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Muhammad T, Pastore SF, Good K, Ausió J, Vincent JB. Chromatin gatekeeper and modifier CHD proteins in development, and in autism and other neurological disorders. Psychiatr Genet 2023; 33:213-232. [PMID: 37851134 DOI: 10.1097/ypg.0000000000000353] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2023]
Abstract
Chromatin, a protein-DNA complex, is a dynamic structure that stores genetic information within the nucleus and responds to molecular/cellular changes in its structure, providing conditional access to the genetic machinery. ATP-dependent chromatin modifiers regulate access of transcription factors and RNA polymerases to DNA by either "opening" or "closing" the structure of chromatin, and its aberrant regulation leads to a variety of neurodevelopmental disorders. The chromodomain helicase DNA-binding (CHD) proteins are ATP-dependent chromatin modifiers involved in the organization of chromatin structure, act as gatekeepers of genomic access, and deposit histone variants required for gene regulation. In this review, we first discuss the structural and functional domains of the CHD proteins, and their binding sites, and phosphorylation, acetylation, and methylation sites. The conservation of important amino acids in SWItch/sucrose non-fermenting (SWI/SNF) domains, and their protein and mRNA tissue expression profiles are discussed. Next, we convey the important binding partners of CHD proteins, their protein complexes and activities, and their involvements in epigenetic regulation. We also show the ChIP-seq binding dynamics for CHD1, CHD2, CHD4, and CHD7 proteins at promoter regions of histone genes, as well as several genes that are critical for neurodevelopment. The role of CHD proteins in development is also discussed. Finally, this review provides information about CHD protein mutations reported in autism and neurodevelopmental disorders, and their pathogenicity. Overall, this review provides information on the progress of research into CHD proteins, their structural and functional domains, epigenetics, and their role in stem cell, development, and neurological disorders.
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Affiliation(s)
- Tahir Muhammad
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health
- Institute of Medical Science, University of Toronto, Toronto, ON
| | - Stephen F Pastore
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health
- Institute of Medical Science, University of Toronto, Toronto, ON
| | - Katrina Good
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC
| | - John B Vincent
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health
- Institute of Medical Science, University of Toronto, Toronto, ON
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
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2
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Shi W, Scialdone AP, Emerson JI, Mei L, Wasson LK, Davies HA, Seidman CE, Seidman JG, Cook JG, Conlon FL. Missense Mutation in Human CHD4 Causes Ventricular Noncompaction by Repressing ADAMTS1. Circ Res 2023; 133:48-67. [PMID: 37254794 PMCID: PMC10284140 DOI: 10.1161/circresaha.122.322223] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 05/02/2023] [Accepted: 05/05/2023] [Indexed: 06/01/2023]
Abstract
BACKGROUND Left ventricular noncompaction (LVNC) is a prevalent cardiomyopathy associated with excessive trabeculation and thin compact myocardium. Patients with LVNC are vulnerable to cardiac dysfunction and at high risk of sudden death. Although sporadic and inherited mutations in cardiac genes are implicated in LVNC, understanding of the mechanisms responsible for human LVNC is limited. METHODS We screened the complete exome sequence database of the Pediatrics Cardiac Genomics Consortium and identified a cohort with a de novo CHD4 (chromodomain helicase DNA-binding protein 4) proband, CHD4M202I, with congenital heart defects. We engineered a humanized mouse model of CHD4M202I (mouse CHD4M195I). Histological analysis, immunohistochemistry, flow cytometry, transmission electron microscopy, and echocardiography were used to analyze cardiac anatomy and function. Ex vivo culture, immunopurification coupled with mass spectrometry, transcriptional profiling, and chromatin immunoprecipitation were performed to deduce the mechanism of CHD4M195I-mediated ventricular wall defects. RESULTS CHD4M195I/M195I mice developed biventricular hypertrabeculation and noncompaction and died at birth. Proliferation of cardiomyocytes was significantly increased in CHD4M195I hearts, and the excessive trabeculation was associated with accumulation of ECM (extracellular matrix) proteins and a reduction of ADAMTS1 (ADAM metallopeptidase with thrombospondin type 1 motif 1), an ECM protease. We rescued the hyperproliferation and hypertrabeculation defects in CHD4M195I hearts by administration of ADAMTS1. Mechanistically, the CHD4M195I protein showed augmented affinity to endocardial BRG1 (SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily A, member 4). This enhanced affinity resulted in the failure of derepression of Adamts1 transcription such that ADAMTS1-mediated trabeculation termination was impaired. CONCLUSIONS Our study reveals how a single mutation in the chromatin remodeler CHD4, in mice or humans, modulates ventricular chamber maturation and that cardiac defects associated with the missense mutation CHD4M195I can be attenuated by the administration of ADAMTS1.
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Affiliation(s)
- Wei Shi
- Department of Biology and Genetics, McAllister Heart Institute (W.S., A.P.S., J.I.E., H.A.D., F.L.C.), the University of North Carolina at Chapel Hill
| | - Angel P. Scialdone
- Department of Biology and Genetics, McAllister Heart Institute (W.S., A.P.S., J.I.E., H.A.D., F.L.C.), the University of North Carolina at Chapel Hill
| | - James I. Emerson
- Department of Biology and Genetics, McAllister Heart Institute (W.S., A.P.S., J.I.E., H.A.D., F.L.C.), the University of North Carolina at Chapel Hill
| | - Liu Mei
- Department of Biochemistry & Biophysics (L.M., J.G.C.), the University of North Carolina at Chapel Hill
| | - Lauren K. Wasson
- Department of Genetics, Harvard Medical School, Boston, MA (L.K.W., C.E.S., J.G.S.)
- Howard Hughes Medical Institute, Chevy Chase, MD (L.K.W., C.E.S.)
| | - Haley A. Davies
- Department of Biology and Genetics, McAllister Heart Institute (W.S., A.P.S., J.I.E., H.A.D., F.L.C.), the University of North Carolina at Chapel Hill
| | - Christine E. Seidman
- Department of Genetics, Harvard Medical School, Boston, MA (L.K.W., C.E.S., J.G.S.)
- Howard Hughes Medical Institute, Chevy Chase, MD (L.K.W., C.E.S.)
- Division of Cardiovascular Medicine, Brigham and Women’s Hospital, Boston, MA (C.E.S.)
| | - Jonathan G. Seidman
- Department of Biochemistry & Biophysics (L.M., J.G.C.), the University of North Carolina at Chapel Hill
- Department of Genetics, Harvard Medical School, Boston, MA (L.K.W., C.E.S., J.G.S.)
| | - Jeanette G. Cook
- Department of Biology and Genetics, McAllister Heart Institute (W.S., A.P.S., J.I.E., H.A.D., F.L.C.), the University of North Carolina at Chapel Hill
- Department of Biochemistry & Biophysics (L.M., J.G.C.), the University of North Carolina at Chapel Hill
- Lineberger Comprehensive Cancer Center (F.L.C.), the University of North Carolina at Chapel Hill
- Department of Genetics, Harvard Medical School, Boston, MA (L.K.W., C.E.S., J.G.S.)
- Howard Hughes Medical Institute, Chevy Chase, MD (L.K.W., C.E.S.)
- Division of Cardiovascular Medicine, Brigham and Women’s Hospital, Boston, MA (C.E.S.)
| | - Frank L. Conlon
- Department of Biology and Genetics, McAllister Heart Institute (W.S., A.P.S., J.I.E., H.A.D., F.L.C.), the University of North Carolina at Chapel Hill
- Lineberger Comprehensive Cancer Center (F.L.C.), the University of North Carolina at Chapel Hill
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3
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Herchenröther A, Gossen S, Friedrich T, Reim A, Daus N, Diegmüller F, Leers J, Sani HM, Gerstner S, Schwarz L, Stellmacher I, Szymkowiak LV, Nist A, Stiewe T, Borggrefe T, Mann M, Mackay JP, Bartkuhn M, Borchers A, Lan J, Hake SB. The H2A.Z and NuRD associated protein HMG20A controls early head and heart developmental transcription programs. Nat Commun 2023; 14:472. [PMID: 36709316 PMCID: PMC9884267 DOI: 10.1038/s41467-023-36114-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 01/17/2023] [Indexed: 01/30/2023] Open
Abstract
Specialized chromatin-binding proteins are required for DNA-based processes during development. We recently established PWWP2A as a direct histone variant H2A.Z interactor involved in mitosis and craniofacial development. Here, we identify the H2A.Z/PWWP2A-associated protein HMG20A as part of several chromatin-modifying complexes, including NuRD, and show that it localizes to distinct genomic regulatory regions. Hmg20a depletion causes severe head and heart developmental defects in Xenopus laevis. Our data indicate that craniofacial malformations are caused by defects in neural crest cell (NCC) migration and cartilage formation. These developmental failures are phenocopied in Hmg20a-depleted mESCs, which show inefficient differentiation into NCCs and cardiomyocytes (CM). Consequently, loss of HMG20A, which marks open promoters and enhancers, results in chromatin accessibility changes and a striking deregulation of transcription programs involved in epithelial-mesenchymal transition (EMT) and differentiation processes. Collectively, our findings implicate HMG20A as part of the H2A.Z/PWWP2A/NuRD-axis and reveal it as a key modulator of intricate developmental transcription programs that guide the differentiation of NCCs and CMs.
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Affiliation(s)
| | - Stefanie Gossen
- Department of Biology, Molecular Embryology, Philipps University Marburg, Marburg, Germany
| | - Tobias Friedrich
- Institute for Biochemistry, Justus-Liebig University Giessen, Giessen, Germany.,Biomedical Informatics and Systems Medicine, Science Unit for Basic and Clinical Medicine, Institute for lung health, Justus-Liebig University Giessen, Giessen, Germany
| | - Alexander Reim
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Nadine Daus
- Institute for Genetics, Justus-Liebig University Giessen, Giessen, Germany
| | - Felix Diegmüller
- Institute for Genetics, Justus-Liebig University Giessen, Giessen, Germany
| | - Jörg Leers
- Institute for Genetics, Justus-Liebig University Giessen, Giessen, Germany
| | - Hakimeh Moghaddas Sani
- School of Life and Environmental Sciences, University of Sydney, New South Wales, Australia
| | - Sarah Gerstner
- Department of Biology, Molecular Embryology, Philipps University Marburg, Marburg, Germany
| | - Leah Schwarz
- Department of Biology, Molecular Embryology, Philipps University Marburg, Marburg, Germany
| | - Inga Stellmacher
- Institute for Genetics, Justus-Liebig University Giessen, Giessen, Germany
| | - Laura Victoria Szymkowiak
- Institute for Genetics, Justus-Liebig University Giessen, Giessen, Germany.,Institute for Physiological Chemistry, Technical University Dresden, Dresden, Germany
| | - Andrea Nist
- Genomics Core Facility, Institute of Molecular Oncology, Universities of Giessen and Marburg Lung Center, Member of the German Center for Lung Research (DZL), Philipps-University Marburg, Marburg, Germany
| | - Thorsten Stiewe
- Genomics Core Facility, Institute of Molecular Oncology, Universities of Giessen and Marburg Lung Center, Member of the German Center for Lung Research (DZL), Philipps-University Marburg, Marburg, Germany
| | - Tilman Borggrefe
- Institute for Biochemistry, Justus-Liebig University Giessen, Giessen, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, New South Wales, Australia
| | - Marek Bartkuhn
- Biomedical Informatics and Systems Medicine, Science Unit for Basic and Clinical Medicine, Institute for lung health, Justus-Liebig University Giessen, Giessen, Germany.
| | - Annette Borchers
- Department of Biology, Molecular Embryology, Philipps University Marburg, Marburg, Germany.
| | - Jie Lan
- Institute for Genetics, Justus-Liebig University Giessen, Giessen, Germany.
| | - Sandra B Hake
- Institute for Genetics, Justus-Liebig University Giessen, Giessen, Germany.
