151
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Bode D, Yu L, Tate P, Pardo M, Choudhary J. Characterization of Two Distinct Nucleosome Remodeling and Deacetylase (NuRD) Complex Assemblies in Embryonic Stem Cells. Mol Cell Proteomics 2015; 15:878-91. [PMID: 26714524 PMCID: PMC4813707 DOI: 10.1074/mcp.m115.053207] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Indexed: 11/26/2022] Open
Abstract
Pluripotency and self-renewal, the defining properties of embryonic stem cells, are brought about by transcriptional programs involving an intricate network of transcription factors and chromatin remodeling complexes. The Nucleosome Remodeling and Deacetylase (NuRD) complex plays a crucial and dynamic role in the regulation of stemness and differentiation. Several NuRD-associated factors have been reported but how they are organized has not been investigated in detail. Here, we have combined affinity purification and blue native polyacrylamide gel electrophoresis followed by protein identification by mass spectrometry and protein correlation profiling to characterize the topology of the NuRD complex. Our data show that in mouse embryonic stem cells the NuRD complex is present as two distinct assemblies of differing topology with different binding partners. Cell cycle regulator Cdk2ap1 and transcription factor Sall4 associate only with the higher mass NuRD assembly. We further establish that only isoform Sall4a, and not Sall4b, associates with NuRD. By contrast, Suz12, a component of the PRC2 Polycomb repressor complex, associates with the lower mass entity. In addition, we identify and validate a novel NuRD-associated protein, Wdr5, a regulatory subunit of the MLL histone methyltransferase complex, which associates with both NuRD entities. Bioinformatic analyses of published target gene sets of these chromatin binding proteins are in agreement with these structural observations. In summary, this study provides an interesting insight into mechanistic aspects of NuRD function in stem cell biology. The relevance of our work has broader implications because of the ubiquitous nature of the NuRD complex. The strategy described here can be more broadly applicable to investigate the topology of the multiple complexes an individual protein can participate in.
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Affiliation(s)
- Daniel Bode
- From the ‡Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Lu Yu
- From the ‡Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Peri Tate
- §Stem Cell Engineering, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Mercedes Pardo
- From the ‡Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK;
| | - Jyoti Choudhary
- From the ‡Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
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152
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Aranda S, Mas G, Di Croce L. Regulation of gene transcription by Polycomb proteins. SCIENCE ADVANCES 2015; 1:e1500737. [PMID: 26665172 PMCID: PMC4672759 DOI: 10.1126/sciadv.1500737] [Citation(s) in RCA: 237] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Accepted: 09/17/2015] [Indexed: 05/14/2023]
Abstract
The Polycomb group (PcG) of proteins defines a subset of factors that physically associate and function to maintain the positional identity of cells from the embryo to adult stages. PcG has long been considered a paradigmatic model for epigenetic maintenance of gene transcription programs. Despite intensive research efforts to unveil the molecular mechanisms of action of PcG proteins, several fundamental questions remain unresolved: How many different PcG complexes exist in mammalian cells? How are PcG complexes targeted to specific loci? How does PcG regulate transcription? In this review, we discuss the diversity of PcG complexes in mammalian cells, examine newly identified modes of recruitment to chromatin, and highlight the latest insights into the molecular mechanisms underlying the function of PcGs in transcription regulation and three-dimensional chromatin conformation.
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Affiliation(s)
- Sergi Aranda
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain
| | - Gloria Mas
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain
| | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain
- Institucio Catalana de Recerca i Estudis Avançats, Pg Lluis Companys 23, Barcelona 08010, Spain
- Corresponding author. E-mail:
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153
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Campos EI, Smits AH, Kang YH, Landry S, Escobar TM, Nayak S, Ueberheide BM, Durocher D, Vermeulen M, Hurwitz J, Reinberg D. Analysis of the Histone H3.1 Interactome: A Suitable Chaperone for the Right Event. Mol Cell 2015; 60:697-709. [PMID: 26527279 DOI: 10.1016/j.molcel.2015.08.005] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 06/17/2015] [Accepted: 08/07/2015] [Indexed: 11/17/2022]
Abstract
Despite minimal disparity at the sequence level, mammalian H3 variants bind to distinct sets of polypeptides. Although histone H3.1 predominates in cycling cells, our knowledge of the soluble complexes that it forms en route to deposition or following eviction from chromatin remains limited. Here, we provide a comprehensive analysis of the H3.1-binding proteome, with emphasis on its interactions with histone chaperones and components of the replication fork. Quantitative mass spectrometry revealed 170 protein interactions, whereas a large-scale biochemical fractionation of H3.1 and associated enzymatic activities uncovered over twenty stable protein complexes in dividing human cells. The sNASP and ASF1 chaperones play pivotal roles in the processing of soluble histones but do not associate with the active CDC45/MCM2-7/GINS (CMG) replicative helicase. We also find TONSL-MMS22L to function as a H3-H4 histone chaperone. It associates with the regulatory MCM5 subunit of the replicative helicase.
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Affiliation(s)
- Eric I Campos
- Howard Hughes Medical Institute, New York University School of Medicine, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, NY 10016, USA
| | - Arne H Smits
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands 6525 GA
| | - Young-Hoon Kang
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, NY 10021, USA
| | - Sébastien Landry
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, and Department of Molecular Genetics, University of Toronto, Toronto M5G 1X5, Canada
| | - Thelma M Escobar
- Howard Hughes Medical Institute, New York University School of Medicine, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, NY 10016, USA
| | - Shruti Nayak
- Office of Collaborative Science, New York University School of Medicine, NY 10016, USA
| | - Beatrix M Ueberheide
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, NY 10016, USA
| | - Daniel Durocher
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, and Department of Molecular Genetics, University of Toronto, Toronto M5G 1X5, Canada
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands 6525 GA
| | - Jerard Hurwitz
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, NY 10021, USA
| | - Danny Reinberg
- Howard Hughes Medical Institute, New York University School of Medicine, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, NY 10016, USA.
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154
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Brien GL, Healy E, Jerman E, Conway E, Fadda E, O'Donovan D, Krivtsov AV, Rice AM, Kearney CJ, Flaus A, McDade SS, Martin SJ, McLysaght A, O'Connell DJ, Armstrong SA, Bracken AP. A chromatin-independent role of Polycomb-like 1 to stabilize p53 and promote cellular quiescence. Genes Dev 2015; 29:2231-43. [PMID: 26494712 PMCID: PMC4647557 DOI: 10.1101/gad.267930.115] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 10/02/2015] [Indexed: 12/05/2022]
Abstract
Brien et al. show that while Polycomb-like proteins PCL2 and PCL3 are E2F-regulated genes expressed in proliferating cells, PCL1 is a p53 target gene predominantly expressed in quiescent cells. PCL1 binds to and stabilizes p53 to block cellular proliferation, and depletion of PCL1 phenocopies the defects in maintaining cellular quiescence associated with p53 loss. Polycomb-like proteins 1–3 (PCL1–3) are substoichiometric components of the Polycomb-repressive complex 2 (PRC2) that are essential for association of the complex with chromatin. However, it remains unclear why three proteins with such apparent functional redundancy exist in mammals. Here we characterize their divergent roles in both positively and negatively regulating cellular proliferation. We show that while PCL2 and PCL3 are E2F-regulated genes expressed in proliferating cells, PCL1 is a p53 target gene predominantly expressed in quiescent cells. Ectopic expression of any PCL protein recruits PRC2 to repress the INK4A gene; however, only PCL2 and PCL3 confer an INK4A-dependent proliferative advantage. Remarkably, PCL1 has evolved a PRC2- and chromatin-independent function to negatively regulate proliferation. We show that PCL1 binds to and stabilizes p53 to induce cellular quiescence. Moreover, depletion of PCL1 phenocopies the defects in maintaining cellular quiescence associated with p53 loss. This newly evolved function is achieved by the binding of the PCL1 N-terminal PHD domain to the C-terminal domain of p53 through two unique serine residues, which were acquired during recent vertebrate evolution. This study illustrates the functional bifurcation of PCL proteins, which act in both a chromatin-dependent and a chromatin-independent manner to regulate the INK4A and p53 pathways.
