to deposition onto DNA. Hereby, DAXX provides a molecular mechanism for de novo H3K9me3 deposition and heterochromatin assembly. Collectively, our findings provide a framework for understanding how cells orchestrate histone supply and employ targeted deposition of modified histones to underpin specialized chromatin states.
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Affiliation(s)
- Massimo Carraro
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ivo A Hendriks
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Colin M Hammond
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | | | | | - Jonas D Elsborg
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Melanie B Weisser
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christos Spanos
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK; Technische Universität Berlin, Chair of Bioanalytics, Berlin, Germany
| | - Guillermo Montoya
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Juri Rappsilber
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK; Technische Universität Berlin, Chair of Bioanalytics, Berlin, Germany
| | - Axel Imhof
- EpiQMAx GmbH, Planegg, Germany; Faculty of Medicine, Biomedical Center, Protein Analysis Unit, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Michael L Nielsen
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Anja Groth
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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6
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López-Rivera F, Chuang J, Spatt D, Gopalakrishnan R, Winston F. Suppressor mutations that make the essential transcription factor Spn1/Iws1 dispensable in Saccharomyces cerevisiae. Genetics 2022; 222:iyac125. [PMID: 35977387 PMCID: PMC9526074 DOI: 10.1093/genetics/iyac125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/11/2022] [Indexed: 11/12/2022] Open
Abstract
Spn1/Iws1 is an essential eukaryotic transcription elongation factor that is conserved from yeast to humans as an integral member of the RNA polymerase II elongation complex. Several studies have shown that Spn1 functions as a histone chaperone to control transcription, RNA splicing, genome stability, and histone modifications. However, the precise role of Spn1 is not understood, and there is little understanding of why it is essential for viability. To address these issues, we have isolated 8 suppressor mutations that bypass the essential requirement for Spn1 in Saccharomyces cerevisiae. Unexpectedly, the suppressors identify several functionally distinct complexes and activities, including the histone chaperone FACT, the histone methyltransferase Set2, the Rpd3S histone deacetylase complex, the histone acetyltransferase Rtt109, the nucleosome remodeler Chd1, and a member of the SAGA coactivator complex, Sgf73. The identification of these distinct groups suggests that there are multiple ways in which Spn1 bypass can occur, including changes in histone acetylation and alterations in other histone chaperones. Thus, Spn1 may function to overcome repressive chromatin by multiple mechanisms during transcription. Our results suggest that bypassing a subset of these functions allows viability in the absence of Spn1.
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Affiliation(s)
| | - James Chuang
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Dan Spatt
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | | | - Fred Winston
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
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7
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Yin L, Tang Y, Xiao M, Li M, Huang Fu ZM, Wang YL. The role of histone chaperone spty2d1 in human colorectal cancer. Mol Cell Probes 2022; 64:101832. [PMID: 35691597 DOI: 10.1016/j.mcp.2022.101832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/17/2022] [Accepted: 05/31/2022] [Indexed: 11/30/2022]
Abstract
Colorectal cancer (CRC) remains a major public health concern, associated with a high rate of morbidity and mortality. Several factors have been implicated in its occurrence and development, which includes histone chaperones. The role of spty2d1 (spt2)-a novel histone chaperone protein-has rarely been investigated in CRC. Therefore, we demonstrated in this study that spt2 undergoes different genetic alterations in colorectal adenocarcinoma datasets and that it was associated with the proliferation of colon carcinoma. Spt2 silencing can reduce the ability of proliferation and increase the rate of apoptosis of LoVo cells. Regarding the overall survival associated with spt2, only the quartile disease-free survival of colon adenocarcinoma (COAD) was found to be statistically significant, while that of rectum adenocarcinoma (READ) was not. The positive (+++) expression of spt2 was correlated with a deeper invasion depth in colorectal adenocarcinoma, and this effect was more pronounced in COAD. These data collectively suggest that spt2 can influence the progression and prognosis in some subtypes of colorectal adenocarcinoma. Therefore, we propose spt2 as a potential target for application in enhancing the overall therapeutic efficacy in some specific subtypes of colorectal adenocarcinoma.
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Affiliation(s)
- Ling Yin
- Department of Pathology, School of Basic Medicine, Chongqing Medical University, Chongqing, 400016, People's Republic of China.
| | - Yi Tang
- Department of Pathology, School of Basic Medicine, Chongqing Medical University, Chongqing, 400016, People's Republic of China; Molecular Medicine Diagnostic and Testing Center, Chongqing Medical University, Chongqing, 400016, People's Republic of China; Department of Pathology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People's Republic of China.
| | - Ming Xiao
- Department of Pathology, School of Basic Medicine, Chongqing Medical University, Chongqing, 400016, People's Republic of China; Molecular Medicine Diagnostic and Testing Center, Chongqing Medical University, Chongqing, 400016, People's Republic of China; Department of Pathology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People's Republic of China.
| | - Ming Li
- Department of Pathology, School of Basic Medicine, Chongqing Medical University, Chongqing, 400016, People's Republic of China; Molecular Medicine Diagnostic and Testing Center, Chongqing Medical University, Chongqing, 400016, People's Republic of China; Department of Pathology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People's Republic of China.
| | - Zhi-Min Huang Fu
- Department of Pathology, School of Basic Medicine, Chongqing Medical University, Chongqing, 400016, People's Republic of China.
| | - Ya-Lan Wang
- Department of Pathology, School of Basic Medicine, Chongqing Medical University, Chongqing, 400016, People's Republic of China; Molecular Medicine Diagnostic and Testing Center, Chongqing Medical University, Chongqing, 400016, People's Republic of China; Department of Pathology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People's Republic of China.
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8
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Dalui S, Dasgupta A, Adhikari S, Das C, Roy S. Human testis-specific Y-encoded protein-like protein 5 is a histone H3/H4-specific chaperone that facilitates histone deposition in vitro. J Biol Chem 2022; 298:102200. [PMID: 35772497 PMCID: PMC9305336 DOI: 10.1016/j.jbc.2022.102200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 06/16/2022] [Accepted: 06/18/2022] [Indexed: 11/20/2022] Open
Abstract
DNA and core histones are hierarchically packaged into a complex organization called chromatin. The nucleosome assembly protein (NAP) family of histone chaperones is involved in the deposition of histone complexes H2A/H2B and H3/H4 onto DNA and prevents nonspecific aggregation of histones. Testis-specific Y-encoded protein (TSPY)–like protein 5 (TSPYL5) is a member of the TSPY-like protein family, which has been previously reported to interact with ubiquitin-specific protease USP7 and regulate cell proliferation and is thus implicated in various cancers, but its interaction with chromatin has not been investigated. In this study, we characterized the chromatin association of TSPYL5 and found that it preferentially binds histone H3/H4 via its C-terminal NAP-like domain both in vitro and ex vivo. We identified the critical residues involved in the TSPYL5–H3/H4 interaction and further quantified the binding affinity of TSPYL5 toward H3/H4 using biolayer interferometry. We then determined the binding stoichiometry of the TSPYL5–H3/H4 complex in vitro using a chemical cross-linking assay and size-exclusion chromatography coupled with multiangle laser light scattering. Our results indicate that a TSPYL5 dimer binds to either two histone H3/H4 dimers or a single tetramer. We further demonstrated that TSPYL5 has a specific affinity toward longer DNA fragments and that the same histone-binding residues are also critically involved in its DNA binding. Finally, employing histone deposition and supercoiling assays, we confirmed that TSPYL5 is a histone chaperone responsible for histone H3/H4 deposition and nucleosome assembly. We conclude that TSPYL5 is likely a new member of the NAP histone chaperone family.
