1
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Ntini E, Budach S, Vang Ørom UA, Marsico A. Genome-wide measurement of RNA dissociation from chromatin classifies transcripts by their dynamics and reveals rapid dissociation of enhancer lncRNAs. Cell Syst 2023; 14:906-922.e6. [PMID: 37857083 DOI: 10.1016/j.cels.2023.09.005] [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: 10/30/2022] [Revised: 05/24/2023] [Accepted: 09/20/2023] [Indexed: 10/21/2023]
Abstract
Long non-coding RNAs (lncRNAs) are involved in gene expression regulation in cis. Although enriched in the cell chromatin fraction, to what degree this defines their regulatory potential remains unclear. Furthermore, the factors underlying lncRNA chromatin tethering, as well as the molecular basis of efficient lncRNA chromatin dissociation and its impact on enhancer activity and target gene expression, remain to be resolved. Here, we developed chrTT-seq, which combines the pulse-chase metabolic labeling of nascent RNA with chromatin fractionation and transient transcriptome sequencing to follow nascent RNA transcripts from their transcription on chromatin to release and allows the quantification of dissociation dynamics. By incorporating genomic, transcriptomic, and epigenetic metrics, as well as RNA-binding protein propensities, in machine learning models, we identify features that define transcript groups of different chromatin dissociation dynamics. Notably, lncRNAs transcribed from enhancers display reduced chromatin retention, suggesting that, in addition to splicing, their chromatin dissociation may shape enhancer activity.
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Affiliation(s)
- Evgenia Ntini
- Max-Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Freie Universität Berlin, 14195 Berlin, Germany; Institute of Molecular Biology and Biotechnology, IMBB-FORTH, 70013 Heraklio, Greece.
| | - Stefan Budach
- Max-Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Freie Universität Berlin, 14195 Berlin, Germany
| | - Ulf A Vang Ørom
- Aarhus University, Department of Molecular Biology and Genetics, 8000 Aarhus, Denmark
| | - Annalisa Marsico
- Max-Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Freie Universität Berlin, 14195 Berlin, Germany; Computational Health Center, Helmholtz Center Munich, Munich, Germany.
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2
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Liu Y, Yu K, Kong X, Zhang K, Wang L, Zhang N, Chen Q, Niu M, Li W, Zhong X, Wu S, Zhang J, Liu Y. FOXA1 O-GlcNAcylation-mediated transcriptional switch governs metastasis capacity in breast cancer. SCIENCE ADVANCES 2023; 9:eadg7112. [PMID: 37595040 PMCID: PMC10438466 DOI: 10.1126/sciadv.adg7112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 07/19/2023] [Indexed: 08/20/2023]
Abstract
FOXA1, a transcription factor involved in epigenetic reprogramming, is crucial for breast cancer progression. However, the mechanisms by which FOXA1 achieves its oncogenic functions remain elusive. Here, we demonstrate that the O-linked β-N-acetylglucosamine modification (O-GlcNAcylation) of FOXA1 promotes breast cancer metastasis by orchestrating the transcription of numerous metastasis regulators. O-GlcNAcylation at Thr432, Ser441, and Ser443 regulates the stability of FOXA1 and promotes its assembly with chromatin. O-GlcNAcylation shapes the FOXA1 interactome, especially triggering the recruitment of the transcriptional repressor methyl-CpG binding protein 2 and consequently stimulating FOXA1 chromatin-binding sites to switch to chromatin loci of adhesion-related genes, including EPB41L3 and COL9A2. Site-specific depletion of O-GlcNAcylation on FOXA1 affects the expression of various downstream genes and thus inhibits breast cancer proliferation and metastasis both in vitro and in vivo. Our data establish the importance of aberrant FOXA1 O-GlcNAcylation in breast cancer progression and indicate that targeting O-GlcNAcylation is a therapeutic strategy for metastatic breast cancer.
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Affiliation(s)
- Yajie Liu
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, China
| | - Kairan Yu
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, China
| | - Xiaotian Kong
- Faculty of Environment and Life, Beijing University of Technology, Beijing, China
- Beijing International Science and Technology Cooperation Base for Intelligent Physiological Measurement and Clinical Transformation, Beijing, China
| | - Keren Zhang
- Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen, China
| | - Lingyan Wang
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, China
| | - Nana Zhang
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, China
| | - Qiushi Chen
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Hong Kong Science Park, Science Park West Avenue, Hong Kong, China
| | - Mingshan Niu
- Blood Diseases Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Wenli Li
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, China
| | - Xiaomin Zhong
- Department of Oncology, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huai'an, China
| | - Sijin Wu
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Jianing Zhang
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, China
| | - Yubo Liu
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, China
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3
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Zhang Q, Ma S, Liu Z, Zhu B, Zhou Z, Li G, Meana JJ, González-Maeso J, Lu C. Droplet-based bisulfite sequencing for high-throughput profiling of single-cell DNA methylomes. Nat Commun 2023; 14:4672. [PMID: 37537185 PMCID: PMC10400590 DOI: 10.1038/s41467-023-40411-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 07/26/2023] [Indexed: 08/05/2023] Open
Abstract
The genome-wide DNA methylation profile, or DNA methylome, is a critical component of the overall epigenomic landscape that modulates gene activities and cell fate. Single-cell DNA methylomic studies offer unprecedented resolution for detecting and profiling cell subsets based on methylomic features. However, existing single-cell methylomic technologies are based on use of tubes or well plates and these platforms are not easily scalable for handling a large number of single cells. Here we demonstrate a droplet-based microfluidic technology, Drop-BS, to construct single-cell bisulfite sequencing libraries for DNA methylome profiling. Drop-BS takes advantage of the ultrahigh throughput offered by droplet microfluidics to prepare bisulfite sequencing libraries of up to 10,000 single cells within 2 days. We apply the technology to profile mixed cell lines, mouse and human brain tissues to reveal cell type heterogeneity. Drop-BS offers a promising solution for single-cell methylomic studies requiring examination of a large cell population.
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Affiliation(s)
- Qiang Zhang
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Sai Ma
- Department of Biomedical Engineering and Mechanics, Virginia Tech, Blacksburg, VA, 24061, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Zhengzhi Liu
- Department of Biomedical Engineering and Mechanics, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Bohan Zhu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Zirui Zhou
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Gaoshan Li
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, 24061, USA
| | - J Javier Meana
- Department of Pharmacology, University of the Basque Country UPV/EHU, CIBERSAM, Biocruces Health Research Institute, E-48940, Leioa, Bizkaia, Spain
| | - Javier González-Maeso
- Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, VA, 23298, USA
| | - Chang Lu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, 24061, USA.
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4
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Schmolka N, Karemaker ID, Cardoso da Silva R, Recchia DC, Spegg V, Bhaskaran J, Teske M, de Wagenaar NP, Altmeyer M, Baubec T. Dissecting the roles of MBD2 isoforms and domains in regulating NuRD complex function during cellular differentiation. Nat Commun 2023; 14:3848. [PMID: 37385984 PMCID: PMC10310694 DOI: 10.1038/s41467-023-39551-w] [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: 04/20/2022] [Accepted: 06/19/2023] [Indexed: 07/01/2023] Open
Abstract
The Nucleosome Remodeling and Deacetylation (NuRD) complex is a crucial regulator of cellular differentiation. Two members of the Methyl-CpG-binding domain (MBD) protein family, MBD2 and MBD3, are known to be integral, but mutually exclusive subunits of the NuRD complex. Several MBD2 and MBD3 isoforms are present in mammalian cells, resulting in distinct MBD-NuRD complexes. Whether these different complexes serve distinct functional activities during differentiation is not fully explored. Based on the essential role of MBD3 in lineage commitment, we systematically investigated a diverse set of MBD2 and MBD3 variants for their potential to rescue the differentiation block observed for mouse embryonic stem cells (ESCs) lacking MBD3. While MBD3 is indeed crucial for ESC differentiation to neuronal cells, it functions independently of its MBD domain. We further identify that MBD2 isoforms can replace MBD3 during lineage commitment, however with different potential. Full-length MBD2a only partially rescues the differentiation block, while MBD2b, an isoform lacking an N-terminal GR-rich repeat, fully rescues the Mbd3 KO phenotype. In case of MBD2a, we further show that removing the methylated DNA binding capacity or the GR-rich repeat enables full redundancy to MBD3, highlighting the synergistic requirements for these domains in diversifying NuRD complex function.
