51
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Donnaloja F, Raimondi MT, Messa L, Barzaghini B, Carnevali F, Colombo E, Mazza D, Martinelli C, Boeri L, Rey F, Cereda C, Osellame R, Cerullo G, Carelli S, Soncini M, Jacchetti E. 3D photopolymerized microstructured scaffolds influence nuclear deformation, nucleo/cytoskeletal protein organization, and gene regulation in mesenchymal stem cells. APL Bioeng 2023; 7:036112. [PMID: 37692376 PMCID: PMC10491463 DOI: 10.1063/5.0153215] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 08/21/2023] [Indexed: 09/12/2023] Open
Abstract
Mechanical stimuli from the extracellular environment affect cell morphology and functionality. Recently, we reported that mesenchymal stem cells (MSCs) grown in a custom-made 3D microscaffold, the Nichoid, are able to express higher levels of stemness markers. In fact, the Nichoid is an interesting device for autologous MSC expansion in clinical translation and would appear to regulate gene activity by altering intracellular force transmission. To corroborate this hypothesis, we investigated mechanotransduction-related nuclear mechanisms, and we also treated spread cells with a drug that destroys the actin cytoskeleton. We observed a roundish nuclear shape in MSCs cultured in the Nichoid and correlated the nuclear curvature with the import of transcription factors. We observed a more homogeneous euchromatin distribution in cells cultured in the Nichoid with respect to the Flat sample, corresponding to a standard glass coverslip. These results suggest a different gene regulation, which we confirmed by an RNA-seq analysis that revealed the dysregulation of 1843 genes. We also observed a low structured lamina mesh, which, according to the implemented molecular dynamic simulations, indicates reduced damping activity, thus supporting the hypothesis of low intracellular force transmission. Also, our investigations regarding lamin expression and spatial organization support the hypothesis that the gene dysregulation induced by the Nichoid is mainly related to a reduction in force transmission. In conclusion, our findings revealing the Nichoid's effects on MSC behavior is a step forward in the control of stem cells via mechanical manipulation, thus paving the way to new strategies for MSC translation to clinical applications.
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Affiliation(s)
- Francesca Donnaloja
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta,” Politecnico di Milano, Milan, Italy
| | - Manuela Teresa Raimondi
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta,” Politecnico di Milano, Milan, Italy
| | | | - Bianca Barzaghini
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta,” Politecnico di Milano, Milan, Italy
| | - Federica Carnevali
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta,” Politecnico di Milano, Milan, Italy
| | | | - Davide Mazza
- Istituto Scientifico Ospedale San Raffaele, Centro di Imaging Sperimentale, Milan, Italy
| | - Chiara Martinelli
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta,” Politecnico di Milano, Milan, Italy
| | - Lucia Boeri
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta,” Politecnico di Milano, Milan, Italy
| | - Federica Rey
- Pediatric Research Center “Romeo ed Enrica Invernizzi,” Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | - Cristina Cereda
- Center of Functional Genomic and Rare Diseases, “V. Buzzi” Children's Hospital, 20154 Milan, Italy
| | - Roberto Osellame
- Institute for Photonics and Nanotechnologies—CNR, and Physics Department, Politecnico di Milano, Milan, Italy
| | - Giulio Cerullo
- Institute for Photonics and Nanotechnologies—CNR, and Physics Department, Politecnico di Milano, Milan, Italy
| | | | - Monica Soncini
- Department of Electronics, Information and Bioengineering, Politecnico di Milano, Milan, Italy
| | - Emanuela Jacchetti
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta,” Politecnico di Milano, Milan, Italy
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52
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Pruvost M, Patzig J, Yattah C, Selcen I, Hernandez M, Park HJ, Moyon S, Liu S, Morioka MS, Shopland L, Al-Dalahmah O, Bendl J, Fullard JF, Roussos P, Goldman J, He Y, Dupree JL, Casaccia P. The stability of the myelinating oligodendrocyte transcriptome is regulated by the nuclear lamina. Cell Rep 2023; 42:112848. [PMID: 37515770 PMCID: PMC10600948 DOI: 10.1016/j.celrep.2023.112848] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 05/26/2023] [Accepted: 07/07/2023] [Indexed: 07/31/2023] Open
Abstract
Oligodendrocytes are specialized cells that insulate and support axons with their myelin membrane, allowing proper brain function. Here, we identify lamin A/C (LMNA/C) as essential for transcriptional and functional stability of myelinating oligodendrocytes. We show that LMNA/C levels increase with differentiation of progenitors and that loss of Lmna in differentiated oligodendrocytes profoundly alters their chromatin accessibility and transcriptional signature. Lmna deletion in myelinating glia is compatible with normal developmental myelination. However, altered chromatin accessibility is detected in fully differentiated oligodendrocytes together with increased expression of progenitor genes and decreased levels of lipid-related transcription factors and inner mitochondrial membrane transcripts. These changes are accompanied by altered brain metabolism, lower levels of myelin-related lipids, and altered mitochondrial structure in oligodendrocytes, thereby resulting in myelin thinning and the development of a progressively worsening motor phenotype. Overall, our data identify LMNA/C as essential for maintaining the transcriptional and functional stability of myelinating oligodendrocytes.
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Affiliation(s)
- Mathilde Pruvost
- Neuroscience Initiative at the Advanced Science Research Center of the Graduate Center of the City University of New York, 85 St. Nicholas Terrace, New York, NY 10031, USA
| | - Julia Patzig
- Neuroscience Initiative at the Advanced Science Research Center of the Graduate Center of the City University of New York, 85 St. Nicholas Terrace, New York, NY 10031, USA
| | - Camila Yattah
- Neuroscience Initiative at the Advanced Science Research Center of the Graduate Center of the City University of New York, 85 St. Nicholas Terrace, New York, NY 10031, USA; Graduate Program in Biochemistry, The Graduate Center of The City University of New York, 365 5(th) Avenue, New York, NY 10016, USA
| | - Ipek Selcen
- Neuroscience Initiative at the Advanced Science Research Center of the Graduate Center of the City University of New York, 85 St. Nicholas Terrace, New York, NY 10031, USA; Graduate Program in Biochemistry, The Graduate Center of The City University of New York, 365 5(th) Avenue, New York, NY 10016, USA
| | - Marylens Hernandez
- Graduate School of Biological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hye-Jin Park
- Neuroscience Initiative at the Advanced Science Research Center of the Graduate Center of the City University of New York, 85 St. Nicholas Terrace, New York, NY 10031, USA
| | - Sarah Moyon
- Neuroscience Initiative at the Advanced Science Research Center of the Graduate Center of the City University of New York, 85 St. Nicholas Terrace, New York, NY 10031, USA
| | - Shibo Liu
- Neuroscience Initiative at the Advanced Science Research Center of the Graduate Center of the City University of New York, 85 St. Nicholas Terrace, New York, NY 10031, USA; Structural Biology Initiative, Advanced Science Research Center at the Graduate Center, City University of New York, New York, NY 10031, USA
| | - Malia S Morioka
- Neuroscience Initiative at the Advanced Science Research Center of the Graduate Center of the City University of New York, 85 St. Nicholas Terrace, New York, NY 10031, USA; Macaulay Honors College, City College of New York, New York, NY 10031, USA
| | - Lindsay Shopland
- Jackson Laboratory, 1650 Santa Ana Ave, Sacramento, CA 95835, USA
| | - Osama Al-Dalahmah
- Department of Pathology and Cell Biology, Division of Neuropathology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, and the New York Presbyterian Hospital, New York, NY 10032, USA
| | - Jaroslav Bendl
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - John F Fullard
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Panos Roussos
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Mental Illness Research, Education, and Clinical Center (VISN 2 South), James J. Peters VA Medical Center, Bronx, NY 10468, USA; Center for Dementia Research, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY 10962, USA
| | - James Goldman
- Department of Pathology and Cell Biology, Division of Neuropathology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, and the New York Presbyterian Hospital, New York, NY 10032, USA
| | - Ye He
- Neuroscience Initiative at the Advanced Science Research Center of the Graduate Center of the City University of New York, 85 St. Nicholas Terrace, New York, NY 10031, USA; Macaulay Honors College, City College of New York, New York, NY 10031, USA
| | - Jeffrey L Dupree
- Department of Anatomy and Neurobiology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Patrizia Casaccia
- Neuroscience Initiative at the Advanced Science Research Center of the Graduate Center of the City University of New York, 85 St. Nicholas Terrace, New York, NY 10031, USA; Graduate Program in Biochemistry, The Graduate Center of The City University of New York, 365 5(th) Avenue, New York, NY 10016, USA; Graduate School of Biological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate Program in Biology, The Graduate Center of The City University of New York, 365 5th Avenue, New York, NY 10016, USA.
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53
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Shaban HA, Gasser SM. Dynamic 3D genome reorganization during senescence: defining cell states through chromatin. Cell Death Differ 2023:10.1038/s41418-023-01197-y. [PMID: 37596440 DOI: 10.1038/s41418-023-01197-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 08/20/2023] Open
Abstract
Cellular senescence, a cell state characterized by growth arrest and insensitivity to growth stimulatory hormones, is accompanied by a massive change in chromatin organization. Senescence can be induced by a range of physiological signals and pathological stresses and was originally thought to be an irreversible state, implicated in normal development, wound healing, tumor suppression and aging. Recently cellular senescence was shown to be reversible in some cases, with exit being triggered by the modulation of the cell's transcriptional program by the four Yamanaka factors, the suppression of p53 or H3K9me3, PDK1, and/or depletion of AP-1. Coincident with senescence reversal are changes in chromatin organization, most notably the loss of senescence-associated heterochromatin foci (SAHF) found in oncogene-induced senescence. In addition to fixed-cell imaging, chromatin conformation capture and multi-omics have been used to examine chromatin reorganization at different spatial resolutions during senescence. They identify determinants of SAHF formation and other key features that differentiate distinct types of senescence. Not surprisingly, multiple factors, including the time of induction, the type of stress experienced, and the type of cell involved, influence the global reorganization of chromatin in senescence. Here we discuss how changes in the three-dimensional organization of the genome contribute to the regulation of transcription at different stages of senescence. In particular, the distinct contributions of heterochromatin- and lamina-mediated interactions, changes in gene expression, and other cellular control mechanisms are discussed. We propose that high-resolution temporal and spatial analyses of the chromatin landscape during senescence will identify early markers of the different senescence states to help guide clinical diagnosis.
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Affiliation(s)
- Haitham A Shaban
- Precision Oncology Center, Department of Oncology, Lausanne University Hospital, 1005, Lausanne, Switzerland.
- Agora Cancer Research Center Lausanne, Rue du Bugnon 25A, 1005, Lausanne, Switzerland.