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Affiliation(s)
- Sambit Dalui
- Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology, Kolkata, India
| | - Anirban Dasgupta
- Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology, Kolkata, India
| | - Swagata Adhikari
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India; Homi Bhaba National Institute, Mumbai, India
| | - Chandrima Das
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India; Homi Bhaba National Institute, Mumbai, India
| | - Siddhartha Roy
- Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology, Kolkata, India.
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9
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Kasiliauskaite A, Kubicek K, Klumpler T, Zanova M, Zapletal D, Koutna E, Novacek J, Stefl R. Cooperation between intrinsically disordered and ordered regions of Spt6 regulates nucleosome and Pol II CTD binding, and nucleosome assembly. Nucleic Acids Res 2022; 50:5961-5973. [PMID: 35640611 PMCID: PMC9177984 DOI: 10.1093/nar/gkac451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 04/29/2022] [Accepted: 05/16/2022] [Indexed: 11/14/2022] Open
Abstract
Transcription elongation factor Spt6 associates with RNA polymerase II (Pol II) and acts as a histone chaperone, which promotes the reassembly of nucleosomes following the passage of Pol II. The precise mechanism of nucleosome reassembly mediated by Spt6 remains unclear. In this study, we used a hybrid approach combining cryo-electron microscopy and small-angle X-ray scattering to visualize the architecture of Spt6 from Saccharomyces cerevisiae. The reconstructed overall architecture of Spt6 reveals not only the core of Spt6, but also its flexible N- and C-termini, which are critical for Spt6's function. We found that the acidic N-terminal region of Spt6 prevents the binding of Spt6 not only to the Pol II CTD and Pol II CTD-linker, but also to pre-formed intact nucleosomes and nucleosomal DNA. The N-terminal region of Spt6 self-associates with the tSH2 domain and the core of Spt6 and thus controls binding to Pol II and nucleosomes. Furthermore, we found that Spt6 promotes the assembly of nucleosomes in vitro. These data indicate that the cooperation between the intrinsically disordered and structured regions of Spt6 regulates nucleosome and Pol II CTD binding, and also nucleosome assembly.
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Affiliation(s)
- Aiste Kasiliauskaite
- CEITEC-Central European Institute of Technology, Masaryk University, Brno CZ-62500, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno CZ-62500, Czech Republic
| | - Karel Kubicek
- CEITEC-Central European Institute of Technology, Masaryk University, Brno CZ-62500, Czech Republic.,Department of Condensed Matter Physics, Faculty of Science, Masaryk University, Brno CZ-61137, Czech Republic
| | - Tomas Klumpler
- CEITEC-Central European Institute of Technology, Masaryk University, Brno CZ-62500, Czech Republic
| | - Martina Zanova
- CEITEC-Central European Institute of Technology, Masaryk University, Brno CZ-62500, Czech Republic.,Department of Condensed Matter Physics, Faculty of Science, Masaryk University, Brno CZ-61137, Czech Republic
| | - David Zapletal
- CEITEC-Central European Institute of Technology, Masaryk University, Brno CZ-62500, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno CZ-62500, Czech Republic
| | - Eliska Koutna
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.,Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jiri Novacek
- CEITEC-Central European Institute of Technology, Masaryk University, Brno CZ-62500, Czech Republic
| | - Richard Stefl
- CEITEC-Central European Institute of Technology, Masaryk University, Brno CZ-62500, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno CZ-62500, Czech Republic
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10
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Li S, Edwards G, Radebaugh CA, Luger K, A Stargell L. Spn1 and its dynamic interactions with Spt6, histones and nucleosomes. J Mol Biol 2022; 434:167630. [PMID: 35595162 DOI: 10.1016/j.jmb.2022.167630] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/06/2022] [Accepted: 05/10/2022] [Indexed: 11/25/2022]
Abstract
Histone chaperones facilitate the assembly and disassembly of nucleosomes and regulate DNA accessibility for critical cellular processes. Spn1 is an essential, highly conserved histone chaperone that functions in transcription initiation and elongation in a chromatin context. Here we demonstrate that Spn1 binds H3-H4 with low nanomolar affinity, residues 85-99 within the acidic N-terminal region of Spn1 are required for H3-H4 binding, and Spn1 binding to H3-H4 dimers does not impede (H3-H4)2 tetramer formation. Previous work has shown the central region of Spn1 (residues 141-305) is important for interaction with Spt6, another conserved and essential histone chaperone. We show that the C-terminal region of Spn1 also contributes to Spt6 binding and is critical for Spn1 binding to nucleosomes. We also show Spt6 preferentially binds H3-H4 tetramers and Spt6 competes with nucleosomes for Spn1 binding. Combined with previous results, this indicates the Spn1-Spt6 complex does not bind nucleosomes. In contrast to nucleosome binding, we found that the Spn1-Spt6 complex can bind H3-H4 dimers and tetramers and H2A-H2B to form ternary complexes. These important results provide new information about the functions of Spn1, Spt6, and the Spn1-Spt6 complex, two essential and highly conserved histone chaperones.
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Affiliation(s)
- Sha Li
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523-1870, USA; Department of Biochemistry, University of Colorado, Boulder, CO, 80309, USA
| | - Garrett Edwards
- Department of Biochemistry, University of Colorado, Boulder, CO, 80309, USA
| | - Catherine A Radebaugh
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523-1870, USA
| | - Karolin Luger
- Department of Biochemistry, University of Colorado, Boulder, CO, 80309, USA; Howard Hughes Medical Institute, University of Colorado, Boulder, CO, 80309, USA
| | - Laurie A Stargell
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523-1870, USA
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11
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Jeronimo C, Robert F. The histone chaperone FACT: a guardian of chromatin structure integrity. Transcription 2022; 13:16-38. [PMID: 35485711 PMCID: PMC9467567 DOI: 10.1080/21541264.2022.2069995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The identification of FACT as a histone chaperone enabling transcription through chromatin in vitro has strongly shaped how its roles are envisioned. However, FACT has been implicated in essentially all aspects of chromatin biology, from transcription to DNA replication, DNA repair, and chromosome segregation. In this review, we focus on recent literature describing the role and mechanisms of FACT during transcription. We highlight the prime importance of FACT in preserving chromatin integrity during transcription and challenge its role as an elongation factor. We also review evidence for FACT's role as a cell-type/gene-specificregulator of gene expression and briefly summarize current efforts at using FACT inhibition as an anti-cancerstrategy.
