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Jurkovic CM, Raisch J, Tran S, Nguyen HD, Lévesque D, Scott MS, Campos EI, Boisvert FM. Replisome Proximal Protein Associations and Dynamic Proteomic Changes at Stalled Replication Forks. Mol Cell Proteomics 2024; 23:100767. [PMID: 38615877 PMCID: PMC11101681 DOI: 10.1016/j.mcpro.2024.100767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 03/19/2024] [Accepted: 04/11/2024] [Indexed: 04/16/2024] Open
Abstract
DNA replication is a fundamental cellular process that ensures the transfer of genetic information during cell division. Genome duplication takes place in S phase and requires a dynamic and highly coordinated recruitment of multiple proteins at replication forks. Various genotoxic stressors lead to fork instability and collapse, hence the need for DNA repair pathways. By identifying the multitude of protein interactions implicated in those events, we can better grasp the complex and dynamic molecular mechanisms that facilitate DNA replication and repair. Proximity-dependent biotin identification was used to identify associations with 17 proteins within four core replication components, namely the CDC45/MCM2-7/GINS helicase that unwinds DNA, the DNA polymerases, replication protein A subunits, and histone chaperones needed to disassemble and reassemble chromatin. We further investigated the impact of genotoxic stress on these interactions. This analysis revealed a vast proximity association network with 108 nuclear proteins further modulated in the presence of hydroxyurea; 45 being enriched and 63 depleted. Interestingly, hydroxyurea treatment also caused a redistribution of associations with 11 interactors, meaning that the replisome is dynamically reorganized when stressed. The analysis identified several poorly characterized proteins, thereby uncovering new putative players in the cellular response to DNA replication arrest. It also provides a new comprehensive proteomic framework to understand how cells respond to obstacles during DNA replication.
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Affiliation(s)
- Carla-Marie Jurkovic
- Faculty of Medicine and Health Sciences, Department of Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Jennifer Raisch
- Faculty of Medicine and Health Sciences, Department of Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Stephanie Tran
- Genetics & Genome Biology Program, Department of Molecular Biology, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Hoang Dong Nguyen
- Faculty of Medicine and Health Sciences, Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Dominique Lévesque
- Faculty of Medicine and Health Sciences, Department of Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Michelle S Scott
- Faculty of Medicine and Health Sciences, Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Eric I Campos
- Genetics & Genome Biology Program, Department of Molecular Biology, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada.
| | - François-Michel Boisvert
- Faculty of Medicine and Health Sciences, Department of Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, Québec, Canada.
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Klett-Mingo JI, Pinto-Díez C, Cambronero-Plaza J, Carrión-Marchante R, Barragán-Usero M, Pérez-Morgado MI, Rodríguez-Martín E, del Val Toledo-Lobo M, González VM, Martín ME. Potential Therapeutic Use of Aptamers against HAT1 in Lung Cancer. Cancers (Basel) 2022; 15:cancers15010227. [PMID: 36612223 PMCID: PMC9818519 DOI: 10.3390/cancers15010227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/14/2022] [Accepted: 12/26/2022] [Indexed: 12/31/2022] Open
Abstract
Lung cancer is one of the leading causes of death worldwide and the most common of all cancer types. Histone acetyltransferase 1 (HAT1) has attracted increasing interest as a potential therapeutic target due to its involvement in multiple pathologies, including cancer. Aptamers are single-stranded RNA or DNA molecules whose three-dimensional structure allows them to bind to a target molecule with high specificity and affinity, thus making them exceptional candidates for use as diagnostic or therapeutic tools. In this work, aptamers against HAT1 were obtained, subsequently characterized, and optimized, showing high affinity and specificity for HAT1 and the ability to inhibit acetyltransferase activity in vitro. Of those tested, the apHAT610 aptamer reduced cell viability, induced apoptosis and cell cycle arrest, and inhibited colony formation in lung cancer cell lines. All these results indicate that the apHAT610 aptamer is a potential drug for the treatment of lung cancer.
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Affiliation(s)
- José Ignacio Klett-Mingo
- Grupo de Aptámeros, Departamento de Bioquímica-Investigación, IRYCIS-Hospital Universitario Ramón y Cajal, Carretera de Colmenar Viejo Km. 9.100, 28034 Madrid, Spain
| | - Celia Pinto-Díez
- Aptus Biotech SL, Av. Cardenal Herrera Oria 298, 28035 Madrid, Spain
| | - Julio Cambronero-Plaza
- Grupo de Aptámeros, Departamento de Bioquímica-Investigación, IRYCIS-Hospital Universitario Ramón y Cajal, Carretera de Colmenar Viejo Km. 9.100, 28034 Madrid, Spain
| | - Rebeca Carrión-Marchante
- Grupo de Aptámeros, Departamento de Bioquímica-Investigación, IRYCIS-Hospital Universitario Ramón y Cajal, Carretera de Colmenar Viejo Km. 9.100, 28034 Madrid, Spain
| | - Miriam Barragán-Usero
- Grupo de Aptámeros, Departamento de Bioquímica-Investigación, IRYCIS-Hospital Universitario Ramón y Cajal, Carretera de Colmenar Viejo Km. 9.100, 28034 Madrid, Spain
| | - María Isabel Pérez-Morgado
- Grupo de Aptámeros, Departamento de Bioquímica-Investigación, IRYCIS-Hospital Universitario Ramón y Cajal, Carretera de Colmenar Viejo Km. 9.100, 28034 Madrid, Spain
| | - Eulalia Rodríguez-Martín
- Departamento de Inmunología, IRYCIS-Hospital Universitario Ramón y Cajal, Carretera de Colmenar Viejo Km. 9.100, 28034 Madrid, Spain
| | - María del Val Toledo-Lobo
- Unidad de Biología Celular, Departamento de Biomedicina y Biotecnología, Universidad de Alcalá, 28871 Alcalá de Henares, Spain
| | - Víctor M. González
- Grupo de Aptámeros, Departamento de Bioquímica-Investigación, IRYCIS-Hospital Universitario Ramón y Cajal, Carretera de Colmenar Viejo Km. 9.100, 28034 Madrid, Spain
- Correspondence: (V.M.G.); (M.E.M.); Tel.: +34-913368173 (V.M.G. & M.E.M.)
| | - Maria Elena Martín
- Grupo de Aptámeros, Departamento de Bioquímica-Investigación, IRYCIS-Hospital Universitario Ramón y Cajal, Carretera de Colmenar Viejo Km. 9.100, 28034 Madrid, Spain
- Correspondence: (V.M.G.); (M.E.M.); Tel.: +34-913368173 (V.M.G. & M.E.M.)