- Spectroscopy Department, Institute of Physics Research National Research Centre, Cairo, 33 El-Behouth St., Dokki, Giza, 12311, Egypt.
| | - Susan M Gasser
- Fondation ISREC, Rue du Bugnon 25A, 1005, Lausanne, Switzerland
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland
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54
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Benarroch L, Madsen-Østerbye J, Abdelhalim M, Mamchaoui K, Ohana J, Bigot A, Mouly V, Bonne G, Bertrand AT, Collas P. Cellular and Genomic Features of Muscle Differentiation from Isogenic Fibroblasts and Myoblasts. Cells 2023; 12:1995. [PMID: 37566074 PMCID: PMC10417614 DOI: 10.3390/cells12151995] [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: 06/30/2023] [Revised: 07/27/2023] [Accepted: 07/31/2023] [Indexed: 08/12/2023] Open
Abstract
The ability to recapitulate muscle differentiation in vitro enables the exploration of mechanisms underlying myogenesis and muscle diseases. However, obtaining myoblasts from patients with neuromuscular diseases or from healthy subjects poses ethical and procedural challenges that limit such investigations. An alternative consists in converting skin fibroblasts into myogenic cells by forcing the expression of the myogenic regulator MYOD. Here, we directly compared cellular phenotype, transcriptome, and nuclear lamina-associated domains (LADs) in myo-converted human fibroblasts and myotubes differentiated from myoblasts. We used isogenic cells from a 16-year-old donor, ruling out, for the first time to our knowledge, genetic factors as a source of variations between the two myogenic models. We show that myo-conversion of fibroblasts upregulates genes controlling myogenic pathways leading to multinucleated cells expressing muscle cell markers. However, myotubes are more advanced in myogenesis than myo-converted fibroblasts at the phenotypic and transcriptomic levels. While most LADs are shared between the two cell types, each also displays unique domains of lamin A/C interactions. Furthermore, myotube-specific LADs are more gene-rich and less heterochromatic than shared LADs or LADs unique to myo-converted fibroblasts, and they uniquely sequester developmental genes. Thus, myo-converted fibroblasts and myotubes retain cell type-specific features of radial and functional genome organization. Our results favor a view of myo-converted fibroblasts as a practical model to investigate the phenotypic and genomic properties of muscle cell differentiation in normal and pathological contexts, but also highlight current limitations in using fibroblasts as a source of myogenic cells.
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Affiliation(s)
- Louise Benarroch
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, 75013 Paris, France; (L.B.); (K.M.); (J.O.); (A.B.); (V.M.); (G.B.)
| | - Julia Madsen-Østerbye
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0372 Oslo, Norway; (J.M.-Ø.); (M.A.)
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, 0372 Oslo, Norway
| | - Mohamed Abdelhalim
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0372 Oslo, Norway; (J.M.-Ø.); (M.A.)
| | - Kamel Mamchaoui
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, 75013 Paris, France; (L.B.); (K.M.); (J.O.); (A.B.); (V.M.); (G.B.)
| | - Jessica Ohana
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, 75013 Paris, France; (L.B.); (K.M.); (J.O.); (A.B.); (V.M.); (G.B.)
| | - Anne Bigot
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, 75013 Paris, France; (L.B.); (K.M.); (J.O.); (A.B.); (V.M.); (G.B.)
| | - Vincent Mouly
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, 75013 Paris, France; (L.B.); (K.M.); (J.O.); (A.B.); (V.M.); (G.B.)
| | - Gisèle Bonne
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, 75013 Paris, France; (L.B.); (K.M.); (J.O.); (A.B.); (V.M.); (G.B.)
| | - Anne T. Bertrand
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, 75013 Paris, France; (L.B.); (K.M.); (J.O.); (A.B.); (V.M.); (G.B.)
| | - Philippe Collas
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0372 Oslo, Norway; (J.M.-Ø.); (M.A.)
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, 0372 Oslo, Norway
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55
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Liu H, Tsai H, Yang M, Li G, Bian Q, Ding G, Wu D, Dai J. Three-dimensional genome structure and function. MedComm (Beijing) 2023; 4:e326. [PMID: 37426677 PMCID: PMC10329473 DOI: 10.1002/mco2.326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 05/31/2023] [Accepted: 06/09/2023] [Indexed: 07/11/2023] Open
Abstract
Linear DNA undergoes a series of compression and folding events, forming various three-dimensional (3D) structural units in mammalian cells, including chromosomal territory, compartment, topologically associating domain, and chromatin loop. These structures play crucial roles in regulating gene expression, cell differentiation, and disease progression. Deciphering the principles underlying 3D genome folding and the molecular mechanisms governing cell fate determination remains a challenge. With advancements in high-throughput sequencing and imaging techniques, the hierarchical organization and functional roles of higher-order chromatin structures have been gradually illuminated. This review systematically discussed the structural hierarchy of the 3D genome, the effects and mechanisms of cis-regulatory elements interaction in the 3D genome for regulating spatiotemporally specific gene expression, the roles and mechanisms of dynamic changes in 3D chromatin conformation during embryonic development, and the pathological mechanisms of diseases such as congenital developmental abnormalities and cancer, which are attributed to alterations in 3D genome organization and aberrations in key structural proteins. Finally, prospects were made for the research about 3D genome structure, function, and genetic intervention, and the roles in disease development, prevention, and treatment, which may offer some clues for precise diagnosis and treatment of related diseases.
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Affiliation(s)
- Hao Liu
- Department of Oral and Cranio‐Maxillofacial SurgeryShanghai Ninth People's Hospital, Shanghai Jiao Tong University School of MedicineCollege of Stomatology, Shanghai Jiao Tong UniversityNational Center for StomatologyNational Clinical Research Center for Oral DiseasesShanghai Key Laboratory of StomatologyShanghaiChina
- School of StomatologyWeifang Medical UniversityWeifangChina
| | - Hsiangyu Tsai
- Department of Oral and Cranio‐Maxillofacial SurgeryShanghai Ninth People's Hospital, Shanghai Jiao Tong University School of MedicineCollege of Stomatology, Shanghai Jiao Tong UniversityNational Center for StomatologyNational Clinical Research Center for Oral DiseasesShanghai Key Laboratory of StomatologyShanghaiChina
| | - Maoquan Yang
- School of Clinical MedicineWeifang Medical UniversityWeifangChina
| | - Guozhi Li
- Department of Oral and Cranio‐Maxillofacial SurgeryShanghai Ninth People's Hospital, Shanghai Jiao Tong University School of MedicineCollege of Stomatology, Shanghai Jiao Tong UniversityNational Center for StomatologyNational Clinical Research Center for Oral DiseasesShanghai Key Laboratory of StomatologyShanghaiChina
| | - Qian Bian
- Shanghai Institute of Precision MedicineShanghaiChina
| | - Gang Ding
- School of StomatologyWeifang Medical UniversityWeifangChina
| | - Dandan Wu
- Department of Oral and Cranio‐Maxillofacial SurgeryShanghai Ninth People's Hospital, Shanghai Jiao Tong University School of MedicineCollege of Stomatology, Shanghai Jiao Tong UniversityNational Center for StomatologyNational Clinical Research Center for Oral DiseasesShanghai Key Laboratory of StomatologyShanghaiChina
| | - Jiewen Dai
- Department of Oral and Cranio‐Maxillofacial SurgeryShanghai Ninth People's Hospital, Shanghai Jiao Tong University School of MedicineCollege of Stomatology, Shanghai Jiao Tong UniversityNational Center for StomatologyNational Clinical Research Center for Oral DiseasesShanghai Key Laboratory of StomatologyShanghaiChina
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56
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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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57
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Chen Y, Wang L, Guo F, Dai X, Zhang X. Epigenetic reprogramming during the maternal-to-zygotic transition. MedComm (Beijing) 2023; 4:e331. [PMID: 37547174 PMCID: PMC10397483 DOI: 10.1002/mco2.331] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 08/08/2023] Open
Abstract
After fertilization, sperm and oocyte fused and gave rise to a zygote which is the beginning of a new life. Then the embryonic development is monitored and regulated precisely from the transition of oocyte to the embryo at the early stage of embryogenesis, and this process is termed maternal-to-zygotic transition (MZT). MZT involves two major events that are maternal components degradation and zygotic genome activation. The epigenetic reprogramming plays crucial roles in regulating the process of MZT and supervising the normal development of early development of embryos. In recent years, benefited from the rapid development of low-input epigenome profiling technologies, new epigenetic modifications are found to be reprogrammed dramatically and may play different roles during MZT whose dysregulation will cause an abnormal development of embryos even abortion at various stages. In this review, we summarized and discussed the important novel findings on epigenetic reprogramming and the underlying molecular mechanisms regulating MZT in mammalian embryos. Our work provided comprehensive and detailed references for the in deep understanding of epigenetic regulatory network in this key biological process and also shed light on the critical roles for epigenetic reprogramming on embryonic failure during artificial reproductive technology and nature fertilization.
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Affiliation(s)
- Yurong Chen
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education First Hospital of Jilin University Changchun China
- National-Local Joint Engineering Laboratory of Animal Models for Human Disease First Hospital of Jilin University Changchun China
| | - Luyao Wang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education First Hospital of Jilin University Changchun China
- National-Local Joint Engineering Laboratory of Animal Models for Human Disease First Hospital of Jilin University Changchun China
| | - Fucheng Guo
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education First Hospital of Jilin University Changchun China
- National-Local Joint Engineering Laboratory of Animal Models for Human Disease First Hospital of Jilin University Changchun China
| | - Xiangpeng Dai
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education First Hospital of Jilin University Changchun China
- National-Local Joint Engineering Laboratory of Animal Models for Human Disease First Hospital of Jilin University Changchun China
| | - Xiaoling Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education First Hospital of Jilin University Changchun China
- National-Local Joint Engineering Laboratory of Animal Models for Human Disease First Hospital of Jilin University Changchun China
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58
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Karpova A, Samer S, Turacak R, Yuanxiang P, Kreutz MR. Integration of nuclear Ca 2+ transients and subnuclear protein shuttling provides a novel mechanism for the regulation of CREB-dependent gene expression. Cell Mol Life Sci 2023; 80:228. [PMID: 37491479 PMCID: PMC10368568 DOI: 10.1007/s00018-023-04876-8] [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: 03/04/2023] [Revised: 07/02/2023] [Accepted: 07/12/2023] [Indexed: 07/27/2023]
Abstract
Nuclear Ca2+ waves elicited by NMDAR and L-type voltage-gated Ca2+-channels as well as protein transport from synapse-to-nucleus are both instrumental in control of plasticity-related gene expression. At present it is not known whether fast [Ca2+]n transients converge in the nucleus with signaling of synapto-nuclear protein messenger. Jacob is a protein that translocate a signalosome from N-methyl-D-aspartate receptors (NMDAR) to the nucleus and that docks this signalosome to the transcription factor CREB. Here we show that the residing time of Jacob in the nucleoplasm strictly correlates with nuclear [Ca2+]n transients elicited by neuronal activity. A steep increase in [Ca2+]n induces instantaneous uncoupling of Jacob from LaminB1 at the nuclear lamina and promotes the association with the transcription factor cAMP-responsive element-binding protein (CREB) in hippocampal neurons. The size of the Jacob pool at the nuclear lamina is controlled by previous activity-dependent nuclear import, and thereby captures the previous history of NMDAR-induced nucleocytoplasmic shuttling. Moreover, the localization of Jacob at the nuclear lamina strongly correlates with synaptic activity and [Ca2+]n waves reflecting ongoing neuronal activity. In consequence, the resulting extension of the nuclear residing time of Jacob amplifies the capacity of the Jacob signalosome to regulate CREB-dependent gene expression and will, thereby, compensate for the relatively small number of molecules reaching the nucleus from individual synapses.