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Affiliation(s)
- Gerard L Brien
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Evan Healy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Emilia Jerman
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Eric Conway
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Elisa Fadda
- Department of Chemistry, National University of Ireland, Maynooth, Ireland
| | | | - Andrei V Krivtsov
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Alan M Rice
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Conor J Kearney
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Andrew Flaus
- Centre for Chromosome Biology, School of Life Sciences, National University of Ireland Galway, Galway, Ireland
| | - Simon S McDade
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast BT9 7BL, United Kingdom
| | - Seamus J Martin
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Aoife McLysaght
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | | | - Scott A Armstrong
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Adrian P Bracken
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
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155
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Hein MY, Hubner NC, Poser I, Cox J, Nagaraj N, Toyoda Y, Gak IA, Weisswange I, Mansfeld J, Buchholz F, Hyman AA, Mann M. A human interactome in three quantitative dimensions organized by stoichiometries and abundances. Cell 2015; 163:712-23. [PMID: 26496610 DOI: 10.1016/j.cell.2015.09.053] [Citation(s) in RCA: 889] [Impact Index Per Article: 98.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 07/06/2015] [Accepted: 09/17/2015] [Indexed: 02/06/2023]
Abstract
The organization of a cell emerges from the interactions in protein networks. The interactome is critically dependent on the strengths of interactions and the cellular abundances of the connected proteins, both of which span orders of magnitude. However, these aspects have not yet been analyzed globally. Here, we have generated a library of HeLa cell lines expressing 1,125 GFP-tagged proteins under near-endogenous control, which we used as input for a next-generation interaction survey. Using quantitative proteomics, we detect specific interactions, estimate interaction stoichiometries, and measure cellular abundances of interacting proteins. These three quantitative dimensions reveal that the protein network is dominated by weak, substoichiometric interactions that play a pivotal role in defining network topology. The minority of stable complexes can be identified by their unique stoichiometry signature. This study provides a rich interaction dataset connecting thousands of proteins and introduces a framework for quantitative network analysis.
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Affiliation(s)
- Marco Y Hein
- Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Nina C Hubner
- Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Ina Poser
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Jürgen Cox
- Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | | | - Yusuke Toyoda
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Igor A Gak
- Cell Cycle, Biotechnology Center, TU Dresden, 01307 Dresden, Germany
| | - Ina Weisswange
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; Eupheria Biotech GmbH, 01307 Dresden, Germany
| | - Jörg Mansfeld
- Cell Cycle, Biotechnology Center, TU Dresden, 01307 Dresden, Germany
| | - Frank Buchholz
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany; Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany
| | - Anthony A Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.
| | - Matthias Mann
- Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.
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156
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Pervasive lncRNA binding by epigenetic modifying complexes--The challenges ahead. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:93-101. [PMID: 26463275 DOI: 10.1016/j.bbagrm.2015.10.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 10/01/2015] [Accepted: 10/08/2015] [Indexed: 02/08/2023]
Abstract
Epigenetic modifying factors are fundamental regulators of chromatin structure and gene expression during development and differentiation through the induction of chemical modifications on histones, DNA or via remodeling of the chromatin structure. Protein complexes involved in these three processes contain non-canonical RNA-binding components that interact with long non-coding RNAs, in many cases in the absence of any sequence or structural signatures. However, there is growing evidence of the role of such protein-lncRNA interactions in the regulation of the epigenetic landscape in vivo. This review summarizes the growing number of epigenetic modifying factors described to interact with lncRNAs in mouse and human, and then discusses the challenges that lay ahead in understanding lncRNAs as part of the intricate networks of epigenetic regulation. A combination of protein and RNA-centric approaches is required for this purpose. This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa.
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157
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Masson A, Kamrath MZ, Perez MAS, Glover MS, Rothlisberger U, Clemmer DE, Rizzo TR. Infrared Spectroscopy of Mobility-Selected H+-Gly-Pro-Gly-Gly (GPGG). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1444-54. [PMID: 26091889 DOI: 10.1007/s13361-015-1172-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 04/16/2015] [Accepted: 04/18/2015] [Indexed: 05/14/2023]
Abstract
We report the first results from a new instrument capable of acquiring infrared spectra of mobility-selected ions. This demonstration involves using ion mobility to first separate the protonated peptide Gly-Pro-Gly-Gly (GPGG) into two conformational families with collisional cross-sections of 93.8 and 96.8 Å(2). After separation, each family is independently analyzed by acquiring the infrared predissociation spectrum of the H(2)-tagged molecules. The ion mobility and spectroscopic data combined with density functional theory (DFT) based molecular dynamics simulations confirm the presence of one major conformer per family, which arises from cis/trans isomerization about the proline residue. We induce isomerization between the two conformers by using collisional activation in the drift tube and monitor the evolution of the ion distribution with ion mobility and infrared spectroscopy. While the cis-proline species is the preferred gas-phase structure, its relative population is smaller than that of the trans-proline species in the initial ion mobility drift distribution. This suggests that a portion of the trans-proline ion population is kinetically trapped as a higher energy conformer and may retain structural elements from solution.
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Affiliation(s)
- Antoine Masson
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015, Lausanne, Switzerland
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158
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Meyer K, Selbach M. Quantitative affinity purification mass spectrometry: a versatile technology to study protein-protein interactions. Front Genet 2015; 6:237. [PMID: 26236332 PMCID: PMC4500955 DOI: 10.3389/fgene.2015.00237] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 06/25/2015] [Indexed: 01/11/2023] Open
Abstract
While the genomic revolution has dramatically accelerated the discovery of disease-associated genes, the functional characterization of the corresponding proteins lags behind. Most proteins fulfill their tasks in complexes with other proteins, and analysis of protein–protein interactions (PPIs) can therefore provide insights into protein function. Several methods can be used to generate large-scale protein interaction networks. However, most of these approaches are not quantitative and therefore cannot reveal how perturbations affect the network. Here, we illustrate how a clever combination of quantitative mass spectrometry with different biochemical methods provides a rich toolkit to study different aspects of PPIs including topology, subunit stoichiometry, and dynamic behavior.
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Affiliation(s)
- Katrina Meyer
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine , Berlin, Germany
| | - Matthias Selbach
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine , Berlin, Germany
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159
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Burg JM, Link JE, Morgan BS, Heller FJ, Hargrove AE, McCafferty DG. KDM1 class flavin-dependent protein lysine demethylases. Biopolymers 2015; 104:213-46. [PMID: 25787087 PMCID: PMC4747437 DOI: 10.1002/bip.22643] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 03/02/2015] [Accepted: 03/07/2015] [Indexed: 12/11/2022]
Abstract
Flavin-dependent, lysine-specific protein demethylases (KDM1s) are a subfamily of amine oxidases that catalyze the selective posttranslational oxidative demethylation of methyllysine side chains within protein and peptide substrates. KDM1s participate in the widespread epigenetic regulation of both normal and disease state transcriptional programs. Their activities are central to various cellular functions, such as hematopoietic and neuronal differentiation, cancer proliferation and metastasis, and viral lytic replication and establishment of latency. Interestingly, KDM1s function as catalytic subunits within complexes with coregulatory molecules that modulate enzymatic activity of the demethylases and coordinate their access to specific substrates at distinct sites within the cell and chromatin. Although several classes of KDM1-selective small molecule inhibitors have been recently developed, these pan-active site inhibition strategies lack the ability to selectively discriminate between KDM1 activity in specific, and occasionally opposing, functional contexts within these complexes. Here we review the discovery of this class of demethylases, their structures, chemical mechanisms, and specificity. Additionally, we review inhibition of this class of enzymes as well as emerging interactions with coregulatory molecules that regulate demethylase activity in highly specific functional contexts of biological and potential therapeutic importance.
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160
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Torchy MP, Hamiche A, Klaholz BP. Structure and function insights into the NuRD chromatin remodeling complex. Cell Mol Life Sci 2015; 72:2491-507. [PMID: 25796366 PMCID: PMC11114056 DOI: 10.1007/s00018-015-1880-8] [Citation(s) in RCA: 139] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 03/02/2015] [Accepted: 03/04/2015] [Indexed: 01/09/2023]
Abstract
Transcription regulation through chromatin compaction and decompaction is regulated through various chromatin-remodeling complexes such as nucleosome remodeling and histone deacetylation (NuRD) complex. NuRD is a 1 MDa multi-subunit protein complex which comprises many different subunits, among which histone deacetylases HDAC1/2, ATP-dependent remodeling enzymes CHD3/4, histone chaperones RbAp46/48, CpG-binding proteins MBD2/3, the GATAD2a (p66α) and/or GATAD2b (p66β) and specific DNA-binding proteins MTA1/2/3. Here, we review the currently known crystal and NMR structures of these subunits, the functional data and their relevance for biomedical research considering the implication of NuRD subunits in cancer and various other diseases. The complexity of this macromolecular assembly, and its poorly understood mode of interaction with the nucleosome, the repeating unit of chromatin, illustrate that this complex is a major challenge for structure-function relationship studies which will be tackled best by an integrated biology approach.