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3
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Hammond-Martel I, Verreault A, Wurtele H. Chromatin dynamics and DNA replication roadblocks. DNA Repair (Amst) 2021; 104:103140. [PMID: 34087728 DOI: 10.1016/j.dnarep.2021.103140] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/18/2021] [Accepted: 05/20/2021] [Indexed: 11/27/2022]
Abstract
A broad spectrum of spontaneous and genotoxin-induced DNA lesions impede replication fork progression. The DNA damage response that acts to promote completion of DNA replication is associated with dynamic changes in chromatin structure that include two distinct processes which operate genome-wide during S-phase. The first, often referred to as histone recycling or parental histone segregation, is characterized by the transfer of parental histones located ahead of replication forks onto nascent DNA. The second, known as de novo chromatin assembly, consists of the deposition of new histone molecules onto nascent DNA. Because these two processes occur at all replication forks, their potential to influence a multitude of DNA repair and DNA damage tolerance mechanisms is considerable. The purpose of this review is to provide a description of parental histone segregation and de novo chromatin assembly, and to illustrate how these processes influence cellular responses to DNA replication roadblocks.
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Affiliation(s)
- Ian Hammond-Martel
- Centre de recherche de l'Hôpital Maisonneuve-Rosemont, 5415 boulevard de l'Assomption, Montreal, H1T 2M4, Canada
| | - Alain Verreault
- Institute for Research in Immunology and Cancer, Université de Montréal, P.O. Box 6128, Succursale Centre-Ville, Montreal, H3C 3J7, Canada; Département de Pathologie et Biologie Cellulaire, Université de Montréal, 2900 Edouard Montpetit Blvd, Montreal, H3T 1J4, Canada
| | - Hugo Wurtele
- Centre de recherche de l'Hôpital Maisonneuve-Rosemont, 5415 boulevard de l'Assomption, Montreal, H1T 2M4, Canada; Département de Médecine, Université de Montréal, Université de Montréal, 2900 Edouard Montpetit Blvd, Montreal, H3T 1J4, Canada.
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4
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Young TJ, Cui Y, Pfeffer C, Hobbs E, Liu W, Irudayaraj J, Kirchmaier AL. CAF-1 and Rtt101p function within the replication-coupled chromatin assembly network to promote H4 K16ac, preventing ectopic silencing. PLoS Genet 2020; 16:e1009226. [PMID: 33284793 PMCID: PMC7746308 DOI: 10.1371/journal.pgen.1009226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 12/17/2020] [Accepted: 10/26/2020] [Indexed: 11/18/2022] Open
Abstract
Replication-coupled chromatin assembly is achieved by a network of alternate pathways containing different chromatin assembly factors and histone-modifying enzymes that coordinate deposition of nucleosomes at the replication fork. Here we describe the organization of a CAF-1-dependent pathway in Saccharomyces cerevisiae that regulates acetylation of histone H4 K16. We demonstrate factors that function in this CAF-1-dependent pathway are important for preventing establishment of silenced states at inappropriate genomic sites using a crippled HMR locus as a model, while factors specific to other assembly pathways do not. This CAF-1-dependent pathway required the cullin Rtt101p, but was functionally distinct from an alternate pathway involving Rtt101p-dependent ubiquitination of histone H3 and the chromatin assembly factor Rtt106p. A major implication from this work is that cells have the inherent ability to create different chromatin modification patterns during DNA replication via differential processing and deposition of histones by distinct chromatin assembly pathways within the network.
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Affiliation(s)
- Tiffany J. Young
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, United States of America
- Purdue University Center for Cancer Research, West Lafayette, Indiana, United States of America
- Bindley Bioscience Center, Purdue University, West Lafayette, Indiana, United States of America
| | - Yi Cui
- Purdue University Center for Cancer Research, West Lafayette, Indiana, United States of America
- Bindley Bioscience Center, Purdue University, West Lafayette, Indiana, United States of America
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, Indiana, United States of America
| | - Claire Pfeffer
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, United States of America
| | - Emilie Hobbs
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, United States of America
| | - Wenjie Liu
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, Indiana, United States of America
- Department of Bioengineering, Cancer Center at Illinois, Micro and Nanotechnology Laboratory, University of Illinois at Urbana Champaign, Urbana, Illinois, United States of America
| | - Joseph Irudayaraj
- Purdue University Center for Cancer Research, West Lafayette, Indiana, United States of America
- Bindley Bioscience Center, Purdue University, West Lafayette, Indiana, United States of America
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, Indiana, United States of America
- Department of Bioengineering, Cancer Center at Illinois, Micro and Nanotechnology Laboratory, University of Illinois at Urbana Champaign, Urbana, Illinois, United States of America
| | - Ann L. Kirchmaier
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, United States of America
- Purdue University Center for Cancer Research, West Lafayette, Indiana, United States of America
- Bindley Bioscience Center, Purdue University, West Lafayette, Indiana, United States of America
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5
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Sharma S, Ahmed M, Akhter Y. Fungal acetyltransferases structures, mechanisms and inhibitors: A review. Int J Biol Macromol 2019; 157:626-640. [PMID: 31786301 DOI: 10.1016/j.ijbiomac.2019.11.214] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 11/26/2019] [Accepted: 11/26/2019] [Indexed: 12/31/2022]
Abstract
Acetylation of proteins is vital and mediate many processes within the cells like protein interactions, intercellular localization, protein stability, transcriptional regulation, enzyme activity and many more. Acetylation, an evolutionarily conserved process, attracted more attention due to its key regulatory role in many cellular processes and its effect on proteome and metabolome. In eukaryotes, protein acetylation also contribute to the epigenetic regulation of gene expression. Acetylation involves the transfer of acetyl group from donor acetyl coenzyme A to a suitable acceptor molecule and the reaction is catalyzed by acetyltransferase enzymes. The review focuses on current understanding of different acetyltransferase families: their discovery, structure and catalytic mechanism in fungal species. Fungal acetyltransferases use divergent catalytic mechanisms and carry out catalysis in a substrate-specific manner. The studies have explored different fungal acetyltransferases in relation to secondary metabolite production and the fungal pathogenesis. Although, the functions and catalytic mechanism of acetyltransferases are well known, however further enhanced knowledge may improve their utilization in various applications of biotechnology.