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4
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Zhong Y, Moghaddas Sani H, Paudel BP, Low JKK, Silva APG, Mueller S, Deshpande C, Panjikar S, Reid XJ, Bedward MJ, van Oijen AM, Mackay JP. The role of auxiliary domains in modulating CHD4 activity suggests mechanistic commonality between enzyme families. Nat Commun 2022; 13:7524. [PMID: 36473839 PMCID: PMC9726900 DOI: 10.1038/s41467-022-35002-0] [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: 06/13/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022] Open
Abstract
CHD4 is an essential, widely conserved ATP-dependent translocase that is also a broad tumour dependency. In common with other SF2-family chromatin remodelling enzymes, it alters chromatin accessibility by repositioning histone octamers. Besides the helicase and adjacent tandem chromodomains and PHD domains, CHD4 features 1000 residues of N- and C-terminal sequence with unknown structure and function. We demonstrate that these regions regulate CHD4 activity through different mechanisms. An N-terminal intrinsically disordered region (IDR) promotes remodelling integrity in a manner that depends on the composition but not sequence of the IDR. The C-terminal region harbours an auto-inhibitory region that contacts the helicase domain. Auto-inhibition is relieved by a previously unrecognized C-terminal SANT-SLIDE domain split by ~150 residues of disordered sequence, most likely by binding of this domain to substrate DNA. Our data shed light on CHD4 regulation and reveal strong mechanistic commonality between CHD family members, as well as with ISWI-family remodellers.
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Affiliation(s)
- Yichen Zhong
- grid.1013.30000 0004 1936 834XSchool of Life and Environmental Sciences, University of Sydney, The University of Sydney, NSW 2006 Australia
| | - Hakimeh Moghaddas Sani
- grid.1013.30000 0004 1936 834XSchool of Life and Environmental Sciences, University of Sydney, The University of Sydney, NSW 2006 Australia
| | - Bishnu P. Paudel
- grid.1007.60000 0004 0486 528XMolecular Horizons, School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522 Australia ,grid.510958.0Illawarra Health and Medical Research Institute, Wollongong, NSW 2522 Australia
| | - Jason K. K. Low
- grid.1013.30000 0004 1936 834XSchool of Life and Environmental Sciences, University of Sydney, The University of Sydney, NSW 2006 Australia
| | - Ana P. G. Silva
- grid.1013.30000 0004 1936 834XSchool of Life and Environmental Sciences, University of Sydney, The University of Sydney, NSW 2006 Australia
| | - Stefan Mueller
- grid.1007.60000 0004 0486 528XMolecular Horizons, School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522 Australia ,grid.510958.0Illawarra Health and Medical Research Institute, Wollongong, NSW 2522 Australia
| | - Chandrika Deshpande
- grid.1013.30000 0004 1936 834XSchool of Life and Environmental Sciences, University of Sydney, The University of Sydney, NSW 2006 Australia
| | - Santosh Panjikar
- grid.248753.f0000 0004 0562 0567Australian Synchrotron, Clayton, VIC 3168 Australia ,grid.1002.30000 0004 1936 7857Department of Molecular Biology and Biochemistry, Monash University, Clayton, VIC 3800 Australia
| | - Xavier J. Reid
- grid.1013.30000 0004 1936 834XSchool of Life and Environmental Sciences, University of Sydney, The University of Sydney, NSW 2006 Australia
| | - Max J. Bedward
- grid.1013.30000 0004 1936 834XSchool of Life and Environmental Sciences, University of Sydney, The University of Sydney, NSW 2006 Australia
| | - Antoine M. van Oijen
- grid.1007.60000 0004 0486 528XMolecular Horizons, School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522 Australia ,grid.510958.0Illawarra Health and Medical Research Institute, Wollongong, NSW 2522 Australia
| | - Joel P. Mackay
- grid.1013.30000 0004 1936 834XSchool of Life and Environmental Sciences, University of Sydney, The University of Sydney, NSW 2006 Australia
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5
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Zong W, Gong Y, Sun W, Li T, Wang ZQ. PARP1: Liaison of Chromatin Remodeling and Transcription. Cancers (Basel) 2022; 14:cancers14174162. [PMID: 36077699 PMCID: PMC9454564 DOI: 10.3390/cancers14174162] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/18/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
Poly(ADP-ribosyl)ation (PARylation) is a covalent post-translational modification and plays a key role in the immediate response of cells to stress signals. Poly(ADP-ribose) polymerase 1 (PARP1), the founding member of the PARP superfamily, synthesizes long and branched polymers of ADP-ribose (PAR) onto acceptor proteins, thereby modulating their function and their local surrounding. PARP1 is the most prominent of the PARPs and is responsible for the production of about 90% of PAR in the cell. Therefore, PARP1 and PARylation play a pleotropic role in a wide range of cellular processes, such as DNA repair and genomic stability, cell death, chromatin remodeling, inflammatory response and gene transcription. PARP1 has DNA-binding and catalytic activities that are important for DNA repair, yet also modulate chromatin conformation and gene transcription, which can be independent of DNA damage response. PARP1 and PARylation homeostasis have also been implicated in multiple diseases, including inflammation, stroke, diabetes and cancer. Studies of the molecular action and biological function of PARP1 and PARylation provide a basis for the development of pharmaceutic strategies for clinical applications. This review focuses primarily on the role of PARP1 in the regulation of chromatin remodeling and transcriptional activation.
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Affiliation(s)
- Wen Zong
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
- Correspondence: (W.Z.); or (Z.-Q.W.)
| | - Yamin Gong
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), 07745 Jena, Germany
- College of Basic Medical Sciences, Shenzhen University Medical School, Shenzhen 518055, China
| | - Wenli Sun
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Tangliang Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Zhao-Qi Wang
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), 07745 Jena, Germany
- Faculty of Biological Sciences, Friedrich-Schiller-University of Jena, 07743 Jena, Germany
- Correspondence: (W.Z.); or (Z.-Q.W.)
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6
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Ullah I, Thölken C, Zhong Y, John M, Rossbach O, Lenz J, Gößringer M, Nist A, Albert L, Stiewe T, Hartmann R, Vázquez O, Chung HR, Mackay JP, Brehm A. RNA inhibits dMi-2/CHD4 chromatin binding and nucleosome remodeling. Cell Rep 2022; 39:110895. [PMID: 35649367 DOI: 10.1016/j.celrep.2022.110895] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 03/30/2022] [Accepted: 05/09/2022] [Indexed: 11/03/2022] Open
Abstract
The ATP-dependent nucleosome remodeler Mi-2/CHD4 broadly modulates chromatin landscapes to repress transcription and to maintain genome integrity. Here we use individual nucleotide resolution crosslinking and immunoprecipitation (iCLIP) to show that Drosophila Mi-2 associates with thousands of mRNA molecules in vivo. Biochemical data reveal that recombinant dMi-2 preferentially binds to G-rich RNA molecules using two intrinsically disordered regions of unclear function. Pharmacological inhibition of transcription and RNase digestion approaches establish that RNA inhibits the association of dMi-2 with chromatin. We also show that RNA inhibits dMi-2-mediated nucleosome mobilization by competing with the nucleosome substrate. Importantly, this activity is shared by CHD4, the human homolog of dMi-2, strongly suggesting that RNA-mediated regulation of remodeler activity is an evolutionary conserved mechanism. Our data support a model in which RNA serves to protect actively transcribed regions of the genome from dMi-2/CHD4-mediated establishment of repressive chromatin structures.
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Affiliation(s)
- Ikram Ullah
- Institute of Molecular Biology and Tumor Research, Biomedical Research Center, Philipps-University, Marburg, Germany
| | - Clemens Thölken
- Institute for Medical Bioinformatics and Biostatistic, Philipps-University, Marburg, Germany
| | - Yichen Zhong
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Mara John
- Institute of Molecular Biology and Tumor Research, Biomedical Research Center, Philipps-University, Marburg, Germany
| | - Oliver Rossbach
- Institute of Biochemistry, Department of Biology and Chemistry, Justus Liebig University Giessen, Giessen, Germany
| | - Jonathan Lenz
- Institute of Molecular Biology and Tumor Research, Biomedical Research Center, Philipps-University, Marburg, Germany
| | - Markus Gößringer
- Institute of Pharmaceutical Chemistry, Philipps-University, Marburg, Germany
| | - Andrea Nist
- Genomics Core Facility, Institute of Molecular Oncology, Member of the German Center for Lung Research (DZL), Philipps-University, Marburg, Germany
| | - Lea Albert
- Faculty of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, 35043 Marburg, Germany
| | - Thorsten Stiewe
- Genomics Core Facility, Institute of Molecular Oncology, Member of the German Center for Lung Research (DZL), Philipps-University, Marburg, Germany
| | - Roland Hartmann
- Institute of Pharmaceutical Chemistry, Philipps-University, Marburg, Germany
| | - Olalla Vázquez
- Faculty of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, 35043 Marburg, Germany
| | - Ho-Ryung Chung
- Institute for Medical Bioinformatics and Biostatistic, Philipps-University, Marburg, Germany
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Alexander Brehm
- Institute of Molecular Biology and Tumor Research, Biomedical Research Center, Philipps-University, Marburg, Germany.
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7
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Golden NL, Foley MK, Kim Guisbert KS, Guisbert E. Divergent regulatory roles of NuRD chromatin remodeling complex subunits GATAD2 and CHD4 in Caenorhabditis elegans. Genetics 2022; 221:iyac046. [PMID: 35323946 PMCID: PMC9071545 DOI: 10.1093/genetics/iyac046] [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: 01/16/2022] [Accepted: 03/11/2022] [Indexed: 11/12/2022] Open
Abstract
During proteotoxic stress, a pathway known as the heat shock response is induced to maintain protein-folding homeostasis or proteostasis. Previously, we identified the Caenorhabditis elegans GATAD2 ortholog, dcp-66, as a novel regulator of the heat shock response. Here, we extend these findings to show that dcp-66 positively regulates the heat shock response at the cellular, molecular, and organismal levels. As GATAD2 is a subunit of the nucleosome remodeling and deacetylase chromatin remodeling complex, we examined other nucleosome remodeling and deacetylase subunits and found that the let-418 (CHD4) nucleosome repositioning core also regulates the heat shock response. However, let-418 acts as a negative regulator of the heat shock response, in contrast to positive regulation by dcp-66. The divergent effects of these two nucleosome remodeling and deacetylase subunits extend to the regulation of other stress responses including oxidative, genotoxic, and endoplasmic reticulum stress. Furthermore, a transcriptomic approach reveals additional divergently regulated pathways, including innate immunity and embryogenesis. Taken together, this work establishes new insights into the role of nucleosome remodeling and deacetylase subunits in organismal physiology. We incorporate these findings into a molecular model whereby different mechanisms of recruitment to promoters can result in the divergent effects of nucleosome remodeling and deacetylase subunits.
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Affiliation(s)
- Nicole L Golden
- Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, FL 32901, USA
| | - Michaela K Foley
- Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, FL 32901, USA
| | - Karen S Kim Guisbert
- Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, FL 32901, USA
| | - Eric Guisbert
- Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, FL 32901, USA
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8
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Hagman JR, Arends T, Laborda C, Knapp JR, Harmacek L, O'Connor BP. Chromodomain helicase DNA-binding 4 (CHD4) regulates early B cell identity and V(D)J recombination. Immunol Rev 2021; 305:29-42. [PMID: 34927255 DOI: 10.1111/imr.13054] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 11/22/2021] [Accepted: 12/02/2021] [Indexed: 12/20/2022]
Abstract
B lymphocytes develop from uncommitted precursors into immunoglobulin (antibody)-producing B cells, a major arm of adaptive immunity. Progression of early progenitors to antibody-expressing cells in the bone marrow is orchestrated by the temporal regulation of different gene programs at discrete developmental stages. A major question concerns how B cells control the accessibility of these genes to transcription factors. Research has implicated nucleosome remodeling ATPases as mediators of chromatin accessibility. Here, we describe studies of chromodomain helicase DNA-binding 4 (CHD4; also known as Mi-2β) in early B cell development. CHD4 comprises multiple domains that function in nucleosome mobilization and histone binding. CHD4 is a key component of Nucleosome Remodeling and Deacetylase, or NuRD (Mi-2) complexes, which assemble with other proteins that mediate transcriptional repression. We review data demonstrating that CHD4 is necessary for B lineage identity: early B lineage progression, proliferation in response to interleukin-7, responses to DNA damage, and cell survival in vivo. CHD4-NuRD is also required for the Ig heavy-chain repertoire by promoting utilization of distal variable (VH ) gene segments in V(D)J recombination. In conclusion, the regulation of chromatin accessibility by CHD4 is essential for production of antibodies by B cells, which in turn mediate humoral immune responses to pathogens and disease.
