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Rupasinghe M, Bersaglieri C, Leslie Pedrioli DM, Pedrioli PG, Panatta M, Hottiger MO, Cinelli P, Santoro R. PRAMEL7 and CUL2 decrease NuRD stability to establish ground-state pluripotency. EMBO Rep 2024; 25:1453-1468. [PMID: 38332149 PMCID: PMC10933316 DOI: 10.1038/s44319-024-00083-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 01/05/2024] [Accepted: 01/10/2024] [Indexed: 02/10/2024] Open
Abstract
Pluripotency is established in E4.5 preimplantation epiblast. Embryonic stem cells (ESCs) represent the immortalization of pluripotency, however, their gene expression signature only partially resembles that of developmental ground-state. Induced PRAMEL7 expression, a protein highly expressed in the ICM but lowly expressed in ESCs, reprograms developmentally advanced ESC+serum into ground-state pluripotency by inducing a gene expression signature close to developmental ground-state. However, how PRAMEL7 reprograms gene expression remains elusive. Here we show that PRAMEL7 associates with Cullin2 (CUL2) and this interaction is required to establish ground-state gene expression. PRAMEL7 recruits CUL2 to chromatin and targets regulators of repressive chromatin, including the NuRD complex, for proteasomal degradation. PRAMEL7 antagonizes NuRD-mediated repression of genes implicated in pluripotency by decreasing NuRD stability and promoter association in a CUL2-dependent manner. Our data link proteasome degradation pathways to ground-state gene expression, offering insights to generate in vitro models to reproduce the in vivo ground-state pluripotency.
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Affiliation(s)
- Meneka Rupasinghe
- Department of Molecular Mechanisms of Disease, DMMD, University of Zurich, 8057, Zurich, Switzerland
- Molecular Life Science Program, Life Science Zurich Graduate School, University of Zurich, 8057, Zurich, Switzerland
| | - Cristiana Bersaglieri
- Department of Molecular Mechanisms of Disease, DMMD, University of Zurich, 8057, Zurich, Switzerland
| | - Deena M Leslie Pedrioli
- Department of Molecular Mechanisms of Disease, DMMD, University of Zurich, 8057, Zurich, Switzerland
| | - Patrick Ga Pedrioli
- Department of Health Sciences and Technology, ETH Zurich, 8093, Zurich, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Martina Panatta
- Department of Molecular Mechanisms of Disease, DMMD, University of Zurich, 8057, Zurich, Switzerland
- RNA Biology Program, Life Science Zurich Graduate School, University of Zurich, Zurich, Switzerland
| | - Michael O Hottiger
- Department of Molecular Mechanisms of Disease, DMMD, University of Zurich, 8057, Zurich, Switzerland
| | - Paolo Cinelli
- Department of Trauma Surgery, University Hospital Zurich, University of Zurich, Rämistrasse 100, 8091, Zurich, Switzerland
| | - Raffaella Santoro
- Department of Molecular Mechanisms of Disease, DMMD, University of Zurich, 8057, Zurich, Switzerland.
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2
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Sun Z, Cernilogar FM, Horvatic H, Yeroslaviz A, Abdullah Z, Schotta G, Hornung V. β1 integrin signaling governs necroptosis via the chromatin-remodeling factor CHD4. Cell Rep 2023; 42:113322. [PMID: 37883227 DOI: 10.1016/j.celrep.2023.113322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 08/29/2023] [Accepted: 10/05/2023] [Indexed: 10/28/2023] Open
Abstract
Fibrosis, characterized by sustained activation of myofibroblasts and excessive extracellular matrix (ECM) deposition, is known to be associated with chronic inflammation. Receptor-interacting protein kinase 3 (RIPK3), the central kinase of necroptosis signaling, is upregulated in fibrosis and contributes to tumor necrosis factor (TNF)-mediated inflammation. In bile-duct-ligation-induced liver fibrosis, we found that myofibroblasts are the major cell type expressing RIPK3. Genetic ablation of β1 integrin, the major profibrotic ECM receptor in fibroblasts, not only abolished ECM fibrillogenesis but also blunted RIPK3 expression via a mechanism mediated by the chromatin-remodeling factor chromodomain helicase DNA-binding protein 4 (CHD4). While the function of CHD4 has been conventionally linked to the nucleosome-remodeling deacetylase (NuRD) and CHD4-ADNP-HP1(ChAHP) complexes, we found that CHD4 potently repressed a set of genes, including Ripk3, with high locus specificity but independent of either the NuRD or the ChAHP complex. Thus, our data uncover that β1 integrin intrinsically links fibrotic signaling to RIPK3-driven inflammation via a novel mode of action of CHD4.
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Affiliation(s)
- Zhiqi Sun
- Gene Center and Department of Biochemistry, Ludwig Maximilian University of Munich, Munich, Germany; Research Group Molecular Mechanisms of Inflammation, Max-Planck Institute of Biochemistry, Martinsried, Germany.
| | - Filippo M Cernilogar
- Division of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig Maximilian University of Munich, Munich, Germany
| | - Helena Horvatic
- Institute of Molecular Medicine and Experimental Immunology, University Hospital Bonn, Bonn, Germany
| | - Assa Yeroslaviz
- Computational Biology Group, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Zeinab Abdullah
- Institute of Molecular Medicine and Experimental Immunology, University Hospital Bonn, Bonn, Germany
| | - Gunnar Schotta
- Division of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig Maximilian University of Munich, Munich, Germany
| | - Veit Hornung
- Gene Center and Department of Biochemistry, Ludwig Maximilian University of Munich, Munich, Germany; Research Group Molecular Mechanisms of Inflammation, Max-Planck Institute of Biochemistry, Martinsried, Germany.
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3
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Basu S, Shukron O, Hall D, Parutto P, Ponjavic A, Shah D, Boucher W, Lando D, Zhang W, Reynolds N, Sober LH, Jartseva A, Ragheb R, Ma X, Cramard J, Floyd R, Balmer J, Drury TA, Carr AR, Needham LM, Aubert A, Communie G, Gor K, Steindel M, Morey L, Blanco E, Bartke T, Di Croce L, Berger I, Schaffitzel C, Lee SF, Stevens TJ, Klenerman D, Hendrich BD, Holcman D, Laue ED. Live-cell three-dimensional single-molecule tracking reveals modulation of enhancer dynamics by NuRD. Nat Struct Mol Biol 2023; 30:1628-1639. [PMID: 37770717 PMCID: PMC10643137 DOI: 10.1038/s41594-023-01095-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 08/14/2023] [Indexed: 09/30/2023]
Abstract
To understand how the nucleosome remodeling and deacetylase (NuRD) complex regulates enhancers and enhancer-promoter interactions, we have developed an approach to segment and extract key biophysical parameters from live-cell three-dimensional single-molecule trajectories. Unexpectedly, this has revealed that NuRD binds to chromatin for minutes, decompacts chromatin structure and increases enhancer dynamics. We also uncovered a rare fast-diffusing state of enhancers and found that NuRD restricts the time spent in this state. Hi-C and Cut&Run experiments revealed that NuRD modulates enhancer-promoter interactions in active chromatin, allowing them to contact each other over longer distances. Furthermore, NuRD leads to a marked redistribution of CTCF and, in particular, cohesin. We propose that NuRD promotes a decondensed chromatin environment, where enhancers and promoters can contact each other over longer distances, and where the resetting of enhancer-promoter interactions brought about by the fast decondensed chromatin motions is reduced, leading to more stable, long-lived enhancer-promoter relationships.
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Affiliation(s)
- S Basu
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - O Shukron
- Department of Applied Mathematics and Computational Biology, Ecole Normale Supérieure, Paris, France
| | - D Hall
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - P Parutto
- Department of Applied Mathematics and Computational Biology, Ecole Normale Supérieure, Paris, France
| | - A Ponjavic
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- School of Physics and Astronomy, University of Leeds, Leeds, UK
- School of Food Science and Nutrition, University of Leeds, Leeds, UK
| | - D Shah
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - W Boucher
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - D Lando
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - W Zhang
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - N Reynolds
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - L H Sober
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - A Jartseva
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - R Ragheb
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - X Ma
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - J Cramard
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - R Floyd
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - J Balmer
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - T A Drury
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - A R Carr
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - L-M Needham
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - A Aubert
- The European Molecular Biology Laboratory EMBL, Grenoble, France
| | - G Communie
- The European Molecular Biology Laboratory EMBL, Grenoble, France
| | - K Gor
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
- The European Molecular Biology Laboratory, Heidelberg, Germany
| | - M Steindel
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - L Morey
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Sylvester Comprehensive Cancer Center, Department of Human Genetics, University of Miami Miller School of Medicine, Biomedical Research Building, Miami, FL, USA
| | - E Blanco
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - T Bartke
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Functional Epigenetics, Neuherberg, Germany
| | - L Di Croce
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - I Berger
- School of Biochemistry, University of Bristol, Bristol, UK
| | - C Schaffitzel
- School of Biochemistry, University of Bristol, Bristol, UK
| | - S F Lee
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - T J Stevens
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - D Klenerman
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
| | - B D Hendrich
- Department of Biochemistry, University of Cambridge, Cambridge, UK.
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK.
| | - D Holcman
- Department of Applied Mathematics and Computational Biology, Ecole Normale Supérieure, Paris, France.
| | - E D Laue
- Department of Biochemistry, University of Cambridge, Cambridge, UK.
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK.
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4
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Lenz J, Brehm A. Conserved mechanisms of NuRD function in hematopoetic gene expression. Enzymes 2023; 53:7-32. [PMID: 37748838 DOI: 10.1016/bs.enz.2023.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
The Nucleosome Remodeling and Deacetylating Complex (NuRD) is ubiquitously expressed in all metazoans. It combines nucleosome remodeling and histone deacetylating activities to generate inaccessible chromatin structures and to repress gene transcription. NuRD is involved in the generation and maintenance of a wide variety of lineage-specific gene expression programs during differentiation and in differentiated cells. A close cooperation with a large number of lineage-specific transcription factors is key to allow NuRD to function in many distinct differentiation contexts. The molecular nature of this interplay between transcription factors and NuRD is complex and not well understood. This review uses hematopoiesis as a paradigm to highlight recent advances in our understanding of how transcription factors and NuRD cooperate at the molecular level during differentiation. A comparison of vertebrate and invertebrate systems serves to identify the conserved and fundamental concepts guiding functional interactions between transcription factors and NuRD. We also discuss how the transcription factor-NuRD axis constitutes a potential therapeutic target for the treatment of hemoglobinopathies.
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Affiliation(s)
- Jonathan Lenz
- Institute for Molecular Biology and Tumor Research, Biomedical Research Center, Philipps-University Marburg, Marburg, Germany
| | - Alexander Brehm
- Institute for Molecular Biology and Tumor Research, Biomedical Research Center, Philipps-University Marburg, Marburg, Germany.
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5
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Affar M, Bottardi S, Quansah N, Lemarié M, Ramón AC, Affar EB, Milot E. IKAROS: from chromatin organization to transcriptional elongation control. Cell Death Differ 2023:10.1038/s41418-023-01212-2. [PMID: 37620540 DOI: 10.1038/s41418-023-01212-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 07/26/2023] [Accepted: 08/14/2023] [Indexed: 08/26/2023] Open
Abstract
IKAROS is a master regulator of cell fate determination in lymphoid and other hematopoietic cells. This transcription factor orchestrates the association of epigenetic regulators with chromatin, ensuring the expression pattern of target genes in a developmental and lineage-specific manner. Disruption of IKAROS function has been associated with the development of acute lymphocytic leukemia, lymphoma, chronic myeloid leukemia and immune disorders. Paradoxically, while IKAROS has been shown to be a tumor suppressor, it has also been identified as a key therapeutic target in the treatment of various forms of hematological malignancies, including multiple myeloma. Indeed, targeted proteolysis of IKAROS is associated with decreased proliferation and increased death of malignant cells. Although the molecular mechanisms have not been elucidated, the expression levels of IKAROS are variable during hematopoiesis and could therefore be a key determinant in explaining how its absence can have seemingly opposite effects. Mechanistically, IKAROS collaborates with a variety of proteins and complexes controlling chromatin organization at gene regulatory regions, including the Nucleosome Remodeling and Deacetylase complex, and may facilitate transcriptional repression or activation of specific genes. Several transcriptional regulatory functions of IKAROS have been proposed. An emerging mechanism of action involves the ability of IKAROS to promote gene repression or activation through its interaction with the RNA polymerase II machinery, which influences pausing and productive transcription at specific genes. This control appears to be influenced by IKAROS expression levels and isoform production. In here, we summarize the current state of knowledge about the biological roles and mechanisms by which IKAROS regulates gene expression. We highlight the dynamic regulation of this factor by post-translational modifications. Finally, potential avenues to explain how IKAROS destruction may be favorable in the treatment of certain hematological malignancies are also explored.