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Affiliation(s)
- Morgan P. Torchy
- Department of Integrated Structural Biology, Centre for Integrative Biology (CBI), Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, Illkirch, France
- Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Ali Hamiche
- Department of Integrated Structural Biology, Centre for Integrative Biology (CBI), Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, Illkirch, France
- Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Bruno P. Klaholz
- Department of Integrated Structural Biology, Centre for Integrative Biology (CBI), Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, Illkirch, France
- Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France
- Université de Strasbourg, Strasbourg, France
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161
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van Kruijsbergen I, Hontelez S, Veenstra GJC. Recruiting polycomb to chromatin. Int J Biochem Cell Biol 2015; 67:177-87. [PMID: 25982201 DOI: 10.1016/j.biocel.2015.05.006] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 05/04/2015] [Accepted: 05/05/2015] [Indexed: 10/23/2022]
Abstract
Polycomb group (PcG) proteins are key regulators in establishing a transcriptional repressive state. Polycomb Repressive Complex 2 (PRC2), one of the two major PcG protein complexes, is essential for proper differentiation and maintenance of cellular identity. Multiple factors are involved in recruiting PRC2 to its genomic targets. In this review, we will discuss the role of DNA sequence, transcription factors, pre-existing histone modifications, and RNA in guiding PRC2 towards specific genomic loci. The DNA sequence itself influences the DNA methylation state, which is an important determinant of PRC2 recruitment. Other histone modifications are also important for PRC2 binding as PRC2 can respond to different cellular states via crosstalk between histone modifications. Additionally, PRC2 might be able to sense the transcriptional status of genes by binding to nascent RNA, which could also guide the complex to chromatin. In this review, we will discuss how all these molecular aspects define a local chromatin state which controls accurate, cell-type-specific epigenetic silencing by PRC2. This article is part of a Directed Issue entitled: Epigenetics dynamics in development and disease.
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Affiliation(s)
- Ila van Kruijsbergen
- Radboud University Nijmegen, Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Nijmegen 6500 HB, The Netherlands
| | - Saartje Hontelez
- Radboud University Nijmegen, Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Nijmegen 6500 HB, The Netherlands
| | - Gert Jan C Veenstra
- Radboud University Nijmegen, Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Nijmegen 6500 HB, The Netherlands.
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162
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Knock E, Pereira J, Lombard PD, Dimond A, Leaford D, Livesey FJ, Hendrich B. The methyl binding domain 3/nucleosome remodelling and deacetylase complex regulates neural cell fate determination and terminal differentiation in the cerebral cortex. Neural Dev 2015; 10:13. [PMID: 25934499 PMCID: PMC4432814 DOI: 10.1186/s13064-015-0040-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 04/17/2015] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Chromatin-modifying complexes have key roles in regulating various aspects of neural stem cell biology, including self-renewal and neurogenesis. The methyl binding domain 3/nucleosome remodelling and deacetylation (MBD3/NuRD) co-repressor complex facilitates lineage commitment of pluripotent cells in early mouse embryos and is important for stem cell homeostasis in blood and skin, but its function in neurogenesis had not been described. Here, we show for the first time that MBD3/NuRD function is essential for normal neurogenesis in mice. RESULTS Deletion of MBD3, a structural component of the NuRD complex, in the developing mouse central nervous system resulted in reduced cortical thickness, defects in the proper specification of cortical projection neuron subtypes and neonatal lethality. These phenotypes are due to alterations in PAX6+ apical progenitor cell outputs, as well as aberrant terminal neuronal differentiation programmes of cortical plate neurons. Normal numbers of PAX6+ apical neural progenitor cells were generated in the MBD3/NuRD-mutant cortex; however, the PAX6+ apical progenitor cells generate EOMES+ basal progenitor cells in reduced numbers. Cortical progenitor cells lacking MBD3/NuRD activity generate neurons that express both deep- and upper-layer markers. Using laser capture microdissection, gene expression profiling and chromatin immunoprecipitation, we provide evidence that MBD3/NuRD functions to control gene expression patterns during neural development. CONCLUSIONS Our data suggest that although MBD3/NuRD is not required for neural stem cell lineage commitment, it is required to repress inappropriate transcription in both progenitor cells and neurons to facilitate appropriate cell lineage choice and differentiation programmes.
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Affiliation(s)
- Erin Knock
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, CB2 1QR, UK.
- Tanz Centre for Research in Neurodegenerative Diseases, Krembil Discovery Tower, 6KD-404, 60 Leonard Avenue, Toronto, ON, Canada.
| | - João Pereira
- Gurdon Institute, University of Cambridge, Cambridge, CB2 1QW, UK.
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QN, UK.
| | - Patrick D Lombard
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, CB2 1QR, UK.
| | - Andrew Dimond
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QN, UK.
| | - Donna Leaford
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, CB2 1QR, UK.
| | - Frederick J Livesey
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, CB2 1QR, UK.
- Gurdon Institute, University of Cambridge, Cambridge, CB2 1QW, UK.
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QN, UK.
| | - Brian Hendrich
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, CB2 1QR, UK.
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QN, UK.
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163
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Liefke R, Shi Y. The PRC2-associated factor C17orf96 is a novel CpG island regulator in mouse ES cells. Cell Discov 2015; 1:15008. [PMID: 27462409 PMCID: PMC4860827 DOI: 10.1038/celldisc.2015.8] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 02/14/2015] [Indexed: 12/12/2022] Open
Abstract
CpG islands (CGIs) are key DNA regulatory elements in the vertebrate genome and are often found at gene promoters. In mammalian embryonic stem (ES) cells, CGIs are decorated by either the active or repressive histone marks, H3K4me3 and H3K27me3, respectively, or by both modifications ('bivalent domains'), but their precise regulation is incompletely understood. Remarkably, we find that the polycomb repressive complex 2 (PRC2)-associated protein C17orf96 (a.k.a. esPRC2p48 and E130012A19Rik) is present at most CGIs in mouse ES cells. At PRC2-rich CGIs, loss of C17orf96 results in an increased chromatin binding of Suz12 and elevated H3K27me3 levels concomitant with gene repression. In contrast, at PRC2-poor CGIs, located at actively transcribed genes, C17orf96 colocalizes with RNA polymerase II and its depletion leads to a focusing of H3K4me3 in the core of CGIs. Our findings thus identify C17orf96 as a novel context-dependent CGI regulator.
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Affiliation(s)
- Robert Liefke
- Division of Newborn Medicine and Program in Epigenetics, Department of Medicine, Boston Children's Hospital, Boston, MA, USA; Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Yang Shi
- Division of Newborn Medicine and Program in Epigenetics, Department of Medicine, Boston Children's Hospital, Boston, MA, USA; Department of Cell Biology, Harvard Medical School, Boston, MA, USA
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164
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Desai MA, Webb HD, Sinanan LM, Scarsdale JN, Walavalkar NM, Ginder GD, Williams DC. An intrinsically disordered region of methyl-CpG binding domain protein 2 (MBD2) recruits the histone deacetylase core of the NuRD complex. Nucleic Acids Res 2015; 43:3100-13. [PMID: 25753662 PMCID: PMC4381075 DOI: 10.1093/nar/gkv168] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 02/13/2015] [Accepted: 02/20/2015] [Indexed: 12/20/2022] Open
Abstract
The MBD2-NuRD (Nucleosome Remodeling and Deacetylase) complex is an epigenetic reader of DNA methylation that regulates genes involved in normal development and neoplastic diseases. To delineate the architecture and functional interactions of the MBD2-NuRD complex, we previously solved the structures of MBD2 bound to methylated DNA and a coiled-coil interaction between MBD2 and p66α that recruits the CHD4 nucleosome remodeling protein to the complex. The work presented here identifies novel structural and functional features of a previously uncharacterized domain of MBD2 (MBD2IDR). Biophysical analyses show that the MBD2IDR is an intrinsically disordered region (IDR). However, despite this inherent disorder, MBD2IDR increases the overall binding affinity of MBD2 for methylated DNA. MBD2IDR also recruits the histone deacetylase core components (RbAp48, HDAC2 and MTA2) of NuRD through a critical contact region requiring two contiguous amino acid residues, Arg(286) and Leu(287). Mutating these residues abrogates interaction of MBD2 with the histone deacetylase core and impairs the ability of MBD2 to repress the methylated tumor suppressor gene PRSS8 in MDA-MB-435 breast cancer cells. These findings expand our knowledge of the multi-dimensional interactions of the MBD2-NuRD complex that govern its function.