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Affiliation(s)
- Anna Karpova
- RG Neuroplasticity, Leibniz Institute for Neurobiology, 39118, Magdeburg, Germany.
- Center for Behavioral Brain Sciences, Otto von Guericke University, 39106, Magdeburg, Germany.
| | - Sebastian Samer
- RG Neuroplasticity, Leibniz Institute for Neurobiology, 39118, Magdeburg, Germany
| | - Rabia Turacak
- RG Neuroplasticity, Leibniz Institute for Neurobiology, 39118, Magdeburg, Germany
| | - PingAn Yuanxiang
- RG Neuroplasticity, Leibniz Institute for Neurobiology, 39118, Magdeburg, Germany
| | - Michael R Kreutz
- RG Neuroplasticity, Leibniz Institute for Neurobiology, 39118, Magdeburg, Germany.
- Center for Behavioral Brain Sciences, Otto von Guericke University, 39106, Magdeburg, Germany.
- Leibniz Group 'Dendritic Organelles and Synaptic Function', Center for Molecular Neurobiology, ZMNH, University Medical Center Hamburg-Eppendorf, 20251, Hamburg, Germany.
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Yang M, Ma J. UNADON: transformer-based model to predict genome-wide chromosome spatial position. Bioinformatics 2023; 39:i553-i562. [PMID: 37387176 PMCID: PMC10311299 DOI: 10.1093/bioinformatics/btad246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023] Open
Abstract
MOTIVATION The spatial positioning of chromosomes relative to functional nuclear bodies is intertwined with genome functions such as transcription. However, the sequence patterns and epigenomic features that collectively influence chromatin spatial positioning in a genome-wide manner are not well understood. RESULTS Here, we develop a new transformer-based deep learning model called UNADON, which predicts the genome-wide cytological distance to a specific type of nuclear body, as measured by TSA-seq, using both sequence features and epigenomic signals. Evaluations of UNADON in four cell lines (K562, H1, HFFc6, HCT116) show high accuracy in predicting chromatin spatial positioning to nuclear bodies when trained on a single cell line. UNADON also performed well in an unseen cell type. Importantly, we reveal potential sequence and epigenomic factors that affect large-scale chromatin compartmentalization in nuclear bodies. Together, UNADON provides new insights into the principles between sequence features and large-scale chromatin spatial localization, which has important implications for understanding nuclear structure and function. AVAILABILITY AND IMPLEMENTATION The source code of UNADON can be found at https://github.com/ma-compbio/UNADON.
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Affiliation(s)
- Muyu Yang
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh PA 15213, USA
| | - Jian Ma
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh PA 15213, USA
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Pandupuspitasari NS, Khan FA, Huang C, Ali A, Yousaf MR, Shakeel F, Putri EM, Negara W, Muktiani A, Prasetiyono BWHE, Kustiawan L, Wahyuni DS. Recent advances in chromosome capture techniques unraveling 3D genome architecture in germ cells, health, and disease. Funct Integr Genomics 2023; 23:214. [PMID: 37386239 DOI: 10.1007/s10142-023-01146-5] [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: 04/08/2023] [Revised: 06/16/2023] [Accepted: 06/20/2023] [Indexed: 07/01/2023]
Abstract
In eukaryotes, the genome does not emerge in a specific shape but rather as a hierarchial bundle within the nucleus. This multifaceted genome organization consists of multiresolution cellular structures, such as chromosome territories, compartments, and topologically associating domains, which are frequently defined by architecture, design proteins including CTCF and cohesin, and chromatin loops. This review briefly discusses the advances in understanding the basic rules of control, chromatin folding, and functional areas in early embryogenesis. With the use of chromosome capture techniques, the latest advancements in technologies for visualizing chromatin interactions come close to revealing 3D genome formation frameworks with incredible detail throughout all genomic levels, including at single-cell resolution. The possibility of detecting variations in chromatin architecture might open up new opportunities for disease diagnosis and prevention, infertility treatments, therapeutic approaches, desired exploration, and many other application scenarios.
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Affiliation(s)
- Nuruliarizki Shinta Pandupuspitasari
- Laboratory of Animal Nutrition and Feed Science, Animal Science Department, Faculty of Animal and Agricultural Sciences, Universitas Diponegoro, Semarang, Indonesia.
| | - Faheem Ahmed Khan
- Research Center for Animal Husbandry, National Research and Innovation Agency, Bogor, Indonesia
| | - Chunjie Huang
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong, 226001, China
| | - Azhar Ali
- Laboratory of Molecular Biology and Genomics, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Muhammad Rizwan Yousaf
- Laboratory of Molecular Biology and Genomics, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Farwa Shakeel
- Laboratory of Molecular Biology and Genomics, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Ezi Masdia Putri
- Research Center for Animal Husbandry, National Research and Innovation Agency, Bogor, Indonesia
| | - Windu Negara
- Research Center for Animal Husbandry, National Research and Innovation Agency, Bogor, Indonesia
| | - Anis Muktiani
- Laboratory of Animal Nutrition and Feed Science, Animal Science Department, Faculty of Animal and Agricultural Sciences, Universitas Diponegoro, Semarang, Indonesia
| | - Bambang Waluyo Hadi Eko Prasetiyono
- Laboratory of Feed Technology, Animal Science Department, Faculty of Animal and Agricultural Sciences Universitas Diponegoro, Semarang, Indonesia
| | - Limbang Kustiawan
- Laboratory of Animal Nutrition and Feed Science, Animal Science Department, Faculty of Animal and Agricultural Sciences, Universitas Diponegoro, Semarang, Indonesia
| | - Dimar Sari Wahyuni
- Research Center for Animal Husbandry, National Research and Innovation Agency, Bogor, Indonesia
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Pujadas EM, Wei X, Acosta N, Carter L, Yang J, Almassalha L, Daneshkhah A, Rao SSP, Agrawal V, Seker-Polat F, Aiden EL, Kanemaki MT, Backman V, Adli M. Depletion of lamins B1 and B2 alters chromatin mobility and induces differential gene expression by a mesoscale-motion dependent mechanism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.26.546573. [PMID: 37425796 PMCID: PMC10326988 DOI: 10.1101/2023.06.26.546573] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
BACKGROUND B-type lamins are critical nuclear envelope proteins that interact with the 3D genomic architecture. However, identifying the direct roles of B-lamins on dynamic genome organization has been challenging as their joint depletion severely impacts cell viability. To overcome this, we engineered mammalian cells to rapidly and completely degrade endogenous B-type lamins using Auxin-inducible degron (AID) technology. RESULTS Paired with a suite of novel technologies, live-cell Dual Partial Wave Spectroscopic (Dual-PWS) microscopy, in situ Hi-C, and CRISPR-Sirius, we demonstrate that lamin B1 and lamin B2 depletion transforms chromatin mobility, heterochromatin positioning, gene expression, and loci-positioning with minimal disruption to mesoscale chromatin folding. Using the AID system, we show that the disruption of B-lamins alters gene expression both within and outside lamin associated domains, with distinct mechanistic patterns depending on their localization. Critically, we demonstrate that chromatin dynamics, positioning of constitutive and facultative heterochromatic markers, and chromosome positioning near the nuclear periphery are significantly altered, indicating that the mechanism of action of B-type lamins is derived from their role in maintaining chromatin dynamics and spatial positioning. CONCLUSIONS Our findings suggest that the mechanistic role of B-type lamins is stabilization of heterochromatin and chromosomal positioning along the nuclear periphery. We conclude that degrading lamin B1 and lamin B2 has several functional consequences related to both structural disease and cancer.
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Lin TC, Chung PJ, Shen CA, Nguyen TMH, Lin YS, Lin SC, Hsiao SC, Chiu WT. Depletion of intracellular Ca 2+ induces FOXM1 SUMOylation and accumulation on the inner nuclear membrane and accelerates G2/M cell cycle transition. Eur J Cell Biol 2023; 102:151332. [PMID: 37302175 DOI: 10.1016/j.ejcb.2023.151332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 06/13/2023] Open
Abstract
Intracellular calcium (Ca2+) has been reported to regulate transcription factor activity and cancer development, but how it affects the function of Forkhead box protein M1 (FOXM1), a crucial transcription factor and key oncogene participating in tumorigenesis, remains unclear. Here, we investigated the regulatory role of Ca2+ on FOXM1 and found that Ca2+ depletion caused the distribution of FOXM1 to aggregate on the nuclear envelope, which was also observed in many cell lines. Further experiments revealed that sequestrated FOXM1 colocalized with lamin B in the inner nuclear membrane (INM) and was affected by the activity of nuclear export protein exportin 1 (XPO1). To investigate how intracellular Ca2+ affects FOXM1, we found that among the posttranscriptional modifications, only SUMOylation of FOXM1 showed a pronounced increase under reduced Ca2+, and suppressed SUMOylation rescued FOXM1 sequestration. In addition, Ca2+-dependent SUMOylated FOXM1 appeared to enhance the G2/M transition of the cell cycle and decrease cell apoptosis. In conclusion, our findings provide a molecular basis for the relationship between Ca2+ signaling and FOXM1 regulation, and we look to elucidate Ca2+-dependent FOXM1 SUMOylation-related biological functions in the future.
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Affiliation(s)
- Tzu-Chien Lin
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
| | - Ping-Jung Chung
- Department of Biomedical Engineering, College of Engineering, National Cheng Kung University, Tainan 701, Taiwan
| | - Chen-An Shen
- Department of Biomedical Engineering, College of Engineering, National Cheng Kung University, Tainan 701, Taiwan
| | - Thi My Hang Nguyen
- Department of Biomedical Engineering, College of Engineering, National Cheng Kung University, Tainan 701, Taiwan
| | - Yi-Syuan Lin
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
| | - Shih-Chieh Lin
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
| | - Shih-Chuan Hsiao
- Department of Hematology & Oncology, Saint Martin de Porres Hospital, Chiayi 600, Taiwan.
| | - Wen-Tai Chiu
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan; Department of Biomedical Engineering, College of Engineering, National Cheng Kung University, Tainan 701, Taiwan; Medical Device Innovation Center, National Cheng Kung University, Tainan 701, Taiwan.
