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Wahl N, Espeso-Gil S, Chietera P, Nagel A, Laighneach A, Morris DW, Rajarajan P, Akbarian S, Dechant G, Apostolova G. SATB2 organizes the 3D genome architecture of cognition in cortical neurons. Mol Cell 2024; 84:621-639.e9. [PMID: 38244545 PMCID: PMC10923151 DOI: 10.1016/j.molcel.2023.12.024] [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: 01/27/2023] [Revised: 10/02/2023] [Accepted: 12/15/2023] [Indexed: 01/22/2024]
Abstract
The DNA-binding protein SATB2 is genetically linked to human intelligence. We studied its influence on the three-dimensional (3D) epigenome by mapping chromatin interactions and accessibility in control versus SATB2-deficient cortical neurons. We find that SATB2 affects the chromatin looping between enhancers and promoters of neuronal-activity-regulated genes, thus influencing their expression. It also alters A/B compartments, topologically associating domains, and frequently interacting regions. Genes linked to SATB2-dependent 3D genome changes are implicated in highly specialized neuronal functions and contribute to cognitive ability and risk for neuropsychiatric and neurodevelopmental disorders. Non-coding DNA regions with a SATB2-dependent structure are enriched for common variants associated with educational attainment, intelligence, and schizophrenia. Our data establish SATB2 as a cell-type-specific 3D genome modulator, which operates both independently and in cooperation with CCCTC-binding factor (CTCF) to set up the chromatin landscape of pyramidal neurons for cognitive processes.
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Affiliation(s)
- Nico Wahl
- Institute for Neuroscience, Medical University of Innsbruck, Innsbruck 6020, Austria.
| | - Sergio Espeso-Gil
- Institute for Neuroscience, Medical University of Innsbruck, Innsbruck 6020, Austria; Department of Psychiatry, Friedman Brain Institute, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Paola Chietera
- Institute for Neuroscience, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Amelie Nagel
- Institute for Neuroscience, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Aodán Laighneach
- Centre for Neuroimaging, Cognition and Genomics (NICOG), School of Biological and Chemical Sciences, University of Galway, Galway, H91 TK33, Ireland
| | - Derek W Morris
- Centre for Neuroimaging, Cognition and Genomics (NICOG), School of Biological and Chemical Sciences, University of Galway, Galway, H91 TK33, Ireland
| | - Prashanth Rajarajan
- Department of Psychiatry, Friedman Brain Institute, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Schahram Akbarian
- Department of Psychiatry, Friedman Brain Institute, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Georg Dechant
- Institute for Neuroscience, Medical University of Innsbruck, Innsbruck 6020, Austria.
| | - Galina Apostolova
- Institute for Neuroscience, Medical University of Innsbruck, Innsbruck 6020, Austria.
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Li F, Yan C, Yao Y, Yang Y, Liu Y, Fan D, Zhao J, Tang Z. Transcription Factor SATB2 Regulates Skeletal Muscle Cell Proliferation and Migration via HDAC4 in Pigs. Genes (Basel) 2024; 15:65. [PMID: 38254955 PMCID: PMC10815226 DOI: 10.3390/genes15010065] [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: 12/13/2023] [Revised: 12/26/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024] Open
Abstract
Skeletal muscle development remarkably affects meat production and growth rate, regulated by complex regulatory mechanisms in pigs. Specific AT sequence-binding protein 2 (SATB2) is a classic transcription factor and chromatin organizer, which holds a profound effect in the regulation of chromatin remodeling. However, the regulation role of SATB2 concerning skeletal muscle cell fate through chromatin remodeling in pigs remains largely unknown. Here, we observed that SATB2 was expressed higher in the lean-type compared to the obese-type pigs, which also enriched the pathways of skeletal muscle development, chromatin organization, and histone modification. Functionally, knockdown SATB2 led to decreases in the proliferation and migration markers at the mRNA and protein expression levels, respectively, while overexpression SATB2 had the opposite effects. Further, we found histone deacetylase 4 (HDAC4) was a key downstream target gene of SATB2 related to chromatin remodeling. The binding relationship between SATB2 and HDAC4 was confirmed by a dual-luciferase reporter system and ChIP-qPCR analysis. Besides, we revealed that HDAC4 promoted the skeletal muscle cell proliferation and migration at the mRNA and protein expression levels, respectively. In conclusion, our study indicates that transcription factor SATB2 binding to HDAC4 positively contributes to skeletal muscle cell proliferation and migration, which might mediate the chromatin remodeling to influence myogenesis in pigs. This study develops a novel insight into understanding the molecular regulatory mechanism of myogenesis, and provides a promising gene for genetic breeding in pigs.
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Affiliation(s)
- Fanqinyu Li
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China;
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (C.Y.); (Y.Y.); (Y.L.); (D.F.)
| | - Chao Yan
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (C.Y.); (Y.Y.); (Y.L.); (D.F.)
- Kunpeng Institute of Modern Agriculture at Foshan, Chinese Academy of Agricultural Sciences, Foshan 528226, China;
| | - Yilong Yao
- Kunpeng Institute of Modern Agriculture at Foshan, Chinese Academy of Agricultural Sciences, Foshan 528226, China;
| | - Yalan Yang
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (C.Y.); (Y.Y.); (Y.L.); (D.F.)
- Kunpeng Institute of Modern Agriculture at Foshan, Chinese Academy of Agricultural Sciences, Foshan 528226, China;
| | - Yanwen Liu
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (C.Y.); (Y.Y.); (Y.L.); (D.F.)
