The Nucleosome Remodeling and Deacetylase Complex NuRD Is Built from Preformed Catalytically Active Sub-modules.
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.
Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom.
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Zhang
EMBL Grenoble, 71 avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France.
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Aubert
EMBL Grenoble, 71 avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France.
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Gomez de Segura
EMBL Grenoble, 71 avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France.
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Karuppasamy
Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom.
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Basu
Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom.
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Murthy
Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom.
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Diamante
Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom.
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Drury
Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom.
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Balmer
Wellcome Trust, Medical Research Council Stem Cell Institute, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QR, United Kingdom.
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Cramard
Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom.
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Watson
Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom.
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Lando
Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom.
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Lee
Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom.
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Palayret
Department of Molecular Biology, Radboud Institute of Molecular Life Sciences, M850/3.79 Geert Grooteplein Zuid 30, 6525 GA Nijmegen, the Netherlands.
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Kloet
Department of Molecular Biology, Radboud Institute of Molecular Life Sciences, M850/3.79 Geert Grooteplein Zuid 30, 6525 GA Nijmegen, the Netherlands.
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Smits
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.
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Deery
Department of Molecular Biology, Radboud Institute of Molecular Life Sciences, M850/3.79 Geert Grooteplein Zuid 30, 6525 GA Nijmegen, the Netherlands.
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Vermeulen
Wellcome Trust, Medical Research Council Stem Cell Institute, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QR, United Kingdom.
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Hendrich
Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom.
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Klenerman
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.
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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.
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Berger
Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom.
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Laue
D000818:Animals; D002467:Cell Nucleus / Q000378:metabolism; D002843:Chromatin / Q000378:metabolism; D042002:Chromatin Assembly and Disassembly / Q000502:physiology; D003600:Cytosol / Q000378:metabolism; D004330:Drosophila / Q000378:metabolism; D006655:Histone Deacetylases / Q000378:metabolism*; D056245:Mi-2 Nucleosome Remodeling and Deacetylase Complex / Q000378:metabolism*; D051379:Mice; D009707:Nucleosomes / Q000378:metabolism*; D021122:Protein Subunits / Q000378:metabolism; D013234:Stem Cells / Q000378:metabolism
D002843:Chromatin; D009707:Nucleosomes; D021122:Protein Subunits; D006655:Histone Deacetylases; D056245:Mi-2 Nucleosome Remodeling and Deacetylase Complex
chromatin-remodeling; complex assembly; histone modification; nucleosome remodeling and deacetylase NuRD; transcription