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Affiliation(s)
- Célia Jeronimo
- Institut de recherches cliniques de Montréal, Montréal, Québec, Canada
| | - François Robert
- Institut de recherches cliniques de Montréal, Montréal, Québec, Canada.,Département de Médecine, Faculté de Médecine, Université de Montréal, Montréal, Québec, Canada.,Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
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12
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Zardoni L, Nardini E, Brambati A, Lucca C, Choudhary R, Loperfido F, Sabbioneda S, Liberi G. Elongating RNA polymerase II and RNA:DNA hybrids hinder fork progression and gene expression at sites of head-on replication-transcription collisions. Nucleic Acids Res 2021; 49:12769-12784. [PMID: 34878142 PMCID: PMC8682787 DOI: 10.1093/nar/gkab1146] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 10/26/2021] [Accepted: 11/02/2021] [Indexed: 11/20/2022] Open
Abstract
Uncoordinated clashes between replication forks and transcription cause replication stress and genome instability, which are hallmarks of cancer and neurodegeneration. Here, we investigate the outcomes of head-on replication-transcription collisions, using as a model system budding yeast mutants for the helicase Sen1, the ortholog of human Senataxin. We found that RNA Polymerase II accumulates together with RNA:DNA hybrids at sites of head-on collisions. The replication fork and RNA Polymerase II are both arrested during the clash, leading to DNA damage and, in the long run, the inhibition of gene expression. The inactivation of RNA Polymerase II elongation factors, such as the HMG-like protein Spt2 and the DISF and PAF complexes, but not alterations in chromatin structure, allows replication fork progression through transcribed regions. Attenuation of RNA Polymerase II elongation rescues RNA:DNA hybrid accumulation and DNA damage sensitivity caused by the absence of Sen1, but not of RNase H proteins, suggesting that such enzymes counteract toxic RNA:DNA hybrids at different stages of the cell cycle with Sen1 mainly acting in replication. We suggest that the main obstacle to replication fork progression is the elongating RNA Polymerase II engaged in an R-loop, rather than RNA:DNA hybrids per se or hybrid-associated chromatin modifications.
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Affiliation(s)
- Luca Zardoni
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, 27100 Pavia, Italy.,Scuola Universitaria Superiore IUSS, 27100 Pavia, Italy
| | - Eleonora Nardini
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, 27100 Pavia, Italy
| | - Alessandra Brambati
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, 27100 Pavia, Italy
| | | | | | - Federica Loperfido
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, 27100 Pavia, Italy
| | - Simone Sabbioneda
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, 27100 Pavia, Italy
| | - Giordano Liberi
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, 27100 Pavia, Italy.,IFOM Foundation, 20139 Milan, Italy
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13
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DNAJC9 integrates heat shock molecular chaperones into the histone chaperone network. Mol Cell 2021; 81:2533-2548.e9. [PMID: 33857403 PMCID: PMC8221569 DOI: 10.1016/j.molcel.2021.03.041] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 03/17/2021] [Accepted: 03/25/2021] [Indexed: 12/31/2022]
Abstract
From biosynthesis to assembly into nucleosomes, histones are handed through a cascade of histone chaperones, which shield histones from non-specific interactions. Whether mechanisms exist to safeguard the histone fold during histone chaperone handover events or to release trapped intermediates is unclear. Using structure-guided and functional proteomics, we identify and characterize a histone chaperone function of DNAJC9, a heat shock co-chaperone that promotes HSP70-mediated catalysis. We elucidate the structure of DNAJC9, in a histone H3-H4 co-chaperone complex with MCM2, revealing how this dual histone and heat shock co-chaperone binds histone substrates. We show that DNAJC9 recruits HSP70-type enzymes via its J domain to fold histone H3-H4 substrates: upstream in the histone supply chain, during replication- and transcription-coupled nucleosome assembly, and to clean up spurious interactions. With its dual functionality, DNAJC9 integrates ATP-resourced protein folding into the histone supply pathway to resolve aberrant intermediates throughout the dynamic lives of histones.
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14
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Braberg H, Echeverria I, Bohn S, Cimermancic P, Shiver A, Alexander R, Xu J, Shales M, Dronamraju R, Jiang S, Dwivedi G, Bogdanoff D, Chaung KK, Hüttenhain R, Wang S, Mavor D, Pellarin R, Schneidman D, Bader JS, Fraser JS, Morris J, Haber JE, Strahl BD, Gross CA, Dai J, Boeke JD, Sali A, Krogan NJ. Genetic interaction mapping informs integrative structure determination of protein complexes. Science 2020; 370:eaaz4910. [PMID: 33303586 PMCID: PMC7946025 DOI: 10.1126/science.aaz4910] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 07/23/2020] [Accepted: 10/23/2020] [Indexed: 12/17/2022]
Abstract
Determining structures of protein complexes is crucial for understanding cellular functions. Here, we describe an integrative structure determination approach that relies on in vivo measurements of genetic interactions. We construct phenotypic profiles for point mutations crossed against gene deletions or exposed to environmental perturbations, followed by converting similarities between two profiles into an upper bound on the distance between the mutated residues. We determine the structure of the yeast histone H3-H4 complex based on ~500,000 genetic interactions of 350 mutants. We then apply the method to subunits Rpb1-Rpb2 of yeast RNA polymerase II and subunits RpoB-RpoC of bacterial RNA polymerase. The accuracy is comparable to that based on chemical cross-links; using restraints from both genetic interactions and cross-links further improves model accuracy and precision. The approach provides an efficient means to augment integrative structure determination with in vivo observations.
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Affiliation(s)
- Hannes Braberg
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ignacia Echeverria
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Stefan Bohn
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
- Gladstone Institutes, San Francisco, CA 94158, USA
| | - Peter Cimermancic
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Anthony Shiver
- Graduate Group in Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Richard Alexander
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jiewei Xu
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
- Gladstone Institutes, San Francisco, CA 94158, USA
| | - Michael Shales
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Raghuvar Dronamraju
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Shuangying Jiang
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Gajendradhar Dwivedi
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454, USA
| | - Derek Bogdanoff
- Center for Advanced Technology, Department of Biophysics and Biochemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kaitlin K Chaung
- Center for Advanced Technology, Department of Biophysics and Biochemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ruth Hüttenhain
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
- Gladstone Institutes, San Francisco, CA 94158, USA
| | - Shuyi Wang
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - David Mavor
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Riccardo Pellarin
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Dina Schneidman
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Joel S Bader
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - James S Fraser
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - John Morris
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - James E Haber
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454, USA
| | - Brian D Strahl
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Carol A Gross
- Department of Microbiology and Immunology and Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Junbiao Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Jef D Boeke
- NYU Langone Health, New York, NY 10016, USA.