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Affiliation(s)
- Shikha Sharma
- School of Earth and Environmental Sciences, Central University of Himachal Pradesh, Shahpur, District-Kangra, Himachal Pradesh 176206, India
| | - Mushtaq Ahmed
- School of Earth and Environmental Sciences, Central University of Himachal Pradesh, Shahpur, District-Kangra, Himachal Pradesh 176206, India
| | - Yusuf Akhter
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, VidyaVihar, Raebareli Road, Lucknow, Uttar Pradesh 226025, India.
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6
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He M, Han Z, Liu L, Zheng YG. Untersuchung der epigenetischen Funktionen von Lysin‐Acetyltransferasen mit Methoden der chemischen Biologie. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201704745] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Maomao He
- Department of Pharmaceutical and Biochemical Sciences and Department of Statistics University of Georgia Athens Georgia 30602 USA
| | - Zhen Han
- Department of Pharmaceutical and Biochemical Sciences and Department of Statistics University of Georgia Athens Georgia 30602 USA
| | - Liang Liu
- Department of Pharmaceutical and Biochemical Sciences and Department of Statistics University of Georgia Athens Georgia 30602 USA
| | - Y. George Zheng
- Department of Pharmaceutical and Biochemical Sciences and Department of Statistics University of Georgia Athens Georgia 30602 USA
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7
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He M, Han Z, Liu L, Zheng YG. Chemical Biology Approaches for Investigating the Functions of Lysine Acetyltransferases. Angew Chem Int Ed Engl 2017; 57:1162-1184. [PMID: 28786225 DOI: 10.1002/anie.201704745] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Indexed: 12/20/2022]
Abstract
The side-chain acetylation of lysine residues in histones and non-histone proteins catalyzed by lysine acetyltransferases (KATs) represents a widespread posttranslational modification (PTM) in the eukaryotic cells. Lysine acetylation plays regulatory roles in major cellular pathways inside and outside the nucleus. In particular, KAT-mediated histone acetylation has an effect on all DNA-templated epigenetic processes. Aberrant expression and activation of KATs are commonly observed in human diseases, especially cancer. In recent years, the study of KAT functions in biology and disease has greatly benefited from chemical biology tools and strategies. In this Review, we present the past and current accomplishments in the design of chemical biology approaches for the interrogation of KAT activity and function. These methods and probes are classified according to their mechanisms of action and respective applications, with both strengths and limitations discussed.
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Affiliation(s)
- Maomao He
- Department of Pharmaceutical and Biochemical Sciences and Department of Statistics, University of Georgia, Athens, Georgia, 30602 (U, SA
| | - Zhen Han
- Department of Pharmaceutical and Biochemical Sciences and Department of Statistics, University of Georgia, Athens, Georgia, 30602 (U, SA
| | - Liang Liu
- Department of Pharmaceutical and Biochemical Sciences and Department of Statistics, University of Georgia, Athens, Georgia, 30602 (U, SA
| | - Y George Zheng
- Department of Pharmaceutical and Biochemical Sciences and Department of Statistics, University of Georgia, Athens, Georgia, 30602 (U, SA
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8
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Structural Insights into the Association of Hif1 with Histones H2A-H2B Dimer and H3-H4 Tetramer. Structure 2016; 24:1810-1820. [DOI: 10.1016/j.str.2016.08.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Revised: 08/01/2016] [Accepted: 08/01/2016] [Indexed: 11/22/2022]
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9
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Data for the identification of proteins and post-translational modifications of proteins associated to histones H3 and H4 in S. cerevisiae, using tandem affinity purification coupled with mass spectrometry. Data Brief 2016; 6:965-9. [PMID: 26949727 PMCID: PMC4758224 DOI: 10.1016/j.dib.2016.01.068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 01/28/2016] [Accepted: 01/28/2016] [Indexed: 11/22/2022] Open
Abstract
Tandem affinity purification method (TAP) allows the efficient purification of native protein complexes which incorporate a target protein fused with the TAP tag. Purified multiprotein complexes can then be subjected to diverse types of proteomic analyses. Here we describe the data acquired after applying the TAP strategy on histones H3 and H4 coupled with mass spectrometry to identify associated proteins and protein post-translational modifications in the budding yeast, Saccharomyces cerevisiae. The mass spectrometry dataset described here consists of 14 files generated from four different analyses in a 5600 Triple TOF (Sciex) by information-dependent acquisition (IDA) LC-MS/MS. The above files contain information about protein identification, protein relative abundance, and PTMs identification. The instrumental raw data from these files has been also uploaded to the ProteomeXchange Consortium via the PRIDE partner repository, with the dataset identifier PRIDE: PXD002671 and http://dx.doi.org/10.6019/PXD002671. These data are discussed and interpreted in http://dx.doi.org/10.1016/j.jprot.2016.01.004. Valero et al. (2016) [1].
