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Wong KG, Cheng YCF, Wu VH, Kiseleva AA, Li J, Poleshko A, Smith CL, Epstein JA. Growth factor-induced activation of MSK2 leads to phosphorylation of H3K9me2S10 and corresponding changes in gene expression. SCIENCE ADVANCES 2024; 10:eadm9518. [PMID: 38478612 PMCID: PMC10936876 DOI: 10.1126/sciadv.adm9518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 02/07/2024] [Indexed: 03/17/2024]
Abstract
Extracellular signals are transmitted through kinase cascades to modulate gene expression, but it remains unclear how epigenetic changes regulate this response. Here, we provide evidence that growth factor-stimulated changes in the transcript levels of many responsive genes are accompanied by increases in histone phosphorylation levels, specifically at histone H3 serine-10 when the adjacent lysine-9 is dimethylated (H3K9me2S10). Imaging and proteomic approaches show that epidermal growth factor (EGF) stimulation results in H3K9me2S10 phosphorylation, which occurs in genomic regions enriched for regulatory enhancers of EGF-responsive genes. We also demonstrate that the EGF-induced increase in H3K9me2S10ph is dependent on the nuclear kinase MSK2, and this subset of EGF-induced genes is dependent on MSK2 for transcription. Together, our work indicates that growth factor-induced changes in chromatin state can mediate the activation of downstream genes.
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Affiliation(s)
- Karen G. Wong
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yu-Chia F. Cheng
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Vincent H. Wu
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anna A. Kiseleva
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jun Li
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrey Poleshko
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Cheryl L. Smith
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jonathan A. Epstein
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Medicine and Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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2
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Jain R, Epstein JA. Epigenetics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1441:341-364. [PMID: 38884720 DOI: 10.1007/978-3-031-44087-8_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Epigenetics is the study of heritable changes to the genome and gene expression patterns that are not caused by direct changes to the DNA sequence. Examples of these changes include posttranslational modifications to DNA-bound histone proteins, DNA methylation, and remodeling of nuclear architecture. Collectively, epigenetic changes provide a layer of regulation that affects transcriptional activity of genes while leaving DNA sequences unaltered. Sequence variants or mutations affecting enzymes responsible for modifying or sensing epigenetic marks have been identified in patients with congenital heart disease (CHD), and small-molecule inhibitors of epigenetic complexes have shown promise as therapies for adult heart diseases. Additionally, transgenic mice harboring mutations or deletions of genes encoding epigenetic enzymes recapitulate aspects of human cardiac disease. Taken together, these findings suggest that the evolving field of epigenetics will inform our understanding of congenital and adult cardiac disease and offer new therapeutic opportunities.
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Affiliation(s)
- Rajan Jain
- Departments of Medicine and Cell and Developmental Biology, Institute for Regenerative Medicine, Epigenetics Institute and the Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
| | - Jonathan A Epstein
- Departments of Medicine and Cell and Developmental Biology, Institute for Regenerative Medicine, Epigenetics Institute and the Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
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3
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Oses C, De Rossi MC, Bruno L, Verneri P, Diaz MC, Benítez B, Guberman A, Levi V. From the membrane to the nucleus: mechanical signals and transcription regulation. Biophys Rev 2023; 15:671-683. [PMID: 37681098 PMCID: PMC10480138 DOI: 10.1007/s12551-023-01103-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/20/2023] [Indexed: 09/09/2023] Open
Abstract
Mechanical forces drive and modulate a wide variety of processes in eukaryotic cells including those occurring in the nucleus. Relevantly, forces are fundamental during development since they guide lineage specifications of embryonic stem cells. A sophisticated macromolecular machinery transduces mechanical stimuli received at the cell surface into a biochemical output; a key component in this mechanical communication is the cytoskeleton, a complex network of biofilaments in constant remodeling that links the cell membrane to the nuclear envelope. Recent evidence highlights that forces transmitted through the cytoskeleton directly affect the organization of chromatin and the accessibility of transcription-related molecules to their targets in the DNA. Consequently, mechanical forces can directly modulate transcription and change gene expression programs. Here, we will revise the biophysical toolbox involved in the mechanical communication with the cell nucleus and discuss how mechanical forces impact on the organization of this organelle and more specifically, on transcription. We will also discuss how live-cell fluorescence imaging is producing exquisite information to understand the mechanical response of cells and to quantify the landscape of interactions of transcription factors with chromatin in embryonic stem cells. These studies are building new biophysical insights that could be fundamental to achieve the goal of manipulating forces to guide cell differentiation in culture systems.