- High Throughput Biology Center and Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA
| | - Andrej Sali
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA.
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA.
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
- Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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15
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Jeronimo C, Poitras C, Robert F. Histone Recycling by FACT and Spt6 during Transcription Prevents the Scrambling of Histone Modifications. Cell Rep 2020; 28:1206-1218.e8. [PMID: 31365865 DOI: 10.1016/j.celrep.2019.06.097] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 05/28/2019] [Accepted: 06/27/2019] [Indexed: 12/27/2022] Open
Abstract
Genomic DNA is framed by additional layers of information, referred to as the epigenome. Epigenomic marks such as DNA methylation, histone modifications, and histone variants are concentrated on specific genomic sites, where they can both instruct and reflect gene expression. How this information is maintained, notably in the face of transcription, is not completely understood. Specifically, the extent to which modified histones themselves are retained through RNA polymerase II passage is unclear. Here, we show that several histone modifications are mislocalized when the transcription-coupled histone chaperones FACT or Spt6 are disrupted in Saccharomyces cerevisiae. In the absence of functional FACT or Spt6, transcription generates nucleosome loss, which is partially compensated for by the increased activity of non-transcription-coupled histone chaperones. The random incorporation of transcription-evicted modified histones scrambles epigenomic information. Our work highlights the importance of local recycling of modified histones by FACT and Spt6 during transcription in the maintenance of the epigenomic landscape.
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Affiliation(s)
- Célia Jeronimo
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Christian Poitras
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - François Robert
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada; Département de Médecine, Faculté de Médecine, Université de Montréal, 2900 Boul. Édouard-Montpetit, Montréal, QC, Canada.
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16
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Petty EL, Pillus L. Cell cycle roles for GCN5 revealed through genetic suppression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194625. [PMID: 32798737 DOI: 10.1016/j.bbagrm.2020.194625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 08/11/2020] [Accepted: 08/11/2020] [Indexed: 11/17/2022]
Abstract
The conserved acetyltransferase Gcn5 is a member of several complexes in eukaryotic cells, playing roles in regulating chromatin organization, gene expression, metabolism, and cell growth and differentiation via acetylation of both nuclear and cytoplasmic proteins. Distinct functions of Gcn5 have been revealed through a combination of biochemical and genetic approaches in many in vitro studies and model organisms. In this review, we focus on the unique insights that have been gleaned from suppressor studies of gcn5 phenotypes in the budding yeast Saccharomyces cerevisiae. Such studies were fundamental in the early understanding of the balance of counteracting chromatin activities in regulating transcription. Most recently, suppressor screens have revealed roles for Gcn5 in early cell cycle (G1 to S) gene expression and regulation of chromosome segregation during mitosis. Much has been learned, but many questions remain which will be informed by focused analysis of additional genetic and physical interactions.
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Affiliation(s)
- Emily L Petty
- University of California, San Diego, Division of Biological Sciences, Section of Molecular Biology, UCSD Moores Cancer Center, United States of America.
| | - Lorraine Pillus
- University of California, San Diego, Division of Biological Sciences, Section of Molecular Biology, UCSD Moores Cancer Center, United States of America.
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17
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Attar N, Campos OA, Vogelauer M, Cheng C, Xue Y, Schmollinger S, Salwinski L, Mallipeddi NV, Boone BA, Yen L, Yang S, Zikovich S, Dardine J, Carey MF, Merchant SS, Kurdistani SK. The histone H3-H4 tetramer is a copper reductase enzyme. Science 2020; 369:59-64. [PMID: 32631887 PMCID: PMC7842201 DOI: 10.1126/science.aba8740] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 05/13/2020] [Indexed: 12/16/2022]
Abstract
Eukaryotic histone H3-H4 tetramers contain a putative copper (Cu2+) binding site at the H3-H3' dimerization interface with unknown function. The coincident emergence of eukaryotes with global oxygenation, which challenged cellular copper utilization, raised the possibility that histones may function in cellular copper homeostasis. We report that the recombinant Xenopus laevis H3-H4 tetramer is an oxidoreductase enzyme that binds Cu2+ and catalyzes its reduction to Cu1+ in vitro. Loss- and gain-of-function mutations of the putative active site residues correspondingly altered copper binding and the enzymatic activity, as well as intracellular Cu1+ abundance and copper-dependent mitochondrial respiration and Sod1 function in the yeast Saccharomyces cerevisiae The histone H3-H4 tetramer, therefore, has a role other than chromatin compaction or epigenetic regulation and generates biousable Cu1+ ions in eukaryotes.
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Affiliation(s)
- Narsis Attar
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Oscar A Campos
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Maria Vogelauer
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Chen Cheng
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Yong Xue
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Stefan Schmollinger
- Institute for Genomics and Proteomics, Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Lukasz Salwinski
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- UCLA-DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Nathan V Mallipeddi
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Brandon A Boone
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Linda Yen
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Sichen Yang
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Shannon Zikovich
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Jade Dardine
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Michael F Carey
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Sabeeha S Merchant
- Institute for Genomics and Proteomics, Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Siavash K Kurdistani
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA.
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
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18
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Poramba-Liyanage DW, Korthout T, Cucinotta CE, van Kruijsbergen I, van Welsem T, El Atmioui D, Ovaa H, Tsukiyama T, van Leeuwen F. Inhibition of transcription leads to rewiring of locus-specific chromatin proteomes. Genome Res 2020; 30:635-646. [PMID: 32188699 PMCID: PMC7197482 DOI: 10.1101/gr.256255.119] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 03/11/2020] [Indexed: 12/13/2022]
Abstract
Transcription of a chromatin template involves the concerted interaction of many different proteins and protein complexes. Analyses of specific factors showed that these interactions change during stress and upon developmental switches. However, how the binding of multiple factors at any given locus is coordinated has been technically challenging to investigate. Here we used Epi-Decoder in yeast to systematically decode, at one transcribed locus, the chromatin binding changes of hundreds of proteins in parallel upon perturbation of transcription. By taking advantage of improved Epi-Decoder libraries, we observed broad rewiring of local chromatin proteomes following chemical inhibition of RNA polymerase. Rapid reduction of RNA polymerase II binding was accompanied by reduced binding of many other core transcription proteins and gain of chromatin remodelers. In quiescent cells, where strong transcriptional repression is induced by physiological signals, eviction of the core transcriptional machinery was accompanied by the appearance of quiescent cell–specific repressors and rewiring of the interactions of protein-folding factors and metabolic enzymes. These results show that Epi-Decoder provides a powerful strategy for capturing the temporal binding dynamics of multiple chromatin proteins under varying conditions and cell states. The systematic and comprehensive delineation of dynamic local chromatin proteomes will greatly aid in uncovering protein–protein relationships and protein functions at the chromatin template.