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Affiliation(s)
- James R Hagman
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colorado, USA.,Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA.,Program in Molecular Biology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Tessa Arends
- Program in Molecular Biology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Curtis Laborda
- Center for Genes, Environment, and Health, National Jewish Health, Denver, Colorado, USA
| | - Jennifer R Knapp
- Center for Genes, Environment, and Health, National Jewish Health, Denver, Colorado, USA
| | - Laura Harmacek
- Center for Genes, Environment, and Health, National Jewish Health, Denver, Colorado, USA
| | - Brian P O'Connor
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colorado, USA.,Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA.,Center for Genes, Environment, and Health, National Jewish Health, Denver, Colorado, USA
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9
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Abstract
Chromatin is highly dynamic, undergoing continuous global changes in its structure and type of histone and DNA modifications governed by processes such as transcription, repair, replication, and recombination. Members of the chromodomain helicase DNA-binding (CHD) family of enzymes are ATP-dependent chromatin remodelers that are intimately involved in the regulation of chromatin dynamics, altering nucleosomal structure and DNA accessibility. Genetic studies in yeast, fruit flies, zebrafish, and mice underscore essential roles of CHD enzymes in regulating cellular fate and identity, as well as proper embryonic development. With the advent of next-generation sequencing, evidence is emerging that these enzymes are subjected to frequent DNA copy number alterations or mutations and show aberrant expression in malignancies and other human diseases. As such, they might prove to be valuable biomarkers or targets for therapeutic intervention.
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Affiliation(s)
- Andrej Alendar
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam 1066CX, The Netherlands
| | - Anton Berns
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam 1066CX, The Netherlands
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10
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Sinha S, Molla S, Kundu CN. PARP1-modulated chromatin remodeling is a new target for cancer treatment. Med Oncol 2021; 38:118. [PMID: 34432161 DOI: 10.1007/s12032-021-01570-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 08/20/2021] [Indexed: 12/13/2022]
Abstract
Cancer progression requires certain tumorigenic mutations in genes encoding for different cellular and nuclear proteins. Altered expressions of these mutated genes are mediated by post-translational modifications and chromatin remodeling. Chromatin remodeling is mainly regulated by the chromatin remodeling enzyme complexes and histone modifications. Upon DNA damage, Poly-(ADP-ribose) Polymerase1 (PARP1) plays a very important role in the induction of chromatin modifications and activation of DNA repair pathways to repair the DNA lesion. It has been targeted to develop different anti-cancer therapeutic interventions and PARP inhibitors have been approved by the U.S. Food and Drug Administration (FDA) for clinical use. But it has been found that the cancer cells often develop resistance to these PARP inhibitors and chromatin remodeling helps in enhancing this process. Hence, it may be beneficial to target PARP1-mediated chromatin remodeling, which may allow to reverse the drug resistance. In the current review, we have discussed the role of chromatin remodeling in DNA repair, how PARP1 regulates modifications of chromatin dynamics, and the role of chromatin modifications in cancer. It has also been discussed how the PARP1-mediated chromatin remodeling can be targeted by PARP inhibitors alone or in combination with other chemotherapeutic agents to establish novel anti-cancer therapeutics. We have also considered the use of PARG inhibitors that may enhance the action of PARP inhibitors to target different types of cancers.
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Affiliation(s)
- Saptarshi Sinha
- Cancer Biology Division, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Campus-11, Patia, Bhubaneswar, Odisha, 751024, India
| | - Sefinew Molla
- Cancer Biology Division, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Campus-11, Patia, Bhubaneswar, Odisha, 751024, India
| | - Chanakya Nath Kundu
- Cancer Biology Division, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Campus-11, Patia, Bhubaneswar, Odisha, 751024, India.
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11
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Sharifi Tabar M, Giardina C, Feng Y, Francis H, Moghaddas Sani H, Low JKK, Mackay JP, Bailey CG, Rasko JEJ. Unique protein interaction networks define the chromatin remodelling module of the NuRD complex. FEBS J 2021; 289:199-214. [PMID: 34231305 PMCID: PMC9545347 DOI: 10.1111/febs.16112] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/27/2021] [Accepted: 07/06/2021] [Indexed: 01/13/2023]
Abstract
The combination of four proteins and their paralogues including MBD2/3, GATAD2A/B, CDK2AP1 and CHD3/4/5, which we refer to as the MGCC module, form the chromatin remodelling module of the nucleosome remodelling and deacetylase (NuRD) complex. To date, mechanisms by which the MGCC module acquires paralogue-specific function and specificity have not been addressed. Understanding the protein-protein interaction (PPI) network of the MGCC subunits is essential for defining underlying mechanisms of gene regulation. Therefore, using pulldown followed by mass spectrometry analysis (PD-MS), we report a proteome-wide interaction network of the MGCC module in a paralogue-specific manner. Our data also demonstrate that the disordered C-terminal region of CHD3/4/5 is a gateway to incorporate remodelling activity into both ChAHP (CHD4, ADNP, HP1γ) and NuRD complexes in a mutually exclusive manner. We define a short aggregation-prone region (APR) within the C-terminal segment of GATAD2B that is essential for the interaction of CHD4 and CDK2AP1 with the NuRD complex. Finally, we also report an association of CDK2AP1 with the nuclear receptor co-repressor (NCOR) complex. Overall, this study provides insight into the possible mechanisms through which the MGCC module can achieve specificity and diverse biological functions.
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Affiliation(s)
- Mehdi Sharifi Tabar
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW, Australia.,Faculty of Medicine & Health, The University of Sydney, NSW, Australia
| | - Caroline Giardina
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW, Australia
| | - Yue Feng
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW, Australia
| | - Habib Francis
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW, Australia
| | | | - Jason K K Low
- School of Life & Environmental Sciences, The University of Sydney, NSW, Australia
| | - Joel P Mackay
- School of Life & Environmental Sciences, The University of Sydney, NSW, Australia
| | - Charles G Bailey
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW, Australia.,Faculty of Medicine & Health, The University of Sydney, NSW, Australia.,Cancer & Gene Regulation Laboratory Centenary Institute, The University of Sydney, Camperdown, NSW, Australia
| | - John E J Rasko
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW, Australia.,Faculty of Medicine & Health, The University of Sydney, NSW, Australia.,Cell & Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
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12
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Andronikou C, Rottenberg S. Studying PAR-Dependent Chromatin Remodeling to Tackle PARPi Resistance. Trends Mol Med 2021; 27:630-642. [PMID: 34030964 DOI: 10.1016/j.molmed.2021.04.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/29/2021] [Accepted: 04/30/2021] [Indexed: 12/12/2022]
Abstract
Histone eviction and chromatin relaxation are important processes for efficient DNA repair. Poly(ADP) ribose (PAR) polymerase 1 (PARP1) is a key mediator of this process, and disruption of PARP1 activity has a direct impact on chromatin structure. PARP inhibitors (PARPis) have been established as a treatment for BRCA1- or BRCA2-deficient tumors. Unfortunately, PARPi resistance occurs in many patients and the underlying mechanisms are not fully understood. In particular, it remains unclear how chromatin remodelers and histone chaperones compensate for the loss of the PARylation signal. In this Opinion article, we summarize currently known mechanisms of PARPi resistance. We discuss how the study of PARP1-mediated chromatin remodeling may help in further understanding PARPi resistance and finding new therapeutic approaches to overcome it.
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Affiliation(s)
- Christina Andronikou
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands; Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Sven Rottenberg
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands; Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland; Bern Center for Precision Medicine, University of Bern, Bern, Switzerland.
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13
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van Beek L, McClay É, Patel S, Schimpl M, Spagnolo L, Maia de Oliveira T. PARP Power: A Structural Perspective on PARP1, PARP2, and PARP3 in DNA Damage Repair and Nucleosome Remodelling. Int J Mol Sci 2021; 22:ijms22105112. [PMID: 34066057 PMCID: PMC8150716 DOI: 10.3390/ijms22105112] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/04/2021] [Accepted: 05/06/2021] [Indexed: 12/30/2022] Open
Abstract
Poly (ADP-ribose) polymerases (PARP) 1-3 are well-known multi-domain enzymes, catalysing the covalent modification of proteins, DNA, and themselves. They attach mono- or poly-ADP-ribose to targets using NAD+ as a substrate. Poly-ADP-ribosylation (PARylation) is central to the important functions of PARP enzymes in the DNA damage response and nucleosome remodelling. Activation of PARP happens through DNA binding via zinc fingers and/or the WGR domain. Modulation of their activity using PARP inhibitors occupying the NAD+ binding site has proven successful in cancer therapies. For decades, studies set out to elucidate their full-length molecular structure and activation mechanism. In the last five years, significant advances have progressed the structural and functional understanding of PARP1-3, such as understanding allosteric activation via inter-domain contacts, how PARP senses damaged DNA in the crowded nucleus, and the complementary role of histone PARylation factor 1 in modulating the active site of PARP. Here, we review these advances together with the versatility of PARP domains involved in DNA binding, the targets and shape of PARylation and the role of PARPs in nucleosome remodelling.
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Affiliation(s)
- Lotte van Beek
- Structure and Biophysics, Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, UK; (L.v.B.); (M.S.)
| | - Éilís McClay
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, Garscube Campus, University of Glasgow, Glasgow G61 1QQ, UK;
| | - Saleha Patel
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, UK;
| | - Marianne Schimpl
- Structure and Biophysics, Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, UK; (L.v.B.); (M.S.)
| | - Laura Spagnolo
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, Garscube Campus, University of Glasgow, Glasgow G61 1QQ, UK;
- Correspondence: (L.S.); (T.M.d.O.)
| | - Taiana Maia de Oliveira
- Structure and Biophysics, Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, UK; (L.v.B.); (M.S.)
- Correspondence: (L.S.); (T.M.d.O.)
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14
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Novillo A, Fernández-Santander A, Gaibar M, Galán M, Romero-Lorca A, El Abdellaoui-Soussi F, Gómez-Del Arco P. Role of Chromodomain-Helicase-DNA-Binding Protein 4 (CHD4) in Breast Cancer. Front Oncol 2021; 11:633233. [PMID: 33981601 PMCID: PMC8107472 DOI: 10.3389/fonc.2021.633233] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/23/2021] [Indexed: 12/15/2022] Open
Abstract
Chromodomain-helicase-DNA-binding protein 4 (CHD4) is an epigenetic regulator identified as an oncogenic element that may provide a novel therapeutic target for the treatment of breast cancer (BC). CHD4—the core component of the nucleosome remodeling and deacetylase (NuRD) complex—may be mutated in patients with this disease. However, information on CHD4 mutants that might allow their use as biomarkers of therapeutic success and prognosis is lacking. The present work examines mutations in CHD4 reported in patients with breast cancer and included in public databases and attempts to identify their roles in its development. The databases revealed 81 point mutations across different types of breast cancer (19 of which also appeared in endometrial, intestinal, nervous system, kidney, and lymphoid organ cancers). 71.6% of the detected mutations were missense mutations, 13.6% were silent, and 6.2% nonsense. Over 50% affected conserved residues of the ATPase motor (ATPase and helicase domains), and domains of unknown function in the C-terminal region. Thirty one mutations were classified in the databases as either ‘deleterious’, ‘probably/possibly damaging’ or as ‘high/medium pathogenic’; another five nonsense and one splice-site variant were predicted to produce potentially harmful truncated proteins. Eight of the 81 mutations were categorized as putative driver mutations and have been found in other cancer types. Some mutations seem to influence ATPase and DNA translocation activities (R1162W), while others may alter protein stability (R877Q/H, R975H) or disrupt DNA binding and protein activity (R572*, X34_splice) suggesting CHD4 function may be affected. In vivo tumorigenecity studies in endometrial cancer have revealed R975H and R1162W as mutations that lead to CHD4 loss-of-function. Our study provides insight into the molecular mechanism whereby CHD4, and some of its mutants could play a role in breast cancer and suggest important implications for the biological comprehension and prognosis of breast cancer, identifying CHD4 as a novel therapeutic target for BC patients.