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Affiliation(s)
- Malik Affar
- Faculty of Medicine, University of Montreal, Montréal, QC, Canada
- Maisonneuve-Rosemont Hospital Research Center, CIUSSS de l'Est-de-l'Île de Montréal, 5415 boulevard de l'Assomption, Montréal, QC, H1T 2M4, Canada
| | - Stefania Bottardi
- Maisonneuve-Rosemont Hospital Research Center, CIUSSS de l'Est-de-l'Île de Montréal, 5415 boulevard de l'Assomption, Montréal, QC, H1T 2M4, Canada
| | - Norreen Quansah
- Maisonneuve-Rosemont Hospital Research Center, CIUSSS de l'Est-de-l'Île de Montréal, 5415 boulevard de l'Assomption, Montréal, QC, H1T 2M4, Canada
| | - Maud Lemarié
- Faculty of Medicine, University of Montreal, Montréal, QC, Canada
- Maisonneuve-Rosemont Hospital Research Center, CIUSSS de l'Est-de-l'Île de Montréal, 5415 boulevard de l'Assomption, Montréal, QC, H1T 2M4, Canada
| | - Ailyn C Ramón
- Faculty of Medicine, University of Montreal, Montréal, QC, Canada
- Maisonneuve-Rosemont Hospital Research Center, CIUSSS de l'Est-de-l'Île de Montréal, 5415 boulevard de l'Assomption, Montréal, QC, H1T 2M4, Canada
| | - El Bachir Affar
- Faculty of Medicine, University of Montreal, Montréal, QC, Canada.
- Maisonneuve-Rosemont Hospital Research Center, CIUSSS de l'Est-de-l'Île de Montréal, 5415 boulevard de l'Assomption, Montréal, QC, H1T 2M4, Canada.
| | - Eric Milot
- Faculty of Medicine, University of Montreal, Montréal, QC, Canada.
- Maisonneuve-Rosemont Hospital Research Center, CIUSSS de l'Est-de-l'Île de Montréal, 5415 boulevard de l'Assomption, Montréal, QC, H1T 2M4, Canada.
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6
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Fragoso MSI, de Siqueira CM, Vitorino FNL, Vieira AZ, Martins-Duarte ÉS, Faoro H, da Cunha JPC, Ávila AR, Nardelli SC. TgKDAC4: A Unique Deacetylase of Toxoplasma' s Apicoplast. Microorganisms 2023; 11:1558. [PMID: 37375060 DOI: 10.3390/microorganisms11061558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/04/2023] [Accepted: 05/09/2023] [Indexed: 06/29/2023] Open
Abstract
Toxoplasma gondii is an obligate intracellular parasite of the phylum Apicomplexa and causes toxoplasmosis infections, a disease that affects a quarter of the world's population and has no effective cure. Epigenetic regulation is one of the mechanisms controlling gene expression and plays an essential role in all organisms. Lysine deacetylases (KDACs) act as epigenetic regulators affecting gene silencing in many eukaryotes. Here, we focus on TgKDAC4, an enzyme unique to apicomplexan parasites, and a class IV KDAC, the least-studied class of deacetylases so far. This enzyme shares only a portion of the specific KDAC domain with other organisms. Phylogenetic analysis from the TgKDAC4 domain shows a putative prokaryotic origin. Surprisingly, TgKDAC4 is located in the apicoplast, making it the only KDAC found in this organelle to date. Transmission electron microscopy assays confirmed the presence of TgKDAC4 in the periphery of the apicoplast. We identified possible targets or/and partners of TgKDAC4 by immunoprecipitation assays followed by mass spectrometry analysis, including TgCPN60 and TgGAPDH2, both located at the apicoplast and containing acetylation sites. Understanding how the protein works could provide new insights into the metabolism of the apicoplast, an essential organelle for parasite survival.
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Affiliation(s)
| | | | - Francisca Nathália Luna Vitorino
- Special Laboratory of Cell Cycle, Center of Toxins, Immune Response and Cell Signalling (CeTICS), Instituto Butantan, São Paulo 05503-900, Brazil
| | | | - Érica Santos Martins-Duarte
- Department of Parasitology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Helisson Faoro
- Instituto Carlos Chagas, Fundação Oswaldo Cruz, Curitiba 81350-010, Brazil
| | - Júlia Pinheiro Chagas da Cunha
- Special Laboratory of Cell Cycle, Center of Toxins, Immune Response and Cell Signalling (CeTICS), Instituto Butantan, São Paulo 05503-900, Brazil
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7
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Reid XJ, Low JKK, Mackay JP. A NuRD for all seasons. Trends Biochem Sci 2023; 48:11-25. [PMID: 35798615 DOI: 10.1016/j.tibs.2022.06.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/02/2022] [Accepted: 06/08/2022] [Indexed: 12/27/2022]
Abstract
The nucleosome-remodeling and deacetylase (NuRD) complex is an essential transcriptional regulator in all complex animals. All seven core subunits of the complex exist as multiple paralogs, raising the question of whether the complex might utilize paralog switching to achieve cell type-specific functions. We examine the evidence for this idea, making use of published quantitative proteomic data to dissect NuRD composition in 20 different tissues, as well as a large-scale CRISPR knockout screen carried out in >1000 human cancer cell lines. These data, together with recent reports, provide strong support for the idea that distinct permutations of the NuRD complex with tailored functions might regulate tissue-specific gene expression programs.
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Affiliation(s)
- Xavier J Reid
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Jason K K Low
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia.
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8
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Leighton GO, Irvin EM, Kaur P, Liu M, You C, Bhattaram D, Piehler J, Riehn R, Wang H, Pan H, Williams DC. Densely methylated DNA traps Methyl-CpG-binding domain protein 2 but permits free diffusion by Methyl-CpG-binding domain protein 3. J Biol Chem 2022; 298:102428. [PMID: 36037972 PMCID: PMC9520026 DOI: 10.1016/j.jbc.2022.102428] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 08/19/2022] [Accepted: 08/20/2022] [Indexed: 10/29/2022] Open
Abstract
The methyl-CpG-binding domain 2 and 3 proteins (MBD2 and MBD3) provide structural and DNA-binding function for the Nucleosome Remodeling and Deacetylase (NuRD) complex. The two proteins form distinct NuRD complexes and show different binding affinity and selectivity for methylated DNA. Previous studies have shown that MBD2 binds with high affinity and selectivity for a single methylated CpG dinucleotide while MBD3 does not. However, the NuRD complex functions in regions of the genome that contain many CpG dinucleotides (CpG islands). Therefore, in this work, we investigate the binding and diffusion of MBD2 and MBD3 on more biologically relevant DNA templates that contain a large CpG island or limited CpG sites. Using a combination of single-molecule and biophysical analyses, we show that both MBD2 and MBD3 diffuse freely and rapidly across unmethylated CpG-rich DNA. In contrast, we found methylation of large CpG islands traps MBD2 leading to stable and apparently static binding on the CpG island while MBD3 continues to diffuse freely. In addition, we demonstrate both proteins bend DNA, which is augmented by methylation. Together, these studies support a model in which MBD2-NuRD strongly localizes to and compacts methylated CpG islands while MBD3-NuRD can freely mobilize nucleosomes independent of methylation status.
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Affiliation(s)
- Gage O Leighton
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | | | - Parminder Kaur
- Department of Physics, North Carolina State University, Raleigh, North Carolina, USA; Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina, USA
| | - Ming Liu
- Department of Physics, North Carolina State University, Raleigh, North Carolina, USA
| | - Changjiang You
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Universität Osnabrück, Osnabrück, Germany
| | - Dhruv Bhattaram
- Department of Biomedical Engineering, Georgia Institute of Technology & Emory University of Medicine, Atlanta, Georgia, USA
| | - Jacob Piehler
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Universität Osnabrück, Osnabrück, Germany
| | - Robert Riehn
- Department of Physics, North Carolina State University, Raleigh, North Carolina, USA
| | - Hong Wang
- Toxicology Program, North Carolina State University, Raleigh, North Carolina, USA; Department of Physics, North Carolina State University, Raleigh, North Carolina, USA; Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina, USA
| | - Hai Pan
- Department of Physics, North Carolina State University, Raleigh, North Carolina, USA.
| | - David C Williams
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA.
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9
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Arvindekar S, Jackman MJ, Low JKK, Landsberg MJ, Mackay JP, Viswanath S. Molecular architecture of nucleosome remodeling and deacetylase sub-complexes by integrative structure determination. Protein Sci 2022; 31:e4387. [PMID: 36040254 PMCID: PMC9413472 DOI: 10.1002/pro.4387] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 05/18/2022] [Accepted: 06/19/2022] [Indexed: 11/11/2022]
Abstract
The nucleosome remodeling and deacetylase (NuRD) complex is a chromatin-modifying assembly that regulates gene expression and DNA damage repair. Despite its importance, limited structural information describing the complete NuRD complex is available and a detailed understanding of its mechanism is therefore lacking. Drawing on information from SEC-MALLS, DIA-MS, XLMS, negative-stain EM, X-ray crystallography, NMR spectroscopy, secondary structure predictions, and homology models, we applied Bayesian integrative structure determination to investigate the molecular architecture of three NuRD sub-complexes: MTA1-HDAC1-RBBP4, MTA1N -HDAC1-MBD3GATAD2CC , and MTA1-HDAC1-RBBP4-MBD3-GATAD2A [nucleosome deacetylase (NuDe)]. The integrative structures were corroborated by examining independent crosslinks, cryo-EM maps, biochemical assays, known cancer-associated mutations, and structure predictions from AlphaFold. The robustness of the models was assessed by jack-knifing. Localization of the full-length MBD3, which connects the deacetylase and chromatin remodeling modules in NuRD, has not previously been possible; our models indicate two different locations for MBD3, suggesting a mechanism by which MBD3 in the presence of GATAD2A asymmetrically bridges the two modules in NuRD. Further, our models uncovered three previously unrecognized subunit interfaces in NuDe: HDAC1C -MTA1BAH , MTA1BAH -MBD3MBD , and HDAC160-100 -MBD3MBD . Our approach also allowed us to localize regions of unknown structure, such as HDAC1C and MBD3IDR , thereby resulting in the most complete and robustly cross-validated structural characterization of these NuRD sub-complexes so far.
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Affiliation(s)
- Shreyas Arvindekar
- National Centre for Biological SciencesTata Institute of Fundamental ResearchBangaloreIndia
| | - Matthew J. Jackman
- School of Chemistry and Molecular BiosciencesUniversity of QueenslandBrisbaneQueenslandAustralia
| | - Jason K. K. Low
- School of Life and Environmental SciencesUniversity of SydneySydneyNew South WalesAustralia
| | - Michael J. Landsberg
- School of Chemistry and Molecular BiosciencesUniversity of QueenslandBrisbaneQueenslandAustralia
| | - Joel P. Mackay
- School of Life and Environmental SciencesUniversity of SydneySydneyNew South WalesAustralia
| | - Shruthi Viswanath
- National Centre for Biological SciencesTata Institute of Fundamental ResearchBangaloreIndia
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10
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Robbe ZL, Shi W, Wasson LK, Scialdone AP, Wilczewski CM, Sheng X, Hepperla AJ, Akerberg BN, Pu WT, Cristea IM, Davis IJ, Conlon FL. CHD4 is recruited by GATA4 and NKX2-5 to repress noncardiac gene programs in the developing heart. Genes Dev 2022; 36:468-482. [PMID: 35450884 PMCID: PMC9067406 DOI: 10.1101/gad.349154.121] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 03/31/2022] [Indexed: 12/23/2022]
Abstract
The nucleosome remodeling and deacetylase (NuRD) complex is one of the central chromatin remodeling complexes that mediates gene repression. NuRD is essential for numerous developmental events, including heart development. Clinical and genetic studies have provided direct evidence for the role of chromodomain helicase DNA-binding protein 4 (CHD4), the catalytic component of NuRD, in congenital heart disease (CHD), including atrial and ventricular septal defects. Furthermore, it has been demonstrated that CHD4 is essential for mammalian cardiomyocyte formation and function. A key unresolved question is how CHD4/NuRD is localized to specific cardiac target genes, as neither CHD4 nor NuRD can directly bind DNA. Here, we coupled a bioinformatics-based approach with mass spectrometry analyses to demonstrate that CHD4 interacts with the core cardiac transcription factors GATA4, NKX2-5, and TBX5 during embryonic heart development. Using transcriptomics and genome-wide occupancy data, we characterized the genomic landscape of GATA4, NKX2-5, and TBX5 repression and defined the direct cardiac gene targets of the GATA4-CHD4, NKX2-5-CHD4, and TBX5-CHD4 complexes. These data were used to identify putative cis-regulatory elements controlled by these complexes. We genetically interrogated two of these silencers in vivo: Acta1 and Myh11 We show that deletion of these silencers leads to inappropriate skeletal and smooth muscle gene misexpression, respectively, in the embryonic heart. These results delineate how CHD4/NuRD is localized to specific cardiac loci and explicates how mutations in the broadly expressed CHD4 protein lead to cardiac-specific disease states.