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Affiliation(s)
| | - Tessy Korthout
- Division of Gene Regulation, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Christine E Cucinotta
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Ila van Kruijsbergen
- Division of Gene Regulation, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Tibor van Welsem
- Division of Gene Regulation, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Dris El Atmioui
- Leiden Institute for Chemical Immunology, Leiden University Medical Center, 2333ZC Leiden, The Netherlands.,Oncode Institute, Amsterdam University Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Huib Ovaa
- Leiden Institute for Chemical Immunology, Leiden University Medical Center, 2333ZC Leiden, The Netherlands.,Oncode Institute, Amsterdam University Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Toshio Tsukiyama
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Fred van Leeuwen
- Division of Gene Regulation, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands.,Department of Medical Biology, Amsterdam University Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
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19
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Long M, Sun X, Shi W, Yanru A, Leung STC, Ding D, Cheema MS, MacPherson N, Nelson CJ, Ausio J, Yan Y, Ishibashi T. A novel histone H4 variant H4G regulates rDNA transcription in breast cancer. Nucleic Acids Res 2019; 47:8399-8409. [PMID: 31219579 PMCID: PMC6895281 DOI: 10.1093/nar/gkz547] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 06/06/2019] [Accepted: 06/10/2019] [Indexed: 12/20/2022] Open
Abstract
Histone variants, present in various cell types and tissues, are known to exhibit different functions. For example, histone H3.3 and H2A.Z are both involved in gene expression regulation, whereas H2A.X is a specific variant that responds to DNA double-strand breaks. In this study, we characterized H4G, a novel hominidae-specific histone H4 variant. We found that H4G is expressed in a variety of human cell lines and exhibit tumor-stage dependent overexpression in tissues from breast cancer patients. We found that H4G localized primarily to the nucleoli of the cell nucleus. This localization was controlled by the interaction of the alpha-helix 3 of the histone fold motif with a histone chaperone, nucleophosmin 1. In addition, we found that modulating H4G expression affects rRNA expression levels, protein synthesis rates and cell-cycle progression. Our data suggest that H4G expression alters nucleolar chromatin in a way that enhances rDNA transcription in breast cancer tissues.
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Affiliation(s)
- Mengping Long
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, NT, Hong Kong, HKSAR, China
| | - Xulun Sun
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, NT, Hong Kong, HKSAR, China
| | - Wenjin Shi
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, NT, Hong Kong, HKSAR, China
| | - An Yanru
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, NT, Hong Kong, HKSAR, China
| | - Sophia T C Leung
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, NT, Hong Kong, HKSAR, China
| | - Dongbo Ding
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, NT, Hong Kong, HKSAR, China
| | - Manjinder S Cheema
- Department of Biochemistry and Microbiology, University of Victoria, Victoria BC V8W 3P6, Canada
| | - Nicol MacPherson
- Department of Medical Oncology, BC Cancer Vancouver Island Centre, Victoria, BC V8R 6V5, Canada
| | - Christopher J Nelson
- Department of Biochemistry and Microbiology, University of Victoria, Victoria BC V8W 3P6, Canada
| | - Juan Ausio
- Department of Biochemistry and Microbiology, University of Victoria, Victoria BC V8W 3P6, Canada
| | - Yan Yan
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, NT, Hong Kong, HKSAR, China
| | - Toyotaka Ishibashi
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, NT, Hong Kong, HKSAR, China
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20
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Gouot E, Bhat W, Rufiange A, Fournier E, Paquet E, Nourani A. Casein kinase 2 mediated phosphorylation of Spt6 modulates histone dynamics and regulates spurious transcription. Nucleic Acids Res 2019; 46:7612-7630. [PMID: 29905868 PMCID: PMC6125631 DOI: 10.1093/nar/gky515] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 05/24/2018] [Indexed: 12/14/2022] Open
Abstract
CK2 is an essential protein kinase implicated in various cellular processes. In this study, we address a potential role of this kinase in chromatin modulations associated with transcription. We found that CK2 depletion from yeast cells leads to replication-independent increase of histone H3K56 acetylation and global activation of H3 turnover in coding regions. This suggests a positive role of CK2 in maintenance/recycling of the histone H3/H4 tetramers during transcription. Interestingly, strand-specific RNA-seq analyses show that CK2 inhibits global cryptic promoters driving both sense and antisense transcription. This further indicates a role of CK2 in the modulation of chromatin during transcription. Next, we showed that CK2 interacts with the major histone chaperone Spt6, and phosphorylates it in vivo and in vitro. CK2 phosphorylation of Spt6 is required for its cellular levels, for the suppression of histone H3 turnover and for the inhibition of spurious transcription. Finally, we showed that CK2 and Spt6 phosphorylation sites are important to various transcriptional responses suggesting that cryptic intragenic and antisense transcript production are associated with a defective adaptation to environmental cues. Altogether, our data indicate that CK2 mediated phosphorylation of Spt6 regulates chromatin dynamics associated with transcription, and prevents aberrant transcription.
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Affiliation(s)
- Emmanuelle Gouot
- Laval University Cancer Research Center, St-Patrick Research Group in Basic Oncology, Québec, Québec, Canada
| | - Wajid Bhat
- Laval University Cancer Research Center, St-Patrick Research Group in Basic Oncology, Québec, Québec, Canada
| | - Anne Rufiange
- Laval University Cancer Research Center, St-Patrick Research Group in Basic Oncology, Québec, Québec, Canada
| | - Eric Fournier
- Laval University Cancer Research Center, St-Patrick Research Group in Basic Oncology, Québec, Québec, Canada.,CHU de Quebec Research Center - Laval University, Endocrinology and Nephrology CHUL, Québec, Québec, Canada
| | - Eric Paquet
- Laval University Cancer Research Center, St-Patrick Research Group in Basic Oncology, Québec, Québec, Canada.,CHU de Quebec Research Center - Laval University, Endocrinology and Nephrology CHUL, Québec, Québec, Canada.,The Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Amine Nourani
- Laval University Cancer Research Center, St-Patrick Research Group in Basic Oncology, Québec, Québec, Canada
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21
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Structural insights into the ability of nucleoplasmin to assemble and chaperone histone octamers for DNA deposition. Sci Rep 2019; 9:9487. [PMID: 31263230 PMCID: PMC6602930 DOI: 10.1038/s41598-019-45726-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 06/12/2019] [Indexed: 12/13/2022] Open
Abstract
Nucleoplasmin (NP) is a pentameric histone chaperone that regulates the condensation state of chromatin in different cellular processes. We focus here on the interaction of NP with the histone octamer, showing that NP could bind sequentially the histone components to assemble an octamer-like particle, and crosslinked octamers with high affinity. The three-dimensional reconstruction of the NP/octamer complex generated by single-particle cryoelectron microscopy, revealed that several intrinsically disordered tail domains of two NP pentamers, facing each other through their distal face, encage the histone octamer in a nucleosome-like conformation and prevent its dissociation. Formation of this complex depended on post-translational modification and exposure of the acidic tract at the tail domain of NP. Finally, NP was capable of transferring the histone octamers to DNA in vitro, assembling nucleosomes. This activity may have biological relevance for processes in which the histone octamer must be rapidly removed from or deposited onto the DNA.