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Affiliation(s)
- Megha A Desai
- Department of Human and Molecular Genetics and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Heather D Webb
- Department of Pathology and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Leander M Sinanan
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - J Neel Scarsdale
- Institute of Structural Biology and Drug Design, Center for the Study of Biological Complexity, and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Ninad M Walavalkar
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Gordon D Ginder
- Departments of Internal Medicine, Human and Molecular Genetics, and Microbiology and Immunology and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - David C Williams
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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165
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Extracting high confidence protein interactions from affinity purification data: at the crossroads. J Proteomics 2015; 118:63-80. [PMID: 25782749 DOI: 10.1016/j.jprot.2015.03.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 02/27/2015] [Accepted: 03/09/2015] [Indexed: 02/06/2023]
Abstract
UNLABELLED Deriving protein-protein interactions from data generated by affinity-purification and mass spectrometry (AP-MS) techniques requires application of scoring methods to measure the reliability of detected putative interactions. Choosing the appropriate scoring method has become a major challenge. Here we apply six popular scoring methods to the same AP-MS dataset and compare their performance. The comparison was carried out for six distinct datasets from human, fly and yeast, which focus on different biological processes and differ in their coverage of the proteome. Results show that the performance of a given scoring method may vary substantially depending on the dataset. Disturbingly, we find that the high confidence (HC) PPI networks built by applying the six scoring methods to the same raw AP-MS dataset display very poor overlap, with only 1.7-4.1% of the HC interactions present in all the networks built, respectively, from the proteome-wide human, fly or yeast datasets. Various properties of the shared versus unique interactions in each network, including biases in protein abundance, suggest that current scoring methods are able to eliminate only the most obvious contaminants, but still fail to reliably single out specific interactions from the large body of spurious associations detected in the AP-MS experiments. BIOLOGICAL SIGNIFICANCE The fast progress in AP-MS techniques has prompted the development of a multitude of scoring methods, which are relied upon to remove contaminants and non-specific binders. Choosing the appropriate scoring scheme for a given AP-MS dataset has become a major challenge. The comparative analysis of 6 of the most popular scoring methods, presented here, reveals that overall these methods do not perform as expected. Evidence is provided that this is due to 3 closely related issues: the high 'noise' levels of the raw AP-MS data, the limited capacity of current scoring methods to deal with such high noise levels, and the biases introduced using Gold Standard datasets to benchmark the scoring functions and threshold the networks. For the field to move forward, all three issues will have to be addressed. This article is part of a Special Issue entitled: Protein dynamics in health and disease. Guest Editors: Pierre Thibault and Anne-Claude Gingras.
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166
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Maier VK, Feeney CM, Taylor JE, Creech AL, Qiao JW, Szanto A, Das PP, Chevrier N, Cifuentes-Rojas C, Orkin SH, Carr SA, Jaffe JD, Mertins P, Lee JT. Functional Proteomic Analysis of Repressive Histone Methyltransferase Complexes Reveals ZNF518B as a G9A Regulator. Mol Cell Proteomics 2015; 14:1435-46. [PMID: 25680957 DOI: 10.1074/mcp.m114.044586] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Indexed: 01/17/2023] Open
Abstract
Cell-type specific gene silencing by histone H3 lysine 27 and lysine 9 methyltransferase complexes PRC2 and G9A-GLP is crucial both during development and to maintain cell identity. Although studying their interaction partners has yielded valuable insight into their functions, how these factors are regulated on a network level remains incompletely understood. Here, we present a new approach that combines quantitative interaction proteomics with global chromatin profiling to functionally characterize repressive chromatin modifying protein complexes in embryonic stem cells. We define binding stoichiometries of 9 new and 12 known interaction partners of PRC2 and 10 known and 29 new interaction partners of G9A-GLP, respectively. We demonstrate that PRC2 and G9A-GLP interact physically and share several interaction partners, including the zinc finger proteins ZNF518A and ZNF518B. Using global chromatin profiling by targeted mass spectrometry, we discover that even sub-stoichiometric binding partners such as ZNF518B can positively regulate global H3K9me2 levels. Biochemical analysis reveals that ZNF518B directly interacts with EZH2 and G9A. Our systematic analysis suggests that ZNF518B may mediate the structural association between PRC2 and G9A-GLP histone methyltransferases and additionally regulates the activity of G9A-GLP.
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Affiliation(s)
- Verena K Maier
- From the ‡Department of Molecular Biology, Massachusetts General Hospital, Department of Genetics, Harvard Medical School, 185 Cambridge Street, Boston, Massachusetts 02143
| | - Caitlin M Feeney
- §Proteomics Platform, The Broad Institute, 7 Cambridge Center, Cambridge, Massachusetts 02142
| | - Jordan E Taylor
- §Proteomics Platform, The Broad Institute, 7 Cambridge Center, Cambridge, Massachusetts 02142
| | - Amanda L Creech
- §Proteomics Platform, The Broad Institute, 7 Cambridge Center, Cambridge, Massachusetts 02142
| | - Jana W Qiao
- §Proteomics Platform, The Broad Institute, 7 Cambridge Center, Cambridge, Massachusetts 02142
| | - Attila Szanto
- From the ‡Department of Molecular Biology, Massachusetts General Hospital, Department of Genetics, Harvard Medical School, 185 Cambridge Street, Boston, Massachusetts 02143
| | - Partha P Das
- ¶Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts, 02115
| | - Nicholas Chevrier
- ‖FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Catherine Cifuentes-Rojas
- From the ‡Department of Molecular Biology, Massachusetts General Hospital, Department of Genetics, Harvard Medical School, 185 Cambridge Street, Boston, Massachusetts 02143
| | - Stuart H Orkin
- ¶Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts, 02115
| | - Steven A Carr
- §Proteomics Platform, The Broad Institute, 7 Cambridge Center, Cambridge, Massachusetts 02142
| | - Jacob D Jaffe
- §Proteomics Platform, The Broad Institute, 7 Cambridge Center, Cambridge, Massachusetts 02142
| | - Philipp Mertins
- §Proteomics Platform, The Broad Institute, 7 Cambridge Center, Cambridge, Massachusetts 02142;
| | - Jeannie T Lee
- From the ‡Department of Molecular Biology, Massachusetts General Hospital, Department of Genetics, Harvard Medical School, 185 Cambridge Street, Boston, Massachusetts 02143
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167
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Wohlgemuth I, Lenz C, Urlaub H. Studying macromolecular complex stoichiometries by peptide-based mass spectrometry. Proteomics 2015; 15:862-79. [PMID: 25546807 PMCID: PMC5024058 DOI: 10.1002/pmic.201400466] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 11/24/2014] [Accepted: 12/22/2014] [Indexed: 11/11/2022]
Abstract
A majority of cellular functions are carried out by macromolecular complexes. A host of biochemical and spectroscopic methods exists to characterize especially protein/protein complexes, however there has been a lack of a universal method to determine protein stoichiometries. Peptide‐based MS, especially as a complementary method to the MS analysis of intact protein complexes, has now been developed to a point where it can be employed to assay protein stoichiometries in a routine manner. While the experimental demands are still significant, peptide‐based MS has been successfully applied to analyze stoichiometries for a variety of protein complexes from very different biological backgrounds. In this review, we discuss the requirements especially for targeted MS acquisition strategies to be used in this context, with a special focus on the interconnected experimental aspects of sample preparation, protein digestion, and peptide stability. In addition, different strategies for the introduction of quantitative peptide standards and their suitability for different scenarios are compared.