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Affiliation(s)
- Zachary L Robbe
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Wei Shi
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Lauren K Wasson
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Angel P Scialdone
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Caralynn M Wilczewski
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Xinlei Sheng
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Austin J Hepperla
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Brynn N Akerberg
- Department of Cardiology, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - William T Pu
- Department of Cardiology, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Ian J Davis
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Frank L Conlon
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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11
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Steindel M, Orsine de Almeida I, Strawbridge S, Chernova V, Holcman D, Ponjavic A, Basu S. Studying the Dynamics of Chromatin-Binding Proteins in Mammalian Cells Using Single-Molecule Localization Microscopy. Methods Mol Biol 2022; 2476:209-247. [PMID: 35635707 DOI: 10.1007/978-1-0716-2221-6_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Single-molecule localization microscopy (SMLM) allows the super-resolved imaging of proteins within mammalian nuclei at spatial resolutions comparable to that of a nucleosome itself (~20 nm). The technique is therefore well suited to the study of chromatin structure. Fixed-cell SMLM has already allowed temporal "snapshots" of how proteins are arranged on chromatin within mammalian nuclei. In this chapter, we focus on how recent developments, for example in selective plane illumination, 3D SMLM, and protein labeling, have led to a range of live-cell SMLM studies. We describe how to carry out single-particle tracking (SPT) of single proteins and, by analyzing their diffusion parameters, how to determine whether proteins interact with chromatin, diffuse freely, or do both. We can study the numbers of proteins that interact with chromatin and also determine their residence time on chromatin. We can determine whether these proteins form functional clusters within the nucleus as well as whether they form specific nuclear structures.
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Affiliation(s)
- Maike Steindel
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | | | - Stanley Strawbridge
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Valentyna Chernova
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - David Holcman
- Group of Computational Biology and Applied Mathematics, Institute of Biology, Ecole Normale Supérieure, Paris, France
| | - Aleks Ponjavic
- School of Physics and Astronomy and School of Food Science and Nutrition, University of Leeds, Leeds, UK.
| | - Srinjan Basu
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
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12
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Kohli S, Gulati P, Narang A, Maini J, Shamsudheen KV, Pandey R, Scaria V, Sivasubbu S, Brahmachari V. Genome and transcriptome analysis of the mealybug Maconellicoccus hirsutus: Correlation with its unique phenotypes. Genomics 2021; 113:2483-2494. [PMID: 34022346 DOI: 10.1016/j.ygeno.2021.05.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 04/02/2021] [Accepted: 05/17/2021] [Indexed: 11/27/2022]
Abstract
Mealybugs are aggressive pests with world-wide distribution and are suitable for the study of different phenomena like genomic imprinting and epigenetics. Genomic approaches facilitate these studies in absence of robust genetics in this system. We sequenced, de novo assembled, annotated Maconellicoccus hirsutus genome. We carried out comparative genomics it with four mealybug and eight other insect species, to identify expanded, specific and contracted gene classes that relate to pesticide and desiccation resistance. We identified horizontally transferred genes adding to the mutualism between the mealybug and its endosymbionts. Male and female transcriptome analysis indicates differential expression of metabolic pathway genes correlating with their physiology and the genes for sexual dimorphism. The significantly lower expression of endosymbiont genes in males relates to the depletion of endosymbionts in males during development.
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Affiliation(s)
- Surbhi Kohli
- Dr.B.R.Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| | - Parul Gulati
- Dr.B.R.Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| | - Ankita Narang
- Dr.B.R.Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India.
| | - Jayant Maini
- Dr.B.R.Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| | - K V Shamsudheen
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Rajesh Pandey
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Vinod Scaria
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | | | - Vani Brahmachari
- Dr.B.R.Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India.
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13
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Larrigan S, Shah S, Fernandes A, Mattar P. Chromatin Remodeling in the Brain-a NuRDevelopmental Odyssey. Int J Mol Sci 2021; 22:ijms22094768. [PMID: 33946340 PMCID: PMC8125410 DOI: 10.3390/ijms22094768] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 04/27/2021] [Indexed: 01/07/2023] Open
Abstract
During brain development, the genome must be repeatedly reconfigured in order to facilitate neuronal and glial differentiation. A host of chromatin remodeling complexes facilitates this process. At the genetic level, the non-redundancy of these complexes suggests that neurodevelopment may require a lexicon of remodelers with different specificities and activities. Here, we focus on the nucleosome remodeling and deacetylase (NuRD) complex. We review NuRD biochemistry, genetics, and functions in neural progenitors and neurons.
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Affiliation(s)
- Sarah Larrigan
- Department of Cell and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (S.L.); (S.S.); (A.F.)
- Ottawa Health Research Institute (OHRI), Ottawa, ON K1H 8L6, Canada
| | - Sujay Shah
- Department of Cell and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (S.L.); (S.S.); (A.F.)
- Ottawa Health Research Institute (OHRI), Ottawa, ON K1H 8L6, Canada
| | - Alex Fernandes
- Department of Cell and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (S.L.); (S.S.); (A.F.)
- Ottawa Health Research Institute (OHRI), Ottawa, ON K1H 8L6, Canada
| | - Pierre Mattar
- Department of Cell and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (S.L.); (S.S.); (A.F.)
- Ottawa Health Research Institute (OHRI), Ottawa, ON K1H 8L6, Canada
- Correspondence:
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14
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Hart P', Hommen P, Noisier A, Krzyzanowski A, Schüler D, Porfetye AT, Akbarzadeh M, Vetter IR, Adihou H, Waldmann H. Structure Based Design of Bicyclic Peptide Inhibitors of RbAp48. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202009749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Peter 't Hart
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Chemical Genomics Centre of the Max Planck Society Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Pascal Hommen
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Chemical Genomics Centre of the Max Planck Society Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Anaïs Noisier
- Medicinal Chemistry, Research and Early Development Cardiovascular Renal and Metabolism, BioPharmaceutical R&D AstraZeneca Gothenburg Sweden
| | - Adrian Krzyzanowski
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Darijan Schüler
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Arthur T. Porfetye
- Department of Mechanistic Cell Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Mohammad Akbarzadeh
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Ingrid R. Vetter
- Department of Mechanistic Cell Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Hélène Adihou
- Medicinal Chemistry, Research and Early Development Cardiovascular Renal and Metabolism, BioPharmaceutical R&D AstraZeneca Gothenburg Sweden
- AstraZeneca MPI Satellite Unit Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Herbert Waldmann
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
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15
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Hart P', Hommen P, Noisier A, Krzyzanowski A, Schüler D, Porfetye AT, Akbarzadeh M, Vetter IR, Adihou H, Waldmann H. Structure Based Design of Bicyclic Peptide Inhibitors of RbAp48. Angew Chem Int Ed Engl 2021; 60:1813-1820. [PMID: 33022847 PMCID: PMC7894522 DOI: 10.1002/anie.202009749] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Indexed: 12/11/2022]
Abstract
The scaffolding protein RbAp48 is part of several epigenetic regulation complexes and is overexpressed in a variety of cancers. In order to develop tool compounds for the study of RbAp48 function, we have developed peptide inhibitors targeting the protein-protein interaction interface between RbAp48 and the scaffold protein MTA1. Based on a MTA1-derived linear peptide with low micromolar affinity and informed by crystallographic analysis, a bicyclic peptide was developed that inhibits the RbAp48/MTA1 interaction with a very low nanomolar KD value of 8.56 nM, and which showed appreciable stability against cellular proteases. Design included exchange of a polar amide cyclization strategy to hydrophobic aromatic linkers enabling mono- and bicyclization by means of cysteine alkylation, which improved affinity by direct interaction of the linkers with a hydrophobic residue on RbAp48. Our results demonstrate that stepwise evolution of a structure-based design is a suitable strategy for inhibitor development targeting PPIs.
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Affiliation(s)
- Peter 't Hart
- Department of Chemical BiologyMax Planck Institute of Molecular PhysiologyOtto-Hahn-Strasse 1144227DortmundGermany
- Chemical Genomics Centre of the Max Planck SocietyMax Planck Institute of Molecular PhysiologyOtto-Hahn-Strasse 1144227DortmundGermany
| | - Pascal Hommen
- Department of Chemical BiologyMax Planck Institute of Molecular PhysiologyOtto-Hahn-Strasse 1144227DortmundGermany
- Chemical Genomics Centre of the Max Planck SocietyMax Planck Institute of Molecular PhysiologyOtto-Hahn-Strasse 1144227DortmundGermany
| | - Anaïs Noisier
- Medicinal Chemistry, Research and Early Development CardiovascularRenal and Metabolism, BioPharmaceutical R&DAstraZenecaGothenburgSweden
| | - Adrian Krzyzanowski
- Department of Chemical BiologyMax Planck Institute of Molecular PhysiologyOtto-Hahn-Strasse 1144227DortmundGermany
| | - Darijan Schüler
- Department of Chemical BiologyMax Planck Institute of Molecular PhysiologyOtto-Hahn-Strasse 1144227DortmundGermany
| | - Arthur T. Porfetye
- Department of Mechanistic Cell BiologyMax Planck Institute of Molecular PhysiologyOtto-Hahn-Strasse 1144227DortmundGermany
| | - Mohammad Akbarzadeh
- Department of Chemical BiologyMax Planck Institute of Molecular PhysiologyOtto-Hahn-Strasse 1144227DortmundGermany
| | - Ingrid R. Vetter
- Department of Mechanistic Cell BiologyMax Planck Institute of Molecular PhysiologyOtto-Hahn-Strasse 1144227DortmundGermany
| | - Hélène Adihou
- Medicinal Chemistry, Research and Early Development CardiovascularRenal and Metabolism, BioPharmaceutical R&DAstraZenecaGothenburgSweden
- AstraZeneca MPI Satellite UnitDepartment of Chemical BiologyMax Planck Institute of Molecular PhysiologyOtto-Hahn-Strasse 1144227DortmundGermany
| | - Herbert Waldmann
- Department of Chemical BiologyMax Planck Institute of Molecular PhysiologyOtto-Hahn-Strasse 1144227DortmundGermany
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16
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Xu G, Lyu H, Yi Y, Peng Y, Feng Q, Song Q, Gong C, Peng X, Palli SR, Zheng S. Intragenic DNA methylation regulates insect gene expression and reproduction through the MBD/Tip60 complex. iScience 2021; 24:102040. [PMID: 33521602 PMCID: PMC7820559 DOI: 10.1016/j.isci.2021.102040] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/12/2020] [Accepted: 01/04/2021] [Indexed: 12/31/2022] Open
Abstract
DNA methylation is an important epigenetic modification. However, the regulations and functions of insect intragenic DNA methylation remain unknown. Here, we demonstrate that a regulatory mechanism involving intragenic DNA methylation controls ovarian and embryonic developmental processes in Bombyx mori. In B. mori, DNA methylation is found near the transcription start site (TSS) of ovarian genes. By promoter activity analysis, we observed that 5′ UTR methylation enhances gene expression. Moreover, methyl-DNA-binding domain protein 2/3 (MBD2/3) binds to the intragenic methyl-CpG fragment and recruits acetyltransferase Tip60 to promote histone H3K27 acetylation and gene expression. Additionally, genome-wide analyses showed that the peak of H3K27 acetylation appears near the TSS of methyl-modified genes, and DNA methylation is enriched in genes involved in protein synthesis in the B. mori ovary, with MBD2/3 knockdown resulting in decreased fecundity. These data uncover a mechanism of gene body methylation for regulating insect gene expression and reproduction. Insect intragenic 5mC enhances gene expression through histone H3K27 acetylation MBD2/3 binds the intragenic 5mC and recruits Tip60 to promote H3K27 acetylation Intragenic 5mCs modify protein synthesis-related genes in insect ovaries The intragenic 5mC plays a role in insect reproduction
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Affiliation(s)
- Guanfeng Xu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Hao Lyu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Yangqin Yi
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Yuling Peng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Qili Feng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Qisheng Song
- Division of Plant Sciences, College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, MO 65211, USA
| | - Chengcheng Gong
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Xuezhen Peng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Subba Reddy Palli
- Department of Entomology, University of Kentucky, Lexington, KY 40546, USA
| | - Sichun Zheng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
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17
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Mazina MY, Vorobyeva NE. Chromatin Modifiers in Transcriptional Regulation: New Findings and Prospects. Acta Naturae 2021; 13:16-30. [PMID: 33959384 PMCID: PMC8084290 DOI: 10.32607/actanaturae.11101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 12/17/2020] [Indexed: 02/04/2023] Open
Abstract
Histone-modifying and remodeling complexes are considered the main coregulators that affect transcription by changing the chromatin structure. Coordinated action by these complexes is essential for the transcriptional activation of any eukaryotic gene. In this review, we discuss current trends in the study of histone modifiers and chromatin remodelers, including the functional impact of transcriptional proteins/ complexes i.e., "pioneers"; remodeling and modification of non-histone proteins by transcriptional complexes; the supplementary functions of the non-catalytic subunits of remodelers, and the participation of histone modifiers in the "pause" of RNA polymerase II. The review also includes a scheme illustrating the mechanisms of recruitment of the main classes of remodelers and chromatin modifiers to various sites in the genome and their functional activities.