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Affiliation(s)
- Nina Schmolka
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Ino D Karemaker
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Richard Cardoso da Silva
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
- Genome Biology and Epigenetics, Institute of Biodynamics and Biocomplexity, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Davide C Recchia
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
- Genome Biology and Epigenetics, Institute of Biodynamics and Biocomplexity, Department of Biology, Utrecht University, Utrecht, The Netherlands
- Molecular Life Science PhD Program of the Life Science Zurich Graduate School, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Vincent Spegg
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
- Molecular Life Science PhD Program of the Life Science Zurich Graduate School, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Jahnavi Bhaskaran
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
- MRC London Institute of Medical Sciences, London, UK
| | - Michael Teske
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
- Molecular Life Science PhD Program of the Life Science Zurich Graduate School, University of Zurich and ETH Zurich, Zurich, Switzerland
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Nathalie P de Wagenaar
- Genome Biology and Epigenetics, Institute of Biodynamics and Biocomplexity, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Matthias Altmeyer
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Tuncay Baubec
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland.
- Genome Biology and Epigenetics, Institute of Biodynamics and Biocomplexity, Department of Biology, Utrecht University, Utrecht, The Netherlands.
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5
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Zhang Q, Ma S, Liu Z, Zhu B, Zhou Z, Li G, Meana JJ, González-Maeso J, Lu C. Droplet-based bisulfite sequencing for high-throughput profiling of single-cell DNA methylomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.26.542421. [PMID: 37293095 PMCID: PMC10245959 DOI: 10.1101/2023.05.26.542421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Genome-wide DNA methylation profile, or DNA methylome, is a critical component of the overall epigenomic landscape that modulates gene activities and cell fate. Single-cell DNA methylomic studies offer unprecedented resolution for detecting and profiling cell subsets based on methylomic features. However, existing single-cell methylomic technologies are all based on use of tubes or well plates and these platforms are not easily scalable for handling a large number of single cells. Here we demonstrate a droplet-based microfluidic technology, Drop-BS, to construct single-cell bisulfite sequencing libraries for DNA methylome profiling. Drop-BS takes advantage of the ultrahigh throughput offered by droplet microfluidics to prepare bisulfite sequencing libraries of up to 10,000 single cells within 2 d. We applied the technology to profile mixed cell lines, mouse and human brain tissues to reveal cell type heterogeneity. Drop-BS will pave the way for single-cell methylomic studies requiring examination of a large cell population.
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Affiliation(s)
- Qiang Zhang
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Sai Ma
- Department of Biomedical Engineering and Mechanics, Virginia Tech, Blacksburg, VA 24061, USA
- Present address: Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zhengzhi Liu
- Department of Biomedical Engineering and Mechanics, Virginia Tech, Blacksburg, VA 24061, USA
| | - Bohan Zhu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Zirui Zhou
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Gaoshan Li
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - J. Javier Meana
- Department of Pharmacology, University of the Basque Country UPV/EHU, CIBERSAM, Biocruces Health Research Institute, E-48940 Leioa, Bizkaia, Spain
| | - Javier González-Maeso
- Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA
| | - Chang Lu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061, USA
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6
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Boulasiki P, Tan XW, Spinelli M, Riccio A. The NuRD Complex in Neurodevelopment and Disease: A Case of Sliding Doors. Cells 2023; 12:cells12081179. [PMID: 37190088 DOI: 10.3390/cells12081179] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/12/2023] [Accepted: 04/14/2023] [Indexed: 05/17/2023] Open
Abstract
The Nucleosome Remodelling and Deacetylase (NuRD) complex represents one of the major chromatin remodelling complexes in mammalian cells, uniquely coupling the ability to "open" the chromatin by inducing nucleosome sliding with histone deacetylase activity. At the core of the NuRD complex are a family of ATPases named CHDs that utilise the energy produced by the hydrolysis of the ATP to induce chromatin structural changes. Recent studies have highlighted the prominent role played by the NuRD in regulating gene expression during brain development and in maintaining neuronal circuitry in the adult cerebellum. Importantly, components of the NuRD complex have been found to carry mutations that profoundly affect neurological and cognitive development in humans. Here, we discuss recent literature concerning the molecular structure of NuRD complexes and how the subunit composition and numerous permutations greatly determine their functions in the nervous system. We will also discuss the role of the CHD family members in an array of neurodevelopmental disorders. Special emphasis will be given to the mechanisms that regulate the NuRD complex composition and assembly in the cortex and how subtle mutations may result in profound defects of brain development and the adult nervous system.
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Affiliation(s)
- Paraskevi Boulasiki
- UCL Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Xiao Wei Tan
- UCL Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Matteo Spinelli
- UCL Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
- Neuroscience Department, Catholic University of the Sacred Heart, 00168 Rome, Italy
| | - Antonella Riccio
- UCL Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
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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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Batsché E, Yi J, Mauger O, Kornobis E, Hopkins B, Hanmer-Lloyd C, Muchardt C. CD44 alternative splicing senses intragenic DNA methylation in tumors via direct and indirect mechanisms. Nucleic Acids Res 2021; 49:6213-6237. [PMID: 34086943 PMCID: PMC8216461 DOI: 10.1093/nar/gkab437] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/30/2021] [Accepted: 05/05/2021] [Indexed: 02/07/2023] Open
Abstract
DNA methylation (meDNA) is a modulator of alternative splicing, and splicing perturbations are involved in tumorigenesis nearly as frequently as DNA mutations. However, the impact of meDNA on tumorigenesis via splicing-mediated mechanisms has not been thoroughly explored. Here, we found that HCT116 colon carcinoma cells inactivated for the DNA methylases DNMT1/3b undergo a partial epithelial to mesenchymal transition associated with increased CD44 variant exon skipping. These skipping events are directly mediated by the loss of intragenic meDNA and the chromatin factors MBD1/2/3 and HP1γ and are also linked to phosphorylation changes in elongating RNA polymerase II. The role of meDNA in alternative splicing was confirmed by using the dCas9/DNMT3b tool. We further tested whether the meDNA level could have predictive value in the MCF10A model for breast cancer progression and in patients with acute lymphoblastic leukemia (B ALL). We found that a small number of differentially spliced genes, mostly involved in splicing and signal transduction, are correlated with the local modulation of meDNA. Our observations suggest that, although DNA methylation has multiple avenues to affect alternative splicing, its indirect effect may also be mediated through alternative splicing isoforms of these meDNA sensors.
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Affiliation(s)
- Eric Batsché
- Epigenetics and RNA metabolism in human diseases. CNRS UMR8256 - Biological Adaptation and Ageing. Institut de Biologie Paris-Seine. Sciences Sorbonne Université. 7–9 Quai Saint Bernard, 75005 Paris, France
- Unité de Régulation Epigénétique, Institut Pasteur, Paris, France
- UMR3738, CNRS, Paris, France
| | - Jia Yi
- Unité de Régulation Epigénétique, Institut Pasteur, Paris, France
- UMR3738, CNRS, Paris, France
- Ecole Doctorale Complexite du Vivant (ED515), Sorbonne Université, Paris, France
| | - Oriane Mauger
- Unité de Régulation Epigénétique, Institut Pasteur, Paris, France
- UMR3738, CNRS, Paris, France
- Ecole Doctorale Complexite du Vivant (ED515), Sorbonne Université, Paris, France
| | - Etienne Kornobis
- Unité de Régulation Epigénétique, Institut Pasteur, Paris, France
- UMR3738, CNRS, Paris, France
| | - Benjamin Hopkins
- Unité de Régulation Epigénétique, Institut Pasteur, Paris, France
- UMR3738, CNRS, Paris, France
- Keele University, Keele, Staffordshire ST5 5BG UK
| | - Charlotte Hanmer-Lloyd
- Unité de Régulation Epigénétique, Institut Pasteur, Paris, France
- UMR3738, CNRS, Paris, France
- Keele University, Keele, Staffordshire ST5 5BG UK
| | - Christian Muchardt
- Epigenetics and RNA metabolism in human diseases. CNRS UMR8256 - Biological Adaptation and Ageing. Institut de Biologie Paris-Seine. Sciences Sorbonne Université. 7–9 Quai Saint Bernard, 75005 Paris, France
- Unité de Régulation Epigénétique, Institut Pasteur, Paris, France
- UMR3738, CNRS, Paris, France
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10
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Osman S, Mohammad E, Lidschreiber M, Stuetzer A, Bazsó FL, Maier KC, Urlaub H, Cramer P. The Cdk8 kinase module regulates interaction of the mediator complex with RNA polymerase II. J Biol Chem 2021; 296:100734. [PMID: 33933450 PMCID: PMC8191332 DOI: 10.1016/j.jbc.2021.100734] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 04/20/2021] [Accepted: 04/28/2021] [Indexed: 11/17/2022] Open
Abstract
The Cdk8 kinase module (CKM) is a dissociable part of the coactivator complex mediator, which regulates gene transcription by RNA polymerase II. The CKM has both negative and positive functions in gene transcription that remain poorly understood at the mechanistic level. In order to reconstitute the role of the CKM in transcription initiation, we prepared recombinant CKM from the yeast Saccharomyces cerevisiae. We showed that CKM bound to the core mediator (cMed) complex, sterically inhibiting cMed from binding to the polymerase II preinitiation complex (PIC) in vitro. We further showed that the Cdk8 kinase activity of the CKM weakened CKM-cMed interaction, thereby facilitating dissociation of the CKM and enabling mediator to bind the PIC in order to stimulate transcription initiation. Finally, we report that the kinase activity of Cdk8 is required for gene activation during the stressful condition of heat shock in vivo but not under steady-state growth conditions. Based on these results, we propose a model in which the CKM negatively regulates mediator function at upstream-activating sequences by preventing mediator binding to the PIC at the gene promoter. However, during gene activation in response to stress, the Cdk8 kinase activity of the CKM may release mediator and allow its binding to the PIC, thereby accounting for the positive function of CKM. This may impart improved adaptability to stress by allowing a rapid transcriptional response to environmental changes, and we speculate that a similar mechanism in metazoans may allow the precise timing of developmental transcription programs.