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Affiliation(s)
- Ingo Wohlgemuth
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Goettingen, Germany
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168
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Basta J, Rauchman M. The nucleosome remodeling and deacetylase complex in development and disease. Transl Res 2015; 165:36-47. [PMID: 24880148 PMCID: PMC4793962 DOI: 10.1016/j.trsl.2014.05.003] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 05/02/2014] [Accepted: 05/05/2014] [Indexed: 02/07/2023]
Abstract
The nucleosome remodeling and deacetylase (NuRD) complex is one of the major chromatin remodeling complexes found in cells. It plays an important role in regulating gene transcription, genome integrity, and cell cycle progression. Through its impact on these basic cellular processes, increasing evidence indicates that alterations in the activity of this macromolecular complex can lead to developmental defects, oncogenesis, and accelerated aging. Recent genetic and biochemical studies have elucidated the mechanisms of NuRD action in modifying the chromatin landscape. These advances have the potential to lead to new therapeutic approaches to birth defects and cancer.
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Affiliation(s)
- Jeannine Basta
- Department of Internal Medicine, Saint Louis University, St. Louis, Missouri; Department of Biochemistry and Molecular Biology, Saint Louis University, St. Louis, Missouri; John Cochran Division, VA St. Louis Health Care System, St. Louis, Missouri
| | - Michael Rauchman
- Department of Internal Medicine, Saint Louis University, St. Louis, Missouri; Department of Biochemistry and Molecular Biology, Saint Louis University, St. Louis, Missouri; John Cochran Division, VA St. Louis Health Care System, St. Louis, Missouri.
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169
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Vizán P, Beringer M, Ballaré C, Di Croce L. Role of PRC2-associated factors in stem cells and disease. FEBS J 2014; 282:1723-35. [PMID: 25271128 DOI: 10.1111/febs.13083] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 09/19/2014] [Accepted: 09/26/2014] [Indexed: 01/01/2023]
Abstract
The Polycomb group (PcG) of proteins form chromatin-binding complexes with histone-modifying activity. The two main PcG repressive complexes studied (PRC1 and PRC2) are generally associated with chromatin in its repressed state. PRC2 is responsible for methylation of histone H3 at lysine 27 (H3K27me3), an epigenetic mark that is linked with numerous biological processes, including development, adult homeostasis and cancer. The core canonical complex PRC2, which contains the EZH1/2, SUZ12 and EED proteins, may be extended and functionally manipulated through interactions with several other proteins. In this review, we focus on these PRC2-associated proteins. As PRC2 functions are diverse, the variability conferred by these sub-stoichiometrically associated members may help to understand specific changes in PRC2 activity, chromatin recruitment and distribution required for gene repression.
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Affiliation(s)
- Pedro Vizán
- Centre for Genomic Regulation, Barcelona, Spain; Universitat Pompeu Fabra, Barcelona, Spain
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170
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Kloet SL, Baymaz HI, Makowski M, Groenewold V, Jansen PWTC, Berendsen M, Niazi H, Kops GJ, Vermeulen M. Towards elucidating the stability, dynamics and architecture of the nucleosome remodeling and deacetylase complex by using quantitative interaction proteomics. FEBS J 2014; 282:1774-85. [PMID: 25123934 DOI: 10.1111/febs.12972] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 08/07/2014] [Accepted: 08/12/2014] [Indexed: 12/30/2022]
Abstract
UNLABELLED The nucleosome remodeling and deacetylase (NuRD) complex is an evolutionarily conserved chromatin-associated protein complex. Although the subunit composition of the mammalian complex is fairly well characterized, less is known about the stability and dynamics of these interactions. Furthermore, detailed information regarding protein-protein interaction surfaces within the complex is still largely lacking. Here, we show that the NuRD complex interacts with a number of substoichiometric zinc finger-containing proteins. Some of these interactions are salt-sensitive (ZNF512B and SALL4), whereas others (ZMYND8) are not. The stoichiometry of the core subunits is not affected by high salt concentrations, indicating that the core complex is stabilized by hydrophobic interactions. Interestingly, the RBBP4 and RBBP7 proteins are sensitive to high nonionic detergent concentrations during affinity purification. In a subunit exchange assay with stable isotope labeling by amino acids in cell culture (SILAC)-treated nuclear extracts, RBBP4 and RBBP7 were identified as dynamic core subunits of the NuRD complex, consistent with their proposed role as histone chaperones. Finally, using cross-linking MS, we have uncovered novel features of NuRD molecular architecture that complement our affinity purification-MS/MS data. Altogether, these findings extend our understanding of MBD3-NuRD structure and stability. STRUCTURED DIGITAL ABSTRACT MBD3 physically interacts with ZNF512B, HDAC1, ZMYND8, GATAD2B, SALL4, GATAD2A, ZNF592, MTA3, ZNF687, CDK2AP1, CHD3, ZNF532, HDAC2, MTA2, CHD4, MTA1, KPNA2, CHD5, RBBP4 and RBBP7 by pull down (View interaction) CDK2AP1 physically interacts with MBD3, MTA3, HDAC2, GATAD2A, CHD4, CDK2AP1, MTA2, HDAC1, MTA1, CHD3, GATAD2B, MBD2, RBBP4 and RBBP7 by pull down (View interaction) MBD3 physically interacts with MTA2, MTA3, RBBP4, RBBP7, HDAC2, HDAC1, CHD4, CHD3 and MTA1 by cross-linking study (View interaction).
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Affiliation(s)
- Susan L Kloet
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, the Netherlands
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171
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Hyun BR, McElwee JL, Soloway PD. Single molecule and single cell epigenomics. Methods 2014; 72:41-50. [PMID: 25204781 DOI: 10.1016/j.ymeth.2014.08.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Revised: 08/19/2014] [Accepted: 08/27/2014] [Indexed: 01/24/2023] Open
Abstract
Dynamically regulated changes in chromatin states are vital for normal development and can produce disease when they go awry. Accordingly, much effort has been devoted to characterizing these states under normal and pathological conditions. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is the most widely used method to characterize where in the genome transcription factors, modified histones, modified nucleotides and chromatin binding proteins are found; bisulfite sequencing (BS-seq) and its variants are commonly used to characterize the locations of DNA modifications. Though very powerful, these methods are not without limitations. Notably, they are best at characterizing one chromatin feature at a time, yet chromatin features arise and function in combination. Investigators commonly superimpose separate ChIP-seq or BS-seq datasets, and then infer where chromatin features are found together. While these inferences might be correct, they can be misleading when the chromatin source has distinct cell types, or when a given cell type exhibits any cell to cell variation in chromatin state. These ambiguities can be eliminated by robust methods that directly characterize the existence and genomic locations of combinations of chromatin features in very small inputs of cells or ideally, single cells. Here we review single molecule epigenomic methods under development to overcome these limitations, the technical challenges associated with single molecule methods and their potential application to single cells.
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Affiliation(s)
- Byung-Ryool Hyun
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - John L McElwee
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Paul D Soloway
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA.
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172
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Fabre B, Lambour T, Bouyssié D, Menneteau T, Monsarrat B, Burlet-Schiltz O, Bousquet-Dubouch MP. Comparison of label-free quantification methods for the determination of protein complexes subunits stoichiometry. EUPA OPEN PROTEOMICS 2014. [DOI: 10.1016/j.euprot.2014.06.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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173
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Alqarni SSM, Murthy A, Zhang W, Przewloka MR, Silva APG, Watson AA, Lejon S, Pei XY, Smits AH, Kloet SL, Wang H, Shepherd NE, Stokes PH, Blobel GA, Vermeulen M, Glover DM, Mackay JP, Laue ED. Insight into the architecture of the NuRD complex: structure of the RbAp48-MTA1 subcomplex. J Biol Chem 2014; 289:21844-55. [PMID: 24920672 PMCID: PMC4139204 DOI: 10.1074/jbc.m114.558940] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 05/30/2014] [Indexed: 12/22/2022] Open
Abstract
The nucleosome remodeling and deacetylase (NuRD) complex is a widely conserved transcriptional co-regulator that harbors both nucleosome remodeling and histone deacetylase activities. It plays a critical role in the early stages of ES cell differentiation and the reprogramming of somatic to induced pluripotent stem cells. Abnormalities in several NuRD proteins are associated with cancer and aging. We have investigated the architecture of NuRD by determining the structure of a subcomplex comprising RbAp48 and MTA1. Surprisingly, RbAp48 recognizes MTA1 using the same site that it uses to bind histone H4, showing that assembly into NuRD modulates RbAp46/48 interactions with histones. Taken together with other results, our data show that the MTA proteins act as scaffolds for NuRD complex assembly. We further show that the RbAp48-MTA1 interaction is essential for the in vivo integration of RbAp46/48 into the NuRD complex.