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Affiliation(s)
- M. Yu. Mazina
- Institute of Gene Biology RAS, Group of transcriptional complexes dynamics, Moscow, 119334 Russia
| | - N. E. Vorobyeva
- Institute of Gene Biology RAS, Group of transcriptional complexes dynamics, Moscow, 119334 Russia
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18
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Millard CJ, Fairall L, Ragan TJ, Savva CG, Schwabe JWR. The topology of chromatin-binding domains in the NuRD deacetylase complex. Nucleic Acids Res 2020; 48:12972-12982. [PMID: 33264408 PMCID: PMC7736783 DOI: 10.1093/nar/gkaa1121] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/22/2020] [Accepted: 11/03/2020] [Indexed: 01/22/2023] Open
Abstract
Class I histone deacetylase complexes play essential roles in many nuclear processes. Whilst they contain a common catalytic subunit, they have diverse modes of action determined by associated factors in the distinct complexes. The deacetylase module from the NuRD complex contains three protein domains that control the recruitment of chromatin to the deacetylase enzyme, HDAC1/2. Using biochemical approaches and cryo-electron microscopy, we have determined how three chromatin-binding domains (MTA1-BAH, MBD2/3 and RBBP4/7) are assembled in relation to the core complex so as to facilitate interaction of the complex with the genome. We observe a striking arrangement of the BAH domains suggesting a potential mechanism for binding to di-nucleosomes. We also find that the WD40 domains from RBBP4 are linked to the core with surprising flexibility that is likely important for chromatin engagement. A single MBD2 protein binds asymmetrically to the dimerisation interface of the complex. This symmetry mismatch explains the stoichiometry of the complex. Finally, our structures suggest how the holo-NuRD might assemble on a di-nucleosome substrate.
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Affiliation(s)
- Christopher J Millard
- The Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Louise Fairall
- The Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Timothy J Ragan
- The Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Christos G Savva
- The Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - John W R Schwabe
- The Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
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19
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Spruijt CG, Gräwe C, Kleinendorst SC, Baltissen MPA, Vermeulen M. Cross-linking mass spectrometry reveals the structural topology of peripheral NuRD subunits relative to the core complex. FEBS J 2020; 288:3231-3245. [PMID: 33283408 PMCID: PMC8246863 DOI: 10.1111/febs.15650] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 10/23/2020] [Accepted: 11/27/2020] [Indexed: 01/08/2023]
Abstract
The multi‐subunit nucleosome remodeling and deacetylase (NuRD) complex consists of seven subunits, each of which comprises two or three paralogs in vertebrates. These paralogs define mutually exclusive and functionally distinct complexes. In addition, several proteins in the complex are multimeric, which complicates structural studies. Attempts to purify sufficient amounts of endogenous complex or recombinantly reconstitute the complex for structural studies have proven quite challenging. Until now, only substructures of individual domains or proteins and low‐resolution densities of (partial) complexes have been reported. In this study, we comprehensively investigated the relative orientation of different subunits within the NuRD complex using multiple cross‐link IP mass spectrometry (xIP‐MS) experiments. Our results confirm that the core of the complex is formed by MTA, RBBP, and HDAC proteins. Assembly of a copy of MBD and GATAD2 onto this core enables binding of the peripheral CHD and CDK2AP proteins. Furthermore, our experiments reveal that not only CDK2AP1 but also CDK2AP2 interacts with the NuRD complex. This interaction requires the C terminus of CHD proteins. Our data provide a more detailed understanding of the topology of the peripheral NuRD subunits relative to the core complex. Database Proteomics data are available in the PRIDE database under the accession numbers PXD017244 and PXD017378.
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Affiliation(s)
- Cornelia G Spruijt
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Cathrin Gräwe
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Simone C Kleinendorst
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Marijke P A Baltissen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
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20
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Low JKK, Silva APG, Sharifi Tabar M, Torrado M, Webb SR, Parker BL, Sana M, Smits C, Schmidberger JW, Brillault L, Jackman MJ, Williams DC, Blobel GA, Hake SB, Shepherd NE, Landsberg MJ, Mackay JP. The Nucleosome Remodeling and Deacetylase Complex Has an Asymmetric, Dynamic, and Modular Architecture. Cell Rep 2020; 33:108450. [PMID: 33264611 PMCID: PMC8908386 DOI: 10.1016/j.celrep.2020.108450] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 09/23/2020] [Accepted: 11/09/2020] [Indexed: 12/15/2022] Open
Abstract
The nucleosome remodeling and deacetylase (NuRD) complex is essential for metazoan development but has been refractory to biochemical analysis. We present an integrated analysis of the native mammalian NuRD complex, combining quantitative mass spectrometry, cross-linking, protein biochemistry, and electron microscopy to define the architecture of the complex. NuRD is built from a 2:2:4 (MTA, HDAC, and RBBP) deacetylase module and a 1:1:1 (MBD, GATAD2, and Chromodomain-Helicase-DNA-binding [CHD]) remodeling module, and the complex displays considerable structural dynamics. The enigmatic GATAD2 controls the asymmetry of the complex and directly recruits the CHD remodeler. The MTA-MBD interaction acts as a point of functional switching, with the transcriptional regulator PWWP2A competing with MBD for binding to the MTA-HDAC-RBBP subcomplex. Overall, our data address the long-running controversy over NuRD stoichiometry, provide imaging of the mammalian NuRD complex, and establish the biochemical mechanism by which PWWP2A can regulate NuRD composition. Low et al. examine the architecture of the nucleosome remodeling and deacetylase complex. They define its stoichiometry, use cross-linking mass spectrometry to define subunit locations, and use electron microscopy to reveal large-scale dynamics. They also demonstrate that PWWP2A competes with MBD3 to sequester the HDAC-MTA-RBBP module from NuRD.
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Affiliation(s)
- Jason K K Low
- School of Life and Environmental Sciences, University of Sydney, NSW, Australia.
| | - Ana P G Silva
- School of Life and Environmental Sciences, University of Sydney, NSW, Australia
| | - Mehdi Sharifi Tabar
- School of Life and Environmental Sciences, University of Sydney, NSW, Australia
| | - Mario Torrado
- School of Life and Environmental Sciences, University of Sydney, NSW, Australia
| | - Sarah R Webb
- School of Life and Environmental Sciences, University of Sydney, NSW, Australia
| | - Benjamin L Parker
- School of Life and Environmental Sciences, University of Sydney, NSW, Australia
| | - Maryam Sana
- School of Life and Environmental Sciences, University of Sydney, NSW, Australia
| | | | | | - Lou Brillault
- School of Chemistry and Molecular Biosciences, University of Queensland, QLD, Australia
| | - Matthew J Jackman
- School of Chemistry and Molecular Biosciences, University of Queensland, QLD, Australia
| | - David C Williams
- Dept of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, NC, USA
| | - Gerd A Blobel
- The Division of Hematology, Children's Hospital of Philadelphia, and the Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sandra B Hake
- Institute for Genetics, FB08 Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Nicholas E Shepherd
- School of Life and Environmental Sciences, University of Sydney, NSW, Australia
| | - Michael J Landsberg
- School of Chemistry and Molecular Biosciences, University of Queensland, QLD, Australia.
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, NSW, Australia.
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21
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Liu X, Wang J. The nucleosome remodeling and deacetylase complex has prognostic significance and associates with immune microenvironment in skin cutaneous melanoma. Int Immunopharmacol 2020; 88:106887. [PMID: 32799111 DOI: 10.1016/j.intimp.2020.106887] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/04/2020] [Accepted: 08/07/2020] [Indexed: 02/08/2023]
Abstract
PURPOSE The Nucleosome Remodeling and Deacetylase (NuRD) complex is an important marker in multiple biological processes whose clinical significance has rarely previously been reported in cancers. In this study, we proposed to estimate the potential of NuRD complex as prognostic signature in skin cutaneous melanoma (SKCM) patients. METHODS SKCM samples were obtained from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). Sample clustering was performed based on the mRNA levels of core subunits of NuRD complex. Survival analysis was carried out by using Kaplan-Meier method. SKCM samples were grouped into prognostically good and poor groups according to their overall survival (OS). Logistic regression analysis was adopted to construct a model based on the optimal subunits of NuRD complex to estimate prognosis of SKCM samples. RESULTS Samples from TCGA were grouped into four clusters which were then divided into good and poor prognostic groups. Significant differences existed in immune microenvironment and mutational rates of frequently mutated genes between good and poor prognostic groups. Besides, several immune-related pathways were significantly activated in good prognostic group. A logistic regression model was constructed by using patients' prognostic group and mRNA expressions of NuRD complex from TCGA as categorical responsive values and continuous predictive variables, respectively, which could independently distinguish prognostically different SKCM patients from another three independent GEO datasets. CONCLUSION In conclusion, we first reported the potential prognostic value and roles in immune microenvironment of NuRD complex in SKCM, which should be helpful for experimental and clinical research in SKCM.
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Affiliation(s)
- Xinhua Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou 311121, China.
| | - Ju Wang
- School of Biomedical Engineering and Technology, Tianjin Medical University, Tianjin 300070, PR China.
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22
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Abstract
Derivation of induced Pluripotent Stem Cells (iPSCs) by reprogramming somatic cells to a pluripotent state has revolutionized stem cell research. Ensuing this, various groups have used genetic and non-genetic approaches to generate iPSCs from numerous cell types. However, achieving a pluripotent state in most of the reprogramming studies is marred by serious limitations such as low reprogramming efficiency and slow kinetics. These limitations are mainly due to the presence of potent barriers that exist during reprogramming when a mature cell is coaxed to achieve a pluripotent state. Several studies have revealed that intrinsic factors such as non-optimal stoichiometry of reprogramming factors, specific signaling pathways, cellular senescence, pluripotency-inhibiting transcription factors and microRNAs act as a roadblock. In addition, the epigenetic state of somatic cells and specific epigenetic modifications that occur during reprogramming also remarkably impede the generation of iPSCs. In this review, we present a comprehensive overview of the barriers that inhibit reprogramming and the understanding of which will pave the way to develop safe strategies for efficient reprogramming.
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23
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Marques JG, Gryder BE, Pavlovic B, Chung Y, Ngo QA, Frommelt F, Gstaiger M, Song Y, Benischke K, Laubscher D, Wachtel M, Khan J, Schäfer BW. NuRD subunit CHD4 regulates super-enhancer accessibility in rhabdomyosarcoma and represents a general tumor dependency. eLife 2020; 9:54993. [PMID: 32744500 PMCID: PMC7438112 DOI: 10.7554/elife.54993] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 08/02/2020] [Indexed: 12/15/2022] Open
Abstract
The NuRD complex subunit CHD4 is essential for fusion-positive rhabdomyosarcoma (FP-RMS) survival, but the mechanisms underlying this dependency are not understood. Here, a NuRD-specific CRISPR screen demonstrates that FP-RMS is particularly sensitive to CHD4 amongst the NuRD members. Mechanistically, NuRD complex containing CHD4 localizes to super-enhancers where CHD4 generates a chromatin architecture permissive for the binding of the tumor driver and fusion protein PAX3-FOXO1, allowing downstream transcription of its oncogenic program. Moreover, CHD4 depletion removes HDAC2 from the chromatin, leading to an increase and spread of histone acetylation, and prevents the positioning of RNA Polymerase 2 at promoters impeding transcription initiation. Strikingly, analysis of genome-wide cancer dependency databases identifies CHD4 as a general cancer vulnerability. Our findings describe CHD4, a classically defined repressor, as positive regulator of transcription and super-enhancer accessibility as well as establish this remodeler as an unexpected broad tumor susceptibility and promising drug target for cancer therapy.