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Affiliation(s)
- Apolonia Novillo
- Department of Pre-clinical Dentistry, Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, Villaviciosa de Odón, Madrid, Spain
| | - Ana Fernández-Santander
- Department of Medicine, Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, Villaviciosa de Odón, Madrid, Spain
| | - Maria Gaibar
- Department of Health Sciences, Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, Villaviciosa de Odón, Madrid, Spain
| | - Miguel Galán
- Department of Health Sciences, Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, Villaviciosa de Odón, Madrid, Spain
| | - Alicia Romero-Lorca
- Department of Medicine, Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, Villaviciosa de Odón, Madrid, Spain
| | | | - Pablo Gómez-Del Arco
- Institute of Rare Diseases Research, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
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15
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Hoffmeister H, Fuchs A, Komives E, Groebner-Ferreira R, Strobl L, Nazet J, Heizinger L, Merkl R, Dove S, Längst G. Sequence and functional differences in the ATPase domains of CHD3 and SNF2H promise potential for selective regulability and drugability. FEBS J 2021; 288:4000-4023. [PMID: 33403747 DOI: 10.1111/febs.15699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 11/19/2020] [Accepted: 01/04/2021] [Indexed: 11/26/2022]
Abstract
Chromatin remodelers use the energy of ATP hydrolysis to regulate chromatin dynamics. Their impact for development and disease requires strict enzymatic control. Here, we address the differential regulability of the ATPase domain of hSNF2H and hCHD3, exhibiting similar substrate affinities and enzymatic activities. Both enzymes are comparably strongly inhibited in their ATP hydrolysis activity by the competitive ATPase inhibitor ADP. However, the nucleosome remodeling activity of SNF2H is more strongly affected than that of CHD3. Beside ADP, also IP6 inhibits the nucleosome translocation of both enzymes to varying degrees, following a competitive inhibition mode at CHD3, but not at SNF2H. Our observations are further substantiated by mutating conserved Q- and K-residues of ATPase domain motifs. The variants still bind both substrates and exhibit a wild-type similar, basal ATP hydrolysis. Apart from three CHD3 variants, none of the variants can translocate nucleosomes, suggesting for the first time that the basal ATPase activity of CHD3 is sufficient for nucleosome remodeling. Together with the ADP data, our results propose a more efficient coupling of ATP hydrolysis and remodeling in CHD3. This aspect correlates with findings that CHD3 nucleosome translocation is visible at much lower ATP concentrations than SNF2H. We propose sequence differences between the ATPase domains of both enzymes as an explanation for the functional differences and suggest that aa interactions, including the conserved Q- and K-residues distinctly regulate ATPase-dependent functions of both proteins. Our data emphasize the benefits of remodeler ATPase domains for selective drugability and/or regulability of chromatin dynamics.
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Affiliation(s)
- Helen Hoffmeister
- Department of Biochemistry, Genetics and Microbiology, Biochemistry III, University of Regensburg, Germany
| | - Andreas Fuchs
- Department of Biochemistry, Genetics and Microbiology, Biochemistry III, University of Regensburg, Germany
| | - Elizabeth Komives
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Regina Groebner-Ferreira
- Department of Biochemistry, Genetics and Microbiology, Biochemistry III, University of Regensburg, Germany
| | - Laura Strobl
- Department of Biochemistry, Genetics and Microbiology, Biochemistry III, University of Regensburg, Germany
| | - Julian Nazet
- Department of Biochemistry II, University of Regensburg, Germany
| | | | - Rainer Merkl
- Department of Biochemistry II, University of Regensburg, Germany
| | - Stefan Dove
- Department of Pharmaceutical and Medical Chemistry II, University of Regensburg, Germany
| | - Gernot Längst
- Department of Biochemistry, Genetics and Microbiology, Biochemistry III, University of Regensburg, Germany
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16
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Farnung L, Ochmann M, Cramer P. Nucleosome-CHD4 chromatin remodeler structure maps human disease mutations. eLife 2020; 9:56178. [PMID: 32543371 PMCID: PMC7338049 DOI: 10.7554/elife.56178] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 06/15/2020] [Indexed: 12/13/2022] Open
Abstract
Chromatin remodeling plays important roles in gene regulation during development, differentiation and in disease. The chromatin remodeling enzyme CHD4 is a component of the NuRD and ChAHP complexes that are involved in gene repression. Here, we report the cryo-electron microscopy (cryo-EM) structure of Homo sapiens CHD4 engaged with a nucleosome core particle in the presence of the non-hydrolysable ATP analogue AMP-PNP at an overall resolution of 3.1 Å. The ATPase motor of CHD4 binds and distorts nucleosomal DNA at superhelical location (SHL) +2, supporting the ‘twist defect’ model of chromatin remodeling. CHD4 does not induce unwrapping of terminal DNA, in contrast to its homologue Chd1, which functions in gene activation. Our structure also maps CHD4 mutations that are associated with human cancer or the intellectual disability disorder Sifrim-Hitz-Weiss syndrome.
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Affiliation(s)
- Lucas Farnung
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Göttingen, Germany
| | - Moritz Ochmann
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Göttingen, Germany
| | - Patrick Cramer
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Göttingen, Germany
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17
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Smith R, Lebeaupin T, Juhász S, Chapuis C, D'Augustin O, Dutertre S, Burkovics P, Biertümpfel C, Timinszky G, Huet S. Poly(ADP-ribose)-dependent chromatin unfolding facilitates the association of DNA-binding proteins with DNA at sites of damage. Nucleic Acids Res 2020; 47:11250-11267. [PMID: 31566235 PMCID: PMC6868358 DOI: 10.1093/nar/gkz820] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 09/01/2019] [Accepted: 09/26/2019] [Indexed: 12/19/2022] Open
Abstract
The addition of poly(ADP-ribose) (PAR) chains along the chromatin fiber due to PARP1 activity regulates the recruitment of multiple factors to sites of DNA damage. In this manuscript, we investigated how, besides direct binding to PAR, early chromatin unfolding events controlled by PAR signaling contribute to recruitment to DNA lesions. We observed that different DNA-binding, but not histone-binding, domains accumulate at damaged chromatin in a PAR-dependent manner, and that this recruitment correlates with their affinity for DNA. Our findings indicate that this recruitment is promoted by early PAR-dependent chromatin remodeling rather than direct interaction with PAR. Moreover, recruitment is not the consequence of reduced molecular crowding at unfolded damaged chromatin but instead originates from facilitated binding to more exposed DNA. These findings are further substantiated by the observation that PAR-dependent chromatin remodeling at DNA lesions underlies increased DNAse hypersensitivity. Finally, the relevance of this new mode of PAR-dependent recruitment to DNA lesions is demonstrated by the observation that reducing the affinity for DNA of both CHD4 and HP1α, two proteins shown to be involved in the DNA-damage response, strongly impairs their recruitment to DNA lesions.
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Affiliation(s)
- Rebecca Smith
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F- 35000 Rennes, France
| | - Théo Lebeaupin
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F- 35000 Rennes, France
| | - Szilvia Juhász
- MTA SZBK Lendület DNA damage and nuclear dynamics research group, Institute of Genetics, Biological Research Center, 6276 Szeged, Hungary
| | - Catherine Chapuis
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F- 35000 Rennes, France
| | - Ostiane D'Augustin
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F- 35000 Rennes, France
| | - Stéphanie Dutertre
- Univ Rennes, CNRS, Inserm, BIOSIT (Biologie, Santé, Innovation Technologique de Rennes) - UMS 3480, US 018, F-35000 Rennes, France
| | - Peter Burkovics
- Laboratory of Replication and Genome Stability, Institute of Genetics, Biological Research Center, 6276 Szeged, Hungary
| | - Christian Biertümpfel
- Department of Structural Cell Biology, Molecular Mechanisms of DNA Repair, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Gyula Timinszky
- MTA SZBK Lendület DNA damage and nuclear dynamics research group, Institute of Genetics, Biological Research Center, 6276 Szeged, Hungary
| | - Sébastien Huet
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F- 35000 Rennes, France
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18
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Hou T, Cao Z, Zhang J, Tang M, Tian Y, Li Y, Lu X, Chen Y, Wang H, Wei FZ, Wang L, Yang Y, Zhao Y, Wang Z, Wang H, Zhu WG. SIRT6 coordinates with CHD4 to promote chromatin relaxation and DNA repair. Nucleic Acids Res 2020; 48:2982-3000. [PMID: 31970415 PMCID: PMC7102973 DOI: 10.1093/nar/gkaa006] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 12/02/2019] [Accepted: 01/03/2020] [Indexed: 01/08/2023] Open
Abstract
Genomic instability is an underlying hallmark of cancer and is closely associated with defects in DNA damage repair (DDR). Chromatin relaxation is a prerequisite for DDR, but how chromatin accessibility is regulated remains elusive. Here we report that the histone deacetylase SIRT6 coordinates with the chromatin remodeler CHD4 to promote chromatin relaxation in response to DNA damage. Upon DNA damage, SIRT6 rapidly translocates to DNA damage sites, where it interacts with and recruits CHD4. Once at the damage sites, CHD4 displaces heterochromatin protein 1 (HP1) from histone H3 lysine 9 trimethylation (H3K9me3). Notably, loss of SIRT6 or CHD4 leads to impaired chromatin relaxation and disrupted DNA repair protein recruitment. These molecular changes, in-turn, lead to defective homologous recombination (HR) and cancer cell hypersensitivity to DNA damaging agents. Furthermore, we show that SIRT6-mediated CHD4 recruitment has a specific role in DDR within compacted chromatin by HR in G2 phase, which is an ataxia telangiectasia mutated (ATM)-dependent process. Taken together, our results identify a novel function for SIRT6 in recruiting CHD4 onto DNA double-strand breaks. This newly identified novel molecular mechanism involves CHD4-dependent chromatin relaxation and competitive release of HP1 from H3K9me3 within the damaged chromatin, which are both essential for accurate HR.