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10
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Valero ML, Sendra R, Pamblanco M. Tandem affinity purification of histones, coupled to mass spectrometry, identifies associated proteins and new sites of post-translational modification in Saccharomyces cerevisiae. J Proteomics 2016; 136:183-92. [PMID: 26778144 DOI: 10.1016/j.jprot.2016.01.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 12/17/2015] [Accepted: 01/04/2016] [Indexed: 02/06/2023]
Abstract
Histones and their post-translational modifications contribute to regulating fundamental biological processes in all eukaryotic cells. We have applied a conventional tandem affinity purification strategy to histones H3 and H4 of the yeast Saccharomyces cerevisiae. Mass spectrometry analysis of the co-purified proteins revealed multiple associated proteins, including core histones, which indicates that tagged histones may be incorporated to the nucleosome particle. Among the many other co-isolated proteins there are histone chaperones, elements of chromatin remodeling, of nucleosome assembly/disassembly, and of histone modification complexes. The histone chaperone Rtt106p, two members of chromatin assembly FACT complex and Psh1p, an ubiquitin ligase, were the most abundant proteins obtained with both H3-TAP and H4-TAP, regardless of the cell extraction medium stringency. Our mass spectrometry analyses have also revealed numerous novel post-translational modifications, including 30 new chemical modifications in histones, mainly by ubiquitination. We have discovered not only new sites of ubiquitination but that, besides lysine, also serine and threonine residues are targets of ubiquitination on yeast histones. Our results show the standard tandem affinity purification procedure is suitable for application to yeast histones, in order to isolate and characterize histone-binding proteins and post-translational modifications, avoiding the bias caused by histone purification from a chromatin-enriched fraction.
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Affiliation(s)
- M Luz Valero
- Secció de Proteòmica, Servei Central de Suport a la Investigació Experimental (SCSIE), Universitat de València, C/Dr. Moliner 50, 46100, Burjassot, València, Spain.
| | - Ramon Sendra
- Departament de Bioquímica i Biologia Molecular, Universitat de València, C/Dr. Moliner 50, 46100, Burjassot, València, Spain.
| | - Mercè Pamblanco
- Departament de Bioquímica i Biologia Molecular, Universitat de València, C/Dr. Moliner 50, 46100, Burjassot, València, Spain.
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11
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Boltengagen M, Huang A, Boltengagen A, Trixl L, Lindner H, Kremser L, Offterdinger M, Lusser A. A novel role for the histone acetyltransferase Hat1 in the CENP-A/CID assembly pathway in Drosophila melanogaster. Nucleic Acids Res 2015; 44:2145-59. [PMID: 26586808 PMCID: PMC4797270 DOI: 10.1093/nar/gkv1235] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 11/02/2015] [Indexed: 12/21/2022] Open
Abstract
The incorporation of CENP-A into centromeric chromatin is an essential prerequisite for kinetochore formation. Yet, the molecular mechanisms governing this process are surprisingly divergent in different organisms. While CENP-A loading mechanisms have been studied in some detail in mammals, there are still large gaps to our understanding of CENP-A/Cid loading pathways in Drosophila. Here, we report on the characterization and delineation of at least three different CENP-A preloading complexes in Drosophila. Two complexes contain the CENP-A chaperones CAL1, FACT and/or Caf1/Rbap48. Notably, we identified a novel complex consisting of the histone acetyltransferase Hat1, Caf1 and CENP-A/H4. We show that Hat1 is required for proper CENP-A loading into chromatin, since knock-down in S2 cells leads to reduced incorporation of newly synthesized CENP-A. In addition, we demonstrate that CENP-A/Cid interacts with the HAT1 complex via an N-terminal region, which is acetylated in cytoplasmic but not in nuclear CENP-A. Since Hat1 is not responsible for acetylation of CENP-A/Cid, these results suggest a histone acetyltransferase activity-independent escort function for Hat1. Thus, our results point toward intriguing analogies between the complex processing pathways of newly synthesized CENP-A and canonical histones.
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Affiliation(s)
- Mark Boltengagen
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Anming Huang
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Anastasiya Boltengagen
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Lukas Trixl
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Herbert Lindner
- Division of Clinical Biochemistry, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Leopold Kremser
- Division of Clinical Biochemistry, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Martin Offterdinger
- Division of Neurobiochemistry, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Alexandra Lusser
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
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12
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Vicente-Muñoz S, Romero P, Magraner-Pardo L, Martinez-Jimenez CP, Tordera V, Pamblanco M. Comprehensive analysis of interacting proteins and genome-wide location studies of the Sas3-dependent NuA3 histone acetyltransferase complex. FEBS Open Bio 2014; 4:996-1006. [PMID: 25473596 PMCID: PMC4248121 DOI: 10.1016/j.fob.2014.11.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 11/05/2014] [Accepted: 11/05/2014] [Indexed: 12/22/2022] Open
Abstract
We characterise Sas3p and Gcn5p active HAT complexes in WT and deleted TAP-strains. We confirm that Pdp3p interacts with NuA3, histones and chromatin regulators. Pdp3p MS-analysis reveals its phosphorylation, ubiquitination and methylation. Sas3p can substitute Gcn5p in acetylation of histone H3K14 but not of H3K9. Genome-wide profiling of Sas3p supports its involvement in transcriptional elongation.
Histone acetylation affects several aspects of gene regulation, from chromatin remodelling to gene expression, by modulating the interplay between chromatin and key transcriptional regulators. The exact molecular mechanism underlying acetylation patterns and crosstalk with other epigenetic modifications requires further investigation. In budding yeast, these epigenetic markers are produced partly by histone acetyltransferase enzymes, which act as multi-protein complexes. The Sas3-dependent NuA3 complex has received less attention than other histone acetyltransferases (HAT), such as Gcn5-dependent complexes. Here, we report our analysis of Sas3p-interacting proteins using tandem affinity purification (TAP), coupled with mass spectrometry. This analysis revealed Pdp3p, a recently described component of NuA3, to be one of the most abundant Sas3p-interacting proteins. The PDP3 gene, was TAP-tagged and protein complex purification confirmed that Pdp3p co-purified with the NuA3 protein complex, histones, and several transcription-related and chromatin remodelling proteins. Our results also revealed that the protein complexes associated with Sas3p presented HAT activity even in the absence of Gcn5p and vice versa. We also provide evidence that Sas3p cannot substitute Gcn5p in acetylation of lysine 9 in histone H3 in vivo. Genome-wide occupancy of Sas3p using ChIP-on-chip tiled microarrays showed that Sas3p was located preferentially within the 5′-half of the coding regions of target genes, indicating its probable involvement in the transcriptional elongation process. Hence, this work further characterises the function and regulation of the NuA3 complex by identifying novel post-translational modifications in Pdp3p, additional Pdp3p-co-purifying chromatin regulatory proteins involved in chromatin-modifying complex dynamics and gene regulation, and a subset of genes whose transcriptional elongation is controlled by this complex.