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22
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Ricketts MD, Dasgupta N, Fan J, Han J, Gerace M, Tang Y, Black BE, Adams PD, Marmorstein R. The HIRA histone chaperone complex subunit UBN1 harbors H3/H4- and DNA-binding activity. J Biol Chem 2019; 294:9239-9259. [PMID: 31040182 DOI: 10.1074/jbc.ra119.007480] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 04/01/2019] [Indexed: 02/04/2023] Open
Abstract
The HIRA histone chaperone complex is composed of the proteins HIRA, UBN1, and CABIN1 and cooperates with the histone chaperone ASF1a to specifically bind and deposit H3.3/H4 into chromatin. We recently reported that the UBN1 Hpc2-related domain (HRD) specifically binds to H3.3/H4 over H3.1/H4. However, the mechanism for HIRA complex deposition of H3.3/H4 into nucleosomes remains unclear. Here, we characterize a central region of UBN1 (UBN1 middle domain) that is evolutionarily conserved and predicted to have helical secondary structure. We report that the UBN1 middle domain has dimer formation activity and binds to H3/H4 in a manner that does not discriminate between H3.1 and H3.3. We additionally identify a nearby DNA-binding domain in UBN1, located between the UBN1 HRD and middle domain, which binds DNA through electrostatic contacts involving several conserved lysine residues. Together, these observations suggest a mechanism for HIRA-mediated H3.3/H4 deposition whereby UBN1 associates with DNA and dimerizes to mediate formation of an (H3.3/H4)2 heterotetramer prior to chromatin deposition.
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Affiliation(s)
- M Daniel Ricketts
- From the Department of Biochemistry and Biophysics and.,the Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Nirmalya Dasgupta
- the Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037
| | - Jiayi Fan
- From the Department of Biochemistry and Biophysics and
| | - Joseph Han
- From the Department of Biochemistry and Biophysics and.,the Department of Chemistry Graduate Group and
| | - Morgan Gerace
- From the Department of Biochemistry and Biophysics and
| | - Yong Tang
- the Wistar Institute, Philadelphia, Pennsylvania 19104, and
| | - Ben E Black
- From the Department of Biochemistry and Biophysics and.,the Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Peter D Adams
- the Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037
| | - Ronen Marmorstein
- From the Department of Biochemistry and Biophysics and .,the Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104.,the Department of Chemistry Graduate Group and.,the Wistar Institute, Philadelphia, Pennsylvania 19104, and.,the Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104
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23
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Zhao H, Winogradoff D, Dalal Y, Papoian GA. The Oligomerization Landscape of Histones. Biophys J 2019; 116:1845-1855. [PMID: 31005236 DOI: 10.1016/j.bpj.2019.03.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 03/06/2019] [Accepted: 03/14/2019] [Indexed: 12/29/2022] Open
Abstract
In eukaryotes, DNA is packaged within nucleosomes. The DNA of each nucleosome is typically centered around an octameric histone protein core: one central tetramer plus two separate dimers. Studying the assembly mechanisms of histones is essential for understanding the dynamics of entire nucleosomes and higher-order DNA packaging. Here, we investigate canonical histone assembly and that of the centromere-specific histone variant, centromere protein A (CENP-A), using molecular dynamics simulations. We quantitatively characterize their thermodynamical and dynamical features, showing that two H3/H4 dimers form a structurally floppy, weakly bound complex, the latter exhibiting large instability around the central interface manifested via a swiveling motion of two halves. This finding is consistent with the recently observed DNA handedness flipping of the tetrasome. In contrast, the variant CENP-A encodes distinctive stability to its tetramer with a rigid but twisted interface compared to the crystal structure, implying diverse structural possibilities of the histone variant. Interestingly, the observed tetramer dynamics alter significantly and appear to reach a new balance when H2A/H2B dimers are present. Furthermore, we found that the preferred structure for the (CENP-A/H4)2 tetramer is incongruent with the octameric structure, explaining many of the unusual dynamical behaviors of the CENP-A nucleosome. In all, these data reveal key mechanistic insights and structural details for the assembly of canonical and variant histone tetramers and octamers, providing theoretical quantifications and physical interpretations for longstanding and recent experimental observations. Based on these findings, we propose different chaperone-assisted binding and nucleosome assembly mechanisms for the canonical and CENP-A histone oligomers.
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Affiliation(s)
- Haiqing Zhao
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland; Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - David Winogradoff
- Chemical Physics Program, Institute for Physical Science and Technology
| | - Yamini Dalal
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.
| | - Garegin A Papoian
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland; Chemical Physics Program, Institute for Physical Science and Technology; Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland.
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24
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Doris SM, Chuang J, Viktorovskaya O, Murawska M, Spatt D, Churchman LS, Winston F. Spt6 Is Required for the Fidelity of Promoter Selection. Mol Cell 2018; 72:687-699.e6. [PMID: 30318445 DOI: 10.1016/j.molcel.2018.09.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 08/20/2018] [Accepted: 08/31/2018] [Indexed: 01/06/2023]
Abstract
Spt6 is a conserved factor that controls transcription and chromatin structure across the genome. Although Spt6 is viewed as an elongation factor, spt6 mutations in Saccharomyces cerevisiae allow elevated levels of transcripts from within coding regions, suggesting that Spt6 also controls initiation. To address the requirements for Spt6 in transcription and chromatin structure, we have combined four genome-wide approaches. Our results demonstrate that Spt6 represses transcription initiation at thousands of intragenic promoters. We characterize these intragenic promoters and find sequence features conserved with genic promoters. Finally, we show that Spt6 also regulates transcription initiation at most genic promoters and propose a model of initiation site competition to account for this. Together, our results demonstrate that Spt6 controls the fidelity of transcription initiation throughout the genome.