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Affiliation(s)
- Tianyun Hou
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Ziyang Cao
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Jun Zhang
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, International Cancer Center, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen 518055, China
| | - Ming Tang
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, International Cancer Center, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen 518055, China
| | - Yuan Tian
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, International Cancer Center, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen 518055, China
| | - Yinglu Li
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, International Cancer Center, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen 518055, China
| | - Xiaopeng Lu
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, International Cancer Center, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen 518055, China
| | - Yongcan Chen
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, International Cancer Center, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen 518055, China
| | - Hui Wang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Fu-Zheng Wei
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Lina Wang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Yang Yang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Ying Zhao
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Zimei Wang
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, International Cancer Center, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen 518055, China
| | - Haiying Wang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Wei-Guo Zhu
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.,Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, International Cancer Center, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen 518055, China
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19
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Weiss K, Lazar HP, Kurolap A, Martinez AF, Paperna T, Cohen L, Smeland MF, Whalen S, Heide S, Keren B, Terhal P, Irving M, Takaku M, Roberts JD, Petrovich RM, Schrier Vergano SA, Kenney A, Hove H, DeChene E, Quinonez SC, Colin E, Ziegler A, Rumple M, Jain M, Monteil D, Roeder ER, Nugent K, van Haeringen A, Gambello M, Santani A, Medne L, Krock B, Skraban CM, Zackai EH, Dubbs HA, Smol T, Ghoumid J, Parker MJ, Wright M, Turnpenny P, Clayton-Smith J, Metcalfe K, Kurumizaka H, Gelb BD, Baris Feldman H, Campeau PM, Muenke M, Wade PA, Lachlan K. The CHD4-related syndrome: a comprehensive investigation of the clinical spectrum, genotype-phenotype correlations, and molecular basis. Genet Med 2020; 22:389-397. [PMID: 31388190 PMCID: PMC8900827 DOI: 10.1038/s41436-019-0612-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 07/09/2019] [Indexed: 12/13/2022] Open
Abstract
PURPOSE Sifrim-Hitz-Weiss syndrome (SIHIWES) is a recently described multisystemic neurodevelopmental disorder caused by de novo variants inCHD4. In this study, we investigated the clinical spectrum of the disorder, genotype-phenotype correlations, and the effect of different missense variants on CHD4 function. METHODS We collected clinical and molecular data from 32 individuals with mostly de novo variants in CHD4, identified through next-generation sequencing. We performed adenosine triphosphate (ATP) hydrolysis and nucleosome remodeling assays on variants from five different CHD4 domains. RESULTS The majority of participants had global developmental delay, mild to moderate intellectual disability, brain anomalies, congenital heart defects, and dysmorphic features. Macrocephaly was a frequent but not universal finding. Additional common abnormalities included hypogonadism in males, skeletal and limb anomalies, hearing impairment, and ophthalmic abnormalities. The majority of variants were nontruncating and affected the SNF2-like region of the protein. We did not identify genotype-phenotype correlations based on the type or location of variants. Alterations in ATP hydrolysis and chromatin remodeling activities were observed in variants from different domains. CONCLUSION The CHD4-related syndrome is a multisystemic neurodevelopmental disorder. Missense substitutions in different protein domains alter CHD4 function in a variant-specific manner, but result in a similar phenotype in humans.
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Affiliation(s)
- Karin Weiss
- The Genetics Institute, Rambam Health Care Campus, Haifa, Israel.
| | - Hayley P Lazar
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Alina Kurolap
- The Genetics Institute, Rambam Health Care Campus, Haifa, Israel
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Ariel F Martinez
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Tamar Paperna
- The Genetics Institute, Rambam Health Care Campus, Haifa, Israel
| | - Lior Cohen
- Genetics Institute, Schneider Children's Medical Center, Petah Tikva, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Marie F Smeland
- Department of Medical Genetics, University Hospital of North Norway, Tromsø, Norway
| | - Sandra Whalen
- UF de génétique clinique, Centre de Référence Maladies Rares des Anomalies du développement et syndromes malformatifs, APHP, Hôpital Trousseau, Paris, France
| | - Solveig Heide
- AP-HP, Département de Génétique, Centre de Référence Maladies Rares "Anomalies du développement et syndromes malformatifs" Hôpital de la Pitié Salpêtrière, Paris, France
| | - Boris Keren
- AP-HP, Département de Génétique, Centre de Référence Maladies Rares "Anomalies du développement et syndromes malformatifs" Hôpital de la Pitié Salpêtrière, Paris, France
| | - Pauline Terhal
- Department of Genetics, Utrecht University Medical Center, Utrecht, the Netherlands
| | - Melita Irving
- Department of Clinical Genetics, Guy's Hospital, London, UK
| | - Motoki Takaku
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - John D Roberts
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Robert M Petrovich
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Samantha A Schrier Vergano
- Division of Medical Genetics and Metabolism, Children's Hospital of The King's Daughters, Norfolk, VA, USA
- Department of Pediatrics, Eastern Virginia Medical School, Norfolk, VA, USA
| | - Amy Kenney
- Division of Medical Genetics and Metabolism, Children's Hospital of The King's Daughters, Norfolk, VA, USA
| | - Hanne Hove
- Centre for Rare Diseases, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Elizabeth DeChene
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Shane C Quinonez
- Department of Pediatrics, Division of Genetics, Metabolism and Genomic Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Estelle Colin
- Department of Biochemistry and Genetics, University Hospital Angers, Angers, France
| | - Alban Ziegler
- Department of Biochemistry and Genetics, University Hospital Angers, Angers, France
| | | | - Mahim Jain
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Bone and Osteogenesis Imperfecta Department, Kennedy Krieger Institute, Baltimore, MD, USA
| | - Danielle Monteil
- Department of Pediatrics, Naval Medical Center Portsmouth, Portsmouth, VA, USA
| | - Elizabeth R Roeder
- Departments of Pediatrics and Molecular and Human Genetics, Baylor College of Medicine, San Antonio, TX, USA
| | - Kimberly Nugent
- Departments of Pediatrics and Molecular and Human Genetics, Baylor College of Medicine, San Antonio, TX, USA
| | - Arie van Haeringen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Michael Gambello
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Avni Santani
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Līvija Medne
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Bryan Krock
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Cara M Skraban
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Elaine H Zackai
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Holly A Dubbs
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Thomas Smol
- Department of Clinical Genetics, Lille University Hospital, CHU Lille, Lille, France
- EA7364 RADEME (Research Team on Rare Developmental and Metabolic Diseases), Lille 2 University, Lille, France
| | - Jamal Ghoumid
- Department of Clinical Genetics, Lille University Hospital, CHU Lille, Lille, France
- EA7364 RADEME (Research Team on Rare Developmental and Metabolic Diseases), Lille 2 University, Lille, France
| | - Michael J Parker
- Sheffield Children's Hospital NHS Foundation Trust, Western Bank, Sheffield, UK
| | - Michael Wright
- Northern Genetics Service, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Institute of Human Genetics, International Centre for Life, Newcastle upon Tyne, UK
| | - Peter Turnpenny
- University of Exeter Medical School, Clinical Genetics Royal Devon & Exeter Hospital, Exeter, UK
| | - Jill Clayton-Smith
- Institute of Evolution, Systems and Genomics, Faculty of Medical and Human Sciences, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK
| | - Kay Metcalfe
- Institute of Evolution, Systems and Genomics, Faculty of Medical and Human Sciences, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK
| | - Hitoshi Kurumizaka
- Laboratory of Structural Biology, Graduate School of Advanced Science & Engineering, Waseda University, Tokyo, Japan
| | - Bruce D Gelb
- Mindich Child Health and Development Institute and Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hagit Baris Feldman
- The Genetics Institute, Rambam Health Care Campus, Haifa, Israel
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Philippe M Campeau
- Department of Pediatrics, University of Montreal and CHU Sainte-Justine, Montreal, QC, Canada
| | - Maximilian Muenke
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Paul A Wade
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Katherine Lachlan
- Wessex Clinical Genetics Service, University Hospital Southampton NHS Trust. Department of Human Genetics and Genomic Medicine, Southampton University, Southampton, UK
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20
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Pierson TM, Otero MG, Grand K, Choi A, Graham JM, Young JI, Mackay JP. The NuRD complex and macrocephaly associated neurodevelopmental disorders. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2019; 181:548-556. [PMID: 31737996 DOI: 10.1002/ajmg.c.31752] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 10/08/2019] [Accepted: 10/10/2019] [Indexed: 12/13/2022]
Abstract
The nucleosome remodeling and deacetylase (NuRD) complex is a major regulator of gene expression involved in pluripotency, lineage commitment, and corticogenesis. This important complex is composed of seven different proteins, with mutations in CHD3, CHD4, and GATAD2B being associated with neurodevelopmental disorders presenting with macrocephaly and intellectual disability similar to other overgrowth and intellectual disability (OGID) syndromes. Pathogenic variants in CHD3 and CHD4 primarily involve disruption of enzymatic function. GATAD2B variants include loss-of-function mutations that alter protein dosage and missense variants that involve either of two conserved domains (CR1 and CR2) known to interact with other NuRD proteins. In addition to macrocephaly and intellectual disability, CHD3 variants are associated with inguinal hernias and apraxia of speech; whereas CHD4 variants are associated with skeletal anomalies, deafness, and cardiac defects. GATAD2B-associated neurodevelopmental disorder (GAND) has phenotypic overlap with both of these disorders. Of note, structural models of NuRD indicate that CHD3 and CHD4 require direct contact with the GATAD2B-CR2 domain to interact with the rest of the complex. Therefore, the phenotypic overlaps of CHD3- and CHD4-related disorders with GAND are consistent with a loss in the ability of GATAD2B to recruit CHD3 or CHD4 to the complex. The shared features of these neurodevelopmental disorders may represent a new class of OGID syndrome: the NuRDopathies.
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Affiliation(s)
- Tyler Mark Pierson
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, California.,Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, California.,Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Maria G Otero
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Katheryn Grand
- Department of Pediatrics, Medical Genetics, Cedars-Sinai Medical Center, Los Angeles, California
| | - Andrew Choi
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - John M Graham
- Department of Pediatrics, Medical Genetics, Cedars-Sinai Medical Center, Los Angeles, California
| | - Juan I Young
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
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21
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Leighton G, Williams DC. The Methyl-CpG-Binding Domain 2 and 3 Proteins and Formation of the Nucleosome Remodeling and Deacetylase Complex. J Mol Biol 2019:S0022-2836(19)30599-6. [PMID: 31626804 DOI: 10.1016/j.jmb.2019.10.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 10/08/2019] [Accepted: 10/09/2019] [Indexed: 12/13/2022]
Abstract
The Nucleosome Remodeling and Deacetylase (NuRD) complex uniquely combines both deacetylase and remodeling enzymatic activities in a single macromolecular complex. The methyl-CpG-binding domain 2 and 3 (MBD2 and MBD3) proteins provide a critical structural link between the deacetylase and remodeling components, while MBD2 endows the complex with the ability to selectively recognize methylated DNA. Hence, NuRD combines three major arms of epigenetic gene regulation. Research over the past few decades has revealed much of the structural basis driving formation of this complex and started to uncover the functional roles of NuRD in epigenetic gene regulation. However, we have yet to fully understand the molecular and biophysical basis for methylation-dependent chromatin remodeling and transcription regulation by NuRD. In this review, we discuss the structural information currently available for the complex, the role MBD2 and MBD3 play in forming and recruiting the complex to methylated DNA, and the biological functions of NuRD.
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Affiliation(s)
- Gage Leighton
- Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA.
| | - David C Williams
- Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA.
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22
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Wang HC, Chou CL, Yang CC, Huang WL, Hsu YC, Luo CW, Chen TJ, Li CF, Pan MR. Over-Expression of CHD4 Is an Independent Biomarker of Poor Prognosis in Patients with Rectal Cancers Receiving Concurrent Chemoradiotherapy. Int J Mol Sci 2019; 20:ijms20174087. [PMID: 31438571 PMCID: PMC6747537 DOI: 10.3390/ijms20174087] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/19/2019] [Accepted: 08/19/2019] [Indexed: 12/18/2022] Open
Abstract
Neoadjuvant concurrent chemoradiotherapy (CCRT), followed by radical proctectomy, is the standard treatment for locally advanced rectal cancer. However, a poor response and therapeutic resistance continue to occur despite this treatment. In this study, we analyzed the microarray datasets (GSE68204) of rectal cancer from the Gene Expression Omnibus database, and identified CHD4 as one of the most significantly up-regulated genes among all subunits of the nucleosome remodeling and histone deacetylation (NuRD) complex, in non-responders to CCRT, among locally advanced rectal cancer (LARC) patients. We confirmed the predictive and prognostic significance of CHD4 expression in CCRT treatment, and its correlation with other clinicopathological features, such as tumor regression grade (TRG), therapeutic response, and patient survival. This was carried out by immunohistochemical studies on endoscopic biopsy tissues from 172 rectal cancer patients, receiving neoadjuvant concurrent chemoradiotherapy (CCRT). A high expression of CHD4 was significantly associated with pre-treatment tumor status (p < 0.001) and lymph node metastasis (p < 0.001), post-treatment tumor status (p < 0.001), and lymph node metastasis (p < 0.001), vascular invasion (p = 0.042), and tumor regression grade (p = 0.001). A high expression of CHD4 could also predict poor disease-specific survival and metastasis-free survival (log-rank test, p = 0.0373 and p < 0.0001, respectively). In multivariate Cox proportional-hazards regression analysis, CHD4 overexpression was an independent factor of poor prognosis for metastasis-free survival (HR, 4.575; 95% CI, 1.717–12.192; p = 0.002). By in vitro studies, based on cell line models, we also demonstrated that, the overexpression of CHD4 induced radio-resistance in microsatellite instability-high (MSI-H) colorectal cells (CRCs). On the contrary, the knockdown of CHD4 enhanced radiosensitivity in microsatellite stable (MSS) CRCs. Altogether, we have identified CHD4 as an important regulator of radio-resistance in both MSI-H and MSS CRC cell lines.