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Affiliation(s)
- Saad S M Alqarni
- From the School of Molecular Bioscience, University of Sydney, New South Wales 2006, Australia
| | - Andal Murthy
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Wei Zhang
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Marcin R Przewloka
- Department of Genetics, University of Cambridge, CB2 3EH, United Kingdom
| | - Ana P G Silva
- From the School of Molecular Bioscience, University of Sydney, New South Wales 2006, Australia
| | - Aleksandra A Watson
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Sara Lejon
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Xue Y Pei
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Arne H Smits
- Department of Molecular Cancer Research, UMC Utrecht, Universiteitsweg 100, 3584CG Utrecht, The Netherlands, and
| | - Susan L Kloet
- Department of Molecular Cancer Research, UMC Utrecht, Universiteitsweg 100, 3584CG Utrecht, The Netherlands, and
| | - Hongxin Wang
- Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104
| | - Nicholas E Shepherd
- From the School of Molecular Bioscience, University of Sydney, New South Wales 2006, Australia
| | - Philippa H Stokes
- From the School of Molecular Bioscience, University of Sydney, New South Wales 2006, Australia
| | - Gerd A Blobel
- Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104
| | - Michiel Vermeulen
- Department of Molecular Cancer Research, UMC Utrecht, Universiteitsweg 100, 3584CG Utrecht, The Netherlands, and
| | - David M Glover
- Department of Genetics, University of Cambridge, CB2 3EH, United Kingdom
| | - Joel P Mackay
- From the School of Molecular Bioscience, University of Sydney, New South Wales 2006, Australia,
| | - Ernest D Laue
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom,
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174
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Menafra R, Brinkman AB, Matarese F, Franci G, Bartels SJJ, Nguyen L, Shimbo T, Wade PA, Hubner NC, Stunnenberg HG. Genome-wide binding of MBD2 reveals strong preference for highly methylated loci. PLoS One 2014; 9:e99603. [PMID: 24927503 PMCID: PMC4057170 DOI: 10.1371/journal.pone.0099603] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 05/16/2014] [Indexed: 12/31/2022] Open
Abstract
MBD2 is a subunit of the NuRD complex that is postulated to mediate gene repression via recruitment of the complex to methylated DNA. In this study we adopted an MBD2 tagging-approach to study its genome wide binding characteristics. We show that in vivo MBD2 is mainly recruited to CpG island promoters that are highly methylated. Interestingly, MBD2 binds around 1 kb downstream of the transcription start site of a subset of ∼ 400 CpG island promoters that are characterized by the presence of active histone marks, RNA polymerase II (Pol2) and low to medium gene expression levels and H3K36me3 deposition. These tagged-MBD2 binding sites in MCF-7 show increased methylation in a cohort of primary breast cancers but not in normal breast samples, suggesting a putative role for MBD2 in breast cancer.
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Affiliation(s)
- Roberta Menafra
- Department of Molecular Biology, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Arie B. Brinkman
- Department of Molecular Biology, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Filomena Matarese
- Department of Molecular Biology, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Gianluigi Franci
- Department of Molecular Biology, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Stefanie J. J. Bartels
- Department of Molecular Biology, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Luan Nguyen
- Department of Molecular Biology, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Takashi Shimbo
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
| | - Paul A. Wade
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
| | - Nina C. Hubner
- Department of Molecular Biology, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Hendrik G. Stunnenberg
- Department of Molecular Biology, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
- * E-mail:
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175
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Dai L, LaCava J, Taylor MS, Boeke JD. Expression and detection of LINE-1 ORF-encoded proteins. Mob Genet Elements 2014; 4:e29319. [PMID: 25054082 PMCID: PMC4091050 DOI: 10.4161/mge.29319] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 05/19/2014] [Accepted: 05/22/2014] [Indexed: 11/30/2022] Open
Abstract
LINE-1 (L1) elements are endogenous retrotransposons active in mammalian genomes. The L1 RNA is bicistronic, encoding two non-overlapping open reading frames, ORF1 and ORF2, whose protein products (ORF1p and ORF2p) bind the L1 RNA to form a ribonucleoprotein (RNP) complex that is presumed to be a critical retrotransposition intermediate. However, ORF2p is expressed at a significantly lower level than ORF1p; these differences are thought to be controlled at the level of translation, due to a low frequency ribosome reinitiation mechanism controlling ORF2 expression. As a result, while ORF1p is readily detectable, ORF2p has previously been very challenging to detect in vitro and in vivo. To address this, we recently tested several epitope tags fused to the N- or C-termini of the ORF proteins in an effort to enable robust detection and affinity purification from native (L1RP) and synthetic (ORFeus-Hs) L1 constructs. An analysis of tagged RNPs from both L1RP and ORFeus-Hs showed similar host-cell-derived protein interactors. Our observations also revealed that the tag sequences affected the retrotransposition competency of native and synthetic L1s differently although they encode identical ORF proteins. Unexpectedly, we observed apparently stochastic expression of ORF2p within seemingly homogenous L1-expressing cell populations.
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Affiliation(s)
- Lixin Dai
- High Throughput Biology Center and Department of Molecular Biology and Genetics; Johns Hopkins University School of Medicine; Baltimore, MD USA
| | - John LaCava
- Laboratory of Cellular and Structural Biology; The Rockefeller University; New York, NY USA
| | - Martin S Taylor
- High Throughput Biology Center and Department of Pharmacology and Molecular Sciences; Johns Hopkins University School of Medicine; Baltimore, MD USA
| | - Jef D Boeke
- Institute for Systems Genetics; New York University School of Medicine; New York, NY USA
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176
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Histone H2A monoubiquitination promotes histone H3 methylation in Polycomb repression. Nat Struct Mol Biol 2014; 21:569-71. [PMID: 24837194 DOI: 10.1038/nsmb.2833] [Citation(s) in RCA: 315] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 05/01/2014] [Indexed: 12/23/2022]
Abstract
A key step in gene repression by Polycomb is trimethylation of histone H3 K27 by PCR2 to form H3K27me3. H3K27me3 provides a binding surface for PRC1. We show that monoubiquitination of histone H2A by PRC1-type complexes to form H2Aub creates a binding site for Jarid2-Aebp2-containing PRC2 and promotes H3K27 trimethylation on H2Aub nucleosomes. Jarid2, Aebp2 and H2Aub thus constitute components of a positive feedback loop establishing H3K27me3 chromatin domains.
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177
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Baymaz HI, Fournier A, Laget S, Ji Z, Jansen PWTC, Smits AH, Ferry L, Mensinga A, Poser I, Sharrocks A, Defossez PA, Vermeulen M. MBD5 and MBD6 interact with the human PR-DUB complex through their methyl-CpG-binding domain. Proteomics 2014; 14:2179-89. [DOI: 10.1002/pmic.201400013] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 03/07/2014] [Indexed: 11/06/2022]
Affiliation(s)
- H. Irem Baymaz
- Molecular Cancer Research; Cancer Genomics; University Medical Center Utrecht; Utrecht The Netherlands
| | - Alexandra Fournier
- Epigenetics and Cell Fate; Sorbonne Paris Cité; Université Paris Diderot; Paris France
| | - Sophie Laget
- Epigenetics and Cell Fate; Sorbonne Paris Cité; Université Paris Diderot; Paris France
| | - Zongling Ji
- Faculty of Life Sciences, University of Manchester; Manchester UK
| | - Pascal W. T. C. Jansen
- Molecular Cancer Research; Cancer Genomics; University Medical Center Utrecht; Utrecht The Netherlands
| | - Arne H. Smits
- Molecular Cancer Research; Cancer Genomics; University Medical Center Utrecht; Utrecht The Netherlands
| | - Laure Ferry
- Epigenetics and Cell Fate; Sorbonne Paris Cité; Université Paris Diderot; Paris France
| | - Anneloes Mensinga
- Molecular Cancer Research; Cancer Genomics; University Medical Center Utrecht; Utrecht The Netherlands
| | - Ina Poser
- Max Planck Institute of Molecular Cell Biology and Genetics; Dresden Germany
| | - Andrew Sharrocks
- Faculty of Life Sciences, University of Manchester; Manchester UK
| | | | - Michiel Vermeulen
- Molecular Cancer Research; Cancer Genomics; University Medical Center Utrecht; Utrecht The Netherlands
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178
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Kohli P, Bartram MP, Habbig S, Pahmeyer C, Lamkemeyer T, Benzing T, Schermer B, Rinschen MM. Label-free quantitative proteomic analysis of the YAP/TAZ interactome. Am J Physiol Cell Physiol 2014; 306:C805-18. [PMID: 24573087 DOI: 10.1152/ajpcell.00339.2013] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The function of an individual protein is typically defined by protein-protein interactions orchestrating the formation of large complexes critical for a wide variety of biological processes. Over the last decade the analysis of purified protein complexes by mass spectrometry became a key technique to identify protein-protein interactions. We present a fast and straightforward approach for analyses of interacting proteins combining a Flp-in single-copy cellular integration system and single-step affinity purification with single-shot mass spectrometry analysis. We applied this protocol to the analysis of the YAP and TAZ interactome. YAP and TAZ are the downstream effectors of the mammalian Hippo tumor suppressor pathway. Our study provides comprehensive interactomes for both YAP and TAZ and does not only confirm the majority of previously described interactors but, strikingly, revealed uncharacterized interaction partners that affect YAP/TAZ TEAD-dependent transcription. Among these newly identified candidates are Rassf8, thymopoetin, and the transcription factors CCAAT/enhancer-binding protein (C/EBP)β/δ and core-binding factor subunit β (Cbfb). In addition, our data allowed insights into complex stoichiometry and uncovered discrepancies between the YAP and TAZ interactomes. Taken together, the stringent approach presented here could help to significantly sharpen the understanding of protein-protein networks.