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Affiliation(s)
- Sara Osman
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Eusra Mohammad
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Michael Lidschreiber
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Alexandra Stuetzer
- Bioanalytical Mass Spectrometry Group, Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany; Bioanalytics Research Group, Institute for Clinical Chemistry, University Medical Center, Göttingen, Germany
| | - Fanni Laura Bazsó
- Bioanalytical Mass Spectrometry Group, Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany; Bioanalytics Research Group, Institute for Clinical Chemistry, University Medical Center, Göttingen, Germany
| | - Kerstin C Maier
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany; Bioanalytics Research Group, Institute for Clinical Chemistry, University Medical Center, Göttingen, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
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11
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D'Anna F, Van Dyck L, Xiong J, Zhao H, Berrens RV, Qian J, Bieniasz-Krzywiec P, Chandra V, Schoonjans L, Matthews J, De Smedt J, Minnoye L, Amorim R, Khorasanizadeh S, Yu Q, Zhao L, De Borre M, Savvides SN, Simon MC, Carmeliet P, Reik W, Rastinejad F, Mazzone M, Thienpont B, Lambrechts D. DNA methylation repels binding of hypoxia-inducible transcription factors to maintain tumor immunotolerance. Genome Biol 2020; 21:182. [PMID: 32718321 PMCID: PMC7384226 DOI: 10.1186/s13059-020-02087-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 06/29/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Hypoxia is pervasive in cancer and other diseases. Cells sense and adapt to hypoxia by activating hypoxia-inducible transcription factors (HIFs), but it is still an outstanding question why cell types differ in their transcriptional response to hypoxia. RESULTS We report that HIFs fail to bind CpG dinucleotides that are methylated in their consensus binding sequence, both in in vitro biochemical binding assays and in vivo studies of differentially methylated isogenic cell lines. Based on in silico structural modeling, we show that 5-methylcytosine indeed causes steric hindrance in the HIF binding pocket. A model wherein cell-type-specific methylation landscapes, as laid down by the differential expression and binding of other transcription factors under normoxia, control cell-type-specific hypoxia responses is observed. We also discover ectopic HIF binding sites in repeat regions which are normally methylated. Genetic and pharmacological DNA demethylation, but also cancer-associated DNA hypomethylation, expose these binding sites, inducing HIF-dependent expression of cryptic transcripts. In line with such cryptic transcripts being more prone to cause double-stranded RNA and viral mimicry, we observe low DNA methylation and high cryptic transcript expression in tumors with high immune checkpoint expression, but not in tumors with low immune checkpoint expression, where they would compromise tumor immunotolerance. In a low-immunogenic tumor model, DNA demethylation upregulates cryptic transcript expression in a HIF-dependent manner, causing immune activation and reducing tumor growth. CONCLUSIONS Our data elucidate the mechanism underlying cell-type-specific responses to hypoxia and suggest DNA methylation and hypoxia to underlie tumor immunotolerance.
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Affiliation(s)
- Flora D'Anna
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Laurien Van Dyck
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Jieyi Xiong
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Hui Zhao
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Rebecca V Berrens
- Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT, UK
- The Old Schools, University of Cambridge, Trinity Lane Cambridge, CB2 1TN, UK
| | - Junbin Qian
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Pawel Bieniasz-Krzywiec
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium
- Laboratory of Tumor Inflammation and Angiogenesis, Department of Oncology, KU Leuven, 3000, Leuven, Belgium
| | - Vikas Chandra
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Luc Schoonjans
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium
- State Key Laboratory of Ophthalmology, Zhongsan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, Leuven Cancer Institute, KU Leuven, 3000, Leuven, Belgium
| | - Jason Matthews
- Institute of Basic Medical Sciences, University of Oslo, 0372, Oslo, Norway
| | - Julie De Smedt
- Laboratory of Dermatology, Department of Oncology, KU Leuven, 3000, Leuven, Belgium
| | - Liesbeth Minnoye
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Ricardo Amorim
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium
- Laboratory of Tumor Inflammation and Angiogenesis, Department of Oncology, KU Leuven, 3000, Leuven, Belgium
| | - Sepideh Khorasanizadeh
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Qian Yu
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Liyun Zhao
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Marie De Borre
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Savvas N Savvides
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, 9052, Ghent, Belgium
- VIB Center for Inflammation Research, 9052, Ghent, Belgium
| | - M Celeste Simon
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Peter Carmeliet
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium
- State Key Laboratory of Ophthalmology, Zhongsan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, Leuven Cancer Institute, KU Leuven, 3000, Leuven, Belgium
| | - Wolf Reik
- Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, CB2 3EG, UK
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3EG, UK
| | - Fraydoon Rastinejad
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Clinical and Experimental Endocrinology, Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, 3000, Leuven, Belgium
| | - Massimiliano Mazzone
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium
- Laboratory of Tumor Inflammation and Angiogenesis, Department of Oncology, KU Leuven, 3000, Leuven, Belgium
| | - Bernard Thienpont
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium.
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium.
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium.
| | - Diether Lambrechts
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium.
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium.
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12
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Hernandez-Vargas H, Goldsmith C, Mathot P, Dante R. Stromal-associated cytokines bias the interplay between gene expression and DNA methylation in human breast cancers. Epigenetics 2019; 15:511-523. [PMID: 31838945 DOI: 10.1080/15592294.2019.1699893] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
In human tumours, the crosstalk between cancer cells and their microenvironment is involved in tumour progression, metastasis and resistance to anti-cancer therapies. Among the factors involved in this exchange of information pro-inflammatory cytokines seem to play a crucial role. We observed that a group of pro-inflammatory cytokines, interleukin 6 (IL6), interleukin 1-beta (IL1b), and tumour necrosis factor-alpha (TNFa), preferentially activated genes exhibiting a high basal methylation level at their transcription start sites, in the human breast cancer cell line MCF7. In human breast tumours, these responding genes were also hypermethylated, and some of them (N = 104) were differentially methylated across human breast tumour samples (The Cancer Genome Atlas cohort). While their expression was positively correlated with the stromal content of the tumours and the expression of stromal-associated pro-inflammatory cytokines, the expression of this subset of genes was negatively correlated with their methylation level at their 5' end. Nevertheless, while the methylation level of this subset of genes was not correlated with the stromal cell content of the tumours, this negative correlation was partially lost in tumours with high stromal cell content. Consistently, we observed that the methylation level in this subset of genes influenced the correlation between gene expression and stromal cell content. Thus, these data indicated that the stromal component of breast tumours should be taken into account for DNA methylation and gene expression studies and suggest an additional pathway, via DNA methylation, in the cross-talk between cancer cells and their microenvironment in human breast cancers.