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Affiliation(s)
- Joana G Marques
- Department of Oncology and Children's Research Center, University Children's Hospital, Zurich, Switzerland
| | - Berkley E Gryder
- Oncogenomics Section, Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Blaz Pavlovic
- Department of Oncology and Children's Research Center, University Children's Hospital, Zurich, Switzerland
| | - Yeonjoo Chung
- Department of Oncology and Children's Research Center, University Children's Hospital, Zurich, Switzerland
| | - Quy A Ngo
- Department of Oncology and Children's Research Center, University Children's Hospital, Zurich, Switzerland
| | - Fabian Frommelt
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Matthias Gstaiger
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Young Song
- Oncogenomics Section, Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Katharina Benischke
- Department of Oncology and Children's Research Center, University Children's Hospital, Zurich, Switzerland
| | - Dominik Laubscher
- Department of Oncology and Children's Research Center, University Children's Hospital, Zurich, Switzerland
| | - Marco Wachtel
- Department of Oncology and Children's Research Center, University Children's Hospital, Zurich, Switzerland
| | - Javed Khan
- Oncogenomics Section, Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Beat W Schäfer
- Department of Oncology and Children's Research Center, University Children's Hospital, Zurich, Switzerland
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Differential regulation of lineage commitment in human and mouse primed pluripotent stem cells by the nucleosome remodelling and deacetylation complex. Stem Cell Res 2020; 46:101867. [PMID: 32535494 PMCID: PMC7347010 DOI: 10.1016/j.scr.2020.101867] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 05/04/2020] [Accepted: 05/25/2020] [Indexed: 12/12/2022] Open
Abstract
Differentiation of mammalian pluripotent cells involves large-scale changes in transcription and, among the molecules that orchestrate these changes, chromatin remodellers are essential to initiate, establish and maintain a new gene regulatory network. The Nucleosome Remodelling and Deacetylation (NuRD) complex is a highly conserved chromatin remodeller which fine-tunes gene expression in embryonic stem cells. While the function of NuRD in mouse pluripotent cells has been well defined, no study yet has defined NuRD function in human pluripotent cells. Here we find that while NuRD activity is required for lineage commitment from primed pluripotency in both human and mouse cells, the nature of this requirement is surprisingly different. While mouse embryonic stem cells (mESC) and epiblast stem cells (mEpiSC) require NuRD to maintain an appropriate differentiation trajectory as judged by gene expression profiling, human induced pluripotent stem cells (hiPSC) lacking NuRD fail to even initiate these trajectories. Further, while NuRD activity is dispensable for self-renewal of mESCs and mEpiSCs, hiPSCs require NuRD to maintain a stable self-renewing state. These studies reveal that failure to properly fine-tune gene expression and/or to reduce transcriptional noise through the action of a highly conserved chromatin remodeller can have different consequences in human and mouse pluripotent stem cells.
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25
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Wang ZA, Millard CJ, Lin CL, Gurnett JE, Wu M, Lee K, Fairall L, Schwabe JWR, Cole PA. Diverse nucleosome Site-Selectivity among histone deacetylase complexes. eLife 2020; 9:e57663. [PMID: 32501215 PMCID: PMC7316510 DOI: 10.7554/elife.57663] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 06/04/2020] [Indexed: 02/06/2023] Open
Abstract
Histone acetylation regulates chromatin structure and gene expression and is removed by histone deacetylases (HDACs). HDACs are commonly found in various protein complexes to confer distinct cellular functions, but how the multi-subunit complexes influence deacetylase activities and site-selectivities in chromatin is poorly understood. Previously we reported the results of studies on the HDAC1 containing CoREST complex and acetylated nucleosome substrates which revealed a notable preference for deacetylation of histone H3 acetyl-Lys9 vs. acetyl-Lys14 (Wu et al, 2018). Here we analyze the enzymatic properties of five class I HDAC complexes: CoREST, NuRD, Sin3B, MiDAC and SMRT with site-specific acetylated nucleosome substrates. Our results demonstrate that these HDAC complexes show a wide variety of deacetylase rates in a site-selective manner. A Gly13 in the histone H3 tail is responsible for a sharp reduction in deacetylase activity of the CoREST complex for H3K14ac. These studies provide a framework for connecting enzymatic and biological functions of specific HDAC complexes.
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Affiliation(s)
- Zhipeng A Wang
- Division of Genetics, Department of Medicine, Brigham and Women’s HospitalBostonUnited States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical SchoolBostonUnited States
| | - Christopher J Millard
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of LeicesterLeicesterUnited Kingdom
| | - Chia-Liang Lin
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of LeicesterLeicesterUnited Kingdom
| | - Jennifer E Gurnett
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of LeicesterLeicesterUnited Kingdom
| | - Mingxuan Wu
- Division of Genetics, Department of Medicine, Brigham and Women’s HospitalBostonUnited States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical SchoolBostonUnited States
| | - Kwangwoon Lee
- Division of Genetics, Department of Medicine, Brigham and Women’s HospitalBostonUnited States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical SchoolBostonUnited States
| | - Louise Fairall
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of LeicesterLeicesterUnited Kingdom
| | - John WR Schwabe
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of LeicesterLeicesterUnited Kingdom
| | - Philip A Cole
- Division of Genetics, Department of Medicine, Brigham and Women’s HospitalBostonUnited States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical SchoolBostonUnited States
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26
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Mugat B, Nicot S, Varela-Chavez C, Jourdan C, Sato K, Basyuk E, Juge F, Siomi MC, Pélisson A, Chambeyron S. The Mi-2 nucleosome remodeler and the Rpd3 histone deacetylase are involved in piRNA-guided heterochromatin formation. Nat Commun 2020; 11:2818. [PMID: 32499524 PMCID: PMC7272611 DOI: 10.1038/s41467-020-16635-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 05/11/2020] [Indexed: 12/15/2022] Open
Abstract
In eukaryotes, trimethylation of lysine 9 on histone H3 (H3K9) is associated with transcriptional silencing of transposable elements (TEs). In drosophila ovaries, this heterochromatic repressive mark is thought to be deposited by SetDB1 on TE genomic loci after the initial recognition of nascent transcripts by PIWI-interacting RNAs (piRNAs) loaded on the Piwi protein. Here, we show that the nucleosome remodeler Mi-2, in complex with its partner MEP-1, forms a subunit that is transiently associated, in a MEP-1 C-terminus-dependent manner, with known Piwi interactors, including a recently reported SUMO ligase, Su(var)2-10. Together with the histone deacetylase Rpd3, this module is involved in the piRNA-dependent TE silencing, correlated with H3K9 deacetylation and trimethylation. Therefore, drosophila piRNA-mediated transcriptional silencing involves three epigenetic effectors, a remodeler, Mi-2, an eraser, Rpd3 and a writer, SetDB1, in addition to the Su(var)2-10 SUMO ligase.
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Affiliation(s)
- Bruno Mugat
- Institute of Human Genetics, UMR9002, CNRS and Univ. Montpellier, Montpellier, France
| | - Simon Nicot
- Institute of Human Genetics, UMR9002, CNRS and Univ. Montpellier, Montpellier, France
| | | | - Christophe Jourdan
- Institute of Human Genetics, UMR9002, CNRS and Univ. Montpellier, Montpellier, France
| | - Kaoru Sato
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Eugenia Basyuk
- Institute of Human Genetics, UMR9002, CNRS and Univ. Montpellier, Montpellier, France
| | - François Juge
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Mikiko C Siomi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Alain Pélisson
- Institute of Human Genetics, UMR9002, CNRS and Univ. Montpellier, Montpellier, France
| | - Séverine Chambeyron
- Institute of Human Genetics, UMR9002, CNRS and Univ. Montpellier, Montpellier, France.
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27
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Guo Q, Cheng K, Wang X, Li X, Yu Y, Hua Y, Yang Z. Expression of HDAC1 and RBBP4 correlate with clinicopathologic characteristics and prognosis in breast cancer. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2020; 13:563-572. [PMID: 32269697 PMCID: PMC7137008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 02/07/2020] [Indexed: 06/11/2023]
Abstract
Retinoblastoma binding protein 4 (RBBP4) plays an important role in transcription, cell cycle, and proliferation. Immunohistochemistry was performed to assess HDAC1 and RBBP4 expression in 240 BC patients. The expression of HDAC1 and RBBP4 in 12 pairs of BC tissues and their normal tissues was determined by western blotting. Kaplan-Meier analysis and Cox's proportional hazards regression were applied to evaluate the prognostic significance of HDAC1 and RBBP4. HDAC1 and RBBP4 expression in BC was significantly higher than that in normal tissues. HDAC1 was positively correlated with RBBP4 in breast cancer. HDAC1 and RBBP4 were negatively correlated with ER and PR in BC, respectively. The patients with high expression of RBBP4 had a worse overall survival time. The expression of RBBP4 was found to be significantly correlated with lymph node metastasis. RBBP4 may play a major role though HDAC1 in the development, metastasis, and prognosis of BC.
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Affiliation(s)
- Qingqun Guo
- Department of Thyroid and Breast Surgery, Binzhou Medical University Hospital Binzhou, Shandong, China
| | - Kai Cheng
- Department of Thyroid and Breast Surgery, Binzhou Medical University Hospital Binzhou, Shandong, China
| | - Xiaohong Wang
- Department of Thyroid and Breast Surgery, Binzhou Medical University Hospital Binzhou, Shandong, China
| | - Xiaoqiang Li
- Department of Thyroid and Breast Surgery, Binzhou Medical University Hospital Binzhou, Shandong, China
| | - Yue Yu
- Department of Thyroid and Breast Surgery, Binzhou Medical University Hospital Binzhou, Shandong, China
| | - Yitong Hua
- Department of Thyroid and Breast Surgery, Binzhou Medical University Hospital Binzhou, Shandong, China
| | - Zhenlin Yang
- Department of Thyroid and Breast Surgery, Binzhou Medical University Hospital Binzhou, Shandong, China
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28
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Pierson TM, Otero MG, Grand K, Choi A, Graham JM, Young JI, Mackay JP. The NuRD complex and macrocephaly associated neurodevelopmental disorders. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2019; 181:548-556. [PMID: 31737996 DOI: 10.1002/ajmg.c.31752] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 10/08/2019] [Accepted: 10/10/2019] [Indexed: 12/13/2022]
Abstract
The nucleosome remodeling and deacetylase (NuRD) complex is a major regulator of gene expression involved in pluripotency, lineage commitment, and corticogenesis. This important complex is composed of seven different proteins, with mutations in CHD3, CHD4, and GATAD2B being associated with neurodevelopmental disorders presenting with macrocephaly and intellectual disability similar to other overgrowth and intellectual disability (OGID) syndromes. Pathogenic variants in CHD3 and CHD4 primarily involve disruption of enzymatic function. GATAD2B variants include loss-of-function mutations that alter protein dosage and missense variants that involve either of two conserved domains (CR1 and CR2) known to interact with other NuRD proteins. In addition to macrocephaly and intellectual disability, CHD3 variants are associated with inguinal hernias and apraxia of speech; whereas CHD4 variants are associated with skeletal anomalies, deafness, and cardiac defects. GATAD2B-associated neurodevelopmental disorder (GAND) has phenotypic overlap with both of these disorders. Of note, structural models of NuRD indicate that CHD3 and CHD4 require direct contact with the GATAD2B-CR2 domain to interact with the rest of the complex. Therefore, the phenotypic overlaps of CHD3- and CHD4-related disorders with GAND are consistent with a loss in the ability of GATAD2B to recruit CHD3 or CHD4 to the complex. The shared features of these neurodevelopmental disorders may represent a new class of OGID syndrome: the NuRDopathies.
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Affiliation(s)
- Tyler Mark Pierson
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, California.,Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, California.,Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Maria G Otero
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Katheryn Grand
- Department of Pediatrics, Medical Genetics, Cedars-Sinai Medical Center, Los Angeles, California
| | - Andrew Choi
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - John M Graham
- Department of Pediatrics, Medical Genetics, Cedars-Sinai Medical Center, Los Angeles, California
| | - Juan I Young
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
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29
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Leighton G, Williams DC. The Methyl-CpG-Binding Domain 2 and 3 Proteins and Formation of the Nucleosome Remodeling and Deacetylase Complex. J Mol Biol 2019:S0022-2836(19)30599-6. [PMID: 31626804 DOI: 10.1016/j.jmb.2019.10.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 10/08/2019] [Accepted: 10/09/2019] [Indexed: 12/13/2022]
Abstract
The Nucleosome Remodeling and Deacetylase (NuRD) complex uniquely combines both deacetylase and remodeling enzymatic activities in a single macromolecular complex. The methyl-CpG-binding domain 2 and 3 (MBD2 and MBD3) proteins provide a critical structural link between the deacetylase and remodeling components, while MBD2 endows the complex with the ability to selectively recognize methylated DNA. Hence, NuRD combines three major arms of epigenetic gene regulation. Research over the past few decades has revealed much of the structural basis driving formation of this complex and started to uncover the functional roles of NuRD in epigenetic gene regulation. However, we have yet to fully understand the molecular and biophysical basis for methylation-dependent chromatin remodeling and transcription regulation by NuRD. In this review, we discuss the structural information currently available for the complex, the role MBD2 and MBD3 play in forming and recruiting the complex to methylated DNA, and the biological functions of NuRD.