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Affiliation(s)
- Hui-Ching Wang
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Division of Hematology and Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Chia-Lin Chou
- Division of Colon & Rectal Surgery, Department of Surgery, Chi Mei Medical Center, Tainan 710, Taiwan
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung 804, Taiwan
| | - Ching-Chieh Yang
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung 804, Taiwan
- Department of Radiation Oncology, Chi-Mei Medical Center, Tainan 710, Taiwan
- Department of Pharmacy, Chia-Nan University of Pharmacy and Science, Tainan 71745, Taiwan
| | - Wei-Lun Huang
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Radiation Oncology, Kaohsiung Veterans General Hospital, Kaohsiung 813, Taiwan
| | - Yin-Chou Hsu
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Emergency Medicine, E-Da Hospital, I-Shou University, Kaohsiung 824, Taiwan
| | - Chi-Wen Luo
- Division of Breast Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
| | - Tzu-Ju Chen
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung 804, Taiwan
- Department of Pathology, Chi Mei Medical Center, Tainan 710, Taiwan
- Department of Optometry, Chung Hwa University of Medical Technology, Tainan 717, Taiwan
| | - Chien-Feng Li
- Department of Pathology, Chi Mei Medical Center, Tainan 710, Taiwan
- Department of Medical Research, Chi Mei Medical Center, Tainan 710, Taiwan
- National Institute of Cancer Research, National Health Research Institute, Tainan 704, Taiwan
| | - Mei-Ren Pan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
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23
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Ryan DP, Tremethick DJ. The interplay between H2A.Z and H3K9 methylation in regulating HP1α binding to linker histone-containing chromatin. Nucleic Acids Res 2019; 46:9353-9366. [PMID: 30007360 PMCID: PMC6182156 DOI: 10.1093/nar/gky632] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 07/04/2018] [Indexed: 12/14/2022] Open
Abstract
One of the most intensively studied chromatin binding factors is HP1α. HP1α is associated with silenced, heterochromatic regions of the genome and binds to H3K9me3. While H3K9me3 is necessary for HP1α recruitment to heterochromatin, it is becoming apparent that it is not sufficient suggesting that additional factors are involved. One candidate proposed as a potential regulator of HP1α recruitment is the linker histone H1.4. Changes to the underlying make-up of chromatin, such as the incorporation of the histone variant H2A.Z, has also been linked with regulating HP1 binding to chromatin. Here, we rigorously dissected the effects of H1.4, H2A.Z and H3K9me3 on the nucleosome binding activity of HP1α in vitro employing arrays, mononucleosomes and nucleosome core particles. Unexpectedly, histone H1.4 impedes the binding of HP1α but strikingly, this inhibition is partially relieved by the incorporation of both H2A.Z and H3K9me3 but only in the context of arrays or nucleosome core particles. Our data suggests that there are two modes of interaction of HP1α with nucleosomes. The first primary mode is through interactions with linker DNA. However, when linker DNA is missing or occluded by linker histones, HP1α directly interacts with the nucleosome core and this interaction is enhanced by H2A.Z with H3K9me3.
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Affiliation(s)
- Daniel P Ryan
- Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, ACT 2601, Australia
| | - David J Tremethick
- Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, ACT 2601, Australia
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24
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Smith R, Sellou H, Chapuis C, Huet S, Timinszky G. CHD3 and CHD4 recruitment and chromatin remodeling activity at DNA breaks is promoted by early poly(ADP-ribose)-dependent chromatin relaxation. Nucleic Acids Res 2019; 46:6087-6098. [PMID: 29733391 PMCID: PMC6158744 DOI: 10.1093/nar/gky334] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 04/23/2018] [Indexed: 12/12/2022] Open
Abstract
One of the first events to occur upon DNA damage is the local opening of the compact chromatin architecture, facilitating access of repair proteins to DNA lesions. This early relaxation is triggered by poly(ADP-ribosyl)ation by PARP1 in addition to ATP-dependent chromatin remodeling. CHD4 recruits to DNA breaks in a PAR-dependent manner, although it lacks any recognizable PAR-binding domain, and has the ability to relax chromatin structure. However, its role in chromatin relaxation at the site of DNA damage has not been explored. Using a live cell fluorescence three-hybrid assay, we demonstrate that the recruitment of CHD4 to DNA damage, while being poly(ADP-ribosyl)ation-dependent, is not through binding poly(ADP-ribose). Additionally, we show that CHD3 is recruited to DNA breaks in the same manner as CHD4 and that both CHD3 and CHD4 play active roles in chromatin remodeling at DNA breaks. Together, our findings reveal a two-step mechanism for DNA damage induced chromatin relaxation in which PARP1 and the PAR-binding remodeler activities of Alc1/CHD1L induce an initial chromatin relaxation phase that promotes the subsequent recruitment of CHD3 and CHD4 via binding to DNA for further chromatin remodeling at DNA breaks.
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Affiliation(s)
- Rebecca Smith
- Biomedical Center Munich, Physiological Chemistry, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany.,Univ Rennes, CNRS, Structure fédérative de recherche Biosit, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F- 35000 Rennes, France
| | - Hafida Sellou
- Univ Rennes, CNRS, Structure fédérative de recherche Biosit, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F- 35000 Rennes, France
| | - Catherine Chapuis
- Univ Rennes, CNRS, Structure fédérative de recherche Biosit, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F- 35000 Rennes, France
| | - Sébastien Huet
- Univ Rennes, CNRS, Structure fédérative de recherche Biosit, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F- 35000 Rennes, France
| | - Gyula Timinszky
- Biomedical Center Munich, Physiological Chemistry, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany.,MTA SZBK Lendület DNA damage and nuclear dynamics research group, Biological Research Center of the Hungarian Academy of Sciences, 6276 Szeged, Hungary
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25
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Kumar A, Kumar V, Kumar A. Functional characterization of host toxic EcdB transcription factor protein of echinocandin B biosynthetic gene cluster. Biotechnol Appl Biochem 2019; 66:626-633. [PMID: 31069846 DOI: 10.1002/bab.1763] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 05/07/2019] [Indexed: 11/09/2022]
Abstract
The ecdB is a transcription factor, located in the echinocandin B biosynthetic gene cluster of Emericella rugulosa NRRL11440. Here, we validated the ecdB mRNA sequence for functional expression and to explore the role of EcdB protein in the echinocandin B regulation. The sequence alignment study revealed that the ecdB coding sequence was found 75 bp shorter than the reference mRNA sequence. This coding sequence encodes for EcdB protein and comprises three conserved domains; DNA binding domain (DBD), coiled-coil domain, and signature middle homology region. The full-length and DBD (truncated) DNA sequences were expressed in Escherichia coli BL21(DE3) under different tested conditions. The expression of EcdB protein was found to be toxic, which curbs the cell growth. In contrast to truncated protein (GST:EcdB1-54), the full-length (GST:EcdB) protein was expressed at very low titer and not detectable in SDS-PAGE under the varying isopropyl β-d-1-thiogalactopyranoside (IPTG), temperature, and media conditions. However, GST:EcdB1-54 was successfully purified under standard conditions (0.5 mM IPTG at 0.5OD) with 33 kDa expected size. The functionality of GST:EcdB1-54 was attained by electrophoretic mobility shift assay study as a clear band shifting showed with ecdA promoter. Taken together, we conclude that EcdB interacts with the ecdA promoter that reflected to require for echinocandin B regulation.
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Affiliation(s)
- Arvind Kumar
- Department of Biotechnology, Central University of South Bihar, Panchanpur, Gaya, India
| | - Vinay Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Antresh Kumar
- Department of Biotechnology, Central University of South Bihar, Panchanpur, Gaya, India
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26
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Crowley EL, Rafferty SP. Review of lactose-driven auto-induction expression of isotope-labelled proteins. Protein Expr Purif 2019; 157:70-85. [PMID: 30708035 DOI: 10.1016/j.pep.2019.01.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 01/18/2019] [Indexed: 02/06/2023]
Abstract
NMR is an important method in the structural and functional characterization of proteins, but such experiments typically require isotopic labelling because of the low natural abundance of the nuclei of interest. Isotope-labelled protein for NMR experiments is typically obtained from IPTG-inducible bacterial expression systems in a minimal media that contains labelled carbon or nitrogen sources. Optimization of expression conditions is crucial yet challenging; large amounts of labelled protein are desired, yet protein yields are lower in minimal media, while the labelled precursors are expensive. Faced with these challenges there is a growing body of literature that apply innovative methods of induction to optimize the yield of isotope-labelled protein. A promising technique is lactose-driven auto-induction as it mitigates user intervention and can lead to higher protein yields. This review assesses the current advances and limitations surrounding the ability of researchers to isotope label proteins using auto-induction, and it identifies key components for optimization.
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Affiliation(s)
- Erika L Crowley
- Environmental and Life Sciences Graduate Program, Trent University, 1600 West Bank Drive, Peterborough, ON, K9J 0G2, Canada.
| | - Steven P Rafferty
- Department of Chemistry, Trent University, 1600 West Bank Drive, Peterborough, ON, K9J 0G2, Canada.
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27
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Moore S, Berger ND, Luijsterburg MS, Piett CG, Stanley FKT, Schräder CU, Fang S, Chan JA, Schriemer DC, Nagel ZD, van Attikum H, Goodarzi AA. The CHD6 chromatin remodeler is an oxidative DNA damage response factor. Nat Commun 2019; 10:241. [PMID: 30651562 PMCID: PMC6335469 DOI: 10.1038/s41467-018-08111-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 12/14/2018] [Indexed: 02/07/2023] Open
Abstract
Cell survival after oxidative DNA damage requires signaling, repair and transcriptional events often enabled by nucleosome displacement, exchange or removal by chromatin remodeling enzymes. Here, we show that Chromodomain Helicase DNA-binding protein 6 (CHD6), distinct to other CHD enzymes, is stabilized during oxidative stress via reduced degradation. CHD6 relocates rapidly to DNA damage in a manner dependent upon oxidative lesions and a conserved N-terminal poly(ADP-ribose)-dependent recruitment motif, with later retention requiring the double chromodomain and central core. CHD6 ablation increases reactive oxygen species persistence and impairs anti-oxidant transcriptional responses, leading to elevated DNA breakage and poly(ADP-ribose) induction that cannot be rescued by catalytic or double chromodomain mutants. Despite no overt epigenetic or DNA repair abnormalities, CHD6 loss leads to impaired cell survival after chronic oxidative stress, abnormal chromatin relaxation, amplified DNA damage signaling and checkpoint hypersensitivity. We suggest that CHD6 is a key regulator of the oxidative DNA damage response. Oxidative DNA damage is associated with nucleosome respacing and transcriptional changes requiring chromatin remodeling enzymes. Here, the authors reveal that the CHD6 remodeler is a DNA damage response factor that relocates to damaged sites and promotes cell survival following oxidative damage.