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Affiliation(s)
- Hector Hernandez-Vargas
- Department of Immunity, Virus and Inflammation, Cancer Research Center of Lyon (CRCL), Inserm U 1052, CNRS UMR 5286, Université de Lyon, Centre Léon Bérard, Lyon CEDEX 08, France.,Department of Translational Research and Innovation, Centre Léon Bérard, Lyon CEDEX 08, France
| | - Chloe Goldsmith
- Department of Immunity, Virus and Inflammation, Cancer Research Center of Lyon (CRCL), Inserm U 1052, CNRS UMR 5286, Université de Lyon, Centre Léon Bérard, Lyon CEDEX 08, France
| | - Pauline Mathot
- Dependence Receptors Cancer and Development Laboratory, Department of Signaling of Tumoral Escape, Cancer Research Center of Lyon (CRCL), Inserm U 1052, CNRS UMR 5286, Université de Lyon, Centre Léon Bérard, Lyon CEDEX 08, France
| | - Robert Dante
- Dependence Receptors Cancer and Development Laboratory, Department of Signaling of Tumoral Escape, Cancer Research Center of Lyon (CRCL), Inserm U 1052, CNRS UMR 5286, Université de Lyon, Centre Léon Bérard, Lyon CEDEX 08, France
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13
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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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14
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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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15
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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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16
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Barnes NE, Mendoza KM, Strasburg GM, Velleman SG, Reed KM. Thermal challenge alters the transcriptional profile of the breast muscle in turkey poults. Poult Sci 2019; 98:74-91. [PMID: 30239949 DOI: 10.3382/ps/pey401] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 08/08/2018] [Indexed: 12/25/2022] Open
Abstract
Extremes in temperature represent environmental stressors that impact the well-being and economic value of poultry. As homeotherms, young poultry with immature thermoregulatory systems are especially susceptible to thermal extremes. Genetic variation and differences in gene expression resulting from selection for production traits, likely contribute to thermal stress response. This study was designed to investigate in vivo transcriptional changes in the breast muscle of young turkey poults from an unselected randombred line and one selected for 16 wk body weight under hot and cold thermal challenge. Newly hatched turkey poults were brooded for 3 d at one of 3 temperatures: control (35°C), cold (31°C), or hot (39°C). Samples of the pectoralis major were harvested and subjected to deep RNA sequencing. Significant differential gene expression was observed in both growth-selected and randombred birds at both temperature extremes when compared to control-brooded poults. Growth-selected birds responded to thermal stress through changes in genes predicted to have downstream transcriptional effects and that would result in reduced muscle growth. Slower growing randombred birds responded to thermal stress through modulation of lipid-related genes, suggesting reduction in lipid storage, transport, and synthesis, consistent with changes in energy metabolism required to maintain body temperature.
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Affiliation(s)
- Natalie E Barnes
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, MN 55108, USA
| | - Kristelle M Mendoza
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, MN 55108, USA
| | - Gale M Strasburg
- Department of Food Science and Human Nutrition, Michigan State University, East Lansing, MI 48824, USA
| | - Sandra G Velleman
- Department of Animal Sciences, The Ohio State University/Ohio Agricultural Research and Development Center, Wooster, OH 44691, USA
| | - Kent M Reed
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, MN 55108, USA
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17
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Kraushaar DC, Chen Z, Tang Q, Cui K, Zhang J, Zhao K. The gene repressor complex NuRD interacts with the histone variant H3.3 at promoters of active genes. Genome Res 2018; 28:1646-1655. [PMID: 30254051 PMCID: PMC6211640 DOI: 10.1101/gr.236224.118] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 09/13/2018] [Indexed: 12/13/2022]
Abstract
The histone variant H3.3 is deposited across active genes, regulatory regions, and telomeres. It remains unclear how H3.3 interacts with chromatin modifying enzymes and thereby modulates gene activity. In this study, we performed a co-immunoprecipitation-mass spectrometry analysis of proteins associated with H3.3-containing nucleosomes and identified the nucleosome remodeling and deacetylase complex (NuRD) as a major H3.3-interactor. We show that the H3.3-NuRD interaction is dependent on the H3.3 lysine 4 residue and that NuRD binding occurs when lysine 4 is in its unmodified state. The majority of NuRD binding colocalizes with H3.3 and directly correlates with gene activity. H3.3 depletion led to reduced levels of NuRD at sites previously occupied by H3.3, as well as a global decrease in histone marks associated with gene activation. Our results demonstrate the importance of H3.3 in the maintenance of the cellular epigenetic landscape and reveal a highly prevalent interaction between the histone variant H3.3 and the multiprotein complex NuRD.
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Affiliation(s)
- Daniel C Kraushaar
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Zuozhou Chen
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education; International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
| | - Qingsong Tang
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Kairong Cui
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Junfang Zhang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education; International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
| | - Keji Zhao
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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18
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Modulation of Cellular CpG DNA Methylation by Kaposi's Sarcoma-Associated Herpesvirus. J Virol 2018; 92:JVI.00008-18. [PMID: 29899086 DOI: 10.1128/jvi.00008-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 05/23/2018] [Indexed: 01/08/2023] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV, HHV-8) is a gammaherpesvirus associated with several human malignancies. DNA methylation at CpG dinucleotides is an epigenetic mark dysregulated in many cancer types and in KSHV-infected cells. Several previous studies have analyzed in detail the CpG methylation of the KSHV episomal genomes, but little is known about the impact of KSHV on the human genome. Our knowledge of cellular CpG methylation in the context of KSHV infection is currently limited to four hypermethylated human gene promoters. Therefore, we undertook a comprehensive CpG methylation analysis of the human methylome in KSHV-infected cells and KSHV-associated primary effusion lymphoma (PEL). We performed Infinium HumanMethylation450K and MethylationEpic BeadChip arrays and identified panels of hyper- and hypomethylated cellular promoters in KSHV-infected cells. We combined our genome-wide methylation analysis with high-throughput RNA sequencing (RNA-seq) to add functional outcomes to the virally induced methylation changes. We were able to correlate many downregulated genes with promoter hypermethylation and upregulated genes with hypomethylation. In addition, we show that treating the cells with a demethylating agent leads to reexpression of these downregulated genes, indicating that, indeed, DNA methylation plays a role in the repression of these human genes. Comparison between de novo infection and PEL suggests that the virus induces initial hypermethylation followed by a slow increase in genome-wide hypomethylation. This study extends our understanding of the relationship between epigenetic changes induced by KSHV infection and tumorigenesis.IMPORTANCE In cancer cells, certain promoters become aberrantly methylated, contributing to the phenotype of the tumor. KSHV infection seems to modify cellular CpG methylation, but only a few methylated promoters have been identified in KSHV-infected cells. Here, we investigated the CpG methylation of the human genome in KSHV-associated primary effusion lymphoma (PEL) and KSHV-infected cells. We have identified many hyper- and hypomethylated gene promoters and correlated their methylation with cellular gene expression. These differentially methylated cellular promoters can distinguish KSHV-positive cells from uninfected cells and may serve as the foundation for the use of these differentially methylated regions as potential biomarkers for KSHV-associated malignancies. Drugs that reverse these cancerous methylation patterns have the potential to inhibit tumor growth. Here, we show that treating PEL cells with a demethylating drug (5-aza-2'-deoxycytidine) led to inhibition of cell growth, raising the possibility of testing this drug for the treatment of PEL.
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19
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Ntini E, Louloupi A, Liz J, Muino JM, Marsico A, Ørom UAV. Long ncRNA A-ROD activates its target gene DKK1 at its release from chromatin. Nat Commun 2018; 9:1636. [PMID: 29691407 PMCID: PMC5915440 DOI: 10.1038/s41467-018-04100-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 04/04/2018] [Indexed: 12/20/2022] Open
Abstract
Long ncRNAs are often enriched in the nucleus and at chromatin, but whether their dissociation from chromatin is important for their role in transcription regulation is unclear. Here, we group long ncRNAs using epigenetic marks, expression and strength of chromosomal interactions; we find that long ncRNAs transcribed from loci engaged in strong long-range chromosomal interactions are less abundant at chromatin, suggesting the release from chromatin as a crucial functional aspect of long ncRNAs in transcription regulation of their target genes. To gain mechanistic insight into this, we functionally validate the long ncRNA A-ROD, which enhances DKK1 transcription via its nascent spliced released form. Our data provide evidence that the regulatory interaction requires dissociation of A-ROD from chromatin, with target specificity ensured within the pre-established chromosomal proximity. We propose that the post-transcriptional release of a subset of long ncRNAs from the chromatin-associated template plays an important role in their function as transcription regulators.
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Affiliation(s)
- Evgenia Ntini
- Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany.
| | - Annita Louloupi
- Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany.,Free University Berlin, 14195, Berlin, Germany
| | - Julia Liz
- Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | | | - Annalisa Marsico
- Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany.,Free University Berlin, 14195, Berlin, Germany
| | - Ulf Andersson Vang Ørom
- Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany. .,Institute for Molecular Biology and Genetics, Aarhus University, 8000, Aarhus, Denmark.