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Affiliation(s)
- Camila Oses
- Instituto de Química Biológica de La Facultad de Ciencias Exactas Y Naturales (IQUIBICEN), Facultad de Ciencias Exactas Y Naturales, CONICET-Universidad de Buenos Aires, C1428EGA Buenos Aires, Argentina
| | - María Cecilia De Rossi
- Instituto de Química Biológica de La Facultad de Ciencias Exactas Y Naturales (IQUIBICEN), Facultad de Ciencias Exactas Y Naturales, CONICET-Universidad de Buenos Aires, C1428EGA Buenos Aires, Argentina
| | - Luciana Bruno
- Facultad de Ciencias Exactas Y Naturales, Instituto de Cálculo (IC), CONICET-Universidad de Buenos Aires, C1428EGA Buenos Aires, Argentina
| | - Paula Verneri
- Instituto de Química Biológica de La Facultad de Ciencias Exactas Y Naturales (IQUIBICEN), Facultad de Ciencias Exactas Y Naturales, CONICET-Universidad de Buenos Aires, C1428EGA Buenos Aires, Argentina
| | - María Candelaria Diaz
- Instituto de Química Biológica de La Facultad de Ciencias Exactas Y Naturales (IQUIBICEN), Facultad de Ciencias Exactas Y Naturales, CONICET-Universidad de Buenos Aires, C1428EGA Buenos Aires, Argentina
| | - Belén Benítez
- Instituto de Fisiología, Biología Molecular Y Neurociencias (IFIBYNE), Facultad de Ciencias Exactas Y Naturales, CONICET-Universidad de Buenos Aires, C1428EGA Buenos Aires, Argentina
| | - Alejandra Guberman
- Instituto de Química Biológica de La Facultad de Ciencias Exactas Y Naturales (IQUIBICEN), Facultad de Ciencias Exactas Y Naturales, CONICET-Universidad de Buenos Aires, C1428EGA Buenos Aires, Argentina
- Facultad de Ciencias Exactas Y Naturales, Departamento de Fisiología, Universidad de Buenos Aires, Biología Molecular Y Celular, C1428EGA Buenos Aires, Argentina
| | - Valeria Levi
- Instituto de Química Biológica de La Facultad de Ciencias Exactas Y Naturales (IQUIBICEN), Facultad de Ciencias Exactas Y Naturales, CONICET-Universidad de Buenos Aires, C1428EGA Buenos Aires, Argentina
- Facultad de Ciencias Exactas Y Naturales, Departamento de Química Biológica, Universidad de Buenos Aires, C1428EGA Buenos Aires, Argentina
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4
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McCarthy RL, Zhang J, Zaret KS. Diverse heterochromatin states restricting cell identity and reprogramming. Trends Biochem Sci 2023; 48:513-526. [PMID: 36990958 PMCID: PMC10182259 DOI: 10.1016/j.tibs.2023.02.007] [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: 05/25/2022] [Revised: 02/16/2023] [Accepted: 02/24/2023] [Indexed: 03/29/2023]
Abstract
Heterochromatin is defined as a chromosomal domain harboring repressive H3K9me2/3 or H3K27me3 histone modifications and relevant factors that physically compact the chromatin. Heterochromatin can restrict where transcription factors bind, providing a barrier to gene activation and changes in cell identity. While heterochromatin thus helps maintain cell differentiation, it presents a barrier to overcome during efforts to reprogram cells for biomedical purposes. Recent findings have revealed complexity in the composition and regulation of heterochromatin, and shown that transiently disrupting the machinery of heterochromatin can enhance reprogramming. Here, we discuss how heterochromatin is established and maintained during development, and how our growing understanding of the mechanisms regulating H3K9me3 heterochromatin can be leveraged to improve our ability to direct changes in cell identity.