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Harris HL, Gu H, Olshansky M, Wang A, Farabella I, Eliaz Y, Kalluchi A, Krishna A, Jacobs M, Cauer G, Pham M, Rao SSP, Dudchenko O, Omer A, Mohajeri K, Kim S, Nichols MH, Davis ES, Gkountaroulis D, Udupa D, Aiden AP, Corces VG, Phanstiel DH, Noble WS, Nir G, Di Pierro M, Seo JS, Talkowski ME, Aiden EL, Rowley MJ. Chromatin alternates between A and B compartments at kilobase scale for subgenic organization. Nat Commun 2023; 14:3303. [PMID: 37280210 PMCID: PMC10244318 DOI: 10.1038/s41467-023-38429-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 04/28/2023] [Indexed: 06/08/2023] Open
Abstract
Nuclear compartments are prominent features of 3D chromatin organization, but sequencing depth limitations have impeded investigation at ultra fine-scale. CTCF loops are generally studied at a finer scale, but the impact of looping on proximal interactions remains enigmatic. Here, we critically examine nuclear compartments and CTCF loop-proximal interactions using a combination of in situ Hi-C at unparalleled depth, algorithm development, and biophysical modeling. Producing a large Hi-C map with 33 billion contacts in conjunction with an algorithm for performing principal component analysis on sparse, super massive matrices (POSSUMM), we resolve compartments to 500 bp. Our results demonstrate that essentially all active promoters and distal enhancers localize in the A compartment, even when flanking sequences do not. Furthermore, we find that the TSS and TTS of paused genes are often segregated into separate compartments. We then identify diffuse interactions that radiate from CTCF loop anchors, which correlate with strong enhancer-promoter interactions and proximal transcription. We also find that these diffuse interactions depend on CTCF's RNA binding domains. In this work, we demonstrate features of fine-scale chromatin organization consistent with a revised model in which compartments are more precise than commonly thought while CTCF loops are more protracted.
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Affiliation(s)
- Hannah L Harris
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
| | - Huiya Gu
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Moshe Olshansky
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Ailun Wang
- Center for Theoretical Biological Physics, Northeastern University, Boston, MA, USA
| | - Irene Farabella
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BISB), 17 08028, Barcelona, Spain
- Integrative Nuclear Architecture Laboratory, Center for Human Technologies, Istituto Italiano di Tecnologia, Genova, Italy
| | - Yossi Eliaz
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Achyuth Kalluchi
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
| | - Akshay Krishna
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
| | - Mozes Jacobs
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA
| | - Gesine Cauer
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Melanie Pham
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Suhas S P Rao
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Olga Dudchenko
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Arina Omer
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | | | - Michael H Nichols
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Eric S Davis
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Dimos Gkountaroulis
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Devika Udupa
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
| | - Aviva Presser Aiden
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Victor G Corces
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Douglas H Phanstiel
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Thurston Arthritis Research Center, University of North Carolina, Chapel Hill, NC, USA
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC, USA
| | - William Stafford Noble
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Guy Nir
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Michele Di Pierro
- Center for Theoretical Biological Physics, Northeastern University, Boston, MA, USA
- Department of Physics, Northeastern University, Boston, MA, USA
| | - Jeong-Sun Seo
- Macrogen Inc, Seoul, Republic of Korea
- Asian Genome Institute, Seoul National University Bundang Hospital, Gyeonggi-do, Republic of Korea
| | - Michael E Talkowski
- Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Program in Medical Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Erez Lieberman Aiden
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA.
| | - M Jordan Rowley
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA.
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Tolokh IS, Kinney NA, Sharakhov IV, Onufriev AV. Strong interactions between highly dynamic lamina-associated domains and the nuclear envelope stabilize the 3D architecture of Drosophila interphase chromatin. Epigenetics Chromatin 2023; 16:21. [PMID: 37254161 PMCID: PMC10228000 DOI: 10.1186/s13072-023-00492-9] [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: 01/19/2023] [Accepted: 05/04/2023] [Indexed: 06/01/2023] Open
Abstract
BACKGROUND Interactions among topologically associating domains (TADs), and between the nuclear envelope (NE) and lamina-associated domains (LADs) are expected to shape various aspects of three-dimensional (3D) chromatin structure and dynamics; however, relevant genome-wide experiments that may provide statistically significant conclusions remain difficult. RESULTS We have developed a coarse-grained dynamical model of D. melanogaster nuclei at TAD resolution that explicitly accounts for four distinct epigenetic classes of TADs and LAD-NE interactions. The model is parameterized to reproduce the experimental Hi-C map of the wild type (WT) nuclei; it describes time evolution of the chromatin over the G1 phase of the interphase. The simulations include an ensemble of nuclei, corresponding to the experimentally observed set of several possible mutual arrangements of chromosomal arms. The model is validated against multiple structural features of chromatin from several different experiments not used in model development. Predicted positioning of all LADs at the NE is highly dynamic-the same LAD can attach, detach and move far away from the NE multiple times during interphase. The probabilities of LADs to be in contact with the NE vary by an order of magnitude, despite all having the same affinity to the NE in the model. These probabilities are mostly determined by a highly variable local linear density of LADs along the genome, which also has the same strong effect on the predicted positioning of individual TADs -- higher probability of a TAD to be near NE is largely determined by a higher linear density of LADs surrounding this TAD. The distribution of LADs along the chromosome chains plays a notable role in maintaining a non-random average global structure of chromatin. Relatively high affinity of LADs to the NE in the WT nuclei substantially reduces sensitivity of the global radial chromatin distribution to variations in the strength of TAD-TAD interactions compared to the lamin depleted nuclei, where a small (0.5 kT) increase of cross-type TAD-TAD interactions doubles the chromatin density in the central nucleus region. CONCLUSIONS A dynamical model of the entire fruit fly genome makes multiple genome-wide predictions of biological interest. The distribution of LADs along the chromatin chains affects their probabilities to be in contact with the NE and radial positioning of highly mobile TADs, playing a notable role in creating a non-random average global structure of the chromatin. We conjecture that an important role of attractive LAD-NE interactions is to stabilize global chromatin structure against inevitable cell-to-cell variations in TAD-TAD interactions.
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Affiliation(s)
- Igor S. Tolokh
- Department of Computer Science, Virginia Tech, Blacksburg, VA 24061 USA
| | - Nicholas Allen Kinney
- Department of Computer Science, Virginia Tech, Blacksburg, VA 24061 USA
- Department of Entomology, Virginia Tech, Blacksburg, VA 24061 USA
- Edward Via College of Osteopathic Medicine, 2265 Kraft Drive, Blacksburg, VA 24060 USA
| | | | - Alexey V. Onufriev
- Department of Computer Science, Virginia Tech, Blacksburg, VA 24061 USA
- Department of Physics, Virginia Tech, Blacksburg, VA 24061 USA
- Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA 24061 USA
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65
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Torres DE, Reckard AT, Klocko AD, Seidl MF. Nuclear genome organization in fungi: from gene folding to Rabl chromosomes. FEMS Microbiol Rev 2023; 47:fuad021. [PMID: 37197899 PMCID: PMC10246852 DOI: 10.1093/femsre/fuad021] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/28/2023] [Accepted: 05/08/2023] [Indexed: 05/19/2023] Open
Abstract
Comparative genomics has recently provided unprecedented insights into the biology and evolution of the fungal lineage. In the postgenomics era, a major research interest focuses now on detailing the functions of fungal genomes, i.e. how genomic information manifests into complex phenotypes. Emerging evidence across diverse eukaryotes has revealed that the organization of DNA within the nucleus is critically important. Here, we discuss the current knowledge on the fungal genome organization, from the association of chromosomes within the nucleus to topological structures at individual genes and the genetic factors required for this hierarchical organization. Chromosome conformation capture followed by high-throughput sequencing (Hi-C) has elucidated how fungal genomes are globally organized in Rabl configuration, in which centromere or telomere bundles are associated with opposite faces of the nuclear envelope. Further, fungal genomes are regionally organized into topologically associated domain-like (TAD-like) chromatin structures. We discuss how chromatin organization impacts the proper function of DNA-templated processes across the fungal genome. Nevertheless, this view is limited to a few fungal taxa given the paucity of fungal Hi-C experiments. We advocate for exploring genome organization across diverse fungal lineages to ensure the future understanding of the impact of nuclear organization on fungal genome function.
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Affiliation(s)
- David E Torres
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Laboratory of Phytopathology, Wageningen University and Research,Droevendaalsesteeg 4, 6708 PB Wageningen, The Netherlands
| | - Andrew T Reckard
- Department of Chemistry and Biochemistry, University of Colorado Colorado Springs, 234 Centennial Hall, 1420 Austin Bluffs Pkwy, Colorado Springs, CO 80918 USA
| | - Andrew D Klocko
- Department of Chemistry and Biochemistry, University of Colorado Colorado Springs, 234 Centennial Hall, 1420 Austin Bluffs Pkwy, Colorado Springs, CO 80918 USA
| | - Michael F Seidl
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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Lovejoy CM, Nagarajan P, Parthun MR. Dynamic Reassociation of the Nuclear Lamina with Newly Replicated DNA. RESEARCH SQUARE 2023:rs.3.rs-2846826. [PMID: 37215015 PMCID: PMC10197746 DOI: 10.21203/rs.3.rs-2846826/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The physical association of specific regions of chromatin with components of the nuclear lamina provides the framework for the 3-dimensionl architecture of the genome. The regulation of these interactions plays a critical role in the maintenance of gene expression patterns and cell identity. The breakdown and reassembly of the nuclear membrane as cells transit mitosis plays a central role in the regulation of the interactions between the genome and the nuclear lamina. However, other nuclear processes, such as transcription, have emerged as regulators of the association of DNA with the nuclear lamina. To determine whether DNA replication also has the potential to regulate DNA-nuclear lamina interactions, we adapted proximity ligation-based chromatin assembly assays to analyze the dynamics of nuclear lamina association with newly replicated DNA. We observe that lamin A/C and lamin B, as well as inner nuclear membrane proteins LBR and emerin, are found in proximity to newly replicated DNA. While core histones rapidly reassociate with DNA following passage of the replication fork, the complete reassociation of nuclear lamina components with newly replicated DNA occurs over a period of approximately 30 minutes. We propose models to describe the disassembly and reassembly of nascent chromatin with the nuclear lamina.
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Kai Y, Liu N, Orkin SH, Yuan GC. Identifying Quantitatively Differential Chromosomal Compartmentalization Changes and Their Biological Significance from Hi-C data using DARIC. RESEARCH SQUARE 2023:rs.3.rs-2814806. [PMID: 37162846 PMCID: PMC10168473 DOI: 10.21203/rs.3.rs-2814806/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Background Chromosomal compartmentalization plays a critical role in maintaining proper transcriptional programs in cell differentiation and oncogenesis. However, currently the prevalent method for comparative analysis of compartmentalization landscapes between different cell types is limited to the qualitative switched compartments. Results To identify genomic regions with quantitatively differential compartmentalization changes from genome-wide chromatin conformation data like Hi-C, we developed a computational framework named DARIC. DARIC includes three modules: compartmentalization quantification, normalization, and differential analysis. Comparing DARIC with the conventional compartment switching analysis reveals substantial regions characterized by quantitatively significant compartmentalization changes without switching. These changes are accompanied by changes in gene expression, chromatin accessibility, H3K27ac intensity, as well as the interactions with nuclear lamina proteins and nuclear positioning, highlighting the functional importance of such quantitative changes in gene regulation. We applied DARIC to dissect the quantitative compartmentalization changes during human cardiomyocyte differentiation and identified two distinct mechanisms for gene activation based on the association with compartmentalization changes. Using the quantitative compartmentalization measurement module from DARIC, we further dissected the compartment variability landscape in the human genome by analyzing a compendium of 32 Hi-C datasets from 4DN. We discovered an interesting correlation between compartmentalization variability and sub-compartments. Conclusions DARIC is a useful tool for analyzing quantitative compartmentalization changes and mining novel biological insights from increasing Hi-C data. Our results demonstrate the functional significance of quantitative compartmentalization changes in gene regulation, and provide new insights into the relationship between compartmentalization variability and sub-compartments in the human genome.