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Affiliation(s)
- Priyanka Kohli
- Department II of Internal Medicine and Center for Molecular Medicine, University of Cologne, Cologne, Germany
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179
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Ahn JW, Kim S, Kim EJ, Kim YJ, Kim KJ. Structural insights into the novel ARM-repeat protein CTNNBL1 and its association with the hPrp19-CDC5L complex. ACTA ACUST UNITED AC 2014; 70:780-8. [PMID: 24598747 DOI: 10.1107/s139900471303318x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 12/08/2013] [Indexed: 11/10/2022]
Abstract
The hPrp19-CDC5L complex plays a crucial role during human pre-mRNA splicing by catalytic activation of the spliceosome. In order to elucidate the molecular architecture of the hPrp19-CDC5L complex, the crystal structure of CTNNBL1, one of the major components of this complex, was determined. Unlike canonical ARM-repeat proteins such as β-catenin and importin-α, CTNNBL1 was found to contain a twisted and extended ARM-repeat structure at the C-terminal domain and, more importantly, the protein formed a stable dimer. A highly negatively charged patch formed in the N-terminal ARM-repeat domain of CTNNBL1 provides a binding site for CDC5L, a binding partner of the protein in the hPrp19-CDC5L complex, and these two proteins form a complex with a stoichiometry of 2:2. These findings not only present the crystal structure of a novel ARM-repeat protein, CTNNBL1, but also provide insights into the detailed molecular architecture of the hPrp19-CDC5L complex.
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Affiliation(s)
- Jae-Woo Ahn
- Structural and Molecular Biology Laboratory, School of Life Sciences and Biotechnology, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu 702-701, Republic of Korea
| | - Sangwoo Kim
- School of Nano-Bioscience and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Eun-Jung Kim
- Structural and Molecular Biology Laboratory, School of Life Sciences and Biotechnology, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu 702-701, Republic of Korea
| | - Yeo-Jin Kim
- Structural and Molecular Biology Laboratory, School of Life Sciences and Biotechnology, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu 702-701, Republic of Korea
| | - Kyung-Jin Kim
- Structural and Molecular Biology Laboratory, School of Life Sciences and Biotechnology, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu 702-701, Republic of Korea
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180
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Affinity proteomics reveals human host factors implicated in discrete stages of LINE-1 retrotransposition. Cell 2014; 155:1034-48. [PMID: 24267889 DOI: 10.1016/j.cell.2013.10.021] [Citation(s) in RCA: 149] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 08/25/2013] [Accepted: 09/30/2013] [Indexed: 11/21/2022]
Abstract
LINE-1s are active human DNA parasites that are agents of genome dynamics in evolution and disease. These streamlined elements require host factors to complete their life cycles, whereas hosts have developed mechanisms to combat retrotransposition's mutagenic effects. As such, endogenous L1 expression levels are extremely low, creating a roadblock for detailed interactomic analyses. Here, we describe a system to express and purify highly active L1 RNP complexes from human suspension cell culture and characterize the copurified proteome, identifying 37 high-confidence candidate interactors. These data sets include known interactors PABPC1 and MOV10 and, with in-cell imaging studies, suggest existence of at least three types of compositionally and functionally distinct L1 RNPs. Among the findings, UPF1, a key nonsense-mediated decay factor, and PCNA, the polymerase-delta-associated sliding DNA clamp, were identified and validated. PCNA interacts with ORF2p via a PIP box motif; mechanistic studies suggest that this occurs during or immediately after target-primed reverse transcription.
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181
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Reciprocal interactions of human C10orf12 and C17orf96 with PRC2 revealed by BioTAP-XL cross-linking and affinity purification. Proc Natl Acad Sci U S A 2014; 111:2488-93. [PMID: 24550272 DOI: 10.1073/pnas.1400648111] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Understanding the composition of epigenetic regulators remains an important challenge in chromatin biology. Traditional biochemical analysis of chromatin-associated complexes requires their release from DNA under conditions that can also disrupt key interactions. Here we develop a complementary approach (BioTAP-XL), in which cross-linking (XL) enhances the preservation of protein interactions and also allows the analysis of DNA targets under the same tandem affinity purification (BioTAP) regimen. We demonstrate the power of BioTAP-XL through analysis of human EZH2, a core subunit of polycomb repressive complex 2 (PRC2). We identify and validate two strong interactors, C10orf12 and C17orf96, which display enrichment with EZH2-BioTAP at levels similar to canonical PRC2 components (SUZ12, EED, MTF2, JARID2, PHF1, and AEBP2). ChIP-seq analysis of BioTAP-tagged C10orf12 or C17orf96 revealed the similarity of each binding pattern with the location of EZH2 and the H3K27me3-silencing mark, validating their physical interaction with PRC2 components. Interestingly, analysis by mass spectrometry of C10orf12 and C17orf96 interactions revealed that these proteins may be mutually exclusive PRC2 subunits that fail to interact with each other or with JARID2 and AEBP2. C10orf12, in addition, shows a strong and unexpected association with components of the EHMT1/2 complex, thus potentially connecting PRC2 to another histone methyltransferase. Similarly, results from CBX4-BioTAP protein pulldowns are consistent with reports of a diversity of PRC1 complexes. Our results highlight the importance of reciprocal analyses of multiple subunits and suggest that iterative use of BioTAP-XL has strong potential to reveal networks of chromatin-based interactions in higher organisms.
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182
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Schmidt C, Robinson CV. Dynamic protein ligand interactions--insights from MS. FEBS J 2014; 281:1950-64. [PMID: 24393119 PMCID: PMC4154455 DOI: 10.1111/febs.12707] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 12/19/2013] [Accepted: 12/30/2013] [Indexed: 12/31/2022]
Abstract
Proteins undergo dynamic interactions with carbohydrates, lipids and nucleotides to form catalytic cores, fine‐tuned for different cellular actions. The study of dynamic interactions between proteins and their cognate ligands is therefore fundamental to the understanding of biological systems. During the last two decades MS, and its associated techniques, has become accepted as a method for the study of protein–ligand interactions, not only for covalent complexes, where the use of MS is well established, but also, and significantly for protein–ligand interactions, for noncovalent assemblies. In this review, we employ a broad definition of a ligand to encompass protein subunits, drug molecules, oligonucleotides, carbohydrates, and lipids. Under the appropriate conditions, MS can reveal the composition, heterogeneity and dynamics of these protein–ligand interactions, and in some cases their structural arrangements and binding affinities. Herein, we highlight MS approaches for studying protein–ligand complexes, including those containing integral membrane subunits, and showcase examples from recent literature. Specifically, we tabulate the myriad of methodologies, including hydrogen exchange, proteomics, hydroxyl radical footprinting, intact complexes, and crosslinking, which, when combined with MS, provide insights into conformational changes and subtle modifications in response to ligand‐binding interactions.