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Affiliation(s)
- Ryan L McCarthy
- Institute for Regenerative Medicine, Penn Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jingchao Zhang
- Institute for Regenerative Medicine, Penn Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kenneth S Zaret
- Institute for Regenerative Medicine, Penn Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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5
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Shah PP, Keough KC, Gjoni K, Santini GT, Abdill RJ, Wickramasinghe NM, Dundes CE, Karnay A, Chen A, Salomon REA, Walsh PJ, Nguyen SC, Whalen S, Joyce EF, Loh KM, Dubois N, Pollard KS, Jain R. An atlas of lamina-associated chromatin across twelve human cell types reveals an intermediate chromatin subtype. Genome Biol 2023; 24:16. [PMID: 36691074 PMCID: PMC9869549 DOI: 10.1186/s13059-023-02849-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 01/05/2023] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Association of chromatin with lamin proteins at the nuclear periphery has emerged as a potential mechanism to coordinate cell type-specific gene expression and maintain cellular identity via gene silencing. Unlike many histone modifications and chromatin-associated proteins, lamina-associated domains (LADs) are mapped genome-wide in relatively few genetically normal human cell types, which limits our understanding of the role peripheral chromatin plays in development and disease. RESULTS To address this gap, we map LAMIN B1 occupancy across twelve human cell types encompassing pluripotent stem cells, intermediate progenitors, and differentiated cells from all three germ layers. Integrative analyses of this atlas with gene expression and repressive histone modification maps reveal that lamina-associated chromatin in all twelve cell types is organized into at least two subtypes defined by differences in LAMIN B1 occupancy, gene expression, chromatin accessibility, transposable elements, replication timing, and radial positioning. Imaging of fluorescently labeled DNA in single cells validates these subtypes and shows radial positioning of LADs with higher LAMIN B1 occupancy and heterochromatic histone modifications primarily embedded within the lamina. In contrast, the second subtype of lamina-associated chromatin is relatively gene dense, accessible, dynamic across development, and positioned adjacent to the lamina. Most genes gain or lose LAMIN B1 occupancy consistent with cell types along developmental trajectories; however, we also identify examples where the enhancer, but not the gene body and promoter, changes LAD state. CONCLUSIONS Altogether, this atlas represents the largest resource to date for peripheral chromatin organization studies and reveals an intermediate chromatin subtype.
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Affiliation(s)
- Parisha P Shah
- Departments of Medicine and Cell and Developmental Biology, Penn CVI, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Smilow TRC, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Kathleen C Keough
- University of California, San Francisco, CA, 94117, USA
- Gladstone Institute of Data Science and Biotechnology, 1650 Owens Street, San Francisco, CA, 94158, USA
| | - Ketrin Gjoni
- University of California, San Francisco, CA, 94117, USA
- Gladstone Institute of Data Science and Biotechnology, 1650 Owens Street, San Francisco, CA, 94158, USA
| | - Garrett T Santini
- Departments of Medicine and Cell and Developmental Biology, Penn CVI, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Smilow TRC, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Richard J Abdill
- Departments of Medicine and Cell and Developmental Biology, Penn CVI, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Smilow TRC, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Nadeera M Wickramasinghe
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Carolyn E Dundes
- Department of Developmental Biology and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Ashley Karnay
- Departments of Medicine and Cell and Developmental Biology, Penn CVI, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Smilow TRC, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Angela Chen
- Department of Developmental Biology and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Rachel E A Salomon
- Department of Developmental Biology and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Patrick J Walsh
- Department of Genetics, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Son C Nguyen
- Department of Genetics, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Sean Whalen
- Gladstone Institute of Data Science and Biotechnology, 1650 Owens Street, San Francisco, CA, 94158, USA
| | - Eric F Joyce
- Department of Genetics, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kyle M Loh
- Department of Developmental Biology and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Nicole Dubois
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Katherine S Pollard
- University of California, San Francisco, CA, 94117, USA.
- Gladstone Institute of Data Science and Biotechnology, 1650 Owens Street, San Francisco, CA, 94158, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
| | - Rajan Jain
- Departments of Medicine and Cell and Developmental Biology, Penn CVI, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Smilow TRC, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA.
- Smilow TRC, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA.