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Key Words
- ChIP-on-chip
- ChIP-on-chip, chromatin immunoprecipitation with genome-wide location arrays
- Chromatin
- HAT, histone acetyltransferase
- Histones
- NuA3, nucleosomal acetyltransferase of histone H3
- PTM, post-translational modification
- Pdp3
- RNAPII, RNA polymerase II
- SAGA, Spt-Ada-Gcn acetyltransferase
- TAP, tandem affinity purification
- TAP–MS strategy
- TSS, transcription start site
- WCE, whole cell extract
- WT, wild-type
- Yeast
- nt, nucleotide
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Affiliation(s)
- Sara Vicente-Muñoz
- Structural Biochemistry Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Eduardo Primo Yúfera, 3, 46012 València, Spain
| | - Paco Romero
- Departament de Bioquímica i Biologia Molecular, Universitat de València, C/Dr. Moliner 50, 46100 Burjassot, València, Spain
| | - Lorena Magraner-Pardo
- Departament de Bioquímica i Biologia Molecular, Universitat de València, C/Dr. Moliner 50, 46100 Burjassot, València, Spain
| | - Celia P Martinez-Jimenez
- Departament de Bioquímica i Biologia Molecular, Universitat de València, C/Dr. Moliner 50, 46100 Burjassot, València, Spain
| | - Vicente Tordera
- Departament de Bioquímica i Biologia Molecular, Universitat de València, C/Dr. Moliner 50, 46100 Burjassot, València, Spain
| | - Mercè Pamblanco
- Departament de Bioquímica i Biologia Molecular, Universitat de València, C/Dr. Moliner 50, 46100 Burjassot, València, Spain
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13
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Structural insights into yeast histone chaperone Hif1: a scaffold protein recruiting protein complexes to core histones. Biochem J 2014; 462:465-73. [PMID: 24946827 DOI: 10.1042/bj20131640] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Yeast Hif1 [Hat1 (histone acetyltransferase 1)-interacting factor], a homologue of human NASP (nuclear autoantigenic sperm protein), is a histone chaperone that is involved in various protein complexes which modify histones during telomeric silencing and chromatin reassembly. For elucidating the structural basis of Hif1, in the present paper we demonstrate the crystal structure of Hif1 consisting of a superhelixed TPR (tetratricopeptide repeat) domain and an extended acid loop covering the rear of TPR domain, which represent typical characteristics of SHNi-TPR [Sim3 (start independent of mitosis 3)-Hif1-NASP interrupted TPR] proteins. Our binding assay indicates that Hif1 could bind to the histone octamer via histones H3 and H4. The acid loop is shown to be crucial for the binding of histones and may also change the conformation of the TPR groove. By binding to the core histone complex Hif1 may recruit functional protein complexes to modify histones during chromatin reassembly.
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Pamblanco M, Oliete-Calvo P, García-Oliver E, Luz Valero M, Sanchez del Pino MM, Rodríguez-Navarro S. Unveiling novel interactions of histone chaperone Asf1 linked to TREX-2 factors Sus1 and Thp1. Nucleus 2014; 5:247-59. [PMID: 24824343 DOI: 10.4161/nucl.29155] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Anti-silencing function 1 (Asf1) is a conserved key eukaryotic histone H3/H4 chaperone that participates in a variety of DNA and chromatin-related processes. These include the assembly and disassembly of histones H3 and H4 from chromatin during replication, transcription, and DNA repair. In addition, Asf1 is required for H3K56 acetylation activity dependent on histone acetyltransferase Rtt109. Thus, Asf1 impacts on many aspects of DNA metabolism. To gain insights into the functional links of Asf1 with other cellular machineries, we employed mass spectrometry coupled to tandem affinity purification (TAP) to investigate novel physical interactions of Asf1. Under different TAP-MS analysis conditions, we describe a new repertoire of Asf1 physical interactions and novel Asf1 post-translational modifications as ubiquitination, methylation and acetylation that open up new ways to regulate Asf1 functions. Asf1 co-purifies with several subunits of the TREX-2, SAGA complexes, and with nucleoporins Nup2, Nup60, and Nup57, which are all involved in transcription coupled to mRNA export in eukaryotes. Reciprocally, Thp1 and Sus1 interact with Asf1. Albeit mRNA export and GAL1 transcription are not affected in asf1Δ a strong genetic interaction exists between ASF1 and SUS1. Notably, supporting a functional link between Asf1 and TREX-2, both Sus1 and Thp1 affect the levels of Asf1-dependent histone H3K56 acetylation and histone H3 and H4 incorporation onto chromatin. Additionally, we provide evidence for a role of Asf1 in histone H2B ubiquitination. This work proposes a functional link between Asf1 and TREX-2 components in histone metabolism at the vicinity of the nuclear pore complex.