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183
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Jarid2 Is Implicated in the Initial Xist-Induced Targeting of PRC2 to the Inactive X Chromosome. Mol Cell 2014; 53:301-16. [DOI: 10.1016/j.molcel.2014.01.002] [Citation(s) in RCA: 192] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 12/16/2013] [Accepted: 12/24/2013] [Indexed: 12/16/2022]
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184
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van Heeringen SJ, Akkers RC, van Kruijsbergen I, Arif MA, Hanssen LLP, Sharifi N, Veenstra GJC. Principles of nucleation of H3K27 methylation during embryonic development. Genome Res 2013; 24:401-10. [PMID: 24336765 PMCID: PMC3941105 DOI: 10.1101/gr.159608.113] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
During embryonic development, maintenance of cell identity and lineage commitment requires the Polycomb-group PRC2 complex, which catalyzes histone H3 lysine 27 trimethylation (H3K27me3). However, the developmental origins of this regulation are unknown. Here we show that H3K27me3 enrichment increases from blastula stages onward in embryos of the Western clawed frog (Xenopus tropicalis) within constrained domains strictly defined by sequence. Strikingly, although PRC2 also binds widely to active enhancers, H3K27me3 is only deposited at a small subset of these sites. Using a Support Vector Machine algorithm, these sequences can be predicted accurately on the basis of DNA sequence alone, with a sequence signature conserved between humans, frogs, and fish. These regions correspond to the subset of blastula-stage DNA methylation-free domains that are depleted for activating promoter motifs, and enriched for motifs of developmental factors. These results imply a genetic-default model in which a preexisting absence of DNA methylation is the major determinant of H3K27 methylation when not opposed by transcriptional activation. The sequence and motif signatures reveal the hierarchical and genetically inheritable features of epigenetic cross-talk that impose constraints on Polycomb regulation and guide H3K27 methylation during the exit of pluripotency.
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Affiliation(s)
- Simon J van Heeringen
- Radboud University Nijmegen, Department of Molecular Developmental Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Nijmegen 6500 HB, The Netherlands
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185
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Cdyl, a new partner of the inactive X chromosome and potential reader of H3K27me3 and H3K9me2. Mol Cell Biol 2013; 33:5005-20. [PMID: 24144980 DOI: 10.1128/mcb.00866-13] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
X chromosome inactivation is a remarkable example of chromosome-wide gene silencing and facultative heterochromatin formation. Numerous histone posttranslational modifications, including H3K9me2 and H3K27me3, accompany this process, although our understanding of the enzymes that lay down these marks and the factors that bind to them is still incomplete. Here we identify Cdyl, a chromodomain-containing transcriptional corepressor, as a new chromatin-associated protein partner of the inactive X chromosome (Xi). Using mouse embryonic stem cell lines with mutated histone methyltransferase activities, we show that Cdyl relies on H3K9me2 for its general association with chromatin in vivo. For its association with Xi, Cdyl requires the process of differentiation and the presence of H3K9me2 and H3K27me3, which both become chromosomally enriched following Xist RNA coating. We further show that the removal of the PRC2 component Eed and subsequent loss of H3K27me3 lead to a reduction of both Cdyl and H3K9me2 enrichment on inactive Xi. Finally, we show that Cdyl associates with the H3K9 histone methyltransferase G9a and the MGA protein, both of which are also found on Xi. We propose that the combination of H3K9me2 and H3K27me3 recruits Cdyl to Xi, and this, in turn, may facilitate propagation of the H3K9me2 mark by anchoring G9a.
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186
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van Nuland R, Schram AW, van Schaik FMA, Jansen PWTC, Vermeulen M, Marc Timmers HT. Multivalent engagement of TFIID to nucleosomes. PLoS One 2013; 8:e73495. [PMID: 24039962 PMCID: PMC3770614 DOI: 10.1371/journal.pone.0073495] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 07/20/2013] [Indexed: 12/20/2022] Open
Abstract
The process of eukaryotic transcription initiation involves the assembly of basal transcription factor complexes on the gene promoter. The recruitment of TFIID is an early and important step in this process. Gene promoters contain distinct DNA sequence elements and are marked by the presence of post-translationally modified nucleosomes. The contributions of these individual features for TFIID recruitment remain to be elucidated. Here, we use immobilized reconstituted promoter nucleosomes, conventional biochemistry and quantitative mass spectrometry to investigate the influence of distinct histone modifications and functional DNA-elements on the binding of TFIID. Our data reveal synergistic effects of H3K4me3, H3K14ac and a TATA box sequence on TFIID binding in vitro. Stoichiometry analyses of affinity purified human TFIID identified the presence of a stable dimeric core. Several peripheral TAFs, including those interacting with distinct promoter features, are substoichiometric yet present in substantial amounts. Finally, we find that the TAF3 subunit of TFIID binds to poised promoters in an H3K4me3-dependent manner. Moreover, the PHD-finger of TAF3 is important for rapid induction of target genes. Thus, fine-tuning of TFIID engagement on promoters is driven by synergistic contacts with both DNA-elements and histone modifications, eventually resulting in a high affinity interaction and activation of transcription.
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Affiliation(s)
- Rick van Nuland
- Department of Molecular Cancer Research, University Medical Center Utrecht, Utrecht, The Netherlands
- Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Andrea W. Schram
- Department of Molecular Cancer Research, University Medical Center Utrecht, Utrecht, The Netherlands
- Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Frederik M. A. van Schaik
- Department of Molecular Cancer Research, University Medical Center Utrecht, Utrecht, The Netherlands
- Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Pascal W. T. C. Jansen
- Department of Molecular Cancer Research, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Medical Oncology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Michiel Vermeulen
- Department of Molecular Cancer Research, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Medical Oncology, University Medical Center Utrecht, Utrecht, The Netherlands
- * E-mail: (MV); (HTMT)
| | - H. T. Marc Timmers
- Department of Molecular Cancer Research, University Medical Center Utrecht, Utrecht, The Netherlands
- Netherlands Proteomics Center, Utrecht, The Netherlands
- * E-mail: (MV); (HTMT)
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187
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Quantitative dissection and stoichiometry determination of the human SET1/MLL histone methyltransferase complexes. Mol Cell Biol 2013; 33:2067-77. [PMID: 23508102 DOI: 10.1128/mcb.01742-12] [Citation(s) in RCA: 177] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Methylation of lysine 4 on histone H3 (H3K4) at promoters is tightly linked to transcriptional regulation in human cells. At least six different COMPASS-like multisubunit (SET1/MLL) complexes that contain methyltransferase activity for H3K4 have been described, but a comprehensive and quantitative analysis of these SET1/MLL complexes is lacking. We applied label-free quantitative mass spectrometry to determine the subunit composition and stoichiometry of the human SET1/MLL complexes. We identified both known and novel, unique and shared interactors and determined their distribution and stoichiometry over the different SET1/MLL complexes. In addition to being a core COMPASS subunit, the Dpy30 protein is a genuine subunit of the NURF chromatin remodeling complex. Furthermore, we identified the Bod1 protein as a discriminator between the SET1B and SET1A complexes, and we show that the H3K36me-interactor Psip1 preferentially binds to the MLL2 complex. Finally, absolute protein quantification in crude lysates mirrors many of the observed SET1/MLL complex stoichiometries. Our findings provide a molecular framework for understanding the diversity and abundance of the different SET1/MLL complexes, which together establish the H3K4 methylation landscape in human cells.
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188
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Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives. Cell 2013; 152:1146-59. [PMID: 23434322 DOI: 10.1016/j.cell.2013.02.004] [Citation(s) in RCA: 758] [Impact Index Per Article: 68.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Revised: 01/11/2013] [Accepted: 02/05/2013] [Indexed: 11/21/2022]
Abstract
Tet proteins oxidize 5-methylcytosine (mC) to generate 5-hydroxymethyl (hmC), 5-formyl (fC), and 5-carboxylcytosine (caC). The exact function of these oxidative cytosine bases remains elusive. We applied quantitative mass-spectrometry-based proteomics to identify readers for mC and hmC in mouse embryonic stem cells (mESC), neuronal progenitor cells (NPC), and adult mouse brain tissue. Readers for these modifications are only partially overlapping, and some readers, such as Rfx proteins, display strong specificity. Interactions are dynamic during differentiation, as for example evidenced by the mESC-specific binding of Klf4 to mC and the NPC-specific binding of Uhrf2 to hmC, suggesting specific biological roles for mC and hmC. Oxidized derivatives of mC recruit distinct transcription regulators as well as a large number of DNA repair proteins in mouse ES cells, implicating the DNA damage response as a major player in active DNA demethylation.
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