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Affiliation(s)
| | - Nan Liu
- Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, 310003 Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, 311121, China
| | - Stuart H Orkin
- Howards Hughes Medical Institute, Boston MA 02115, USA
- Lead contact
| | - Guo-Cheng Yuan
- Department of Genetics and Genomic Sciences, Charles Bronfman Institute for Precision Medicine, Icahn School of Medicine at Mount Sinai, New York NY 10029, USA
- Lead contact
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Yamada S, Ko T, Ito M, Sassa T, Nomura S, Okuma H, Sato M, Imasaki T, Kikkawa S, Zhang B, Yamada T, Seki Y, Fujita K, Katoh M, Kubota M, Hatsuse S, Katagiri M, Hayashi H, Hamano M, Takeda N, Morita H, Takada S, Toyoda M, Uchiyama M, Ikeuchi M, Toyooka K, Umezawa A, Yamanishi Y, Nitta R, Aburatani H, Komuro I. TEAD1 trapping by the Q353R-Lamin A/C causes dilated cardiomyopathy. SCIENCE ADVANCES 2023; 9:eade7047. [PMID: 37058558 PMCID: PMC10104473 DOI: 10.1126/sciadv.ade7047] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 03/09/2023] [Indexed: 06/19/2023]
Abstract
Mutations in the LMNA gene encoding Lamin A and C (Lamin A/C), major components of the nuclear lamina, cause laminopathies including dilated cardiomyopathy (DCM), but the underlying molecular mechanisms have not been fully elucidated. Here, by leveraging single-cell RNA sequencing (RNA-seq), assay for transposase-accessible chromatin using sequencing (ATAC-seq), protein array, and electron microscopy analysis, we show that insufficient structural maturation of cardiomyocytes owing to trapping of transcription factor TEA domain transcription factor 1 (TEAD1) by mutant Lamin A/C at the nuclear membrane underlies the pathogenesis of Q353R-LMNA-related DCM. Inhibition of the Hippo pathway rescued the dysregulation of cardiac developmental genes by TEAD1 in LMNA mutant cardiomyocytes. Single-cell RNA-seq of cardiac tissues from patients with DCM with the LMNA mutation confirmed the dysregulated expression of TEAD1 target genes. Our results propose an intervention for transcriptional dysregulation as a potential treatment of LMNA-related DCM.
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Affiliation(s)
- Shintaro Yamada
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Genome Science Division, Research Center for Advanced Science and Technologies, The University of Tokyo, Meguro-ku, Tokyo 153-8904, Japan
| | - Toshiyuki Ko
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masamichi Ito
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Department of Advanced Clinical Science and Therapeutics, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Tatsuro Sassa
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Genome Science Division, Research Center for Advanced Science and Technologies, The University of Tokyo, Meguro-ku, Tokyo 153-8904, Japan
| | - Seitaro Nomura
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Genome Science Division, Research Center for Advanced Science and Technologies, The University of Tokyo, Meguro-ku, Tokyo 153-8904, Japan
| | - Hiromichi Okuma
- Division of Structural Medicine and Anatomy, Department of Physiology and Cell Biology, Kobe University Graduate School of Medicine, Kobe, Hyogo 650-0017, Japan
| | - Mayuko Sato
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Tsuyoshi Imasaki
- Division of Structural Medicine and Anatomy, Department of Physiology and Cell Biology, Kobe University Graduate School of Medicine, Kobe, Hyogo 650-0017, Japan
| | - Satoshi Kikkawa
- Division of Structural Medicine and Anatomy, Department of Physiology and Cell Biology, Kobe University Graduate School of Medicine, Kobe, Hyogo 650-0017, Japan
| | - Bo Zhang
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Genome Science Division, Research Center for Advanced Science and Technologies, The University of Tokyo, Meguro-ku, Tokyo 153-8904, Japan
| | - Takanobu Yamada
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Genome Science Division, Research Center for Advanced Science and Technologies, The University of Tokyo, Meguro-ku, Tokyo 153-8904, Japan
| | - Yuka Seki
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kanna Fujita
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Genome Science Division, Research Center for Advanced Science and Technologies, The University of Tokyo, Meguro-ku, Tokyo 153-8904, Japan
| | - Manami Katoh
- Genome Science Division, Research Center for Advanced Science and Technologies, The University of Tokyo, Meguro-ku, Tokyo 153-8904, Japan
| | - Masayuki Kubota
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Satoshi Hatsuse
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Mikako Katagiri
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiromu Hayashi
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
| | - Momoko Hamano
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
| | - Norifumi Takeda
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroyuki Morita
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shuji Takada
- Department of Systems BioMedicine, National Center for Child Health and Development Research Institute, Setagaya-ku, Tokyo 157-8535, Japan
| | - Masashi Toyoda
- Center for Regenerative Medicine, National Center for Child Health and Development Research Institute, Setagaya-ku, Tokyo 157-8535, Japan
| | - Masanobu Uchiyama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masashi Ikeuchi
- Division of Biofunctional Restoration, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Kiminori Toyooka
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Akihiro Umezawa
- Center for Regenerative Medicine, National Center for Child Health and Development Research Institute, Setagaya-ku, Tokyo 157-8535, Japan
| | - Yoshihiro Yamanishi
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
| | - Ryo Nitta
- Division of Structural Medicine and Anatomy, Department of Physiology and Cell Biology, Kobe University Graduate School of Medicine, Kobe, Hyogo 650-0017, Japan
| | - Hiroyuki Aburatani
- Genome Science Division, Research Center for Advanced Science and Technologies, The University of Tokyo, Meguro-ku, Tokyo 153-8904, Japan
| | - Issei Komuro
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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Walker SG, Langland CJ, Viles J, Hecker LA, Wallrath LL. Drosophila Models Reveal Properties of Mutant Lamins That Give Rise to Distinct Diseases. Cells 2023; 12:cells12081142. [PMID: 37190051 DOI: 10.3390/cells12081142] [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: 01/26/2023] [Revised: 04/06/2023] [Accepted: 04/06/2023] [Indexed: 05/17/2023] Open
Abstract
Mutations in the LMNA gene cause a collection of diseases known as laminopathies, including muscular dystrophies, lipodystrophies, and early-onset aging syndromes. The LMNA gene encodes A-type lamins, lamins A/C, intermediate filaments that form a meshwork underlying the inner nuclear membrane. Lamins have a conserved domain structure consisting of a head, coiled-coil rod, and C-terminal tail domain possessing an Ig-like fold. This study identified differences between two mutant lamins that cause distinct clinical diseases. One of the LMNA mutations encodes lamin A/C p.R527P and the other codes lamin A/C p.R482W, which are typically associated with muscular dystrophy and lipodystrophy, respectively. To determine how these mutations differentially affect muscle, we generated the equivalent mutations in the Drosophila Lamin C (LamC) gene, an orthologue of human LMNA. The muscle-specific expression of the R527P equivalent showed cytoplasmic aggregation of LamC, a reduced larval muscle size, decreased larval motility, and cardiac defects resulting in a reduced adult lifespan. By contrast, the muscle-specific expression of the R482W equivalent caused an abnormal nuclear shape without a change in larval muscle size, larval motility, and adult lifespan compared to controls. Collectively, these studies identified fundamental differences in the properties of mutant lamins that cause clinically distinct phenotypes, providing insights into disease mechanisms.
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Affiliation(s)
- Sydney G Walker
- Department of Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Christopher J Langland
- Department of Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Jill Viles
- Independent Researcher, Gowrie, IA 50543, USA
| | - Laura A Hecker
- Department of Biology, Clarke University, Dubuque, IA 52001, USA
| | - Lori L Wallrath
- Department of Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
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70
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Li Y, Zhu J, Yu Z, Li H, Jin X. The role of Lamin B2 in human diseases. Gene 2023; 870:147423. [PMID: 37044185 DOI: 10.1016/j.gene.2023.147423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 04/02/2023] [Accepted: 04/05/2023] [Indexed: 04/14/2023]
Abstract
Lamin B2 (LMNB2), on the inner side of the nuclear envelope, constitutes the nuclear skeleton by connecting with other nuclear proteins. LMNB2 is involved in a wide range of nuclear functions, including DNA replication and stability, regulation of chromatin, and nuclear stiffness. Moreover, LMNB2 regulates several cellular processes, such as tissue development, cell cycle, cellular proliferation and apoptosis, chromatin localization and stability, and DNA methylation. Besides, the influence of abnormal expression and mutations of LMNB2 has been gradually discovered in cancers and laminopathies. Therefore, this review summarizes the recent advances of LMNB2-associated biological roles in physiological or pathological conditions, with a particular emphasis on cancers and laminopathies, as well as the potential mechanism of LMNB2 in related cancers.
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Affiliation(s)
- Yuxuan Li
- Department of Hepatobiliary and Pancreatic Surgery, Ningbo Medical Center of LiHuiLi Hospital, Ningbo University, Ningbo, Zhejiang 315040, P.R. China; Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Jie Zhu
- Department of Hepatobiliary and Pancreatic Surgery, Ningbo Medical Center of LiHuiLi Hospital, Ningbo University, Ningbo, Zhejiang 315040, P.R. China; Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Zongdong Yu
- Department of Hepatobiliary and Pancreatic Surgery, Ningbo Medical Center of LiHuiLi Hospital, Ningbo University, Ningbo, Zhejiang 315040, P.R. China; Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Hong Li
- Department of Hepatobiliary and Pancreatic Surgery, Ningbo Medical Center of LiHuiLi Hospital, Ningbo University, Ningbo, Zhejiang 315040, P.R. China; Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, P.R. China.
| | - Xiaofeng Jin
- Department of Hepatobiliary and Pancreatic Surgery, Ningbo Medical Center of LiHuiLi Hospital, Ningbo University, Ningbo, Zhejiang 315040, P.R. China; Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, P.R. China.