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Affiliation(s)
- Mercè Pamblanco
- Departament de Bioquímica i Biologia Molecular; Universitat de València; Burjassot, Spain
| | - Paula Oliete-Calvo
- Gene Expression and RNA Metabolism Laboratory; Centro de Investigación Príncipe Felipe (CIPF); València, Spain
| | - Encar García-Oliver
- Gene Expression and RNA Metabolism Laboratory; Centro de Investigación Príncipe Felipe (CIPF); València, Spain
| | - M Luz Valero
- Secció de Proteòmica; Servei Central de Suport a la Investigació Experimental (SCSIE); Universitat de València; Burjassot, Spain
| | | | - Susana Rodríguez-Navarro
- Gene Expression and RNA Metabolism Laboratory; Centro de Investigación Príncipe Felipe (CIPF); València, Spain
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15
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Schiza V, Molina-Serrano D, Kyriakou D, Hadjiantoniou A, Kirmizis A. N-alpha-terminal acetylation of histone H4 regulates arginine methylation and ribosomal DNA silencing. PLoS Genet 2013; 9:e1003805. [PMID: 24068969 PMCID: PMC3778019 DOI: 10.1371/journal.pgen.1003805] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 08/03/2013] [Indexed: 11/24/2022] Open
Abstract
Post-translational modifications of histones play a key role in DNA-based processes, like transcription, by modulating chromatin structure. N-terminal acetylation is unique among the numerous histone modifications because it is deposited on the N-alpha amino group of the first residue instead of the side-chain of amino acids. The function of this modification and its interplay with other internal histone marks has not been previously addressed. Here, we identified N-terminal acetylation of H4 (N-acH4) as a novel regulator of arginine methylation and chromatin silencing in Saccharomyces cerevisiae. Lack of the H4 N-alpha acetyltransferase (Nat4) activity results specifically in increased deposition of asymmetric dimethylation of histone H4 arginine 3 (H4R3me2a) and in enhanced ribosomal-DNA silencing. Consistent with this, H4 N-terminal acetylation impairs the activity of the Hmt1 methyltransferase towards H4R3 in vitro. Furthermore, combinatorial loss of N-acH4 with internal histone acetylation at lysines 5, 8 and 12 has a synergistic induction of H4R3me2a deposition and rDNA silencing that leads to a severe growth defect. This defect is completely rescued by mutating arginine 3 to lysine (H4R3K), suggesting that abnormal deposition of a single histone modification, H4R3me2a, can impact on cell growth. Notably, the cross-talk between N-acH4 and H4R3me2a, which regulates rDNA silencing, is induced under calorie restriction conditions. Collectively, these findings unveil a molecular and biological function for H4 N-terminal acetylation, identify its interplay with internal histone modifications, and provide general mechanistic implications for N-alpha-terminal acetylation, one of the most common protein modifications in eukaryotes. The genome of eukaryotic cells is packaged into nucleosomes consisting of an octamer of histone proteins that is wrapped around by DNA. Histone proteins are often modified with chemical groups that can influence the arrangement of nucleosomes and thereby affect DNA-based processes like transcription. Histone N-terminal acetylation, which comprises the addition of a chemical group at the tip of the histone tail, is an abundant modification whose function is unknown. In this work, we show that N-terminal acetylation of histone H4 can strongly inhibit the occurrence of a neighboring modification, namely dimethylation at the third arginine. To do this, N-terminal acetylation cooperates with other internal lysine acetylation marks. We find that the communication amongst these histone modifications is necessary for controlling the expression of ribosomal RNA genes that are required for protein synthesis and cell growth. Our experiments show that in the absence of both N-terminal acetylation and lysine acetylation there is a strong increase in H4 arginine 3 dimethylation levels leading to cell lethality. This growth defect can be rescued by a point mutation on H4 that blocks methylation at position 3. Together, our results unveil a molecular and biological function for the previously uncharacterized N-terminal acetylation of histones.
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Affiliation(s)
- Vassia Schiza
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | | | - Dimitris Kyriakou
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | | | - Antonis Kirmizis
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
- * E-mail:
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16
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Winnicki K, Polit JT, Maszewski J. Increased transcription in hydroxyurea-treated root meristem cells of Vicia faba. PROTOPLASMA 2013; 250:251-259. [PMID: 22526201 PMCID: PMC3557396 DOI: 10.1007/s00709-012-0402-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Accepted: 03/21/2012] [Indexed: 05/31/2023]
Abstract
Hydroxyurea (HU), an inhibitor of ribonucleotide reductase, prevents cells from progressing through S phase by depletion of deoxyribonucleoside triphosphates. Concurrently, disruption of DNA replication leads to double-strand DNA breaks. In root meristems of Vicia faba, HU triggers cell cycle arrest (preferentially in G1/S phase) and changes an overall metabolism by global activation of transcription both in the nucleoplasmic and nucleolar regions. High level of transcription is accompanied by an increase in the content of RNA polymerase II large subunit (POLR2A). Changes in transcription activation and POLR2A content correlate with posttranslational modifications of histones that play a role in opening up chromatin for transcription. Increase in the level of H4 Lys5 acetylation indicates that global activation of transcription following HU treatment depends on histone modifications.
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Affiliation(s)
- Konrad Winnicki
- Department of Cytophysiology, Institute of Physiology, Cytology and Cytogenetics, University of Lodz, ul. Pomorska 141/143, 90-236 Łódź, Poland.