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20
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Kolendowski B, Hassan H, Krstic M, Isovic M, Thillainadesan G, Chambers AF, Tuck AB, Torchia J. Genome-wide analysis reveals a role for TDG in estrogen receptor-mediated enhancer RNA transcription and 3-dimensional reorganization. Epigenetics Chromatin 2018; 11:5. [PMID: 29378668 PMCID: PMC5787930 DOI: 10.1186/s13072-018-0176-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 01/15/2018] [Indexed: 01/25/2023] Open
Abstract
Background The estrogen receptor (ER) is a ligand-dependant transcription factor expressed in many breast cancers and is the target of many endocrine-based cancer therapies. Genome-wide studies have shown that the ER binds to gene-specific enhancer regions in response to β-estradiol (E2) which undergo transcription producing noncoding enhancer RNA (eRNA). While eRNAs are important for transcriptional activation of neighboring genes, the mechanism remains poorly understood. Results Using ChIP-Seq we generate a global profile of thymine DNA glycosylase (TDG), an ER coactivator that plays an essential role in DNA demethylation, in response to E2 in the MCF7 breast cancer cell line. Remarkably, we found that in response to E2 TDG localized to enhancers which also recruit ERα, RNA Pol II and other coregulators and which are marked by histone modifications indicative of active enhancers. Importantly, depletion of TDG inhibits E2-mediated transcription of eRNAs and transcription of ER-target genes. Functionally, we find that TDG both sensitizes MCF7 cells to tamoxifen-mediated cytostasis and increases migration and invasion of MCF7 cells. Conclusions Taken together we find that TDG plays a central role in mediating transcription at a subset of enhancers and governs how MCF7 cells respond to both estrogenic and anti-estrogenic compounds and may be an effective therapeutic target. Electronic supplementary material The online version of this article (10.1186/s13072-018-0176-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bart Kolendowski
- Department of Biochemistry, Western University, London, ON, Canada.,Department of Oncology, Western University, London, ON, Canada.,The London Regional Cancer Program and the Lawson Health Research Institute, Western University, London, ON, Canada
| | - Haider Hassan
- Department of Biochemistry, Western University, London, ON, Canada.,Department of Oncology, Western University, London, ON, Canada.,The London Regional Cancer Program and the Lawson Health Research Institute, Western University, London, ON, Canada
| | - Milica Krstic
- Department of Pathology, Western University, London, ON, Canada.,The London Regional Cancer Program and the Lawson Health Research Institute, Western University, London, ON, Canada
| | - Majdina Isovic
- Department of Oncology, Western University, London, ON, Canada
| | - Gobi Thillainadesan
- Department of Biochemistry, Western University, London, ON, Canada.,Department of Oncology, Western University, London, ON, Canada
| | - Ann F Chambers
- The London Regional Cancer Program and the Lawson Health Research Institute, Western University, London, ON, Canada
| | - Alan B Tuck
- Department of Oncology, Western University, London, ON, Canada.,Department of Pathology, Western University, London, ON, Canada
| | - Joseph Torchia
- Department of Biochemistry, Western University, London, ON, Canada. .,Department of Oncology, Western University, London, ON, Canada. .,The London Regional Cancer Program and the Lawson Health Research Institute, Western University, London, ON, Canada. .,Cancer Research Laboratories, London Regional Cancer Program, London, ON, N6A 4L6, Canada.
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21
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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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22
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Pan H, Bilinovich SM, Kaur P, Riehn R, Wang H, Williams DC. CpG and methylation-dependent DNA binding and dynamics of the methylcytosine binding domain 2 protein at the single-molecule level. Nucleic Acids Res 2017. [PMID: 28637186 PMCID: PMC5587734 DOI: 10.1093/nar/gkx548] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The methylcytosine-binding domain 2 (MBD2) protein recruits the nucleosome remodeling and deacetylase complex (NuRD) to methylated DNA to modify chromatin and regulate transcription. Importantly, MBD2 functions within CpG islands that contain 100s to 1000s of potential binding sites. Since NuRD physically rearranges nucleosomes, the dynamic mobility of this complex is directly related to function. In these studies, we use NMR and single-molecule atomic force microscopy and fluorescence imaging to study DNA binding dynamics of MBD2. Single-molecule fluorescence tracking on DNA tightropes containing regions with CpG-rich and CpG-free regions reveals that MBD2 carries out unbiased 1D diffusion on CpG-rich DNA but subdiffusion on CpG-free DNA. In contrast, the protein stably and statically binds to methylated CpG (mCpG) regions. The intrinsically disordered region (IDR) on MBD2 both reduces exchange between mCpG sites along the DNA as well as the dissociation from DNA, acting like an anchor that restricts the dynamic mobility of the MBD domain. Unexpectedly, MBD2 binding to methylated CpGs induces DNA bending that is augmented by the IDR region of the protein. These results suggest that MBD2 targets NuRD to unmethylated or methylated CpG islands where its distinct dynamic binding modes help maintain open or closed chromatin, respectively.
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Affiliation(s)
- Hai Pan
- Department of Physics, North Carolina State University, Raleigh, North Carolina, NC 27695, USA
| | - Stephanie M Bilinovich
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Parminder Kaur
- Department of Physics, North Carolina State University, Raleigh, North Carolina, NC 27695, USA
| | - Robert Riehn
- Department of Physics, North Carolina State University, Raleigh, North Carolina, NC 27695, USA
| | - Hong Wang
- Department of Physics, North Carolina State University, Raleigh, North Carolina, NC 27695, USA.,Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina, NC 27695, USA
| | - David C Williams
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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23
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Intragenic DNA methylation and BORIS-mediated cancer-specific splicing contribute to the Warburg effect. Proc Natl Acad Sci U S A 2017; 114:11440-11445. [PMID: 29073069 PMCID: PMC5664520 DOI: 10.1073/pnas.1708447114] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Recent advances in cancer epigenetics have shown the involvement of epigenetic abnormalities in the initiation and progression of cancer, but their role in cancer-specific aberrant splicing is not clear. The identification of upstream epigenetic regulators of cancer-specific splicing will enable us to therapeutically target aberrant splicing and provide an approach to cancer therapy. Here we have demonstrated a mechanism of intragenic DNA methylation-mediated regulation of alternative splicing by Brother of Regulator of Imprinted Sites (BORIS), which can contribute to breast cancer tumorigenesis by favoring the Warburg effect. The reversal of the Warburg effect was achieved by the inhibition of DNA methylation or down-regulation of BORIS, which may serve as a useful approach to inhibit the growth of breast cancer cells. Aberrant alternative splicing and epigenetic changes are both associated with various cancers, but epigenetic regulation of alternative splicing in cancer is largely unknown. Here we report that the intragenic DNA methylation-mediated binding of Brother of Regulator of Imprinted Sites (BORIS) at the alternative exon of Pyruvate Kinase (PKM) is associated with cancer-specific splicing that promotes the Warburg effect and breast cancer progression. Interestingly, the inhibition of DNA methylation, BORIS depletion, or CRISPR/Cas9-mediated deletion of the BORIS binding site leads to a splicing switch from cancer-specific PKM2 to normal PKM1 isoform. This results in the reversal of the Warburg effect and the inhibition of breast cancer cell growth, which may serve as a useful approach to inhibit the growth of breast cancer cells. Importantly, our results show that in addition to PKM splicing, BORIS also regulates the alternative splicing of several genes in a DNA methylation-dependent manner. Our findings highlight the role of intragenic DNA methylation and DNA binding protein BORIS in cancer-specific splicing and its role in tumorigenesis.
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24
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Ludwig AK, Zhang P, Hastert FD, Meyer S, Rausch C, Herce HD, Müller U, Lehmkuhl A, Hellmann I, Trummer C, Storm C, Leonhardt H, Cardoso MC. Binding of MBD proteins to DNA blocks Tet1 function thereby modulating transcriptional noise. Nucleic Acids Res 2017; 45:2438-2457. [PMID: 27923996 PMCID: PMC5389475 DOI: 10.1093/nar/gkw1197] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 11/20/2016] [Indexed: 12/18/2022] Open
Abstract
Aberrant DNA methylation is a hallmark of various human disorders, indicating that the spatial and temporal regulation of methylation readers and modifiers is imperative for development and differentiation. In particular, the cross-regulation between 5-methylcytosine binders (MBD) and modifiers (Tet) has not been investigated. Here, we show that binding of Mecp2 and Mbd2 to DNA protects 5-methylcytosine from Tet1-mediated oxidation. The mechanism is not based on competition for 5-methylcytosine binding but on Mecp2 and Mbd2 directly restricting Tet1 access to DNA. We demonstrate that the efficiency of this process depends on the number of bound MBDs per DNA molecule. Accordingly, we find 5-hydroxymethylcytosine enriched at heterochromatin of Mecp2-deficient neurons of a mouse model for Rett syndrome and Tet1-induced reexpression of silenced major satellite repeats. These data unveil fundamental regulatory mechanisms of Tet enzymes and their potential pathophysiological role in Rett syndrome. Importantly, it suggests that Mecp2 and Mbd2 have an essential physiological role as guardians of the epigenome.