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Affiliation(s)
- Shaun Moore
- Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Departments of Biochemistry & Molecular Biology and/or Oncology, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - N Daniel Berger
- Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Departments of Biochemistry & Molecular Biology and/or Oncology, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Martijn S Luijsterburg
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Cortt G Piett
- Harvard University, School of Public Health, Boston, MA, 02115, USA
| | - Fintan K T Stanley
- Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Departments of Biochemistry & Molecular Biology and/or Oncology, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Christoph U Schräder
- Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Departments of Biochemistry & Molecular Biology and/or Oncology, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Shujuan Fang
- Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Departments of Biochemistry & Molecular Biology and/or Oncology, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Jennifer A Chan
- Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Departments of Biochemistry & Molecular Biology and/or Oncology, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - David C Schriemer
- Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Departments of Biochemistry & Molecular Biology and/or Oncology, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Zachary D Nagel
- Harvard University, School of Public Health, Boston, MA, 02115, USA
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Aaron A Goodarzi
- Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Departments of Biochemistry & Molecular Biology and/or Oncology, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada.
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28
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Rother MB, van Attikum H. DNA repair goes hip-hop: SMARCA and CHD chromatin remodellers join the break dance. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0285. [PMID: 28847822 PMCID: PMC5577463 DOI: 10.1098/rstb.2016.0285] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/07/2017] [Indexed: 12/20/2022] Open
Abstract
Proper signalling and repair of DNA double-strand breaks (DSB) is critical to prevent genome instability and diseases such as cancer. The packaging of DNA into chromatin, however, has evolved as a mere obstacle to these DSB responses. Posttranslational modifications and ATP-dependent chromatin remodelling help to overcome this barrier by modulating nucleosome structures and allow signalling and repair machineries access to DSBs in chromatin. Here we recap our current knowledge on how ATP-dependent SMARCA- and CHD-type chromatin remodellers alter chromatin structure during the signalling and repair of DSBs and discuss how their dysfunction impacts genome stability and human disease. This article is part of the themed issue ‘Chromatin modifiers and remodellers in DNA repair and signalling’.
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Affiliation(s)
- Magdalena B Rother
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
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29
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Wai DCC, Szyszka TN, Campbell AE, Kwong C, Wilkinson-White LE, Silva APG, Low JKK, Kwan AH, Gamsjaeger R, Chalmers JD, Patrick WM, Lu B, Vakoc CR, Blobel GA, Mackay JP. The BRD3 ET domain recognizes a short peptide motif through a mechanism that is conserved across chromatin remodelers and transcriptional regulators. J Biol Chem 2018; 293:7160-7175. [PMID: 29567837 DOI: 10.1074/jbc.ra117.000678] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 02/08/2018] [Indexed: 12/31/2022] Open
Abstract
Members of the bromodomain and extra-terminal domain (BET) family of proteins (bromodomain-containing (BRD) 2, 3, 4, and T) are widely expressed and highly conserved regulators of gene expression in eukaryotes. These proteins have been intimately linked to human disease, and more than a dozen clinical trials are currently underway to test BET-protein inhibitors as modulators of cancer. However, although it is clear that these proteins use their bromodomains to bind both histones and transcription factors bearing acetylated lysine residues, the molecular mechanisms by which BET family proteins regulate gene expression are not well defined. In particular, the functions of the other domains such as the ET domain have been less extensively studied. Here, we examine the properties of the ET domain of BRD3 as a protein/protein interaction module. Using a combination of pulldown and biophysical assays, we demonstrate that BRD3 binds to a range of chromatin-remodeling complexes, including the NuRD, BAF, and INO80 complexes, via a short linear "KIKL" motif in one of the complex subunits. NMR-based structural analysis revealed that, surprisingly, this mode of interaction is shared by the AF9 and ENL transcriptional coregulators that contain an acetyl-lysine-binding YEATS domain and regulate transcriptional elongation. This observation establishes a functional commonality between these two families of cancer-related transcriptional regulators. In summary, our data provide insight into the mechanisms by which BET family proteins might link chromatin acetylation to transcriptional outcomes and uncover an unexpected functional similarity between BET and YEATS family proteins.
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Affiliation(s)
- Dorothy C C Wai
- School of Life and Environmental Sciences, University of Sydney New South Wales 2006, Australia
| | - Taylor N Szyszka
- School of Life and Environmental Sciences, University of Sydney New South Wales 2006, Australia
| | - Amy E Campbell
- Division of Hematology, Children's Hospital of Philadelphia, and the Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Cherry Kwong
- School of Life and Environmental Sciences, University of Sydney New South Wales 2006, Australia
| | - Lorna E Wilkinson-White
- School of Life and Environmental Sciences, University of Sydney New South Wales 2006, Australia
| | - Ana P G Silva
- School of Life and Environmental Sciences, University of Sydney New South Wales 2006, Australia
| | - Jason K K Low
- School of Life and Environmental Sciences, University of Sydney New South Wales 2006, Australia
| | - Ann H Kwan
- School of Life and Environmental Sciences, University of Sydney New South Wales 2006, Australia
| | - Roland Gamsjaeger
- School of Life and Environmental Sciences, University of Sydney New South Wales 2006, Australia
| | - James D Chalmers
- Department of Biochemistry, University of Otago, Dunedin 9016, New Zealand
| | - Wayne M Patrick
- Department of Biochemistry, University of Otago, Dunedin 9016, New Zealand
| | - Bin Lu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | | | - Gerd A Blobel
- Division of Hematology, Children's Hospital of Philadelphia, and the Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney New South Wales 2006, Australia.
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30
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Corbeski I, Horn V, van der Valk RA, le Paige UB, Dame RT, van Ingen H. Microscale Thermophoresis Analysis of Chromatin Interactions. Methods Mol Biol 2018; 1837:177-197. [PMID: 30109612 DOI: 10.1007/978-1-4939-8675-0_11] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Architectural DNA-binding proteins are key to the organization and compaction of genomic DNA inside cells. The activity of architectural proteins is often subject to further modulation and regulation through the interaction with a diverse array of other protein factors. Detailed knowledge on the binding modes involved is crucial for our understanding of how these protein-protein and protein-DNA interactions shape the functional landscape of chromatin in all kingdoms of life: bacteria, archaea, and eukarya.Microscale thermophoresis (MST) is a biophysical technique that has seen increasing application in the study of biomolecular interactions thanks to its solution-based nature, its rapid application, modest sample demand, and the sensitivity of the thermophoresis effect to binding events. Here, we describe the use of MST in the study of chromatin interactions, with emphasis on the wide range of ways in which these experiments are set up and the diverse types of information they reveal. These aspects are illustrated with four very different systems: the sequence-dependent DNA compaction by architectural protein HMfB; the sequential binding of core histone complexes to histone chaperone APLF; the impact of the nucleosomal context on the recognition of histone modifications; and the binding of a LANA-derived peptide to nucleosome core. Special emphasis is given to the key steps in the design, execution, and analysis of MST experiments in the context of the provided examples.
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Affiliation(s)
- Ivan Corbeski
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Velten Horn
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | | | - Ulric B le Paige
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Remus T Dame
- Leiden Institute of Chemistry and Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Hugo van Ingen
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands.
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands.
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31
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Accessibility of the histone H3 tail in the nucleosome for binding of paired readers. Nat Commun 2017; 8:1489. [PMID: 29138400 PMCID: PMC5686127 DOI: 10.1038/s41467-017-01598-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 10/03/2017] [Indexed: 12/03/2022] Open
Abstract
Combinatorial polyvalent contacts of histone-binding domains or readers commonly mediate localization and activities of chromatin-associated proteins. A pair of readers, the PHD fingers of the protein CHD4, has been shown to bivalently recognize histone H3 tails. Here we describe a mechanism by which these linked but independent readers bind to the intact nucleosome core particle (NCP). Comprehensive NMR, chemical reactivity, molecular dynamics, and fluorescence analyses point to the critical roles of intra-nucleosomal histone-DNA interactions that reduce the accessibility of H3 tails in NCP, the nucleosomal DNA, and the linker between readers in modulating nucleosome- and/or histone-binding activities of the readers. We show that the second PHD finger of CHD4 initiates recruitment to the nucleosome, however both PHDs are required to alter the NCP dynamics. Our findings reveal a distinctive regulatory mechanism for the association of paired readers with the nucleosome that provides an intricate balance between cooperative and individual activities of the readers. The chromatin remodeller CHD4 contains two PHD finger reader domains that have been shown to bivalently recognize H3 histone tails. Here, the authors describe a mechanism by which the PHD fingers bind to the intact nucleosome core particle, revealing both cooperative and individual interactions.
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32
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Torrado M, Low JKK, Silva APG, Schmidberger JW, Sana M, Sharifi Tabar M, Isilak ME, Winning CS, Kwong C, Bedward MJ, Sperlazza MJ, Williams DC, Shepherd NE, Mackay JP. Refinement of the subunit interaction network within the nucleosome remodelling and deacetylase (NuRD) complex. FEBS J 2017; 284:4216-4232. [PMID: 29063705 DOI: 10.1111/febs.14301] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 07/19/2017] [Accepted: 10/18/2017] [Indexed: 01/29/2023]
Abstract
The nucleosome remodelling and deacetylase (NuRD) complex is essential for the development of complex animals. NuRD has roles in regulating gene expression and repairing damaged DNA. The complex comprises at least six proteins with two or more paralogues of each protein routinely identified when the complex is purified from cell extracts. To understand the structure and function of NuRD, a map of direct subunit interactions is needed. Dozens of published studies have attempted to define direct inter-subunit connectivities. We propose that conclusions reported in many such studies are in fact ambiguous for one of several reasons. First, the expression of many NuRD subunits in bacteria is unlikely to lead to folded, active protein. Second, interaction studies carried out in cells that contain endogenous NuRD complex can lead to false positives through bridging of target proteins by endogenous components. Combining existing information on NuRD structure with a protocol designed to minimize false positives, we report a conservative and robust interaction map for the NuRD complex. We also suggest a 3D model of the complex that brings together the existing data on the complex. The issues and strategies discussed herein are also applicable to the analysis of a wide range of multi-subunit complexes. ENZYMES Micrococcal nuclease (MNase), EC 3.1.31.1; histone deacetylase (HDAC), EC 3.5.1.98.
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Affiliation(s)
- Mario Torrado
- School of Life and Environmental Sciences, University of Sydney, Australia
| | - Jason K K Low
- School of Life and Environmental Sciences, University of Sydney, Australia
| | - Ana P G Silva
- School of Life and Environmental Sciences, University of Sydney, Australia
| | | | - Maryam Sana
- School of Life and Environmental Sciences, University of Sydney, Australia
| | | | - Musa E Isilak
- School of Life and Environmental Sciences, University of Sydney, Australia
| | - Courtney S Winning
- School of Life and Environmental Sciences, University of Sydney, Australia
| | - Cherry Kwong
- School of Life and Environmental Sciences, University of Sydney, Australia
| | - Max J Bedward
- School of Life and Environmental Sciences, University of Sydney, Australia
| | - Mary J Sperlazza
- Department of Pathology and Laboratory Medicine, The University of North Carolina - Chapel Hill, NC, USA
| | - David C Williams
- Department of Pathology and Laboratory Medicine, The University of North Carolina - Chapel Hill, NC, USA
| | - Nicholas E Shepherd
- Institute for Molecular Biosciences, The University of Queensland, St Lucia, Australia
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, Australia
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33
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Hoffmeister H, Fuchs A, Erdel F, Pinz S, Gröbner-Ferreira R, Bruckmann A, Deutzmann R, Schwartz U, Maldonado R, Huber C, Dendorfer AS, Rippe K, Längst G. CHD3 and CHD4 form distinct NuRD complexes with different yet overlapping functionality. Nucleic Acids Res 2017; 45:10534-10554. [PMID: 28977666 PMCID: PMC5737555 DOI: 10.1093/nar/gkx711] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 08/08/2017] [Indexed: 12/22/2022] Open
Abstract
CHD3 and CHD4 (Chromodomain Helicase DNA binding protein), two highly similar representatives of the Mi-2 subfamily of SF2 helicases, are coexpressed in many cell lines and tissues and have been reported to act as the motor subunit of the NuRD complex (nucleosome remodeling and deacetylase activities). Besides CHD proteins, NuRD contains several repressors like HDAC1/2, MTA2/3 and MBD2/3, arguing for a role as a transcriptional repressor. However, the subunit composition varies among cell- and tissue types and physiological conditions. In particular, it is unclear if CHD3 and CHD4 coexist in the same NuRD complex or whether they form distinct NuRD complexes with specific functions. We mapped the CHD composition of NuRD complexes in mammalian cells and discovered that they are isoform-specific, containing either the monomeric CHD3 or CHD4 ATPase. Both types of complexes exhibit similar intranuclear mobility, interact with HP1 and rapidly accumulate at UV-induced DNA repair sites. But, CHD3 and CHD4 exhibit distinct nuclear localization patterns in unperturbed cells, revealing a subset of specific target genes. Furthermore, CHD3 and CHD4 differ in their nucleosome remodeling and positioning behaviour in vitro. The proteins form distinct CHD3- and CHD4-NuRD complexes that do not only repress, but can just as well activate gene transcription of overlapping and specific target genes.