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6
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Smith CL, Lan Y, Jain R, Epstein JA, Poleshko A. Global chromatin relabeling accompanies spatial inversion of chromatin in rod photoreceptors. SCIENCE ADVANCES 2021; 7:eabj3035. [PMID: 34559565 PMCID: PMC8462898 DOI: 10.1126/sciadv.abj3035] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 08/04/2021] [Indexed: 06/13/2023]
Abstract
The nuclear architecture of rod photoreceptor cells in nocturnal mammals is unlike that of other animal cells. Murine rod cells have an “inverted” chromatin organization with euchromatin at the nuclear periphery and heterochromatin packed in the center of the nucleus. In conventional nuclear architecture, euchromatin is mostly in the interior, and heterochromatin is largely at the nuclear periphery. We demonstrate that inverted nuclear architecture is achieved through global relabeling of the rod cell epigenome. During rod cell maturation, H3K9me2-labeled nuclear peripheral heterochromatin is relabeled with H3K9me3 and repositioned to the nuclear center, while transcriptionally active euchromatin is labeled with H3K9me2 and positioned at the nuclear periphery. Global chromatin relabeling is correlated with spatial rearrangement, suggesting a critical role for histone modifications, specifically H3K9 methylation, in nuclear architecture. These results reveal a dramatic example of genome-wide epigenetic relabeling of chromatin that accompanies altered nuclear architecture in a postnatal, postmitotic cell.
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Affiliation(s)
- Cheryl L. Smith
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yemin Lan
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rajan Jain
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, Penn Cardiovascular Institute, and Institute of Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jonathan A. Epstein
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, Penn Cardiovascular Institute, and Institute of Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrey Poleshko
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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7
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Shah PP, Lv W, Rhoades JH, Poleshko A, Abbey D, Caporizzo MA, Linares-Saldana R, Heffler JG, Sayed N, Thomas D, Wang Q, Stanton LJ, Bedi K, Morley MP, Cappola TP, Owens AT, Margulies KB, Frank DB, Wu JC, Rader DJ, Yang W, Prosser BL, Musunuru K, Jain R. Pathogenic LMNA variants disrupt cardiac lamina-chromatin interactions and de-repress alternative fate genes. Cell Stem Cell 2021; 28:938-954.e9. [PMID: 33529599 PMCID: PMC8106635 DOI: 10.1016/j.stem.2020.12.016] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 10/13/2020] [Accepted: 12/18/2020] [Indexed: 01/08/2023]
Abstract
Pathogenic mutations in LAMIN A/C (LMNA) cause abnormal nuclear structure and laminopathies. These diseases have myriad tissue-specific phenotypes, including dilated cardiomyopathy (DCM), but how LMNA mutations result in tissue-restricted disease phenotypes remains unclear. We introduced LMNA mutations from individuals with DCM into human induced pluripotent stem cells (hiPSCs) and found that hiPSC-derived cardiomyocytes, in contrast to hepatocytes or adipocytes, exhibit aberrant nuclear morphology and specific disruptions in peripheral chromatin. Disrupted regions were enriched for transcriptionally active genes and regions with lower LAMIN B1 contact frequency. The lamina-chromatin interactions disrupted in mutant cardiomyocytes were enriched for genes associated with non-myocyte lineages and correlated with higher expression of those genes. Myocardium from individuals with LMNA variants similarly showed aberrant expression of non-myocyte pathways. We propose that the lamina network safeguards cellular identity and that pathogenic LMNA variants disrupt peripheral chromatin with specific epigenetic and molecular characteristics, causing misexpression of genes normally expressed in other cell types.
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Affiliation(s)
- Parisha P Shah
- Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Penn Cardiovascular Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA
| | - Wenjian Lv
- Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Penn Cardiovascular Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA
| | - Joshua H Rhoades
- Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Penn Cardiovascular Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Institute for Biomedical Informatics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA
| | - Andrey Poleshko
- Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA
| | - Deepti Abbey
- Penn Cardiovascular Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA
| | - Matthew A Caporizzo
- Penn Cardiovascular Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Department of Physiology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Pennsylvania Muscle Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA
| | - Ricardo Linares-Saldana
- Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Penn Cardiovascular Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA
| | - Julie G Heffler
- Penn Cardiovascular Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Department of Physiology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Pennsylvania Muscle Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA
| | - Nazish Sayed
- Stanford Cardiovascular Institute, Department of Surgery, Division of Vascular Surgery, Stanford University, Stanford, CA 94305, USA
| | - Dilip Thomas
- Stanford Cardiovascular Institute, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Qiaohong Wang
- Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Penn Cardiovascular Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA
| | - Liam J Stanton
- Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Penn Cardiovascular Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA
| | - Kenneth Bedi
- Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Penn Cardiovascular Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA
| | - Michael P Morley
- Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Penn Cardiovascular Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Penn Lung Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA
| | - Thomas P Cappola
- Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Penn Cardiovascular Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA
| | - Anjali T Owens
- Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Penn Cardiovascular Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA
| | - Kenneth B Margulies
- Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Penn Cardiovascular Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA
| | - David B Frank
- Penn Cardiovascular Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Department of Pediatrics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA
| | - Joseph C Wu
- Stanford Cardiovascular Institute, Department of Medicine, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Daniel J Rader
- Penn Cardiovascular Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA
| | - Wenli Yang
- Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Penn Cardiovascular Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Institute for Regenerative Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA
| | - Benjamin L Prosser
- Penn Cardiovascular Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Department of Physiology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Pennsylvania Muscle Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA
| | - Kiran Musunuru
- Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Penn Cardiovascular Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA.
| | - Rajan Jain
- Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Penn Cardiovascular Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Institute for Regenerative Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA.