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Danyang Fan
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (C.Y.); (Y.Y.); (Y.L.); (D.F.)
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Junxing Zhao
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China;
| | - Zhonglin Tang
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China;
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (C.Y.); (Y.Y.); (Y.L.); (D.F.)
- Kunpeng Institute of Modern Agriculture at Foshan, Chinese Academy of Agricultural Sciences, Foshan 528226, China;
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
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3
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Benada J, Alsowaida D, Megeney LA, Sørensen CS. Self-inflicted DNA breaks in cell differentiation and cancer. Trends Cell Biol 2023; 33:850-859. [PMID: 36997393 DOI: 10.1016/j.tcb.2023.03.002] [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: 12/01/2022] [Revised: 03/05/2023] [Accepted: 03/08/2023] [Indexed: 03/30/2023]
Abstract
Self-inflicted DNA strand breaks are canonically linked with cell death pathways and the establishment of genetic diversity in immune and germline cells. Moreover, this form of DNA damage is an established source of genome instability in cancer development. However, recent studies indicate that nonlethal self-inflicted DNA strand breaks play an indispensable but underappreciated role in a variety of cell processes, including differentiation and cancer therapy responses. Mechanistically, these physiological DNA breaks originate from the activation of nucleases, which are best characterized for inducing DNA fragmentation in apoptotic cell death. In this review, we outline the emerging biology of one critical nuclease, caspase-activated DNase (CAD), and how directed activation or deployment of this enzyme can lead to divergent cell fate outcomes.
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Affiliation(s)
- Jan Benada
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen 2200 N, Denmark
| | - Dalal Alsowaida
- Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute and the Departments of Medicine and Cellular and Molecular Medicine, University of Ottawa, Ottawa, K1H 8L6, Canada; Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Lynn A Megeney
- Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute and the Departments of Medicine and Cellular and Molecular Medicine, University of Ottawa, Ottawa, K1H 8L6, Canada.
| | - Claus S Sørensen
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen 2200 N, Denmark.
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Yuan W, Weaver YM, Earnest S, Taylor CA, Cobb MH, Weaver BP. Modulating p38 MAPK signaling by proteostasis mechanisms supports tissue integrity during growth and aging. Nat Commun 2023; 14:4543. [PMID: 37507441 PMCID: PMC10382525 DOI: 10.1038/s41467-023-40317-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
The conserved p38 MAPK family is activated by phosphorylation during stress responses and inactivated by phosphatases. C. elegans PMK-1 p38 MAPK initiates innate immune responses and blocks development when hyperactivated. Here we show that PMK-1 signaling is enhanced during early aging by modulating the stoichiometry of non-phospho-PMK-1 to promote tissue integrity and longevity. Loss of pmk-1 function accelerates progressive declines in neuronal integrity and lysosome function compromising longevity which has both cell autonomous and cell non-autonomous contributions. CED-3 caspase cleavage limits phosphorylated PMK-1. Enhancing p38 signaling with caspase cleavage-resistant PMK-1 protects lysosomal and neuronal integrity extending a youthful phase. PMK-1 works through a complex transcriptional program to regulate lysosome formation. During early aging, the absolute phospho-p38 amount is maintained but the reservoir of non-phospho-p38 diminishes to enhance signaling without hyperactivation. Our findings show that modulating the stoichiometry of non-phospho-p38 dynamically supports tissue-homeostasis during aging without hyper-activation of stress response.
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Affiliation(s)
- Wang Yuan
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yi M Weaver
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Svetlana Earnest
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Clinton A Taylor
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Melanie H Cobb
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Benjamin P Weaver
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, USA.
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Bencze M. Mechanisms of Myofibre Death in Muscular Dystrophies: The Emergence of the Regulated Forms of Necrosis in Myology. Int J Mol Sci 2022; 24:ijms24010362. [PMID: 36613804 PMCID: PMC9820579 DOI: 10.3390/ijms24010362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/08/2022] [Accepted: 12/09/2022] [Indexed: 12/28/2022] Open
Abstract
Myofibre necrosis is a central pathogenic process in muscular dystrophies (MD). As post-lesional regeneration cannot fully compensate for chronic myofibre loss, interstitial tissue accumulates and impairs muscle function. Muscle regeneration has been extensively studied over the last decades, however, the pathway(s) controlling muscle necrosis remains largely unknown. The recent discovery of several regulated cell death (RCD) pathways with necrotic morphology challenged the dogma of necrosis as an uncontrolled process, opening interesting perspectives for many degenerative disorders. In this review, we focus on how cell death affects myofibres in MDs, integrating the latest research in the cell death field, with specific emphasis on Duchenne muscular dystrophy, the best-known and most common hereditary MD. The role of regulated forms of necrosis in myology is still in its infancy but there is increasing evidence that necroptosis, a genetically programmed form of necrosis, is involved in muscle degenerating disorders. The existence of apoptosis in myofibre demise will be questioned, while other forms of non-apoptotic RCDs may also have a role in myonecrosis, illustrating the complexity and possibly the heterogeneity of the cell death pathways in muscle degenerating conditions.
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Affiliation(s)
- Maximilien Bencze
- “Biology of the Neuromuscular System” Team, Institut Mondor de Recherche Biomédicale (IMRB), University Paris-Est Créteil, INSERM, U955 IMRB, 94010 Créteil, France;
- École Nationale Vétérinaire d’Alfort, IMRB, 94700 Maisons-Alfort, France
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