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Affiliation(s)
- Stephen M Doris
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - James Chuang
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | | | | | - Dan Spatt
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | | | - Fred Winston
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
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25
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Zhang L, Serra-Cardona A, Zhou H, Wang M, Yang N, Zhang Z, Xu RM. Multisite Substrate Recognition in Asf1-Dependent Acetylation of Histone H3 K56 by Rtt109. Cell 2018; 174:818-830.e11. [PMID: 30057113 DOI: 10.1016/j.cell.2018.07.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 04/08/2018] [Accepted: 07/03/2018] [Indexed: 12/19/2022]
Abstract
Rtt109 is a unique histone acetyltransferase acetylating histone H3 lysine 56 (H3K56), a modification critical for DNA replication-coupled nucleosome assembly and genome stability. In cells, histone chaperone Asf1 is essential for H3K56 acetylation, yet the mechanisms for H3K56 specificity and Asf1 requirement remain unknown. We have determined the crystal structure of the Rtt109-Asf1-H3-H4 complex and found that unwinding of histone H3 αN, where K56 is normally located, and stabilization of the very C-terminal β strand of histone H4 by Asf1 are prerequisites for H3K56 acetylation. Unexpectedly, an interaction between Rtt109 and the central helix of histone H3 is also required. The observed multiprotein, multisite substrate recognition mechanism among histone modification enzymes provides mechanistic understandings of Rtt109 and Asf1 in H3K56 acetylation, as well as valuable insights into substrate recognition by histone modification enzymes in general.
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Affiliation(s)
- Lin Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China; University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Albert Serra-Cardona
- Institute for Cancer Genetics, Departments of Pediatrics and Genetics and Development and Irving Cancer Research Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Hui Zhou
- Institute for Cancer Genetics, Departments of Pediatrics and Genetics and Development and Irving Cancer Research Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Mingzhu Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China
| | - Na Yang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, 300353 Tianjin, China
| | - Zhiguo Zhang
- Institute for Cancer Genetics, Departments of Pediatrics and Genetics and Development and Irving Cancer Research Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.
| | - Rui-Ming Xu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China; University of Chinese Academy of Sciences, 100049 Beijing, China.
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26
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Warren C, Shechter D. Fly Fishing for Histones: Catch and Release by Histone Chaperone Intrinsically Disordered Regions and Acidic Stretches. J Mol Biol 2017; 429:2401-2426. [PMID: 28610839 DOI: 10.1016/j.jmb.2017.06.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 06/05/2017] [Accepted: 06/06/2017] [Indexed: 01/21/2023]
Abstract
Chromatin is the complex of eukaryotic DNA and proteins required for the efficient compaction of the nearly 2-meter-long human genome into a roughly 10-micron-diameter cell nucleus. The fundamental repeating unit of chromatin is the nucleosome: 147bp of DNA wrapped about an octamer of histone proteins. Nucleosomes are stable enough to organize the genome yet must be dynamically displaced and reassembled to allow access to the underlying DNA for transcription, replication, and DNA damage repair. Histone chaperones are a non-catalytic group of proteins that are central to the processes of nucleosome assembly and disassembly and thus the fluidity of the ever-changing chromatin landscape. Histone chaperones are responsible for binding the highly basic histone proteins, shielding them from non-specific interactions, facilitating their deposition onto DNA, and aiding in their eviction from DNA. Although most histone chaperones perform these common functions, recent structural studies of many different histone chaperones reveal that there are few commonalities in their folds. Importantly, sequence-based predictions show that histone chaperones are highly enriched in intrinsically disordered regions (IDRs) and acidic stretches. In this review, we focus on the molecular mechanisms underpinning histone binding, selectivity, and regulation of these highly dynamic protein regions. We highlight new evidence suggesting that IDRs are often critical for histone chaperone function and play key roles in chromatin assembly and disassembly pathways.
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Affiliation(s)
- Christopher Warren
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - David Shechter
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA.
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27
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Reddy BA, Jeronimo C, Robert F. Recent Perspectives on the Roles of Histone Chaperones in Transcription Regulation. ACTA ACUST UNITED AC 2017. [DOI: 10.1007/s40610-017-0049-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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28
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Hammond CM, Strømme CB, Huang H, Patel DJ, Groth A. Histone chaperone networks shaping chromatin function. Nat Rev Mol Cell Biol 2017; 18:141-158. [PMID: 28053344 DOI: 10.1038/nrm.2016.159] [Citation(s) in RCA: 337] [Impact Index Per Article: 48.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The association of histones with specific chaperone complexes is important for their folding, oligomerization, post-translational modification, nuclear import, stability, assembly and genomic localization. In this way, the chaperoning of soluble histones is a key determinant of histone availability and fate, which affects all chromosomal processes, including gene expression, chromosome segregation and genome replication and repair. Here, we review the distinct structural and functional properties of the expanding network of histone chaperones. We emphasize how chaperones cooperate in the histone chaperone network and via co-chaperone complexes to match histone supply with demand, thereby promoting proper nucleosome assembly and maintaining epigenetic information by recycling modified histones evicted from chromatin.
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Affiliation(s)
- Colin M Hammond
- Biotech Research and Innovation Centre (BRIC) and Centre for Epigenetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Caroline B Strømme
- Biotech Research and Innovation Centre (BRIC) and Centre for Epigenetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Hongda Huang
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Anja Groth
- Biotech Research and Innovation Centre (BRIC) and Centre for Epigenetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark
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29
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Qi YK, He QQ, Ai HS, Guo J, Li JB. The convergent chemical synthesis of histone H3 protein for site-specific acetylation at Lys56 and ubiquitination at Lys122. Chem Commun (Camb) 2017; 53:4148-4151. [DOI: 10.1039/c7cc01721a] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The first total chemical synthesis of modified H3 bearing Lys56 acetylation and Lys122 ubiquitination.
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Affiliation(s)
- Yun-Kun Qi
- Tsinghua-Peking Center for Life Sciences
- Department of Chemistry
- Tsinghua University
- Beijing 100084
- China
| | - Qiao-Qiao He
- Tsinghua-Peking Center for Life Sciences
- Department of Chemistry
- Tsinghua University
- Beijing 100084
- China
| | - Hua-Song Ai
- Tsinghua-Peking Center for Life Sciences
- Department of Chemistry
- Tsinghua University
- Beijing 100084
- China
| | - Jing Guo
- Tsinghua-Peking Center for Life Sciences
- Department of Chemistry
- Tsinghua University
- Beijing 100084
- China
| | - Jia-Bin Li
- Tsinghua-Peking Center for Life Sciences
- Department of Chemistry
- Tsinghua University
- Beijing 100084
- China
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30
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A Molecular Prospective for HIRA Complex Assembly and H3.3-Specific Histone Chaperone Function. J Mol Biol 2016; 429:1924-1933. [PMID: 27871933 DOI: 10.1016/j.jmb.2016.11.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/14/2016] [Accepted: 11/15/2016] [Indexed: 11/24/2022]
Abstract
Incorporation of variant histone sequences, in addition to post-translational modification of histones, serves to modulate the chromatin environment. Different histone chaperone proteins mediate the storage and chromatin deposition of variant histones. Although the two non-centromeric histone H3 variants, H3.1 and H3.3, differ by only 5 aa, replacement of histone H3.1 with H3.3 can modulate the transcription for highly expressed and developmentally required genes, lead to the formation of repressive heterochromatin, or aid in DNA and chromatin repair. The human histone cell cycle regulator (HIRA) complex composed of HIRA, ubinuclein-1, CABIN1, and transiently anti-silencing function 1, forms one of the two complexes that bind and deposit H3.3/H4 into chromatin. A number of recent biochemical and structural studies have revealed important details underlying how these proteins assemble and function together as a multiprotein H3.3-specific histone chaperone complex. Here, we present a review of existing data and present a new model for the assembly of the HIRA complex and for the HIRA-mediated incorporation of H3.3/H4 into chromatin.