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71
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Zhang B, Powers JD, McCulloch AD, Chi NC. Nuclear mechanosignaling in striated muscle diseases. Front Physiol 2023; 14:1126111. [PMID: 36960155 PMCID: PMC10027932 DOI: 10.3389/fphys.2023.1126111] [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: 12/17/2022] [Accepted: 02/22/2023] [Indexed: 03/09/2023] Open
Abstract
Mechanosignaling describes processes by which biomechanical stimuli are transduced into cellular responses. External biophysical forces can be transmitted via structural protein networks that span from the cellular membrane to the cytoskeleton and the nucleus, where they can regulate gene expression through a series of biomechanical and/or biochemical mechanosensitive mechanisms, including chromatin remodeling, translocation of transcriptional regulators, and epigenetic factors. Striated muscle cells, including cardiac and skeletal muscle myocytes, utilize these nuclear mechanosignaling mechanisms to respond to changes in their intracellular and extracellular mechanical environment and mediate gene expression and cell remodeling. In this brief review, we highlight and discuss recent experimental work focused on the pathway of biomechanical stimulus propagation at the nucleus-cytoskeleton interface of striated muscles, and the mechanisms by which these pathways regulate gene regulation, muscle structure, and function. Furthermore, we discuss nuclear protein mutations that affect mechanosignaling function in human and animal models of cardiomyopathy. Furthermore, current open questions and future challenges in investigating striated muscle nuclear mechanosignaling are further discussed.
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Affiliation(s)
- Bo Zhang
- Department of Bioengineering, University of California San Diego, La Jolla, CA, United States
| | - Joseph D. Powers
- Department of Bioengineering, University of California San Diego, La Jolla, CA, United States
| | - Andrew D. McCulloch
- Department of Bioengineering, University of California San Diego, La Jolla, CA, United States
- Institute for Engineering in Medicine, University of California San Diego, La Jolla, CA, United States
| | - Neil C. Chi
- Department of Bioengineering, University of California San Diego, La Jolla, CA, United States
- Institute for Engineering in Medicine, University of California San Diego, La Jolla, CA, United States
- Department of Medicine, Division of Cardiovascular Medicine, University of California San Diego, La Jolla, CA, United States
- Institute of Genomic Medicine, University of California San Diego, La Jolla, CA, United States
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72
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How Epstein-Barr Virus Induces the Reorganization of Cellular Chromatin. mBio 2023; 14:e0268622. [PMID: 36625581 PMCID: PMC9973336 DOI: 10.1128/mbio.02686-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
We have discovered how Epstein-Barr virus (EBV) induces the reorganization of cellular chromatin (ROCC), in which host chromatin is compacted and marginated within the nucleus, with viral DNA replication occurring in the chromatin-free regions. Five families of DNA viruses induce ROCC: herpesviruses, adenoviruses, parvoviruses, baculoviruses, and geminiviruses. These families infect a variety of hosts, including vertebrates, insects, and plants. They also share several characteristics: they replicate and encapsidate their genomes in the host nucleus and package their genomes unbound by histones. We have identified the viral genes and processes required for EBV's ROCC. Each of EBV's seven core DNA synthesis genes and its origin of lytic replication (oriLyt), in trans, are required, while its protein kinase, BGLF4, and its true late genes are not. Following these findings, we tested the role of EBV lytic DNA amplification in driving ROCC. Surprisingly, the inhibition of EBV's lytic DNA synthesis still supports chromatin compaction but blocks its margination. We propose a two-step model for ROCC. First, the initiation of viral lytic DNA synthesis induces a cellular response that results in global chromatin compaction. Second, the histone-free, productive viral DNA synthesis leads to the margination of compacted chromatin to the nuclear periphery. We have tested this model by asking if the histone-associated simian virus 40 (SV40) DNA synthesis could substitute for oriLyt-mediated synthesis and found that EBV's ROCC is incompatible with SV40 DNA replication. Elucidating EBV's induction of ROCC both illuminates how other viruses can do so and indicates how this spatial control of cellular chromatin benefits them. IMPORTANCE Five families of viruses support the reorganization of cellular chromatin (ROCC), the compaction and margination of host chromatin, upon their productive infection. That they all share this phenotype implies the importance of ROCC in viral life cycles. With Epstein-Barr virus (EBV), a herpesvirus, we show that the viral replication complex and origin of lytic replication (oriLyt) are essential for ROCC. In contrast, its protein kinase and true late genes are not. We show that, unexpectedly, the viral lytic amplification is not required for chromatin compaction but is required for its margination. We propose a two-step model for ROCC: first, global chromatin compaction occurs as a cellular response to the initiation of viral DNA synthesis; then, the accumulation of newly synthesized, histone-free viral DNA leads to cellular chromatin margination. Taken together, our findings provide insights into a process contributing to the productive phase of five families of viruses.
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73
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Tuning between Nuclear Organization and Functionality in Health and Disease. Cells 2023; 12:cells12050706. [PMID: 36899842 PMCID: PMC10000962 DOI: 10.3390/cells12050706] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/08/2023] [Accepted: 02/20/2023] [Indexed: 02/25/2023] Open
Abstract
The organization of eukaryotic genome in the nucleus, a double-membraned organelle separated from the cytoplasm, is highly complex and dynamic. The functional architecture of the nucleus is confined by the layers of internal and cytoplasmic elements, including chromatin organization, nuclear envelope associated proteome and transport, nuclear-cytoskeletal contacts, and the mechano-regulatory signaling cascades. The size and morphology of the nucleus could impose a significant impact on nuclear mechanics, chromatin organization, gene expression, cell functionality and disease development. The maintenance of nuclear organization during genetic or physical perturbation is crucial for the viability and lifespan of the cell. Abnormal nuclear envelope morphologies, such as invagination and blebbing, have functional implications in several human disorders, including cancer, accelerated aging, thyroid disorders, and different types of neuro-muscular diseases. Despite the evident interplay between nuclear structure and nuclear function, our knowledge about the underlying molecular mechanisms for regulation of nuclear morphology and cell functionality during health and illness is rather poor. This review highlights the essential nuclear, cellular, and extracellular components that govern the organization of nuclei and functional consequences associated with nuclear morphometric aberrations. Finally, we discuss the recent developments with diagnostic and therapeutic implications targeting nuclear morphology in health and disease.
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74
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Choi M, Kwon H, Pak Y. Caveolin-2 in association with nuclear lamina controls adipocyte hypertrophy. FASEB J 2023; 37:e22745. [PMID: 36637913 DOI: 10.1096/fj.202201028rr] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 12/13/2022] [Accepted: 12/19/2022] [Indexed: 01/14/2023]
Abstract
Here, we identify that Caveolin-2 (Cav-2), an integral membrane protein, controls adipocyte hypertrophy in association with nuclear lamina. In the hypertrophy stage of adipogenesis, pY19-Cav-2 association with lamin A/C facilitated the disengagement of CCAAT/enhancer-binding protein α (C/EBPα) and peroxisome proliferator-activated receptor γ (PPARγ) from lamin A/C and repressed Cav-2 promoter at the nuclear periphery for epigenetic activation of Cav-2, and thereby promoted C/EBPα and PPARγ-induced adipocyte hypertrophy. Stable expression of Cav-2 was required and retained by phosphorylation, deubiquitination, and association with lamin A/C for the adipocyte hypertrophy. However, obese adipocytes exhibited augmented Cav-2 stability resulting from the up-regulation of lamin A/C over lamin B1, protein tyrosine phosphatase 1B (PTP1B), and nuclear deubiquitinating enzyme (DUB), Uchl5. Our findings show a novel epigenetic regulatory mechanism of adipocyte hypertrophy by Cav-2 at the nuclear periphery.
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Affiliation(s)
- Moonjeong Choi
- Division of Life Science, Graduate School of Applied Life Science (BK21 Plus Program), PMBBRC, Gyeongsang National University, Jinju, South Korea
| | - Hayeong Kwon
- Division of Life Science, Graduate School of Applied Life Science (BK21 Plus Program), PMBBRC, Gyeongsang National University, Jinju, South Korea
| | - Yunbae Pak
- Division of Life Science, Graduate School of Applied Life Science (BK21 Plus Program), PMBBRC, Gyeongsang National University, Jinju, South Korea
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75
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Madsen-Østerbye J, Abdelhalim M, Pickering SH, Collas P. Gene Regulatory Interactions at Lamina-Associated Domains. Genes (Basel) 2023; 14:genes14020334. [PMID: 36833261 PMCID: PMC9957430 DOI: 10.3390/genes14020334] [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: 12/24/2022] [Revised: 01/20/2023] [Accepted: 01/26/2023] [Indexed: 01/31/2023] Open
Abstract
The nuclear lamina provides a repressive chromatin environment at the nuclear periphery. However, whereas most genes in lamina-associated domains (LADs) are inactive, over ten percent reside in local euchromatic contexts and are expressed. How these genes are regulated and whether they are able to interact with regulatory elements remain unclear. Here, we integrate publicly available enhancer-capture Hi-C data with our own chromatin state and transcriptomic datasets to show that inferred enhancers of active genes in LADs are able to form connections with other enhancers within LADs and outside LADs. Fluorescence in situ hybridization analyses show proximity changes between differentially expressed genes in LADs and distant enhancers upon the induction of adipogenic differentiation. We also provide evidence of involvement of lamin A/C, but not lamin B1, in repressing genes at the border of an in-LAD active region within a topological domain. Our data favor a model where the spatial topology of chromatin at the nuclear lamina is compatible with gene expression in this dynamic nuclear compartment.
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Affiliation(s)
- Julia Madsen-Østerbye
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0317 Oslo, Norway
| | - Mohamed Abdelhalim
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0317 Oslo, Norway
| | - Sarah Hazell Pickering
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0317 Oslo, Norway
| | - Philippe Collas
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0317 Oslo, Norway
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, 0424 Oslo, Norway
- Correspondence:
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76
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Walker RR, Rentia Z, Chiappinelli KB. Epigenetically programmed resistance to chemo- and immuno-therapies. Adv Cancer Res 2023; 158:41-71. [PMID: 36990538 PMCID: PMC10184181 DOI: 10.1016/bs.acr.2022.12.001] [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] [Indexed: 01/29/2023]
Abstract
Resistance to cancer treatments remains a major barrier in developing cancer cures. While promising combination chemotherapy treatments and novel immunotherapies have improved patient outcomes, resistance to these treatments remains poorly understood. New insights into the dysregulation of the epigenome show how it promotes tumor growth and resistance to therapy. By altering control of gene expression, tumor cells can evade immune cell recognition, ignore apoptotic cues, and reverse DNA damage induced by chemotherapies. In this chapter, we summarize the data on epigenetic remodeling during cancer progression and treatment that enable cancer cell survival and describe how these epigenetic changes are being targeted clinically to overcome resistance.
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Affiliation(s)
- Reddick R Walker
- The George Washington University Cancer Center (GWCC), Washington, DC, United States; Department of Microbiology, Immunology & Tropical Medicine, The George Washington University, Washington, DC, United States
| | - Zainab Rentia
- The George Washington University Cancer Center (GWCC), Washington, DC, United States
| | - Katherine B Chiappinelli
- The George Washington University Cancer Center (GWCC), Washington, DC, United States; Department of Microbiology, Immunology & Tropical Medicine, The George Washington University, Washington, DC, United States.