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Affiliation(s)
- Anne K Ludwig
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Peng Zhang
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Florian D Hastert
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Stephanie Meyer
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Cathia Rausch
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Henry D Herce
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Udo Müller
- Human Biology and BioImaging, Department of Biology II, LMU Munich, 82152 Martinsried, Germany
| | - Anne Lehmkuhl
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Ines Hellmann
- Anthropology and Human Genomics, Department Biology II, LMU Munich, 82152 Martinsried, Germany
| | - Carina Trummer
- Human Biology and BioImaging, Department of Biology II, LMU Munich, 82152 Martinsried, Germany
| | - Christian Storm
- Chemical Plant Ecology, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Heinrich Leonhardt
- Human Biology and BioImaging, Department of Biology II, LMU Munich, 82152 Martinsried, Germany
| | - M Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
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25
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Sarda S, Das A, Vinson C, Hannenhalli S. Distal CpG islands can serve as alternative promoters to transcribe genes with silenced proximal promoters. Genome Res 2017; 27:553-566. [PMID: 28223400 PMCID: PMC5378174 DOI: 10.1101/gr.212050.116] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 02/21/2017] [Indexed: 12/31/2022]
Abstract
DNA methylation at the promoter of a gene is presumed to render it silent, yet a sizable fraction of genes with methylated proximal promoters exhibit elevated expression. Here, we show, through extensive analysis of the methylome and transcriptome in 34 tissues, that in many such cases, transcription is initiated by a distal upstream CpG island (CGI) located several kilobases away that functions as an alternative promoter. Specifically, such genes are expressed precisely when the neighboring CGI is unmethylated but remain silenced otherwise. Based on CAGE and Pol II localization data, we found strong evidence of transcription initiation at the upstream CGI and a lack thereof at the methylated proximal promoter itself. Consistent with their alternative promoter activity, CGI-initiated transcripts are associated with signals of stable elongation and splicing that extend into the gene body, as evidenced by tissue-specific RNA-seq and other DNA-encoded splice signals. Furthermore, based on both inter- and intra-species analyses, such CGIs were found to be under greater purifying selection relative to CGIs upstream of silenced genes. Overall, our study describes a hitherto unreported conserved mechanism of transcription of genes with methylated proximal promoters in a tissue-specific fashion. Importantly, this phenomenon explains the aberrant expression patterns of some cancer driver genes, potentially due to aberrant hypomethylation of distal CGIs, despite methylation at proximal promoters.
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Affiliation(s)
- Shrutii Sarda
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland 20742, USA
| | - Avinash Das
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland 20742, USA
| | - Charles Vinson
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Sridhar Hannenhalli
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland 20742, USA
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26
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Gigek CO, Chen ES, Smith MAC. Methyl-CpG-Binding Protein (MBD) Family: Epigenomic Read-Outs Functions and Roles in Tumorigenesis and Psychiatric Diseases. J Cell Biochem 2016. [PMID: 26205787 DOI: 10.1002/jcb.25281] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Epigenetics is the study of the heritable changes on gene expression that are responsible for the regulation of development and that have an impact on several diseases. However, it is of equal importance to understand how epigenetic machinery works. DNA methylation is the most studied epigenetic mark and is generally associated with the regulation of gene expression through the repression of promoter activity and by affecting genome stability. Therefore, the ability of the cell to interpret correct methylation marks and/or the correct interpretation of methylation plays a role in many diseases. The major family of proteins that bind methylated DNA is the methyl-CpG binding domain proteins, or the MBDs. Here, we discuss the structure that makes these proteins a family, the main functions and interactions of all protein family members and their role in human disease such as psychiatric disorders and cancer.
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Affiliation(s)
- Carolina Oliveira Gigek
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo (UNIFESP), Rua Botucatu, 740, Edifício Leitão da Cunha, 1, ° andar, CEP 04023-900, São Paulo, SP, Brazil.,Disciplina de Gastroenterologia Cirúrgica, Departamento de Cirurgia, Universidade Federal de São Paulo (UNIFESP), R. Napoleão de Barros, 715, 2º andar, CEP:04024-002, São Paulo, Brazil
| | - Elizabeth Suchi Chen
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo (UNIFESP), Rua Botucatu, 740, Edifício Leitão da Cunha, 1, ° andar, CEP 04023-900, São Paulo, SP, Brazil
| | - Marilia Arruda Cardoso Smith
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo (UNIFESP), Rua Botucatu, 740, Edifício Leitão da Cunha, 1, ° andar, CEP 04023-900, São Paulo, SP, Brazil
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27
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Hainer SJ, McCannell KN, Yu J, Ee LS, Zhu LJ, Rando OJ, Fazzio TG. DNA methylation directs genomic localization of Mbd2 and Mbd3 in embryonic stem cells. eLife 2016; 5. [PMID: 27849519 PMCID: PMC5111885 DOI: 10.7554/elife.21964] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 11/01/2016] [Indexed: 12/22/2022] Open
Abstract
Cytosine methylation is an epigenetic and regulatory mark that functions in part through recruitment of chromatin remodeling complexes containing methyl-CpG binding domain (MBD) proteins. Two MBD proteins, Mbd2 and Mbd3, were previously shown to bind methylated or hydroxymethylated DNA, respectively; however, both of these findings have been disputed. Here, we investigated this controversy using experimental approaches and re-analysis of published data and find no evidence for methylation-independent functions of Mbd2 or Mbd3. We show that chromatin localization of Mbd2 and Mbd3 is highly overlapping and, unexpectedly, we find Mbd2 and Mbd3 are interdependent for chromatin association. Further investigation reveals that both proteins are required for normal levels of cytosine methylation and hydroxymethylation in murine embryonic stem cells. Furthermore, Mbd2 and Mbd3 regulate overlapping sets of genes that are also regulated by DNA methylation/hydroxymethylation factors. These findings reveal an interdependent regulatory mechanism mediated by the DNA methylation machinery and its readers.
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Affiliation(s)
- Sarah J Hainer
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, United States
| | - Kurtis N McCannell
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, United States
| | - Jun Yu
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, United States
| | - Ly-Sha Ee
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, United States
| | - Lihua J Zhu
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, United States.,Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, United States.,Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States
| | - Oliver J Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Thomas G Fazzio
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, United States.,Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States
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28
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Methyl-CpG-binding protein MBD2 plays a key role in maintenance and spread of DNA methylation at CpG islands and shores in cancer. Oncogene 2016; 36:1328-1338. [PMID: 27593931 DOI: 10.1038/onc.2016.297] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 07/04/2016] [Accepted: 07/17/2016] [Indexed: 02/07/2023]
Abstract
Cancer is characterised by DNA hypermethylation and gene silencing of CpG island-associated promoters, including tumour-suppressor genes. The methyl-CpG-binding domain (MBD) family of proteins bind to methylated DNA and can aid in the mediation of gene silencing through interaction with histone deacetylases and histone methyltransferases. However, the mechanisms responsible for eliciting CpG island hypermethylation in cancer, and the potential role that MBD proteins play in modulation of the methylome remain unclear. Our previous work demonstrated that MBD2 preferentially binds to the hypermethylated GSTP1 promoter CpG island in prostate cancer cells. Here, we use functional genetic approaches to investigate if MBD2 plays an active role in reshaping the DNA methylation landscape at this locus and genome-wide. First, we show that loss of MBD2 results in inhibition of both maintenance and spread of de novo methylation of a transfected construct containing the GSTP1 promoter CpG island in prostate cancer cells and Mbd2-/- mouse fibroblasts. De novo methylation was rescued by transient expression of Mbd2 in Mbd2-/- cells. Second, we show that MBD2 depletion triggers significant hypomethylation genome-wide in prostate cancer cells with concomitant loss of MBD2 binding at promoter and enhancer regulatory regions. Finally, CpG islands and shores that become hypomethylated after MBD2 depletion in LNCaP cancer cells show significant hypermethylation in clinical prostate cancer samples, highlighting a potential active role of MBD2 in promoting cancer-specific hypermethylation. Importantly, co-immunoprecipiation of MBD2 shows that MBD2 associates with DNA methyltransferase enzymes 1 and 3A. Together our results demonstrate that MBD2 has a critical role in 'rewriting' the cancer methylome at specific regulatory regions.
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29
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Georgiou G, van Heeringen SJ. fluff: exploratory analysis and visualization of high-throughput sequencing data. PeerJ 2016; 4:e2209. [PMID: 27547532 PMCID: PMC4957989 DOI: 10.7717/peerj.2209] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 06/13/2016] [Indexed: 01/07/2023] Open
Abstract
Summary. In this article we describe fluff, a software package that allows for simple exploration, clustering and visualization of high-throughput sequencing data mapped to a reference genome. The package contains three command-line tools to generate publication-quality figures in an uncomplicated manner using sensible defaults. Genome-wide data can be aggregated, clustered and visualized in a heatmap, according to different clustering methods. This includes a predefined setting to identify dynamic clusters between different conditions or developmental stages. Alternatively, clustered data can be visualized in a bandplot. Finally, fluff includes a tool to generate genomic profiles. As command-line tools, the fluff programs can easily be integrated into standard analysis pipelines. The installation is straightforward and documentation is available at http://fluff.readthedocs.org. Availability. fluff is implemented in Python and runs on Linux. The source code is freely available for download at https://github.com/simonvh/fluff.