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Affiliation(s)
- Helen Hoffmeister
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Andreas Fuchs
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Fabian Erdel
- BioQuant, University of Heidelberg, 69120 Heidelberg, Germany
| | - Sophia Pinz
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Regina Gröbner-Ferreira
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Astrid Bruckmann
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Rainer Deutzmann
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Uwe Schwartz
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Rodrigo Maldonado
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Claudia Huber
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Anne-Sarah Dendorfer
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Karsten Rippe
- BioQuant, University of Heidelberg, 69120 Heidelberg, Germany
| | - Gernot Längst
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053 Regensburg, Germany
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34
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Regulation of DNA Repair Mechanisms: How the Chromatin Environment Regulates the DNA Damage Response. Int J Mol Sci 2017; 18:ijms18081715. [PMID: 28783053 PMCID: PMC5578105 DOI: 10.3390/ijms18081715] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 07/17/2017] [Accepted: 08/02/2017] [Indexed: 01/21/2023] Open
Abstract
Cellular DNA is constantly challenged by damage-inducing factors derived from exogenous or endogenous sources. In order to maintain genome stability and integrity, cells have evolved a wide variety of DNA repair pathways which counteract different types of DNA lesions, also referred to as the DNA damage response (DDR). However, DNA in eukaryotes is highly organized and compacted into chromatin representing major constraints for all cellular pathways, including DNA repair pathways, which require DNA as their substrate. Therefore, the chromatin configuration surrounding the lesion site undergoes dramatic remodeling to facilitate access of DNA repair factors and subsequent removal of the DNA lesion. In this review, we focus on the question of how the cellular DNA repair pathways overcome the chromatin barrier, how the chromatin environment is rearranged to facilitate efficient DNA repair, which proteins mediate this re-organization process and, consequently, how the altered chromatin landscape is involved in the regulation of DNA damage responses.
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35
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Mohanty B, Helder S, Silva APG, Mackay JP, Ryan DP. The Chromatin Remodelling Protein CHD1 Contains a Previously Unrecognised C-Terminal Helical Domain. J Mol Biol 2016; 428:4298-4314. [PMID: 27591891 DOI: 10.1016/j.jmb.2016.08.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 08/25/2016] [Accepted: 08/26/2016] [Indexed: 10/21/2022]
Abstract
The packaging of eukaryotic DNA into nucleosomes, and the organisation of these nucleosomes into chromatin, plays a critical role in regulating all DNA-associated processes. Chromodomain helicase DNA-binding protein 1 (CHD1) is an ATP-dependent chromatin remodelling protein that is conserved throughout eukaryotes and has an ability to assemble and organise nucleosomes both in vitro and in vivo. This activity is involved in the regulation of transcription and is implicated in mammalian development and stem cell biology. CHD1 is classically depicted as possessing a pair of tandem chromodomains that directly precede a core catalytic helicase-like domain that is then followed by a SANT-SLIDE DNA-binding domain. Here, we have identified an additional conserved domain C-terminal to the SANT-SLIDE domain and determined its structure by multidimensional heteronuclear NMR spectroscopy. We have termed this domain the CHD1 helical C-terminal (CHCT) domain as it is comprised of five α-helices arranged in a variant helical bundle topology. CHCT has a conserved, positively charged surface and is able to bind DNA and nucleosomes. In addition, we have identified another group of proteins, the as yet uncharacterised C17orf64 proteins, as also containing a conserved CHCT domain. Our data provide new structural insights into the CHD1 enzyme family.
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Affiliation(s)
- Biswaranjan Mohanty
- School of Life and Environmental Sciences, The University of Sydney, Building G08, Corner Butlin Avenue and Maze Crescent, Sydney, New South Wales, 2006, Australia; Faculty of Pharmacy and Pharmaceutical Sciences, Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria, 3052, Australia
| | - Stephanie Helder
- School of Life and Environmental Sciences, The University of Sydney, Building G08, Corner Butlin Avenue and Maze Crescent, Sydney, New South Wales, 2006, Australia
| | - Ana P G Silva
- School of Life and Environmental Sciences, The University of Sydney, Building G08, Corner Butlin Avenue and Maze Crescent, Sydney, New South Wales, 2006, Australia
| | - Joel P Mackay
- School of Life and Environmental Sciences, The University of Sydney, Building G08, Corner Butlin Avenue and Maze Crescent, Sydney, New South Wales, 2006, Australia.
| | - Daniel P Ryan
- Department of Genome Sciences, The John Curtin School of Medical Research, Building 131, Garran Road, The Australian National University, Canberra, Australian Capital Territory, 2601, Australia.
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36
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Low JKK, Webb SR, Silva APG, Saathoff H, Ryan DP, Torrado M, Brofelth M, Parker BL, Shepherd NE, Mackay JP. CHD4 Is a Peripheral Component of the Nucleosome Remodeling and Deacetylase Complex. J Biol Chem 2016; 291:15853-66. [PMID: 27235397 DOI: 10.1074/jbc.m115.707018] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Indexed: 01/08/2023] Open
Abstract
Chromatin remodeling enzymes act to dynamically regulate gene accessibility. In many cases, these enzymes function as large multicomponent complexes that in general comprise a central ATP-dependent Snf2 family helicase that is decorated with a variable number of regulatory subunits. The nucleosome remodeling and deacetylase (NuRD) complex, which is essential for normal development in higher organisms, is one such macromolecular machine. The NuRD complex comprises ∼10 subunits, including the histone deacetylases 1 and 2 (HDAC1 and HDAC2), and is defined by the presence of a CHD family remodeling enzyme, most commonly CHD4 (chromodomain helicase DNA-binding protein 4). The existing paradigm holds that CHD4 acts as the central hub upon which the complex is built. We show here that this paradigm does not, in fact, hold and that CHD4 is a peripheral component of the NuRD complex. A complex lacking CHD4 that has HDAC activity can exist as a stable species. The addition of recombinant CHD4 to this nucleosome deacetylase complex reconstitutes a NuRD complex with nucleosome remodeling activity. These data contribute to our understanding of the architecture of the NuRD complex.
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Affiliation(s)
- Jason K K Low
- From the School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia and
| | - Sarah R Webb
- From the School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia and
| | - Ana P G Silva
- From the School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia and
| | - Hinnerk Saathoff
- From the School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia and
| | - Daniel P Ryan
- the Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Acton, Australian Capital Territory 2601, Australia
| | - Mario Torrado
- From the School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia and
| | - Mattias Brofelth
- From the School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia and
| | - Benjamin L Parker
- From the School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia and
| | - Nicholas E Shepherd
- From the School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia and
| | - Joel P Mackay
- From the School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia and
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37
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Zhang W, Aubert A, Gomez de Segura JM, Karuppasamy M, Basu S, Murthy AS, Diamante A, Drury TA, Balmer J, Cramard J, Watson AA, Lando D, Lee SF, Palayret M, Kloet SL, Smits AH, Deery MJ, Vermeulen M, Hendrich B, Klenerman D, Schaffitzel C, Berger I, Laue ED. The Nucleosome Remodeling and Deacetylase Complex NuRD Is Built from Preformed Catalytically Active Sub-modules. J Mol Biol 2016; 428:2931-42. [PMID: 27117189 PMCID: PMC4942838 DOI: 10.1016/j.jmb.2016.04.025] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 04/18/2016] [Indexed: 11/26/2022]
Abstract
The nucleosome remodeling deacetylase (NuRD) complex is a highly conserved regulator of chromatin structure and transcription. Structural studies have shed light on this and other chromatin modifying machines, but much less is known about how they assemble and whether stable and functional sub-modules exist that retain enzymatic activity. Purification of the endogenous Drosophila NuRD complex shows that it consists of a stable core of subunits, while others, in particular the chromatin remodeler CHD4, associate transiently. To dissect the assembly and activity of NuRD, we systematically produced all possible combinations of different components using the MultiBac system, and determined their activity and biophysical properties. We carried out single-molecule imaging of CHD4 in live mouse embryonic stem cells, in the presence and absence of one of core components (MBD3), to show how the core deacetylase and chromatin-remodeling sub-modules associate in vivo. Our experiments suggest a pathway for the assembly of NuRD via preformed and active sub-modules. These retain enzymatic activity and are present in both the nucleus and the cytosol, an outcome with important implications for understanding NuRD function. We have studied Drosophila nucleosome remodeling deacetylase (NuRD) assembly. NuRD consists of a core deacetylase complex, where MTA-like acts as the scaffold. This transiently associates with a chromatin remodeling sub-module including CHD4. Single-molecule imaging shows that the two sub-modules associate through MBD-like. NuRD comprises catalytically active sub-modules in both the cytosol and the nucleus.
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Affiliation(s)
- W Zhang
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - A Aubert
- EMBL Grenoble, 71 avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - J M Gomez de Segura
- EMBL Grenoble, 71 avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - M Karuppasamy
- EMBL Grenoble, 71 avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - S Basu
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - A S Murthy
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - A Diamante
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - T A Drury
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - J Balmer
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - J Cramard
- Wellcome Trust, Medical Research Council Stem Cell Institute, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QR, United Kingdom
| | - A A Watson
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - D Lando
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - S F Lee
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - M Palayret
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - S L Kloet
- Department of Molecular Biology, Radboud Institute of Molecular Life Sciences, M850/3.79 Geert Grooteplein Zuid 30, 6525 GA Nijmegen, the Netherlands
| | - A H Smits
- Department of Molecular Biology, Radboud Institute of Molecular Life Sciences, M850/3.79 Geert Grooteplein Zuid 30, 6525 GA Nijmegen, the Netherlands
| | - M J Deery
- Cambridge Centre for Proteomics, Cambridge System Biology Centre, Wellcome Trust Stem Cell building, University of Cambridge, Department of Biochemistry, Tennis Court Road, Cambridge CB2 1QR, United Kingdom
| | - M Vermeulen
- Department of Molecular Biology, Radboud Institute of Molecular Life Sciences, M850/3.79 Geert Grooteplein Zuid 30, 6525 GA Nijmegen, the Netherlands
| | - B Hendrich
- Wellcome Trust, Medical Research Council Stem Cell Institute, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QR, United Kingdom
| | - D Klenerman
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - C Schaffitzel
- EMBL Grenoble, 71 avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France; The School of Biochemistry, University of Bristol, University Walk, Clifton BS8 1TD, United Kingdom
| | - I Berger
- EMBL Grenoble, 71 avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France; The School of Biochemistry, University of Bristol, University Walk, Clifton BS8 1TD, United Kingdom
| | - E D Laue
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
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