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77
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Mangiavacchi A, Morelli G, Orlando V. Behind the scenes: How RNA orchestrates the epigenetic regulation of gene expression. Front Cell Dev Biol 2023; 11:1123975. [PMID: 36760365 PMCID: PMC9905133 DOI: 10.3389/fcell.2023.1123975] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 01/16/2023] [Indexed: 01/26/2023] Open
Abstract
Non-coding DNA accounts for approximately 98.5% of the human genome. Once labeled as "junk DNA", this portion of the genome has undergone a progressive re-evaluation and it is now clear that some of its transcriptional products, belonging to the non-coding RNAs (ncRNAs), are key players in cell regulatory networks. A growing body of evidence demonstrates the crucial impact of regulatory ncRNAs on mammalian gene expression. Here, we focus on the defined relationship between chromatin-interacting RNAs, particularly long non-coding RNA (lncRNA), enhancer RNA (eRNA), non-coding natural antisense transcript (ncNAT), and circular RNA (circRNA) and epigenome, a common ground where both protein and RNA species converge to regulate cellular functions. Through several examples, this review provides an overview of the variety of targets, interactors, and mechanisms involved in the RNA-mediated modulation of loci-specific epigenetic states, a fundamental evolutive strategy to orchestrate mammalian gene expression in a timely and reversible manner. We will discuss how RNA-mediated epigenetic regulation impacts development and tissue homeostasis and how its alteration contributes to the onset and progression of many different human diseases, particularly cancer.
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78
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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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79
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Stein RA, Thompson LM. Epigenetic changes induced by pathogenic Chlamydia spp. Pathog Dis 2023; 81:ftad034. [PMID: 38031337 DOI: 10.1093/femspd/ftad034] [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: 06/15/2023] [Revised: 11/16/2023] [Accepted: 11/28/2023] [Indexed: 12/01/2023] Open
Abstract
Chlamydia trachomatis, C. pneumoniae, and C. psittaci, the three Chlamydia species known to cause human disease, have been collectively linked to several pathologies, including conjunctivitis, trachoma, respiratory disease, acute and chronic urogenital infections and their complications, and psittacosis. In vitro, animal, and human studies also established additional correlations, such as between C. pneumoniae and atherosclerosis and between C. trachomatis and ovarian cancer. As part of their survival and pathogenesis strategies as obligate intracellular bacteria, Chlamydia spp. modulate all three major types of epigenetic changes, which include deoxyribonucleic acid (DNA) methylation, histone post-translational modifications, and microRNA-mediated gene silencing. Some of these epigenetic changes may be implicated in key aspects of pathogenesis, such as the ability of the Chlamydia spp. to induce epithelial-to-mesenchymal transition, interfere with DNA damage repair, suppress cholesterol efflux from infected macrophages, act as a co-factor in human papillomavirus (HPV)-mediated cervical cancer, prevent apoptosis, and preserve the integrity of mitochondrial networks in infected host cells. A better understanding of the individual and collective contribution of epigenetic changes to pathogenesis will enhance our knowledge about the biology of Chlamydia spp. and facilitate the development of novel therapies and biomarkers. Pathogenic Chlamydia spp. contribute to epigenetically-mediated gene expression changes in host cells by multiple mechanisms.
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Affiliation(s)
- Richard A Stein
- NYU Tandon School of Engineering, Department of Chemical and Biomolecular Engineering, 6 MetroTech Center, Brooklyn, NY 11201, United States
| | - Lily M Thompson
- NYU Tandon School of Engineering, Department of Chemical and Biomolecular Engineering, 6 MetroTech Center, Brooklyn, NY 11201, United States
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80
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Fritz AJ, Ghule PN, Toor R, Dillac L, Perelman J, Boyd J, Lian JB, Gordon JA, Frietze S, Van Wijnen A, Stein JL, Stein GS. Spatiotemporal Epigenetic Control of the Histone Gene Chromatin Landscape during the Cell Cycle. Crit Rev Eukaryot Gene Expr 2023; 33:85-97. [PMID: 37017672 PMCID: PMC10826887 DOI: 10.1615/critreveukaryotgeneexpr.2022046190] [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] [Indexed: 12/23/2022]
Abstract
Higher-order genomic organization supports the activation of histone genes in response to cell cycle regulatory cues that epigenetically mediates stringent control of transcription at the G1/S-phase transition. Histone locus bodies (HLBs) are dynamic, non-membranous, phase-separated nuclear domains where the regulatory machinery for histone gene expression is organized and assembled to support spatiotemporal epigenetic control of histone genes. HLBs provide molecular hubs that support synthesis and processing of DNA replication-dependent histone mRNAs. These regulatory microenvironments support long-range genomic interactions among non-contiguous histone genes within a single topologically associating domain (TAD). HLBs respond to activation of the cyclin E/CDK2/NPAT/HINFP pathway at the G1/S transition. HINFP and its coactivator NPAT form a complex within HLBs that controls histone mRNA transcription to support histone protein synthesis and packaging of newly replicated DNA. Loss of HINFP compromises H4 gene expression and chromatin formation, which may result in DNA damage and impede cell cycle progression. HLBs provide a paradigm for higher-order genomic organization of a subnuclear domain that executes an obligatory cell cycle-controlled function in response to cyclin E/CDK2 signaling. Understanding the coordinately and spatiotemporally organized regulatory programs in focally defined nuclear domains provides insight into molecular infrastructure for responsiveness to cell signaling pathways that mediate biological control of growth, differentiation phenotype, and are compromised in cancer.
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Affiliation(s)
- Andrew J. Fritz
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
- University of Vermont Cancer Center, Burlington, Vermont, USA
| | - Prachi N. Ghule
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
- University of Vermont Cancer Center, Burlington, Vermont, USA
| | - Rabail Toor
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
- University of Vermont Cancer Center, Burlington, Vermont, USA
| | - Louis Dillac
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
- University of Vermont Cancer Center, Burlington, Vermont, USA
| | - Jonah Perelman
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
| | - Joseph Boyd
- College of Nursing and Health Sciences, University of Vermont, Burlington, Vermont, USA
| | - Jane B. Lian
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
- University of Vermont Cancer Center, Burlington, Vermont, USA
| | - Johnathan A.R. Gordon
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
- University of Vermont Cancer Center, Burlington, Vermont, USA
| | - Seth Frietze
- University of Vermont Cancer Center, Burlington, Vermont, USA
- College of Nursing and Health Sciences, University of Vermont, Burlington, Vermont, USA
| | - Andre Van Wijnen
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
| | - Janet L. Stein
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
- University of Vermont Cancer Center, Burlington, Vermont, USA
| | - Gary S. Stein
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
- University of Vermont Cancer Center, Burlington, Vermont, USA
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81
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Zheng Y, Li H, Bo X, Chen H. Ionizing radiation damage and repair from 3D-genomic perspective. Trends Genet 2023; 39:1-4. [PMID: 35934594 DOI: 10.1016/j.tig.2022.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 07/07/2022] [Accepted: 07/11/2022] [Indexed: 10/16/2022]
Abstract
Ionizing radiation (IR)-induced DNA damage and repair are complex and occur at hierarchical chromatin structures; radiobiology needs to be studied from a 3D-genomic perspective. Differences in IR damage and repair throughout the 3D genome may help to explain differences in radiosensitivity.
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Affiliation(s)
- Yang Zheng
- Institute of Health Service and Transfusion Medicine, Beijing 100850, China; State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China
| | - Hao Li
- Institute of Health Service and Transfusion Medicine, Beijing 100850, China
| | - Xiaochen Bo
- Institute of Health Service and Transfusion Medicine, Beijing 100850, China.
| | - Hebing Chen
- Institute of Health Service and Transfusion Medicine, Beijing 100850, China.
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82
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Santini GT, Shah PP, Karnay A, Jain R. Aberrant chromatin organization at the nexus of laminopathy disease pathways. Nucleus 2022; 13:300-312. [PMID: 36503349 PMCID: PMC9746625 DOI: 10.1080/19491034.2022.2153564] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 11/02/2022] [Accepted: 11/11/2022] [Indexed: 12/14/2022] Open
Affiliation(s)
- Garrett T. Santini
- Departments of Medicine and Cell and Developmental Biology, Penn Cardiovascular Institute, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Parisha P. Shah
- Departments of Medicine and Cell and Developmental Biology, Penn Cardiovascular Institute, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Ashley Karnay
- Departments of Medicine and Cell and Developmental Biology, Penn Cardiovascular Institute, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Rajan Jain
- Departments of Medicine and Cell and Developmental Biology, Penn Cardiovascular Institute, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
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83
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Lavia P, Sciamanna I, Spadafora C. An Epigenetic LINE-1-Based Mechanism in Cancer. Int J Mol Sci 2022; 23:14610. [PMID: 36498938 PMCID: PMC9738484 DOI: 10.3390/ijms232314610] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/18/2022] [Accepted: 11/20/2022] [Indexed: 11/24/2022] Open
Abstract
In the last fifty years, large efforts have been deployed in basic research, clinical oncology, and clinical trials, yielding an enormous amount of information regarding the molecular mechanisms of cancer and the design of effective therapies. The knowledge that has accumulated underpins the complexity, multifactoriality, and heterogeneity of cancer, disclosing novel landscapes in cancer biology with a key role of genome plasticity. Here, we propose that cancer onset and progression are determined by a stress-responsive epigenetic mechanism, resulting from the convergence of upregulation of LINE-1 (long interspersed nuclear element 1), the largest family of human retrotransposons, genome damage, nuclear lamina fragmentation, chromatin remodeling, genome reprogramming, and autophagy activation. The upregulated expression of LINE-1 retrotransposons and their protein products plays a key role in these processes, yielding an increased plasticity of the nuclear architecture with the ensuing reprogramming of global gene expression, including the reactivation of embryonic transcription profiles. Cancer phenotypes would thus emerge as a consequence of the unscheduled reactivation of embryonic gene expression patterns in an inappropriate context, triggering de-differentiation and aberrant proliferation in differentiated cells. Depending on the intensity of the stressing stimuli and the level of LINE-1 response, diverse degrees of malignity would be generated.
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Affiliation(s)
- Patrizia Lavia
- Institute of Molecular Biology and Pathology (IBPM), CNR Consiglio Nazionale delle Ricerche, c/o Department of Biology and Biotechnology, Sapienza University of Rome, 00185 Rome, Italy
| | - Ilaria Sciamanna
- Center for Animal Research and Welfare (BENA), ISS Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Corrado Spadafora
- Institute of Translational Pharmacology (IFT), CNR Consiglio Nazionale delle Ricerche, 00133 Rome, Italy
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84
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Fleming M, Nelson F, Wallace I, Eskiw CH. Genome Tectonics: Linking Dynamic Genome Organization with Cellular Nutrients. Lifestyle Genom 2022; 16:21-34. [PMID: 36446341 DOI: 10.1159/000528011] [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: 06/29/2022] [Accepted: 11/06/2022] [Indexed: 12/22/2023] Open
Abstract
BACKGROUND Our daily intake of food provides nutrients for the maintenance of health, growth, and development. The field of nutrigenomics aims to link dietary intake/nutrients to changes in epigenetic status and gene expression. SUMMARY Although the relationship between our diet and our genes in under intense investigation, there is still a significant aspect of our genome that has received little attention with regard to this. In the past 15 years, the importance of genome organization has become increasingly evident, with research identifying small-scale local changes to large segments of the genome dynamically repositioning within the nucleus in response to/or mediating change in gene expression. The discovery of these dynamic processes and organization maybe as significant as dynamic plate tectonics is to geology, there is little information tying genome organization to specific nutrients or dietary intake. KEY MESSAGES Here, we detail key principles of genome organization and structure, with emphasis on genome folding and organization, and link how these contribute to our future understand of nutrigenomics.