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17
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Tscherner M, Stappler E, Hnisz D, Kuchler K. The histone acetyltransferase Hat1 facilitates DNA damage repair and morphogenesis inCandida albicans. Mol Microbiol 2012; 86:1197-214. [DOI: 10.1111/mmi.12051] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2012] [Indexed: 02/02/2023]
Affiliation(s)
- Michael Tscherner
- Medical University of Vienna; Christian Doppler Laboratory for Infection Biology, Max F. Perutz Laboratories; Campus Vienna Biocenter; A-1030; Vienna; Austria
| | - Eva Stappler
- Medical University of Vienna; Christian Doppler Laboratory for Infection Biology, Max F. Perutz Laboratories; Campus Vienna Biocenter; A-1030; Vienna; Austria
| | - Denes Hnisz
- Medical University of Vienna; Christian Doppler Laboratory for Infection Biology, Max F. Perutz Laboratories; Campus Vienna Biocenter; A-1030; Vienna; Austria
| | - Karl Kuchler
- Medical University of Vienna; Christian Doppler Laboratory for Infection Biology, Max F. Perutz Laboratories; Campus Vienna Biocenter; A-1030; Vienna; Austria
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18
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Schizosaccharomyces pombe Hat1 (Kat1) is associated with Mis16 and is required for telomeric silencing. EUKARYOTIC CELL 2012; 11:1095-103. [PMID: 22771823 DOI: 10.1128/ec.00123-12] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The Hat1 histone acetyltransferase has been implicated in the acetylation of histone H4 during chromatin assembly. In this study, we have characterized the Hat1 complex from the fission yeast Schizosaccharomyces pombe and have examined its role in telomeric silencing. Hat1 is found associated with the RbAp46 homologue Mis16, an essential protein. The Hat1 complex acetylates lysines 5 and 12 of histone H4, the sites that are acetylated in newly synthesized H4 in a wide range of eukaryotes. Deletion of hat1 in S. pombe is itself sufficient to cause the loss of silencing at telomeres. This is in contrast to results obtained with an S. cerevisiae hat1Δ strain, which must also carry mutations of specific acetylatable lysines in the H3 tail domain for loss of telomeric silencing to occur. Notably, deletion of hat1 from S. pombe resulted in an increase of acetylation of histone H4 in subtelomeric chromatin, concomitant with derepression of this region. A similar loss of telomeric silencing was also observed after growing cells in the presence of the deacetylase inhibitor trichostatin A. However, deleting hat1 did not cause loss of silencing at centromeres or the silent mating type locus. These results point to a direct link between Hat1, H4 acetylation, and the establishment of repressed telomeric chromatin in fission yeast.
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Verzijlbergen KF, van Welsem T, Sie D, Lenstra TL, Turner DJ, Holstege FCP, Kerkhoven RM, van Leeuwen F. A barcode screen for epigenetic regulators reveals a role for the NuB4/HAT-B histone acetyltransferase complex in histone turnover. PLoS Genet 2011; 7:e1002284. [PMID: 21998594 PMCID: PMC3188528 DOI: 10.1371/journal.pgen.1002284] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2011] [Accepted: 07/29/2011] [Indexed: 11/18/2022] Open
Abstract
Dynamic modification of histone proteins plays a key role in regulating gene expression. However, histones themselves can also be dynamic, which potentially affects the stability of histone modifications. To determine the molecular mechanisms of histone turnover, we developed a parallel screening method for epigenetic regulators by analyzing chromatin states on DNA barcodes. Histone turnover was quantified by employing a genetic pulse-chase technique called RITE, which was combined with chromatin immunoprecipitation and high-throughput sequencing. In this screen, the NuB4/HAT-B complex, containing the conserved type B histone acetyltransferase Hat1, was found to promote histone turnover. Unexpectedly, the three members of this complex could be functionally separated from each other as well as from the known interacting factor and histone chaperone Asf1. Thus, systematic and direct interrogation of chromatin structure on DNA barcodes can lead to the discovery of genes and pathways involved in chromatin modification and dynamics.
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Affiliation(s)
| | - Tibor van Welsem
- Department of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Daoud Sie
- Genome Center, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Netherlands Proteomics Center, Amsterdam, The Netherlands
| | - Tineke L. Lenstra
- Department of Molecular Cancer Research, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Daniel J. Turner
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Frank C. P. Holstege
- Department of Molecular Cancer Research, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ron M. Kerkhoven
- Genome Center, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Netherlands Proteomics Center, Amsterdam, The Netherlands
| | - Fred van Leeuwen
- Department of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands
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20
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Parthun MR. Histone acetyltransferase 1: more than just an enzyme? BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1819:256-63. [PMID: 24459728 DOI: 10.1016/j.bbagrm.2011.07.006] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Revised: 06/29/2011] [Accepted: 07/04/2011] [Indexed: 10/18/2022]
Abstract
Histone acetyltransferase 1 (HAT1) is an enzyme that is likely to be responsible for the acetylation that occurs on lysines 5 and 12 of the NH2-terminal tail of newly synthesized histone H4. Initial studies suggested that, despite its evolutionary conservation, this modification of new histone H4 played only a minor role in chromatin assembly. However, a number of recent studies have brought into focus the important role of both this modification and HAT1 in histone dynamics. Surprisingly, the function of HAT1 in chromatin assembly may extend beyond just its catalytic activity to include its role as a major histone binding protein. These results are incorporated into a model for the function of HAT1 in histone deposition and chromatin assembly. This article is part of a Special issue entitled: Histone chaperones and Chromatin assembly.
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Affiliation(s)
- Mark R Parthun
- Department of Molecular and Cellular Biochemistry, The Ohio State University, Columbus, OH 43210, USA.
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21
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Genetic interactions between POB3 and the acetylation of newly synthesized histones. Curr Genet 2011; 57:271-86. [PMID: 21656278 DOI: 10.1007/s00294-011-0347-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Revised: 05/13/2011] [Accepted: 05/14/2011] [Indexed: 10/18/2022]
Abstract
Pob3p is an essential component of the S. cerevisiae FACT complex (yFACT). Several lines of evidence indicate that the yFACT complex plays an important role in chromatin assembly including the observation that the pob3 Q308K allele is synthetically lethal with an allele of histone H4 that prevents the diacetylation of newly synthesized molecules. We have analyzed the genetic interactions between the Q308K allele of POB3 and mutations in all of the sites of acetylation that have been identified on newly synthesized histones. Genetic interactions were observed between POB3 and sites of acetylation on the NH(2)-terminal tails of H3 and H4. For histone H3, lysine residues 14 and 23 were particularly important when POB3 activity is compromised. Surprisingly, synthetic defects observed when the pob3 Q308K allele was combined with mutations of H4 lysines 5 and 12, were not phenocopied by deletion of HAT1, which encodes the enzyme that is thought to generate this pattern of acetylation on H4. Genetic interactions were also observed between POB3 and sites of acetylation found in the core domain of newly synthesized histones H3 and H4. These include synthetic lethality with an allele of H4 lysine 91 that mimics constitutive acetylation. While the mutations that alter H4 lysines 5, 12 and 91 do not affect binding to Pob3p, mutation of histone H3 lysine 56 decreases the association of histones with Pob3p. These results support the model that the yFACT complex plays a central role in chromatin assembly pathways regulated by acetylation of newly synthesized histones.