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Affiliation(s)
- Gage Leighton
- Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA.
| | - David C Williams
- Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA.
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30
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Hoffmann A, Spengler D. Chromatin Remodeling Complex NuRD in Neurodevelopment and Neurodevelopmental Disorders. Front Genet 2019; 10:682. [PMID: 31396263 PMCID: PMC6667665 DOI: 10.3389/fgene.2019.00682] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 07/01/2019] [Indexed: 01/22/2023] Open
Abstract
The nucleosome remodeling and deacetylase (NuRD) complex presents one of the major chromatin remodeling complexes in mammalian cells. Here, we discuss current evidence for NuRD's role as an important epigenetic regulator of gene expression in neural stem cell (NSC) and neural progenitor cell (NPC) fate decisions in brain development. With the formation of the cerebellar and cerebral cortex, NuRD facilitates experience-dependent cerebellar plasticity and regulates additionally cerebral subtype specification and connectivity in postmitotic neurons. Consistent with these properties, genetic variation in NuRD's subunits emerges as important risk factor in common polygenic forms of neurodevelopmental disorders (NDDs) and neurodevelopment-related psychiatric disorders such as schizophrenia (SCZ) and bipolar disorder (BD). Overall, these findings highlight the critical role of NuRD in chromatin regulation in brain development and in mental health and disease.
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Affiliation(s)
| | - Dietmar Spengler
- Epigenomics of Early Life, Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
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31
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Nichane M, Loh KM. Obliterating Obstacles to an Odyssey. Cell Stem Cell 2019; 23:313-315. [PMID: 30193127 DOI: 10.1016/j.stem.2018.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Why is reprogramming to generate induced pluripotent stem cells (iPSCs) a protracted and inefficient odyssey? In this issue of Cell Stem Cell, Mor et al. (2018) hypothesize that reprogramming factors paradoxically activate and inhibit pluripotency gene expression and show that eliminating Gatad2a (a NuRD corepressor complex subcomponent) rapidly and efficiently reprograms multiple cell types into iPSCs.
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Affiliation(s)
- Massimo Nichane
- Department of Developmental Biology, Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford-UC Berkeley Siebel Stem Cell Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Kyle M Loh
- Department of Developmental Biology, Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford-UC Berkeley Siebel Stem Cell Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
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32
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Bracken AP, Brien GL, Verrijzer CP. Dangerous liaisons: interplay between SWI/SNF, NuRD, and Polycomb in chromatin regulation and cancer. Genes Dev 2019; 33:936-959. [PMID: 31123059 PMCID: PMC6672049 DOI: 10.1101/gad.326066.119] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In this review, Bracken et al. discuss the functional organization and biochemical activities of remodelers and Polycomb and explore how they work together to control cell differentiation and the maintenance of cell identity. They also discuss how mutations in the genes encoding these various chromatin regulators contribute to oncogenesis by disrupting the chromatin equilibrium. Changes in chromatin structure mediated by ATP-dependent nucleosome remodelers and histone modifying enzymes are integral to the process of gene regulation. Here, we review the roles of the SWI/SNF (switch/sucrose nonfermenting) and NuRD (nucleosome remodeling and deacetylase) and the Polycomb system in chromatin regulation and cancer. First, we discuss the basic molecular mechanism of nucleosome remodeling, and how this controls gene transcription. Next, we provide an overview of the functional organization and biochemical activities of SWI/SNF, NuRD, and Polycomb complexes. We describe how, in metazoans, the balance of these activities is central to the proper regulation of gene expression and cellular identity during development. Whereas SWI/SNF counteracts Polycomb, NuRD facilitates Polycomb repression on chromatin. Finally, we discuss how disruptions of this regulatory equilibrium contribute to oncogenesis, and how new insights into the biological functions of remodelers and Polycombs are opening avenues for therapeutic interventions on a broad range of cancer types.
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Affiliation(s)
- Adrian P Bracken
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Gerard L Brien
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - C Peter Verrijzer
- Department of Biochemistry, Erasmus University Medical Center, 3000 DR Rotterdam, the Netherlands
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33
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Burgold T, Barber M, Kloet S, Cramard J, Gharbi S, Floyd R, Kinoshita M, Ralser M, Vermeulen M, Reynolds N, Dietmann S, Hendrich B. The Nucleosome Remodelling and Deacetylation complex suppresses transcriptional noise during lineage commitment. EMBO J 2019; 38:embj.2018100788. [PMID: 31036553 PMCID: PMC6576150 DOI: 10.15252/embj.2018100788] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 03/30/2019] [Accepted: 04/02/2019] [Indexed: 12/11/2022] Open
Abstract
Multiprotein chromatin remodelling complexes show remarkable conservation of function amongst metazoans, even though components present in invertebrates are often found as multiple paralogous proteins in vertebrate complexes. In some cases, these paralogues specify distinct biochemical and/or functional activities in vertebrate cells. Here, we set out to define the biochemical and functional diversity encoded by one such group of proteins within the mammalian Nucleosome Remodelling and Deacetylation (NuRD) complex: Mta1, Mta2 and Mta3. We find that, in contrast to what has been described in somatic cells, MTA proteins are not mutually exclusive within embryonic stem (ES) cell NuRD and, despite subtle differences in chromatin binding and biochemical interactions, serve largely redundant functions. ES cells lacking all three MTA proteins exhibit complete NuRD loss of function and are viable, allowing us to identify a previously unreported function for NuRD in reducing transcriptional noise, which is essential for maintaining a proper differentiation trajectory during early stages of lineage commitment.
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Affiliation(s)
- Thomas Burgold
- Wellcome- MRC Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Michael Barber
- Wellcome- MRC Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Susan Kloet
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University, Nijmegen, The Netherlands
| | - Julie Cramard
- Wellcome- MRC Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Sarah Gharbi
- Wellcome- MRC Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Robin Floyd
- Wellcome- MRC Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Masaki Kinoshita
- Wellcome- MRC Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Meryem Ralser
- Wellcome- MRC Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University, Nijmegen, The Netherlands
| | - Nicola Reynolds
- Wellcome- MRC Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Sabine Dietmann
- Wellcome- MRC Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Brian Hendrich
- Wellcome- MRC Stem Cell Institute, University of Cambridge, Cambridge, UK .,Department of Biochemistry, University of Cambridge, Cambridge, UK
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34
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Sharifi Tabar M, Mackay JP, Low JKK. The stoichiometry and interactome of the Nucleosome Remodeling and Deacetylase (NuRD) complex are conserved across multiple cell lines. FEBS J 2019; 286:2043-2061. [DOI: 10.1111/febs.14800] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 12/27/2018] [Accepted: 03/01/2019] [Indexed: 12/13/2022]
Affiliation(s)
| | - Joel P. Mackay
- School of Life and Environmental Sciences University of Sydney Australia
| | - Jason K. K. Low
- School of Life and Environmental Sciences University of Sydney Australia
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35
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Link S, Spitzer RMM, Sana M, Torrado M, Völker-Albert MC, Keilhauer EC, Burgold T, Pünzeler S, Low JKK, Lindström I, Nist A, Regnard C, Stiewe T, Hendrich B, Imhof A, Mann M, Mackay JP, Bartkuhn M, Hake SB. PWWP2A binds distinct chromatin moieties and interacts with an MTA1-specific core NuRD complex. Nat Commun 2018; 9:4300. [PMID: 30327463 PMCID: PMC6191444 DOI: 10.1038/s41467-018-06665-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 09/17/2018] [Indexed: 12/31/2022] Open
Abstract
Chromatin structure and function is regulated by reader proteins recognizing histone modifications and/or histone variants. We recently identified that PWWP2A tightly binds to H2A.Z-containing nucleosomes and is involved in mitotic progression and cranial-facial development. Here, using in vitro assays, we show that distinct domains of PWWP2A mediate binding to free linker DNA as well as H3K36me3 nucleosomes. In vivo, PWWP2A strongly recognizes H2A.Z-containing regulatory regions and weakly binds H3K36me3-containing gene bodies. Further, PWWP2A binds to an MTA1-specific subcomplex of the NuRD complex (M1HR), which consists solely of MTA1, HDAC1, and RBBP4/7, and excludes CHD, GATAD2 and MBD proteins. Depletion of PWWP2A leads to an increase of acetylation levels on H3K27 as well as H2A.Z, presumably by impaired chromatin recruitment of M1HR. Thus, this study identifies PWWP2A as a complex chromatin-binding protein that serves to direct the deacetylase complex M1HR to H2A.Z-containing chromatin, thereby promoting changes in histone acetylation levels.
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Affiliation(s)
- Stephanie Link
- Department of Molecular Biology, BioMedical Center (BMC), Ludwig-Maximilians-University Munich, 82152, Planegg-Martinsried, Germany
- Institute for Genetics, Justus-Liebig University Giessen, 35392, Giessen, Germany
| | - Ramona M M Spitzer
- Department of Molecular Biology, BioMedical Center (BMC), Ludwig-Maximilians-University Munich, 82152, Planegg-Martinsried, Germany
- Institute for Genetics, Justus-Liebig University Giessen, 35392, Giessen, Germany
| | - Maryam Sana
- School of Life and Environmental Sciences, University of Sydney, New South Wales, 2006, Australia
| | - Mario Torrado
- School of Life and Environmental Sciences, University of Sydney, New South Wales, 2006, Australia
| | - Moritz C Völker-Albert
- Department of Molecular Biology, BioMedical Center (BMC), Ludwig-Maximilians-University Munich, 82152, Planegg-Martinsried, Germany
| | - Eva C Keilhauer
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
- Coriolis Pharma, Fraunhoferstr. 18B, 82152, Planegg, Germany
| | - Thomas Burgold
- Wellcome Trust - MRC Stem Cell Institute and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QR, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Sebastian Pünzeler
- Department of Molecular Biology, BioMedical Center (BMC), Ludwig-Maximilians-University Munich, 82152, Planegg-Martinsried, Germany
- Coparion GmbH & Co. KG, Charles-de-Gaulle-Platz 1d, 50679, Cologne, Germany
| | - Jason K K Low
- School of Life and Environmental Sciences, University of Sydney, New South Wales, 2006, Australia
| | - Ida Lindström
- School of Life and Environmental Sciences, University of Sydney, New South Wales, 2006, Australia
| | - Andrea Nist
- Genomics Core Facility, Philipps-University Marburg, 35043, Marburg, Germany
| | - Catherine Regnard
- Department of Molecular Biology, BioMedical Center (BMC), Ludwig-Maximilians-University Munich, 82152, Planegg-Martinsried, Germany
| | - Thorsten Stiewe
- Genomics Core Facility, Philipps-University Marburg, 35043, Marburg, Germany
- Institute for Molecular Oncology, Philipps-University Marburg, 35043, Marburg, Germany
| | - Brian Hendrich
- Wellcome Trust - MRC Stem Cell Institute and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QR, UK
| | - Axel Imhof
- Department of Molecular Biology, BioMedical Center (BMC), Ludwig-Maximilians-University Munich, 82152, Planegg-Martinsried, Germany
- Center for Integrated Protein Science Munich (CIPSM), 81377, Munich, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
- Center for Integrated Protein Science Munich (CIPSM), 81377, Munich, Germany
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, New South Wales, 2006, Australia
| | - Marek Bartkuhn
- Institute for Genetics, Justus-Liebig University Giessen, 35392, Giessen, Germany.
| | - Sandra B Hake
- Institute for Genetics, Justus-Liebig University Giessen, 35392, Giessen, Germany.
- Center for Integrated Protein Science Munich (CIPSM), 81377, Munich, Germany.