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Affiliation(s)
- Georgios Georgiou
- Radboud University, Molecular Developmental Biology , Nijmegen , The Netherlands
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30
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Wood KH, Zhou Z. Emerging Molecular and Biological Functions of MBD2, a Reader of DNA Methylation. Front Genet 2016; 7:93. [PMID: 27303433 PMCID: PMC4880565 DOI: 10.3389/fgene.2016.00093] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 05/10/2016] [Indexed: 01/25/2023] Open
Abstract
DNA methylation is an epigenetic mark that is essential for many biological processes and is linked to diseases such as cancer. Methylation is usually associated with transcriptional silencing, but new research has challenged this model. Both transcriptional activation and repression have recently been found to be associated with DNA methylation in a context-specific manner. How DNA methylation patterns are interpreted into different functional output remains poorly understood. One mechanism involves the protein ‘readers’ of methylation, which includes the methyl-CpG binding domain (MBD) family of proteins. This review examines the molecular and biological functions of MBD2, which binds to CpG methylation and is an integral part of the nucleosome remodeling and histone deacetylation (NuRD) complex. MBD2 has been linked to immune system function and tumorigenesis, yet little is known about its functions in vivo. Recent studies have found the MBD2 protein is ubiquitously expressed, with relatively high levels in the lung, liver, and colon. Mbd2 null mice surprisingly show relatively mild phenotypes compared to mice with loss of function of other MBD proteins. This evidence has previously been interpreted as functional redundancy between the MBD proteins. Here, we examine and contextualize research that suggests MBD2 has unique properties and functions among the MBD proteins. These functions translate to recently described roles in the development and differentiation of multiple cell lineages, including pluripotent stem cells and various cell types of the immune system, as well as in tumorigenesis. We also consider possible models for the dynamic interactions between MBD2 and NuRD in different tissues in vivo. The functions of MBD2 may have direct therapeutic implications for several areas of human disease, including autoimmune conditions and cancer, in addition to providing insights into the actions of NuRD and chromatin regulation.
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Affiliation(s)
- Kathleen H Wood
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, USA
| | - Zhaolan Zhou
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, USA
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31
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The Chromatin Remodeling Complex Chd4/NuRD Controls Striated Muscle Identity and Metabolic Homeostasis. Cell Metab 2016; 23:881-92. [PMID: 27166947 DOI: 10.1016/j.cmet.2016.04.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 02/19/2016] [Accepted: 04/13/2016] [Indexed: 01/01/2023]
Abstract
Heart muscle maintains blood circulation, while skeletal muscle powers skeletal movement. Despite having similar myofibrilar sarcomeric structures, these striated muscles differentially express specific sarcomere components to meet their distinct contractile requirements. The mechanism responsible is still unclear. We show here that preservation of the identity of the two striated muscle types depends on epigenetic repression of the alternate lineage gene program by the chromatin remodeling complex Chd4/NuRD. Loss of Chd4 in the heart triggers aberrant expression of the skeletal muscle program, causing severe cardiomyopathy and sudden death. Conversely, genetic depletion of Chd4 in skeletal muscle causes inappropriate expression of cardiac genes and myopathy. In both striated tissues, mitochondrial function was also dependent on the Chd4/NuRD complex. We conclude that an epigenetic mechanism controls cardiac and skeletal muscle structural and metabolic identities and that loss of this regulation leads to hybrid striated muscle tissues incompatible with life.
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32
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Takaku M, Grimm SA, Shimbo T, Perera L, Menafra R, Stunnenberg HG, Archer TK, Machida S, Kurumizaka H, Wade PA. GATA3-dependent cellular reprogramming requires activation-domain dependent recruitment of a chromatin remodeler. Genome Biol 2016; 17:36. [PMID: 26922637 PMCID: PMC4769547 DOI: 10.1186/s13059-016-0897-0] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 02/11/2016] [Indexed: 12/13/2022] Open
Abstract
Background Transcription factor-dependent cellular reprogramming is integral to normal development and is central to production of induced pluripotent stem cells. This process typically requires pioneer transcription factors (TFs) to induce de novo formation of enhancers at previously closed chromatin. Mechanistic information on this process is currently sparse. Results Here we explore the mechanistic basis by which GATA3 functions as a pioneer TF in a cellular reprogramming event relevant to breast cancer, the mesenchymal to epithelial transition (MET). In some instances, GATA3 binds previously inaccessible chromatin, characterized by stable, positioned nucleosomes where it induces nucleosome eviction, alters local histone modifications, and remodels local chromatin architecture. At other loci, GATA3 binding induces nucleosome sliding without concomitant generation of accessible chromatin. Deletion of the transactivation domain retains the chromatin binding ability of GATA3 but cripples chromatin reprogramming ability, resulting in failure to induce MET. Conclusions These data provide mechanistic insights into GATA3-mediated chromatin reprogramming during MET, and suggest unexpected complexity to TF pioneering. Successful reprogramming requires stable binding to a nucleosomal site; activation domain-dependent recruitment of co-factors including BRG1, the ATPase subunit of the SWI/SNF chromatin remodeling complex; and appropriate genomic context. The resulting model provides a new conceptual framework for de novo enhancer establishment by a pioneer TF. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-0897-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Motoki Takaku
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Sara A Grimm
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Takashi Shimbo
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Lalith Perera
- Laboratory of Genome Integrity and Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Roberta Menafra
- Department of Molecular Biology, Faculties of Science and Medicine, Radboud University, Nijmegen, Netherlands
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Faculties of Science and Medicine, Radboud University, Nijmegen, Netherlands
| | - Trevor K Archer
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Shinichi Machida
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Paul A Wade
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA.
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33
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Du Q, Luu PL, Stirzaker C, Clark SJ. Methyl-CpG-binding domain proteins: readers of the epigenome. Epigenomics 2015; 7:1051-73. [DOI: 10.2217/epi.15.39] [Citation(s) in RCA: 265] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
How DNA methylation is interpreted and influences genome regulation remains largely unknown. Proteins of the methyl-CpG-binding domain (MBD) family are primary candidates for the readout of DNA methylation as they recruit chromatin remodelers, histone deacetylases and methylases to methylated DNA associated with gene repression. MBD protein binding requires both functional MBD domains and methyl-CpGs; however, some MBD proteins also bind unmethylated DNA and active regulatory regions via alternative regulatory domains or interaction with the nucleosome remodeling deacetylase (NuRD/Mi-2) complex members. Mutations within MBD domains occur in many diseases, including neurological disorders and cancers, leading to loss of MBD binding specificity to methylated sites and gene deregulation. Here, we summarize the current state of knowledge about MBD proteins and their role as readers of the epigenome.
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Affiliation(s)
- Qian Du
- Epigenetics Research Laboratory, Genomics & Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Phuc-Loi Luu
- Epigenetics Research Laboratory, Genomics & Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Clare Stirzaker
- Epigenetics Research Laboratory, Genomics & Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
- St Vincent's Clinical School, University of NSW, Darlinghurst, NSW 2010, Australia
| | - Susan J Clark
- Epigenetics Research Laboratory, Genomics & Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
- St Vincent's Clinical School, University of NSW, Darlinghurst, NSW 2010, Australia
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34
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Devailly G, Grandin M, Perriaud L, Mathot P, Delcros JG, Bidet Y, Morel AP, Bignon JY, Puisieux A, Mehlen P, Dante R. Dynamics of MBD2 deposition across methylated DNA regions during malignant transformation of human mammary epithelial cells. Nucleic Acids Res 2015; 43:5838-54. [PMID: 26007656 PMCID: PMC4499136 DOI: 10.1093/nar/gkv508] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 05/05/2015] [Indexed: 12/26/2022] Open
Abstract
DNA methylation is thought to induce transcriptional silencing through the combination of two mechanisms: the repulsion of transcriptional activators unable to bind their target sites when methylated, and the recruitment of transcriptional repressors with specific affinity for methylated DNA. The Methyl CpG Binding Domain proteins MeCP2, MBD1 and MBD2 belong to the latter category. Here, we present MBD2 ChIPseq data obtained from the endogenous MBD2 in an isogenic cellular model of oncogenic transformation of human mammary cells. In immortalized (HMEC-hTERT) or transformed (HMLER) cells, MBD2 was found in a large proportion of methylated regions and associated with transcriptional silencing. A redistribution of MBD2 on methylated DNA occurred during oncogenic transformation, frequently independently of local DNA methylation changes. Genes downregulated during HMEC-hTERT transformation preferentially gained MBD2 on their promoter. Furthermore, depletion of MBD2 induced an upregulation of MBD2-bound genes methylated at their promoter regions, in HMLER cells. Among the 3,160 genes downregulated in transformed cells, 380 genes were methylated at their promoter regions in both cell lines, specifically associated by MBD2 in HMLER cells, and upregulated upon MBD2 depletion in HMLER. The transcriptional MBD2-dependent downregulation occurring during oncogenic transformation was also observed in two additional models of mammary cell transformation. Thus, the dynamics of MBD2 deposition across methylated DNA regions was associated with the oncogenic transformation of human mammary cells.