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22
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Dose A, Liokatis S, Theillet FX, Selenko P, Schwarzer D. NMR profiling of histone deacetylase and acetyl-transferase activities in real time. ACS Chem Biol 2011; 6:419-24. [PMID: 21302972 DOI: 10.1021/cb1003866] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Histone deacetylases (HDACs) and histone acetyl-transferases (HATs) are universal regulators of eukaryotic transcriptional activity and emerging therapeutic targets for human diseases. Here we describe the generation of isotope-labeled deacetylation and acetylation reporters for simultaneous NMR readouts of multiple deacetylation and acetylation reactions at different histone H4 sites. The site preferences of two prototypic histone deacetylases (Sir2.1 and HDAC8) and two acetyl-transferases (HAT1 and p300/CBP) were studied in intramolecular competition assays. We identify a previously ill-defined acetylation site, lysine 20 of histone H4, as a preferred target of three of theses enzymes. In situ analyses of endogenous deacetylation reactions at H4 sites in HeLa nuclear extracts point to abundant HDAC activities in human cellular environments.
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Affiliation(s)
- Alexander Dose
- Department of Chemical Biology and ‡Department of NMR-assisted Structural Biology, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Robert-Roessle-Strasse 10, 13125 Berlin, Germany
| | - Stamatios Liokatis
- Department of Chemical Biology and ‡Department of NMR-assisted Structural Biology, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Robert-Roessle-Strasse 10, 13125 Berlin, Germany
| | - Francois-Xavier Theillet
- Department of Chemical Biology and ‡Department of NMR-assisted Structural Biology, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Robert-Roessle-Strasse 10, 13125 Berlin, Germany
| | - Philipp Selenko
- Department of Chemical Biology and ‡Department of NMR-assisted Structural Biology, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Robert-Roessle-Strasse 10, 13125 Berlin, Germany
| | - Dirk Schwarzer
- Department of Chemical Biology and ‡Department of NMR-assisted Structural Biology, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Robert-Roessle-Strasse 10, 13125 Berlin, Germany
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23
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Irradiation with heavy-ion particles changes the cellular distribution of human histone acetyltransferase HAT1. Mol Cell Biochem 2010; 339:271-84. [PMID: 20148353 DOI: 10.1007/s11010-010-0390-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2009] [Accepted: 01/25/2010] [Indexed: 12/16/2022]
Abstract
Hat1 was the first histone acetyltransferase identified; however, its biological function is still unclear. In this report, it is shown for the first time that human Hat1 has two isoforms. Isoform a has 418 amino acids (aa) and is localized exclusively in the nuclear matrix of normal human keratinocytes (NHKs). Isoform b has 334 aa and is located in the cytoplasm, the nucleoplasm, attached to the chromatin and to the nuclear matrix. Immunohistochemical analyses revealed that the bulk of Hat1 is confined to the nucleus, with much lesser amounts in the cytoplasm. Cells undergoing mitotic division have an elevated amount of Hat1 compared to those that are non-mitotic. Senescent cells, however, exhibit a higher concentration of Hat1 in the cytoplasm compare to proliferating cells and the amount of Hat1 in the nucleus decreases with the progression of senescence. NHKs exposed to hydrogen peroxide (H(2)O(2)) or to a beam of high mass and energy ion particles displayed bright nuclear staining for Hat1, a phenotype that was not observed in NHKs exposed to gamma-rays. We established that the enhanced nuclear staining for Hat1 in response to these treatments is regulated by the PI3K and the mitogen-activated protein kinase signaling pathways. Our observations clearly implicate Hat1 in the cellular response assuring the survival of the treated cells.
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24
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Current awareness on yeast. Yeast 2008. [DOI: 10.1002/yea.1559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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25
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An easy assay for histone acetyltransferase activity using a PhosphorImager. Anal Biochem 2008; 383:296-300. [DOI: 10.1016/j.ab.2008.08.029] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2008] [Revised: 08/18/2008] [Accepted: 08/26/2008] [Indexed: 11/18/2022]
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26
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Mersfelder EL, Parthun MR. Involvement of Hat1p (Kat1p) catalytic activity and subcellular localization in telomeric silencing. J Biol Chem 2008; 283:29060-8. [PMID: 18753131 DOI: 10.1074/jbc.m802564200] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Previous studies have shown that loss of the type B histone acetyltransferase Hat1p leads to defects in telomeric silencing in Saccharomyces cerevisiae. We used this phenotype to explore a number of functional characteristics of this enzyme. To determine whether the enzymatic activity of Hat1p is necessary for its role in telomeric silencing, a structurally conserved glutamic acid residue (Glu-255) that has been proposed to be the enzymes catalytic base was mutated. Surprisingly neither this residue nor any other acidic residues near the enzymes active site were essential for enzymatic activity. This suggests that Hat1p differs from most histone acetyltransferases in that it does not use an acidic amino acid as a catalytic base. The effects of these Hat1p mutants on enzymatic activity correlated with their effects on telomeric silencing indicating that the ability of Hat1p to acetylate substrates is important for its in vivo function. Despite its presumed role in the acetylation of newly synthesized histones in the cytoplasm, Hat1p was found to be a predominantly nuclear protein. This subcellular localization of Hat1p is important for its in vivo function because a construct that prevents its accumulation in the nucleus caused defects in telomeric silencing similar to those seen with a deletion mutant. Therefore, the presence of catalytically active Hat1p in the cytoplasm is not sufficient to support normal telomeric silencing. Hence both enzymatic activity and nuclear localization are necessary characteristics of Hat1p function in telomeric silencing.
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Affiliation(s)
- Erica L Mersfelder
- Department of Molecular and Cellular Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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