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36
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Zhang T, Wei G, Millard CJ, Fischer R, Konietzny R, Kessler BM, Schwabe JWR, Brockdorff N. A variant NuRD complex containing PWWP2A/B excludes MBD2/3 to regulate transcription at active genes. Nat Commun 2018; 9:3798. [PMID: 30228260 PMCID: PMC6143588 DOI: 10.1038/s41467-018-06235-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 08/03/2018] [Indexed: 02/07/2023] Open
Abstract
Transcriptional regulation by chromatin is a highly dynamic process directed through the recruitment and coordinated action of epigenetic modifiers and readers of these modifications. Using an unbiased proteomic approach to find interactors of H3K36me3, a modification enriched on active chromatin, here we identify PWWP2A and HDAC2 among the top interactors. PWWP2A and its paralog PWWP2B form a stable complex with NuRD subunits MTA1/2/3:HDAC1/2:RBBP4/7, but not with MBD2/3, p66α/β, and CHD3/4. PWWP2A competes with MBD3 for binding to MTA1, thus defining a new variant NuRD complex that is mutually exclusive with the MBD2/3 containing NuRD. In mESCs, PWWP2A/B is most enriched at highly transcribed genes. Loss of PWWP2A/B leads to increases in histone acetylation predominantly at highly expressed genes, accompanied by decreases in Pol II elongation. Collectively, these findings suggest a role for PWWP2A/B in regulating transcription through the fine-tuning of histone acetylation dynamics at actively transcribed genes. Transcription regulation requires recruitment of different epigenetic regulators to the chromatin. Here the authors provide evidence that an H3K36me3 reader PWWP2A forms a variant NuRD complex and plays a role in regulating transcription and histone acetylation dynamics.
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Affiliation(s)
- Tianyi Zhang
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, United Kingdom
| | - Guifeng Wei
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, United Kingdom
| | - Christopher J Millard
- Leicester Institute for Structural and Chemical Biology and Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, United Kingdom
| | - Roman Fischer
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom
| | - Rebecca Konietzny
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom.,Agilent Technologies, Hewlett-Packard-Str. 8, 76337, Waldbronn, Germany
| | - Benedikt M Kessler
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom
| | - John W R Schwabe
- Leicester Institute for Structural and Chemical Biology and Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, United Kingdom
| | - Neil Brockdorff
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, United Kingdom.
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37
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Basu S, Needham LM, Lando D, Taylor EJR, Wohlfahrt KJ, Shah D, Boucher W, Tan YL, Bates LE, Tkachenko O, Cramard J, Lagerholm BC, Eggeling C, Hendrich B, Klenerman D, Lee SF, Laue ED. FRET-enhanced photostability allows improved single-molecule tracking of proteins and protein complexes in live mammalian cells. Nat Commun 2018; 9:2520. [PMID: 29955052 PMCID: PMC6023872 DOI: 10.1038/s41467-018-04486-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 04/27/2018] [Indexed: 11/09/2022] Open
Abstract
A major challenge in single-molecule imaging is tracking the dynamics of proteins or complexes for long periods of time in the dense environments found in living cells. Here, we introduce the concept of using FRET to enhance the photophysical properties of photo-modulatable (PM) fluorophores commonly used in such studies. By developing novel single-molecule FRET pairs, consisting of a PM donor fluorophore (either mEos3.2 or PA-JF549) next to a photostable acceptor dye JF646, we demonstrate that FRET competes with normal photobleaching kinetic pathways to increase the photostability of both donor fluorophores. This effect was further enhanced using a triplet-state quencher. Our approach allows us to significantly improve single-molecule tracking of chromatin-binding proteins in live mammalian cells. In addition, it provides a novel way to track the localization and dynamics of protein complexes by labeling one protein with the PM donor and its interaction partner with the acceptor dye.
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Affiliation(s)
- Srinjan Basu
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Lisa-Maria Needham
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - David Lando
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Edward J R Taylor
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Kai J Wohlfahrt
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Devina Shah
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Wayne Boucher
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Yi Lei Tan
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Lawrence E Bates
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Olga Tkachenko
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Julie Cramard
- Wellcome Trust - MRC Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - B Christoffer Lagerholm
- Medical Research Council Human Immunology Unit and Wolfson Imaging Centre, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford, OX3 9DS, UK
| | - Christian Eggeling
- Medical Research Council Human Immunology Unit and Wolfson Imaging Centre, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford, OX3 9DS, UK
| | - Brian Hendrich
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK.,Wellcome Trust - MRC Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Dave Klenerman
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Steven F Lee
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Ernest D Laue
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK.
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38
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Bornelöv S, Reynolds N, Xenophontos M, Gharbi S, Johnstone E, Floyd R, Ralser M, Signolet J, Loos R, Dietmann S, Bertone P, Hendrich B. The Nucleosome Remodeling and Deacetylation Complex Modulates Chromatin Structure at Sites of Active Transcription to Fine-Tune Gene Expression. Mol Cell 2018; 71:56-72.e4. [PMID: 30008319 PMCID: PMC6039721 DOI: 10.1016/j.molcel.2018.06.003] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 03/20/2018] [Accepted: 05/31/2018] [Indexed: 01/03/2023]
Abstract
Chromatin remodeling complexes play essential roles in metazoan development through widespread control of gene expression, but the precise molecular mechanisms by which they do this in vivo remain ill defined. Using an inducible system with fine temporal resolution, we show that the nucleosome remodeling and deacetylation (NuRD) complex controls chromatin architecture and the protein binding repertoire at regulatory regions during cell state transitions. This is primarily exerted through its nucleosome remodeling activity while deacetylation at H3K27 follows changes in gene expression. Additionally, NuRD activity influences association of RNA polymerase II at transcription start sites and subsequent nascent transcript production, thereby guiding the establishment of lineage-appropriate transcriptional programs. These findings provide a detailed molecular picture of genome-wide modulation of lineage-specific transcription by an essential chromatin remodeling complex as well as insight into the orchestration of molecular events involved in transcriptional transitions in vivo. Video Abstract
NuRD increases nucleosome density, expelling TFs or inhibiting recruitment NuRD displaces RNA Pol II from TSSs, reducing nascent transcription Local gains in TF and Mediator occupancy can be indirect effects of NuRD activity Resetting protein binding at regulatory elements can promote or suppress transcription
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Affiliation(s)
- Susanne Bornelöv
- Wellcome-MRC Stem Cell Institute, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Nicola Reynolds
- Wellcome-MRC Stem Cell Institute, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Maria Xenophontos
- Wellcome-MRC Stem Cell Institute, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QR, UK; European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL), Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
| | - Sarah Gharbi
- Wellcome-MRC Stem Cell Institute, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Ewan Johnstone
- Wellcome-MRC Stem Cell Institute, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QR, UK; European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL), Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
| | - Robin Floyd
- Wellcome-MRC Stem Cell Institute, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Meryem Ralser
- Wellcome-MRC Stem Cell Institute, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Jason Signolet
- Wellcome-MRC Stem Cell Institute, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QR, UK; Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Remco Loos
- Wellcome-MRC Stem Cell Institute, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QR, UK; European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL), Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
| | - Sabine Dietmann
- Wellcome-MRC Stem Cell Institute, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Paul Bertone
- Wellcome-MRC Stem Cell Institute, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QR, UK; European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL), Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK.
| | - Brian Hendrich
- Wellcome-MRC Stem Cell Institute, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QR, UK; Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK.
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39
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Wai DCC, Szyszka TN, Campbell AE, Kwong C, Wilkinson-White LE, Silva APG, Low JKK, Kwan AH, Gamsjaeger R, Chalmers JD, Patrick WM, Lu B, Vakoc CR, Blobel GA, Mackay JP. The BRD3 ET domain recognizes a short peptide motif through a mechanism that is conserved across chromatin remodelers and transcriptional regulators. J Biol Chem 2018; 293:7160-7175. [PMID: 29567837 PMCID: PMC5949996 DOI: 10.1074/jbc.ra117.000678] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 02/08/2018] [Indexed: 12/31/2022] Open
Abstract
Members of the bromodomain and extra-terminal domain (BET) family of proteins (bromodomain-containing (BRD) 2, 3, 4, and T) are widely expressed and highly conserved regulators of gene expression in eukaryotes. These proteins have been intimately linked to human disease, and more than a dozen clinical trials are currently underway to test BET-protein inhibitors as modulators of cancer. However, although it is clear that these proteins use their bromodomains to bind both histones and transcription factors bearing acetylated lysine residues, the molecular mechanisms by which BET family proteins regulate gene expression are not well defined. In particular, the functions of the other domains such as the ET domain have been less extensively studied. Here, we examine the properties of the ET domain of BRD3 as a protein/protein interaction module. Using a combination of pulldown and biophysical assays, we demonstrate that BRD3 binds to a range of chromatin-remodeling complexes, including the NuRD, BAF, and INO80 complexes, via a short linear "KIKL" motif in one of the complex subunits. NMR-based structural analysis revealed that, surprisingly, this mode of interaction is shared by the AF9 and ENL transcriptional coregulators that contain an acetyl-lysine-binding YEATS domain and regulate transcriptional elongation. This observation establishes a functional commonality between these two families of cancer-related transcriptional regulators. In summary, our data provide insight into the mechanisms by which BET family proteins might link chromatin acetylation to transcriptional outcomes and uncover an unexpected functional similarity between BET and YEATS family proteins.
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Affiliation(s)
- Dorothy C C Wai
- School of Life and Environmental Sciences, University of Sydney New South Wales 2006, Australia
| | - Taylor N Szyszka
- School of Life and Environmental Sciences, University of Sydney New South Wales 2006, Australia
| | - Amy E Campbell
- Division of Hematology, Children's Hospital of Philadelphia, and the Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Cherry Kwong
- School of Life and Environmental Sciences, University of Sydney New South Wales 2006, Australia
| | - Lorna E Wilkinson-White
- School of Life and Environmental Sciences, University of Sydney New South Wales 2006, Australia
| | - Ana P G Silva
- School of Life and Environmental Sciences, University of Sydney New South Wales 2006, Australia
| | - Jason K K Low
- School of Life and Environmental Sciences, University of Sydney New South Wales 2006, Australia
| | - Ann H Kwan
- School of Life and Environmental Sciences, University of Sydney New South Wales 2006, Australia
| | - Roland Gamsjaeger
- School of Life and Environmental Sciences, University of Sydney New South Wales 2006, Australia
| | - James D Chalmers
- Department of Biochemistry, University of Otago, Dunedin 9016, New Zealand
| | - Wayne M Patrick
- Department of Biochemistry, University of Otago, Dunedin 9016, New Zealand
| | - Bin Lu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | | | - Gerd A Blobel
- Division of Hematology, Children's Hospital of Philadelphia, and the Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney New South Wales 2006, Australia.
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40
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Torrado M, Low JKK, Silva APG, Schmidberger JW, Sana M, Sharifi Tabar M, Isilak ME, Winning CS, Kwong C, Bedward MJ, Sperlazza MJ, Williams DC, Shepherd NE, Mackay JP. Refinement of the subunit interaction network within the nucleosome remodelling and deacetylase (NuRD) complex. FEBS J 2017; 284:4216-4232. [PMID: 29063705 DOI: 10.1111/febs.14301] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 07/19/2017] [Accepted: 10/18/2017] [Indexed: 01/29/2023]
Abstract
The nucleosome remodelling and deacetylase (NuRD) complex is essential for the development of complex animals. NuRD has roles in regulating gene expression and repairing damaged DNA. The complex comprises at least six proteins with two or more paralogues of each protein routinely identified when the complex is purified from cell extracts. To understand the structure and function of NuRD, a map of direct subunit interactions is needed. Dozens of published studies have attempted to define direct inter-subunit connectivities. We propose that conclusions reported in many such studies are in fact ambiguous for one of several reasons. First, the expression of many NuRD subunits in bacteria is unlikely to lead to folded, active protein. Second, interaction studies carried out in cells that contain endogenous NuRD complex can lead to false positives through bridging of target proteins by endogenous components. Combining existing information on NuRD structure with a protocol designed to minimize false positives, we report a conservative and robust interaction map for the NuRD complex. We also suggest a 3D model of the complex that brings together the existing data on the complex. The issues and strategies discussed herein are also applicable to the analysis of a wide range of multi-subunit complexes. ENZYMES Micrococcal nuclease (MNase), EC 3.1.31.1; histone deacetylase (HDAC), EC 3.5.1.98.