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31
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A Quantitative Characterization of Nucleoplasmin/Histone Complexes Reveals Chaperone Versatility. Sci Rep 2016; 6:32114. [PMID: 27558753 PMCID: PMC4997359 DOI: 10.1038/srep32114] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 08/02/2016] [Indexed: 01/29/2023] Open
Abstract
Nucleoplasmin (NP) is an abundant histone chaperone in vertebrate oocytes and embryos involved in storing and releasing maternal histones to establish and maintain the zygotic epigenome. NP has been considered a H2A-H2B histone chaperone, and recently it has been shown that it can also interact with H3-H4. However, its interaction with different types of histones has not been quantitatively studied so far. We show here that NP binds H2A-H2B, H3-H4 and linker histones with Kd values in the subnanomolar range, forming different complexes. Post-translational modifications of NP regulate exposure of the polyGlu tract at the disordered distal face of the protein and induce an increase in chaperone affinity for all histones. The relative affinity of NP for H2A-H2B and linker histones and the fact that they interact with the distal face of the chaperone could explain their competition for chaperone binding, a relevant process in NP-mediated sperm chromatin remodelling during fertilization. Our data show that NP binds H3-H4 tetramers in a nucleosomal conformation and dimers, transferring them to DNA to form disomes and tetrasomes. This finding might be relevant to elucidate the role of NP in chromatin disassembly and assembly during replication and transcription.
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32
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Tsunaka Y, Fujiwara Y, Oyama T, Hirose S, Morikawa K. Integrated molecular mechanism directing nucleosome reorganization by human FACT. Genes Dev 2016; 30:673-86. [PMID: 26966247 PMCID: PMC4803053 DOI: 10.1101/gad.274183.115] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 02/05/2016] [Indexed: 11/24/2022]
Abstract
Facilitates chromatin transcription (FACT) plays essential roles in chromatin remodeling during DNA transcription, replication, and repair. Tsunaka et al. studied human FACT–histone interactions that present precise views of nucleosome reorganization, conducted by the FACT-SPT16 Mid domain and its adjacent acidic AID segment. Facilitates chromatin transcription (FACT) plays essential roles in chromatin remodeling during DNA transcription, replication, and repair. Our structural and biochemical studies of human FACT–histone interactions present precise views of nucleosome reorganization, conducted by the FACT-SPT16 (suppressor of Ty 16) Mid domain and its adjacent acidic AID segment. AID accesses the H2B N-terminal basic region exposed by partial unwrapping of the nucleosomal DNA, thereby triggering the invasion of FACT into the nucleosome. The crystal structure of the Mid domain complexed with an H3–H4 tetramer exhibits two separate contact sites; the Mid domain forms a novel intermolecular β structure with H4. At the other site, the Mid–H2A steric collision on the H2A-docking surface of the H3–H4 tetramer within the nucleosome induces H2A–H2B displacement. This integrated mechanism results in disrupting the H3 αN helix, which is essential for retaining the nucleosomal DNA ends, and hence facilitates DNA stripping from histone.
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Affiliation(s)
- Yasuo Tsunaka
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, Sakyo-ku, Kyoto 606-8501, Japan; Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan; Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Yoshida-konoemachi, Sakyo-ku, Kyoto 606-8501, Japan; International Institute for Advanced Studies, Kizugawa-shi, Kyoto 619-0225, Japan
| | - Yoshie Fujiwara
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan; Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Yoshida-konoemachi, Sakyo-ku, Kyoto 606-8501, Japan
| | - Takuji Oyama
- Department of Biotechnology, Faculty of Life and Environmental Sciences, University of Yamanashi, Yamanashi 400-8510, Japan
| | - Susumu Hirose
- Department of Developmental Genetics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Kosuke Morikawa
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Yoshida-konoemachi, Sakyo-ku, Kyoto 606-8501, Japan; International Institute for Advanced Studies, Kizugawa-shi, Kyoto 619-0225, Japan
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33
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The Abundant Histone Chaperones Spt6 and FACT Collaborate to Assemble, Inspect, and Maintain Chromatin Structure in Saccharomyces cerevisiae. Genetics 2015; 201:1031-45. [PMID: 26416482 DOI: 10.1534/genetics.115.180794] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 09/20/2015] [Indexed: 11/18/2022] Open
Abstract
Saccharomyces cerevisiae Spt6 protein is a conserved chromatin factor with several distinct functional domains, including a natively unstructured 30-residue N-terminal region that binds competitively with Spn1 or nucleosomes. To uncover physiological roles of these interactions, we isolated histone mutations that suppress defects caused by weakening Spt6:Spn1 binding with the spt6-F249K mutation. The strongest suppressor was H2A-N39K, which perturbs the point of contact between the two H2A-H2B dimers in an assembled nucleosome. Substantial suppression also was observed when the H2A-H2B interface with H3-H4 was altered, and many members of this class of mutations also suppressed a defect in another essential histone chaperone, FACT. Spt6 is best known as an H3-H4 chaperone, but we found that it binds with similar affinity to H2A-H2B or H3-H4. Like FACT, Spt6 is therefore capable of binding each of the individual components of a nucleosome, but unlike FACT, Spt6 did not produce endonuclease-sensitive reorganized nucleosomes and did not displace H2A-H2B dimers from nucleosomes. Spt6 and FACT therefore have distinct activities, but defects can be suppressed by overlapping histone mutations. We also found that Spt6 and FACT together are nearly as abundant as nucleosomes, with ∼24,000 Spt6 molecules, ∼42,000 FACT molecules, and ∼75,000 nucleosomes per cell. Histone mutations that destabilize interfaces within nucleosomes therefore reveal multiple spatial regions that have both common and distinct roles in the functions of these two essential and abundant histone chaperones. We discuss these observations in terms of different potential roles for chaperones in both promoting the assembly of nucleosomes and monitoring their quality.
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34
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Clément C, Almouzni G. MCM2 binding to histones H3–H4 and ASF1 supports a tetramer-to-dimer model for histone inheritance at the replication fork. Nat Struct Mol Biol 2015; 22:587-9. [DOI: 10.1038/nsmb.3067] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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