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Affiliation(s)
- Guillaume Devailly
- Dependence Receptors, Cancer and Development Laboratory - Equipe labellisée 'La Ligue', LabEx DEVweCAN, Centre de Recherche en Cancérologie de Lyon (CRCL), INSERM U1052-CNRS UMR5286, Université de Lyon, Centre Léon Bérard, 69008 Lyon, France
| | - Mélodie Grandin
- Dependence Receptors, Cancer and Development Laboratory - Equipe labellisée 'La Ligue', LabEx DEVweCAN, Centre de Recherche en Cancérologie de Lyon (CRCL), INSERM U1052-CNRS UMR5286, Université de Lyon, Centre Léon Bérard, 69008 Lyon, France
| | - Laury Perriaud
- Institut Curie and INSERM U612, Centre Universitaire, 91405, Orsay, France
| | - Pauline Mathot
- Dependence Receptors, Cancer and Development Laboratory - Equipe labellisée 'La Ligue', LabEx DEVweCAN, Centre de Recherche en Cancérologie de Lyon (CRCL), INSERM U1052-CNRS UMR5286, Université de Lyon, Centre Léon Bérard, 69008 Lyon, France
| | - Jean-Guy Delcros
- Dependence Receptors, Cancer and Development Laboratory - Equipe labellisée 'La Ligue', LabEx DEVweCAN, Centre de Recherche en Cancérologie de Lyon (CRCL), INSERM U1052-CNRS UMR5286, Université de Lyon, Centre Léon Bérard, 69008 Lyon, France
| | - Yannick Bidet
- Laboratoire d'Oncologie Moléculaire, Centre Jean Perrin, 63011 Clermont-Ferrand, France
| | - Anne-Pierre Morel
- EMT and cancer cell plasticity Laboratory - Equipe labellisée 'La Ligue', LabEx DEVweCAN, CRCL, INSERM U1052-CNRS UMR5286, Université de Lyon, Centre Léon Bérard, 69008 Lyon, France
| | - Jean-Yves Bignon
- Laboratoire d'Oncologie Moléculaire, Centre Jean Perrin, 63011 Clermont-Ferrand, France
| | - Alain Puisieux
- EMT and cancer cell plasticity Laboratory - Equipe labellisée 'La Ligue', LabEx DEVweCAN, CRCL, INSERM U1052-CNRS UMR5286, Université de Lyon, Centre Léon Bérard, 69008 Lyon, France
| | - Patrick Mehlen
- Dependence Receptors, Cancer and Development Laboratory - Equipe labellisée 'La Ligue', LabEx DEVweCAN, Centre de Recherche en Cancérologie de Lyon (CRCL), INSERM U1052-CNRS UMR5286, Université de Lyon, Centre Léon Bérard, 69008 Lyon, France
| | - Robert Dante
- Dependence Receptors, Cancer and Development Laboratory - Equipe labellisée 'La Ligue', LabEx DEVweCAN, Centre de Recherche en Cancérologie de Lyon (CRCL), INSERM U1052-CNRS UMR5286, Université de Lyon, Centre Léon Bérard, 69008 Lyon, France
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Aberrant hypermethylation of aldehyde dehydrogenase 2 promoter upstream sequence in rats with experimental myocardial infarction. BIOMED RESEARCH INTERNATIONAL 2015; 2015:503692. [PMID: 25629048 PMCID: PMC4299765 DOI: 10.1155/2015/503692] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 11/13/2014] [Accepted: 11/20/2014] [Indexed: 12/31/2022]
Abstract
Background. Aldehyde dehydrogenase 2 (ALDH2) plays a crucial role in myocardial protection against ischemia. Downregulation of ALDH2 was evidenced after myocardial infarction and the underlying mechanism is not fully understood. DNA methylation can regulate gene transcription in epigenetic level. We thus hypothesized that DNA methylation may affect ALDH2 expression in myocardial infarction (MI). Methods. MI was induced in Sprague-Dawley rats. MI border zone tissues were harvested at 1st week, 2nd week, and 3rd week after MI. Bisulfite sequencing PCR (BSP) was performed to detect the methylation levels of ALDH2 core promoter. Sequenom MassARRAY platform (MassARRAY) was used to examine the methylation levels of ALDH2 promoter upstream sequence. ALDH2 protein and mRNA expression were assayed by Western blot and real-time PCR, respectively. Results. Compared with Sham group, ALDH2 protein and mRNA expression of MI groups was significantly downregulated. Compared with Sham group, DNA methylation level of CpG sites in ALDH2 promoter upstream sequence was significantly higher in MI groups in a time-dependent manner (CpG1, CpG2, and CpG7, P < 0.01). DNA methylation did not affect ALDH2 core promoter sequence during the progress of MI. No significant difference was detected in DNA methylation level of ALDH2 promoter upstream sequence among MI groups. Conclusion. Aberrant hypermethylation of CpG sites in ALDH2 promoter upstream sequence is associated with myocardial ischemia injury and may partly result in ALDH2 downregulation after MI.
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Menafra R, Stunnenberg HG. MBD2 and MBD3: elusive functions and mechanisms. Front Genet 2014; 5:428. [PMID: 25538734 PMCID: PMC4260518 DOI: 10.3389/fgene.2014.00428] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 11/21/2014] [Indexed: 02/05/2023] Open
Abstract
Deoxyribonucleic acid methylation is a long known epigenetic mark involved in many biological processes and the 'readers' of this mark belong to several distinct protein families that 'read' and 'translate' the methylation mark into a function. Methyl-CpG binding domain proteins belong to one of these families that are associated with transcriptional activation/repression, regulation of chromatin structure, pluripotency, development, and differentiation. Discovered decades ago, the systematic determination of the genomic binding sites of these readers and their epigenome make-up at a genome-wide level revealed the tip of the functional iceberg. This review focuses on two members of the methyl binding proteins, namely MBD2 and MBD3 that reside in very similar complexes, yet appear to have very different biological roles. We provide a comprehensive comparison of their genome-wide binding features and emerging roles in gene regulation.
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Affiliation(s)
- Roberta Menafra
- Department of Molecular Biology, Radboud University Nijmegen, Netherlands
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Alteration of Scn3a expression is mediated via CpG methylation and MBD2 in mouse hippocampus during postnatal development and seizure condition. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1849:1-9. [PMID: 25459751 DOI: 10.1016/j.bbagrm.2014.11.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 10/13/2014] [Accepted: 11/12/2014] [Indexed: 12/21/2022]
Abstract
Increased expression of sodium channel SCN3A, an embryonic-expressed gene, has been identified in epileptic tissues, which is believed to contribute to the development of epilepsy. However, the regulatory mechanism of SCN3A expression under epileptic condition is still unknown. Here we showed a high level of Scn3a mRNA expression in mouse embryonic hippocampus with gradually decreasing to a low level during the postnatal development and a methylation of a specific CpG site (-39C) in the Scn3a promoter was increased in hippocampus during postnatal development, corresponding to the downregulation of Scn3a expression. Furthermore, in vitro methylation and -39C>T mutation of the Scn3a promoter decreased the reporter gene expression, suggesting an important role of the -39C site in regulating gene expression. We then demonstrated that the sequence containing -39C was a MBD2-binding motif and the CpG methylation of the promoter region increased the capability of MBD2's binding to the motif. Knockdown of MBD2 in mouse N1E-115 cells led to the -39C methylation and the downregulation of Scn3a transcription by decreasing the Scn3a promoter activity. In the hippocampus of seizure mice, the expressions of Scn3a and Mbd2 were upregulated after 10-day KA treatment. At the same time point, the -39C site was demethylated and the capability of MBD2's binding to the Scn3a promoter motif was decreased. Taken together, these findings suggest that CpG methylation and MBD2 are involved in altering Scn3a expression during postnatal development and seizure condition.
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