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8
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Bertero A, Rosa-Garrido M. Three-dimensional chromatin organization in cardiac development and disease. J Mol Cell Cardiol 2021; 151:89-105. [PMID: 33242466 PMCID: PMC11056610 DOI: 10.1016/j.yjmcc.2020.11.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 11/10/2020] [Accepted: 11/18/2020] [Indexed: 02/07/2023]
Abstract
Recent technological advancements in the field of chromatin biology have rewritten the textbook on nuclear organization. We now appreciate that the folding of chromatin in the three-dimensional space (i.e. its 3D "architecture") is non-random, hierarchical, and highly complex. While 3D chromatin structure is partially encoded in the primary sequence and thereby broadly conserved across cell types and states, a substantial portion of the genome seems to be dynamic during development or in disease. Moreover, there is growing evidence that at least some of the 3D structure of chromatin is functionally linked to gene regulation, both being modulated by and impacting on multiple nuclear processes (including DNA replication, transcription, and RNA splicing). In recent years, these new concepts have nourished several investigations about the functional role of 3D chromatin topology dynamics in the heart during development and disease. This review aims to provide a comprehensive overview of our current understanding in this field, and to discuss how this knowledge can inform further research as well as clinical practice.
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Affiliation(s)
- Alessandro Bertero
- Department of Laboratory Medicine and Pathology, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, WA 98109, USA; Center for Cardiovascular Biology, University of Washington, 850 Republican Street, Brotman Building, Seattle, WA 98109, USA.
| | - Manuel Rosa-Garrido
- Department of Anesthesiology and Perioperative Medicine, David Geffen School of Medicine, University of California, 650 Charles Young Dr, Los Angeles, CA 90095, USA.
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9
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Rullens PMJ, Kind J. Attach and stretch: Emerging roles for genome-lamina contacts in shaping the 3D genome. Curr Opin Cell Biol 2020; 70:51-57. [PMID: 33360765 DOI: 10.1016/j.ceb.2020.11.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/20/2020] [Accepted: 11/25/2020] [Indexed: 11/17/2022]
Abstract
A large proportion of the metazoan genome is spatially segregated at the nuclear periphery through genomic contacts with the nuclear lamina, a thin meshwork of lamin filaments that lines the inner-nuclear membrane. Lamina-associated domains are believed to contribute to the regulation of gene transcription and to provide structural three-dimensional support to the organization of the genome in A and B compartments and topologically associating domains. In this review, we will evaluate recent work addressing the role of lamina-associated domains in three-dimensional genome organization and propose experimental frameworks that may expand our understanding of their interdependence.
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Affiliation(s)
- Pim M J Rullens
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jop Kind
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands.
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10
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Kafer GR, Tanaka Y, Rillo-Bohn R, Shimizu E, Hasegawa K, Carlton PM. Sequential peripheral enrichment of H2A.Zac and H3K9me2 during trophoblast differentiation in human embryonic stem cells. J Cell Sci 2020; 133:jcs.245282. [PMID: 33199519 DOI: 10.1242/jcs.245282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 10/27/2020] [Indexed: 11/20/2022] Open
Abstract
During the transition from pluripotency to a lineage-committed state, chromatin undergoes large-scale changes in structure, involving covalent modification of histone tails, use of histone variants and gene position changes with respect to the nuclear periphery. Here, using high-resolution microscopy and quantitative image analysis, we surveyed a panel of histone modifications for changes in nuclear peripheral enrichment during differentiation of human embryonic stem cells to a trophoblast-like lineage. We found two dynamic modifications at the nuclear periphery, acetylation of histone H2A.Z (H2A.Zac), and dimethylation of histone H3 at lysine 9 (H3K9me2). We demonstrate successive peripheral enrichment of these markers, with H2A.Zac followed by H3K9me2, over the course of 4 days. We find that H3K9me2 increases concomitantly with, but independently of, expression of lamin A, since deletion of lamin A did not affect H3K9me2 enrichment. We further show that inhibition of histone deacetylases causes persistent and increased H2A.Z acetylation at the periphery, delayed H3K9me2 enrichment and failure to differentiate. Our results show a concerted change in the nature of peripheral chromatin occurs upon differentiation into the trophoblast state.