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Affiliation(s)
- Mario Torrado
- School of Life and Environmental Sciences, University of Sydney, Australia
| | - Jason K K Low
- School of Life and Environmental Sciences, University of Sydney, Australia
| | - Ana P G Silva
- School of Life and Environmental Sciences, University of Sydney, Australia
| | | | - Maryam Sana
- School of Life and Environmental Sciences, University of Sydney, Australia
| | | | - Musa E Isilak
- School of Life and Environmental Sciences, University of Sydney, Australia
| | - Courtney S Winning
- School of Life and Environmental Sciences, University of Sydney, Australia
| | - Cherry Kwong
- School of Life and Environmental Sciences, University of Sydney, Australia
| | - Max J Bedward
- School of Life and Environmental Sciences, University of Sydney, Australia
| | - Mary J Sperlazza
- Department of Pathology and Laboratory Medicine, The University of North Carolina - Chapel Hill, NC, USA
| | - David C Williams
- Department of Pathology and Laboratory Medicine, The University of North Carolina - Chapel Hill, NC, USA
| | - Nicholas E Shepherd
- Institute for Molecular Biosciences, The University of Queensland, St Lucia, Australia
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, Australia
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41
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Ginder GD, Williams DC. Readers of DNA methylation, the MBD family as potential therapeutic targets. Pharmacol Ther 2017; 184:98-111. [PMID: 29128342 DOI: 10.1016/j.pharmthera.2017.11.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
DNA methylation represents a fundamental epigenetic modification that regulates chromatin architecture and gene transcription. Many diseases, including cancer, show aberrant methylation patterns that contribute to the disease phenotype. DNA methylation inhibitors have been used to block methylation dependent gene silencing to treat hematopoietic neoplasms and to restore expression of developmentally silenced genes. However, these inhibitors disrupt methylation globally and show significant off-target toxicities. As an alternative approach, we have been studying readers of DNA methylation, the 5-methylcytosine binding domain family of proteins, as potential therapeutic targets to restore expression of aberrantly and developmentally methylated and silenced genes. In this review, we discuss the role of DNA methylation in gene regulation and cancer development, the structure and function of the 5-methylcytosine binding domain family of proteins, and the possibility of targeting the complexes these proteins form to treat human disease.
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Affiliation(s)
- Gordon D Ginder
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA 23298, United States; Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, United States; Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, United States.
| | - David C Williams
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States.
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42
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Carr AR, Ponjavic A, Basu S, McColl J, Santos AM, Davis S, Laue ED, Klenerman D, Lee SF. Three-Dimensional Super-Resolution in Eukaryotic Cells Using the Double-Helix Point Spread Function. Biophys J 2017; 112:1444-1454. [PMID: 28402886 PMCID: PMC5390298 DOI: 10.1016/j.bpj.2017.02.023] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 02/07/2017] [Accepted: 02/21/2017] [Indexed: 02/02/2023] Open
Abstract
Single-molecule localization microscopy, typically based on total internal reflection illumination, has taken our understanding of protein organization and dynamics in cells beyond the diffraction limit. However, biological systems exist in a complicated three-dimensional environment, which has required the development of new techniques, including the double-helix point spread function (DHPSF), to accurately visualize biological processes. The application of the DHPSF approach has so far been limited to the study of relatively small prokaryotic cells. By matching the refractive index of the objective lens immersion liquid to that of the sample media, we demonstrate DHPSF imaging of up to 15-μm-thick whole eukaryotic cell volumes in three to five imaging planes. We illustrate the capabilities of the DHPSF by exploring large-scale membrane reorganization in human T cells after receptor triggering, and by using single-particle tracking to image several mammalian proteins, including membrane, cytoplasmic, and nuclear proteins in T cells and embryonic stem cells.
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Affiliation(s)
- Alexander R. Carr
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Aleks Ponjavic
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Srinjan Basu
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - James McColl
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Ana Mafalda Santos
- Radcliffe Department of Clinical Medicine and Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Simon Davis
- Radcliffe Department of Clinical Medicine and Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Ernest D. Laue
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - David Klenerman
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Steven F. Lee
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom,Corresponding author
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Stevens TJ, Lando D, Basu S, Atkinson LP, Cao Y, Lee SF, Leeb M, Wohlfahrt KJ, Boucher W, O'Shaughnessy-Kirwan A, Cramard J, Faure AJ, Ralser M, Blanco E, Morey L, Sansó M, Palayret MGS, Lehner B, Di Croce L, Wutz A, Hendrich B, Klenerman D, Laue ED. 3D structures of individual mammalian genomes studied by single-cell Hi-C. Nature 2017; 544:59-64. [PMID: 28289288 PMCID: PMC5385134 DOI: 10.1038/nature21429] [Citation(s) in RCA: 505] [Impact Index Per Article: 72.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 01/26/2017] [Indexed: 12/19/2022]
Abstract
The folding of genomic DNA from the beads-on-a-string-like structure of nucleosomes into higher-order assemblies is crucially linked to nuclear processes. Here we calculate 3D structures of entire mammalian genomes using data from a new chromosome conformation capture procedure that allows us to first image and then process single cells. The technique enables genome folding to be examined at a scale of less than 100 kb, and chromosome structures to be validated. The structures of individual topological-associated domains and loops vary substantially from cell to cell. By contrast, A and B compartments, lamina-associated domains and active enhancers and promoters are organized in a consistent way on a genome-wide basis in every cell, suggesting that they could drive chromosome and genome folding. By studying genes regulated by pluripotency factor and nucleosome remodelling deacetylase (NuRD), we illustrate how the determination of single-cell genome structure provides a new approach for investigating biological processes.
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Affiliation(s)
- Tim J Stevens
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - David Lando
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Srinjan Basu
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Liam P Atkinson
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Yang Cao
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Steven F Lee
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Martin Leeb
- Wellcome Trust - MRC Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, United Kingdom
| | - Kai J Wohlfahrt
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Wayne Boucher
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Aoife O'Shaughnessy-Kirwan
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
- Wellcome Trust - MRC Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, United Kingdom
| | - Julie Cramard
- Wellcome Trust - MRC Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, United Kingdom
| | - Andre J Faure
- EMBL-CRG Systems Biology Unit, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain
| | - Meryem Ralser
- Wellcome Trust - MRC Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, United Kingdom
| | - Enrique Blanco
- EMBL-CRG Systems Biology Unit, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain
| | - Lluis Morey
- EMBL-CRG Systems Biology Unit, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain
| | - Miriam Sansó
- EMBL-CRG Systems Biology Unit, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain
| | - Matthieu G S Palayret
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Ben Lehner
- EMBL-CRG Systems Biology Unit, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain
- Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Luciano Di Croce
- EMBL-CRG Systems Biology Unit, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain
- Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Anton Wutz
- Wellcome Trust - MRC Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, United Kingdom
| | - Brian Hendrich
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
- Wellcome Trust - MRC Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, United Kingdom
| | - Dave Klenerman
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Ernest D Laue
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
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Zhao H, Han Z, Liu X, Gu J, Tang F, Wei G, Jin Y. The chromatin remodeler Chd4 maintains embryonic stem cell identity by controlling pluripotency- and differentiation-associated genes. J Biol Chem 2017; 292:8507-8519. [PMID: 28298436 DOI: 10.1074/jbc.m116.770248] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 03/13/2017] [Indexed: 12/23/2022] Open
Abstract
The unique properties of embryonic stem cells (ESCs), including unlimited self-renewal and pluripotent differentiation potential, are sustained by integrated genetic and epigenetic networks composed of transcriptional factors and epigenetic modulators. However, the molecular mechanisms underlying the function of these regulators are not fully elucidated. Chromodomain helicase DNA-binding protein 4 (Chd4), an ATPase subunit of the nucleosome remodeling and deacetylase (NuRD) complex, is highly expressed in ESCs. However, its function in ESC regulation remains elusive. Here we report that Chd4 is required for the maintenance of ESC self-renewal. RNAi-mediated silencing of Chd4 disrupted self-renewal and up-regulated lineage commitment-associated genes under self-renewal culture conditions. During ESC differentiation in embryoid body formation, we observed significantly stronger induction of differentiation-associated genes in Chd4-deficient cells. The phenotype was different from that caused by the deletion of Mbd3, another subunit of the NuRD complex. Transcriptomic analyses revealed that Chd4 secured ESC identity by controlling the expression of subsets of pluripotency- and differentiation-associated genes. Importantly, Chd4 repressed the transcription of T box protein 3 (Tbx3), a transcription factor with important functions in ESC fate determination. Tbx3 knockdown partially rescued aberrant activation of differentiation-associated genes, especially of endoderm-associated genes, induced by Chd4 depletion. Moreover, we identified an interaction of Chd4 with the histone variant H2A.Z. This variant stabilized Chd4 by inhibiting Chd4 protein degradation through the ubiquitin-proteasome pathway. Collectively, this study identifies the Chd4-Tbx3 axis in controlling ESC fate and a role of H2A.Z in maintaining the stability of Chd4 proteins.
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Affiliation(s)
- Haixin Zhao
- Key Laboratory of Stem Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai JiaoTong University School of Medicine, 320 Yueyang Road, Shanghai 200031, China; University of the Chinese Academy of Sciences
| | - Zhijun Han
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xinyuan Liu
- Key Laboratory of Stem Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai JiaoTong University School of Medicine, 320 Yueyang Road, Shanghai 200031, China
| | - Junjie Gu
- Laboratory of Molecular Developmental Biology, Shanghai JiaoTong University School of Medicine, Shanghai 200025, China
| | - Fan Tang
- Laboratory of Molecular Developmental Biology, Shanghai JiaoTong University School of Medicine, Shanghai 200025, China
| | - Gang Wei
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ying Jin
- Key Laboratory of Stem Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai JiaoTong University School of Medicine, 320 Yueyang Road, Shanghai 200031, China; Laboratory of Molecular Developmental Biology, Shanghai JiaoTong University School of Medicine, Shanghai 200025, China.
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Expression, purification and characterization of the human MTA2-RBBP7 complex. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:531-538. [PMID: 28179136 DOI: 10.1016/j.bbapap.2017.02.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 01/23/2017] [Accepted: 02/03/2017] [Indexed: 01/26/2023]
Abstract
The repressive Nucleosome Remodeling and histone Deacetylation (NuRD) complex remodels the chromatin structure by coupling ATP-dependent remodeling activity with histone deacetylase function and plays important roles in regulating gene transcription, DNA damage repair and chromatin assembly. The complex is composed of six subunits: Metastasis Associated proteins MTA1/2/3 initially recruit histone chaperones RBBP4/7 followed by the histone deacetylases HDAC1/2 forming a core complex. Further association of the CpG-binding protein MBD2/3, p66α/β and the ATP-dependent helicase CDH3/4 constitutes the NuRD complex. Recent structural studies on truncated human proteins or orthologous have revealed that the stoichiometry of the MTA1-RBBP4 complex is 2:4. This study reports expression and purification of the intact human MTA2-RBBP7 complex using HEK293F cells as expression system. In analogy with findings on the Drosophila NuRD complex, we find that also the human MTA-RBBP can be isolated in vitro. Taken together with previous findings this suggests, that MTA-RBBP is a stable complex, with a central role in the initial assembly of the human NuRD complex. Refined 3D volumes of the complex generated from negative stain electron microscopy (EM) data reveals an elongated architecture that is capable of hinge like motion around the center of the particle.
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Targeting Class I Histone Deacetylases in a "Complex" Environment. Trends Pharmacol Sci 2017; 38:363-377. [PMID: 28139258 DOI: 10.1016/j.tips.2016.12.006] [Citation(s) in RCA: 120] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 12/16/2016] [Accepted: 12/21/2016] [Indexed: 01/22/2023]
Abstract
Histone deacetylase (HDAC) inhibitors are proven anticancer therapeutics and have potential in the treatment of many other diseases including HIV infection, Alzheimer's disease, and Friedreich's ataxia. A problem with the currently available HDAC inhibitors is that they have limited specificity and target multiple deacetylases. Designing isoform-selective inhibitors has proven challenging due to similarities in the structure and chemistry of HDAC active sites. However, the fact that HDACs 1, 2, and 3 are recruited to several large multi-subunit complexes, each with particular biological functions, raises the possibility of specifically inhibiting individual complexes. This may be assisted by recent structural and functional information about the assembly of these complexes. Here, we review the available structural information and discuss potential targeting strategies.
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Polycomb complexes PRC1 and their function in hematopoiesis. Exp Hematol 2017; 48:12-31. [PMID: 28087428 DOI: 10.1016/j.exphem.2016.12.006] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 12/19/2016] [Accepted: 12/20/2016] [Indexed: 12/31/2022]
Abstract
Hematopoiesis, the process by which blood cells are continuously produced, is one of the best studied differentiation pathways. Hematological diseases are associated with reiterated mutations in genes encoding important gene expression regulators, including chromatin regulators. Among them, the Polycomb group (PcG) of proteins is an essential system of gene silencing involved in the maintenance of cell identities during differentiation. PcG proteins assemble into two major types of Polycomb repressive complexes (PRCs) endowed with distinct histone-tail-modifying activities. PRC1 complexes are histone H2A E3 ubiquitin ligases and PRC2 trimethylates histone H3. Established conceptions about their activities, mostly derived from work in embryonic stem cells, are being modified by new findings in differentiated cells. Here, we focus on PRC1 complexes, reviewing recent evidence on their intricate architecture, the diverse mechanisms of their recruitment to targets, and the different ways in which they engage in transcriptional control. We also discuss hematopoietic PRC1 gain- and loss-of-function mouse strains, including those that model leukemic and lymphoma diseases, in the belief that these genetic analyses provide the ultimate test for molecular mechanisms driving normal hematopoiesis and hematological malignancies.
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