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Affiliation(s)
- Georgia Rose Kafer
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto 606-8501, Japan
| | - Yoshihisa Tanaka
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto 606-8501, Japan
| | - Regina Rillo-Bohn
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto 606-8501, Japan
| | - Eiko Shimizu
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto 606-8501, Japan
| | - Kouichi Hasegawa
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto 606-8501, Japan
| | - Peter M Carlton
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto 606-8501, Japan
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11
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Abstract
Gene expression is needed for the maintenance of heart function under normal conditions and in response to stress. Each cell type of the heart has a specific program controlling transcription. Different types of stress induce modifications of these programs and, if prolonged, can lead to altered cardiac phenotype and, eventually, to heart failure. The transcriptional status of a gene is regulated by the epigenome, a complex network of DNA and histone modifications. Until a few years ago, our understanding of the role of the epigenome in heart disease was limited to that played by histone deacetylation. But over the last decade, the consequences for the maintenance of homeostasis in the heart and for the development of cardiac hypertrophy of a number of other modifications, including DNA methylation and hydroxymethylation, histone methylation and acetylation, and changes in chromatin architecture, have become better understood. Indeed, it is now clear that many levels of regulation contribute to defining the epigenetic landscape required for correct cardiomyocyte function, and that their perturbation is responsible for cardiac hypertrophy and fibrosis. Here, we review these aspects and draw a picture of what epigenetic modification may imply at the therapeutic level for heart failure.
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Affiliation(s)
- Roberto Papait
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy; Humanitas Clinical Research Center-IRCCS, Rozzano, Italy; Humanitas University, Department of Biomedical Sciences, Pieve Emanuele, Italy; and National Research Council of Italy, Institute of Genetics and Biomedical Research, Milan Unit, Rozzano, Italy
| | - Simone Serio
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy; Humanitas Clinical Research Center-IRCCS, Rozzano, Italy; Humanitas University, Department of Biomedical Sciences, Pieve Emanuele, Italy; and National Research Council of Italy, Institute of Genetics and Biomedical Research, Milan Unit, Rozzano, Italy
| | - Gianluigi Condorelli
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy; Humanitas Clinical Research Center-IRCCS, Rozzano, Italy; Humanitas University, Department of Biomedical Sciences, Pieve Emanuele, Italy; and National Research Council of Italy, Institute of Genetics and Biomedical Research, Milan Unit, Rozzano, Italy
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12
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Mizi A, Zhang S, Papantonis A. Genome folding and refolding in differentiation and cellular senescence. Curr Opin Cell Biol 2020; 67:56-63. [PMID: 32911122 DOI: 10.1016/j.ceb.2020.08.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 08/02/2020] [Accepted: 08/03/2020] [Indexed: 12/11/2022]
Abstract
The spatial conformation of chromatin within the confines of eukaryotic cell nuclei is now acknowledged as a decisive epigenetic mechanism for the modulation of such cellular functions as gene expression regulation, DNA replication or DNA damage repair. Of course, these processes are tightly regulated during organismal development and markedly affected by cellular ageing. Thus, the question that arises is to what extent does folding or refolding of the genome in three-dimensional space underlie the progression of development or ageing? Herein, we discuss recent experimental and modelling evidence to address this question and revisit how these seemingly different processed might represent two sides of the same coin.
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Affiliation(s)
- Athanasia Mizi
- Institute of Pathology, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Shu Zhang
- Institute of Pathology, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Argyris Papantonis
- Institute of Pathology, University Medical Center Göttingen, 37075, Göttingen, Germany.
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13
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See K, Kiseleva AA, Smith CL, Liu F, Li J, Poleshko A, Epstein JA. Histone methyltransferase activity programs nuclear peripheral genome positioning. Dev Biol 2020; 466:90-98. [PMID: 32712024 DOI: 10.1016/j.ydbio.2020.07.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/13/2020] [Accepted: 07/14/2020] [Indexed: 11/26/2022]
Abstract
Spatial organization of the genome in the nucleus plays a critical role in development and regulation of transcription. A genomic region that resides at the nuclear periphery is part of the chromatin layer marked with histone H3 lysine 9 dimethyl (H3K9me2), but chromatin reorganization during cell differentiation can cause movement in and out of this nuclear compartment with patterns specific for individual cell fates. Here we describe a CRISPR-based system that allows visualization coupled with forced spatial relocalization of a target genomic locus in live cells. We demonstrate that a specified locus can be tethered to the nuclear periphery through direct binding to a dCas9-Lap2β fusion protein at the nuclear membrane, or via targeting of a histone methyltransferase (HMT), G9a fused to dCas9, that promotes H3K9me2 labeling and localization to the nuclear periphery. The enzymatic activity of the HMT is sufficient to promote this repositioning, while disruption of the catalytic activity abolishes the localization effect. We further demonstrate that dCas9-G9a-mediated localization to the nuclear periphery is independent of nuclear actin polymerization. Our data suggest a function for epigenetic histone modifying enzymes in spatial chromatin organization and provide a system for tracking and labeling targeted genomic regions in live cells.
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Affiliation(s)
- Kelvin See
- Department of Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Anna A Kiseleva
- Department of Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Cheryl L Smith
- Department of Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Feiyan Liu
- Department of Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jun Li
- Department of Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrey Poleshko
- Department of Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jonathan A Epstein
- Department of Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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14
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Rymen B, Kawamura A, Lambolez A, Inagaki S, Takebayashi A, Iwase A, Sakamoto Y, Sako K, Favero DS, Ikeuchi M, Suzuki T, Seki M, Kakutani T, Roudier F, Sugimoto K. Histone acetylation orchestrates wound-induced transcriptional activation and cellular reprogramming in Arabidopsis. Commun Biol 2019; 2:404. [PMID: 31701032 PMCID: PMC6828771 DOI: 10.1038/s42003-019-0646-5] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 10/08/2019] [Indexed: 01/15/2023] Open
Abstract
Plant somatic cells reprogram and regenerate new tissues or organs when they are severely damaged. These physiological processes are associated with dynamic transcriptional responses but how chromatin-based regulation contributes to wound-induced gene expression changes and subsequent cellular reprogramming remains unknown. In this study we investigate the temporal dynamics of the histone modifications H3K9/14ac, H3K27ac, H3K4me3, H3K27me3, and H3K36me3, and analyze their correlation with gene expression at early time points after wounding. We show that a majority of the few thousand genes rapidly induced by wounding are marked with H3K9/14ac and H3K27ac before and/or shortly after wounding, and these include key wound-inducible reprogramming genes such as WIND1, ERF113/RAP2.6 L and LBD16. Our data further demonstrate that inhibition of GNAT-MYST-mediated histone acetylation strongly blocks wound-induced transcriptional activation as well as callus formation at wound sites. This study thus uncovered a key epigenetic mechanism that underlies wound-induced cellular reprogramming in plants.
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Affiliation(s)
- Bart Rymen
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045 Japan
| | - Ayako Kawamura
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045 Japan
| | - Alice Lambolez
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045 Japan
- Department of Biological Sciences, Faculty of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654 Japan
| | - Soichi Inagaki
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540 Japan
- Department of Genetics, School of Life science, The Graduate University for Advanced Studies (SOKENDAI), Shonankokusaimura, Hayama, Kanagawa 240-0193 Japan
- PREST, Japan Science and Technology Agency, 4-1-8, Honcho, Kawaguchi, Saitama 332-0012 Japan
| | - Arika Takebayashi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045 Japan
| | - Akira Iwase
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045 Japan
| | - Yuki Sakamoto
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045 Japan
- Department of Biological Sciences, Faculty of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654 Japan
| | - Kaori Sako
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045 Japan
- Department of Advanced Bioscience, Faculty of Agriculture, Kindai University, Nara, 631-8505 Japan
| | - David S. Favero
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045 Japan
| | - Momoko Ikeuchi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045 Japan
| | - Takamasa Suzuki
- Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501 Japan
| | - Motoaki Seki
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045 Japan
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198 Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, 244-0813 Japan
| | - Tetsuji Kakutani
- Department of Biological Sciences, Faculty of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654 Japan
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540 Japan
- Department of Genetics, School of Life science, The Graduate University for Advanced Studies (SOKENDAI), Shonankokusaimura, Hayama, Kanagawa 240-0193 Japan
| | - François Roudier
- Laboratoire Reproduction et Développement des Plantes, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342 Lyon, France
| | - Keiko Sugimoto
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045 Japan
- Department of Biological Sciences, Faculty of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654 Japan
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15
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Mortimer T, Wainwright EN, Patel H, Siow BM, Jaunmuktane Z, Brandner S, Scaffidi P. Redistribution of EZH2 promotes malignant phenotypes by rewiring developmental programmes. EMBO Rep 2019; 20:e48155. [PMID: 31468686 PMCID: PMC6776892 DOI: 10.15252/embr.201948155] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 08/05/2019] [Accepted: 08/08/2019] [Indexed: 01/08/2023] Open
Abstract
Epigenetic regulators are often hijacked by cancer cells to sustain malignant phenotypes. How cells repurpose key regulators of cell identity as tumour-promoting factors is unclear. The antithetic role of the Polycomb component EZH2 in normal brain and glioma provides a paradigm to dissect how wild-type chromatin modifiers gain a pathological function in cancer. Here, we show that oncogenic signalling induces redistribution of EZH2 across the genome, and through misregulation of homeotic genes corrupts the identity of neural cells. Characterisation of EZH2 targets in de novo transformed cells, combined with analysis of glioma patient datasets and cell lines, reveals that acquisition of tumorigenic potential is accompanied by a transcriptional switch involving de-repression of spinal cord-specifying HOX genes and concomitant silencing of the empty spiracles homologue EMX2, a critical regulator of neurogenesis in the forebrain. Maintenance of tumorigenic potential by glioblastoma cells requires EMX2 repression, since forced EMX2 expression prevents tumour formation. Thus, by redistributing EZH2 across the genome, cancer cells subvert developmental transcriptional programmes that specify normal cell identity and remove physiological breaks that restrain cell proliferation.
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MESH Headings
- Animals
- Carcinogenesis/genetics
- Carcinogenesis/pathology
- Cell Line, Tumor
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Chromatin/metabolism
- DNA Methylation/genetics
- Enhancer of Zeste Homolog 2 Protein/metabolism
- Gene Expression Regulation, Neoplastic
- Genes, Homeobox
- Glioma/genetics
- Glioma/pathology
- Humans
- Male
- Mice, Inbred NOD
- Models, Biological
- Phenotype
- Protein Binding
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Transcription, Genetic
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Affiliation(s)
- Thomas Mortimer
- Cancer Epigenetics LaboratoryThe Francis Crick InstituteLondonUK
| | | | - Harshil Patel
- Bioinformatics and BiostatisticsThe Francis Crick InstituteLondonUK
| | | | - Zane Jaunmuktane
- Department of Clinical and Movement NeurosciencesQueen Square Brain BankUCL Queen Square Institute of NeurologyLondonUK
- Division of NeuropathologyNational Hospital for Neurology and NeurosurgeryUniversity College London Hospitals NHS Foundation TrustLondonUK
| | - Sebastian Brandner
- Division of NeuropathologyNational Hospital for Neurology and NeurosurgeryUniversity College London Hospitals NHS Foundation TrustLondonUK
- Department of Neurodegenerative DiseaseUCL Queen Square Institute of NeurologyLondonUK
| | - Paola Scaffidi
- Cancer Epigenetics LaboratoryThe Francis Crick InstituteLondonUK
- UCL Cancer InstituteUniversity College LondonLondonUK
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16
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Lamina Associated Domains and Gene Regulation in Development and Cancer. Cells 2019; 8:cells8030271. [PMID: 30901978 PMCID: PMC6468596 DOI: 10.3390/cells8030271] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 03/18/2019] [Accepted: 03/19/2019] [Indexed: 12/02/2022] Open
Abstract
The nuclear lamina (NL) is a thin meshwork of filaments that lines the inner nuclear membrane, thereby providing a platform for chromatin binding and supporting genome organization. Genomic regions contacting the NL are lamina associated domains (LADs), which contain thousands of genes that are lowly transcribed, and enriched for repressive histone modifications. LADs are dynamic structures that shift spatial positioning in accordance with cell-type specific gene expression changes during differentiation and development. Furthermore, recent studies have linked the disruption of LADs and alterations in the epigenome with the onset of diseases such as cancer. Here we focus on the role of LADs and the NL in gene regulation during development and cancer.
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