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Affiliation(s)
- Morgan Fleming
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Fina Nelson
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- 21st Street Brewery Inc., Saskatoon, Saskatchewan, Canada
| | - Iain Wallace
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Proxima Research and Development, Saskatoon, Saskatchewan, Canada
| | - Christopher H Eskiw
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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85
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Tomikawa J, Miyamoto K. Structural alteration of the nucleus for the reprogramming of gene expression. FEBS J 2022; 289:7221-7233. [PMID: 33891358 DOI: 10.1111/febs.15894] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/06/2021] [Accepted: 04/19/2021] [Indexed: 01/13/2023]
Abstract
The regulation of gene expression is a critical process for establishing and maintaining cellular identity. Gene expression is controlled through a chromatin-based mechanism in the nucleus of eukaryotic cells. Recent studies suggest that chromatin accessibility and the higher-order structure of chromatin affect transcriptional outcome. This is especially evident when cells change their fate during development and nuclear reprogramming. Furthermore, non-chromosomal contents of the cell nucleus, namely nucleoskeleton proteins, can also affect chromatin and nuclear structures, resulting in transcriptional alterations. Here, we review our current mechanistic understanding about how chromatin and nuclear structures impact transcription in the course of embryonic development, cellular differentiation and nuclear reprogramming, and also discuss unresolved questions that remain to be addressed in the field.
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Affiliation(s)
- Junko Tomikawa
- Graduate School of Biology-Oriented Science and Technology, Kindai University, Wakayama, Japan
| | - Kei Miyamoto
- Graduate School of Biology-Oriented Science and Technology, Kindai University, Wakayama, Japan
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86
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Kervella M, Jahier M, Meli AC, Muchir A. Genome organization in cardiomyocytes expressing mutated A-type lamins. Front Cell Dev Biol 2022; 10:1030950. [PMID: 36274847 PMCID: PMC9585167 DOI: 10.3389/fcell.2022.1030950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 09/26/2022] [Indexed: 11/13/2022] Open
Abstract
Cardiomyopathy is a myocardial disorder, in which the heart muscle is structurally and functionally abnormal, often leading to heart failure. Dilated cardiomyopathy is characterized by a compromised left ventricular function and contributes significantly to the heart failure epidemic, which represents a staggering clinical and public health problem worldwide. Gene mutations have been identified in 35% of patients with dilated cardiomyopathy. Pathogenic variants in LMNA, encoding nuclear A-type lamins, are one of the major causative causes of dilated cardiomyopathy (i.e. CardioLaminopathy). A-type lamins are type V intermediate filament proteins, which are the main components of the nuclear lamina. The nuclear lamina is connected to the cytoskeleton on one side, and to the chromatin on the other side. Among the models proposed to explain how CardioLaminopathy arises, the “chromatin model” posits an effect of mutated A-type lamins on the 3D genome organization and thus on the transcription activity of tissue-specific genes. Chromatin contacts with the nuclear lamina via specific genomic regions called lamina-associated domains lamina-associated domains. These LADs play a role in the chromatin organization and gene expression regulation. This review focuses on the identification of LADs and chromatin remodeling in cardiac muscle cells expressing mutated A-type lamins and discusses the methods and relevance of these findings in disease.
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Affiliation(s)
- Marie Kervella
- PhyMedExp, University of Montpellier, INSERM, CNRS, Montpellier, France
| | - Maureen Jahier
- Sorbonne Université, INSERM U974, Institute of Myology, Center of Research in Myology, Paris, France
| | - Albano C. Meli
- PhyMedExp, University of Montpellier, INSERM, CNRS, Montpellier, France
| | - Antoine Muchir
- Sorbonne Université, INSERM U974, Institute of Myology, Center of Research in Myology, Paris, France
- *Correspondence: Antoine Muchir,
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87
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Rugerio-Martínez CI, Ramos D, Segura-Olvera A, Murillo-Melo NM, Tapia-Guerrero YS, Argüello-García R, Leyva-García N, Hernández-Hernández O, Cisneros B, Suárez-Sánchez R. Dp71 Point Mutations Induce Protein Aggregation, Loss of Nuclear Lamina Integrity and Impaired Braf35 and Ibraf Function in Neuronal Cells. Int J Mol Sci 2022; 23:ijms231911876. [PMID: 36233175 PMCID: PMC9570083 DOI: 10.3390/ijms231911876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/04/2022] [Accepted: 10/04/2022] [Indexed: 11/16/2022] Open
Abstract
Dystrophin Dp71 is the most abundant product of the Duchenne muscular dystrophy gene in the nervous system, and mutations impairing its function have been associated with the neurodevelopmental symptoms present in a third of DMD patients. Dp71 is required for the clustering of neurotransmitter receptors and the neuronal differentiation of cultured cells; nonetheless, its precise role in neuronal cells remains to be poorly understood. In this study, we analyzed the effect of two pathogenic DMD gene point mutations on the Dp71 function in neurons. We engineered C272Y and E299del mutations to express GFP-tagged Dp71 protein variants in N1E-115 and SH-SY5Y neuronal cells. Unexpectedly, the ectopic expression of Dp71 mutants resulted in protein aggregation, which may be mechanistically caused by the effect of the mutations on Dp71 structure, as predicted by protein modeling and molecular dynamics simulations. Interestingly, Dp71 mutant variants acquired a dominant negative function that, in turn, dramatically impaired the distribution of different Dp71 protein partners, including β-dystroglycan, nuclear lamins A/C and B1, the high-mobility group (HMG)-containing protein (BRAF35) and the BRAF35-family-member inhibitor of BRAF35 (iBRAF). Further analysis of Dp71 mutants provided evidence showing a role for Dp71 in modulating both heterochromatin marker H3K9me2 organization and the neuronal genes’ expression, via its interaction with iBRAF and BRAF5.
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Affiliation(s)
- Claudia Ivette Rugerio-Martínez
- Laboratorio de Medicina Genómica, Departamento de Genética, Instituto Nacional de Rehabilitación-Luis Guillermo Ibarra Ibarra, Ciudad de Mexico 14389, Mexico
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de Mexico 07360, Mexico
| | - Daniel Ramos
- Laboratorio de Medicina Genómica, Departamento de Genética, Instituto Nacional de Rehabilitación-Luis Guillermo Ibarra Ibarra, Ciudad de Mexico 14389, Mexico
| | - Abel Segura-Olvera
- Laboratorio de Medicina Genómica, Departamento de Genética, Instituto Nacional de Rehabilitación-Luis Guillermo Ibarra Ibarra, Ciudad de Mexico 14389, Mexico
| | - Nadia Mireya Murillo-Melo
- Laboratorio de Medicina Genómica, Departamento de Genética, Instituto Nacional de Rehabilitación-Luis Guillermo Ibarra Ibarra, Ciudad de Mexico 14389, Mexico
| | - Yessica Sarai Tapia-Guerrero
- Laboratorio de Medicina Genómica, Departamento de Genética, Instituto Nacional de Rehabilitación-Luis Guillermo Ibarra Ibarra, Ciudad de Mexico 14389, Mexico
| | - Raúl Argüello-García
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de Mexico 07360, Mexico
| | - Norberto Leyva-García
- Laboratorio de Medicina Genómica, Departamento de Genética, Instituto Nacional de Rehabilitación-Luis Guillermo Ibarra Ibarra, Ciudad de Mexico 14389, Mexico
| | - Oscar Hernández-Hernández
- Laboratorio de Medicina Genómica, Departamento de Genética, Instituto Nacional de Rehabilitación-Luis Guillermo Ibarra Ibarra, Ciudad de Mexico 14389, Mexico
| | - Bulmaro Cisneros
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de Mexico 07360, Mexico
| | - Rocío Suárez-Sánchez
- Laboratorio de Medicina Genómica, Departamento de Genética, Instituto Nacional de Rehabilitación-Luis Guillermo Ibarra Ibarra, Ciudad de Mexico 14389, Mexico
- Correspondence: or ; Tel.: +52-55-5999-1000 (ext. 14710)
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88
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Martinez-Fundichely A, Dixon A, Khurana E. Modeling tissue-specific breakpoint proximity of structural variations from whole-genomes to identify cancer drivers. Nat Commun 2022; 13:5640. [PMID: 36163358 PMCID: PMC9512825 DOI: 10.1038/s41467-022-32945-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 08/24/2022] [Indexed: 11/11/2022] Open
Abstract
Structural variations (SVs) in cancer cells often impact large genomic regions with functional consequences. However, identification of SVs under positive selection is a challenging task because little is known about the genomic features related to the background breakpoint distribution in different cancers. We report a method that uses a generalized additive model to investigate the breakpoint proximity curves from 2,382 whole-genomes of 32 cancer types. We find that a multivariate model, which includes linear and nonlinear partial contributions of various tissue-specific features and their interaction terms, can explain up to 57% of the observed deviance of breakpoint proximity. In particular, three-dimensional genomic features such as topologically associating domains (TADs), TAD-boundaries and their interaction with other features show significant contributions. The model is validated by identification of known cancer genes and revealed putative drivers in cancers different than those with previous evidence of positive selection.
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Affiliation(s)
- Alexander Martinez-Fundichely
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10021, USA.
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10021, USA.
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA.
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, 10021, USA.
| | - Austin Dixon
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10021, USA
- Children's National Hospital, Washington, DC, 20010, USA
| | - Ekta Khurana
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10021, USA.
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10021, USA.
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA.
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, 10021, USA.
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89
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Jana A, Tran A, Gill A, Kiepas A, Kapania RK, Konstantopoulos K, Nain AS. Sculpting Rupture-Free Nuclear Shapes in Fibrous Environments. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2203011. [PMID: 35863910 PMCID: PMC9443471 DOI: 10.1002/advs.202203011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Indexed: 05/07/2023]
Abstract
Cytoskeleton-mediated force transmission regulates nucleus morphology. How nuclei shaping occurs in fibrous in vivo environments remains poorly understood. Here suspended nanofiber networks of precisely tunable (nm-µm) diameters are used to quantify nucleus plasticity in fibrous environments mimicking the natural extracellular matrix. Contrary to the apical cap over the nucleus in cells on 2-dimensional surfaces, the cytoskeleton of cells on fibers displays a uniform actin network caging the nucleus. The role of contractility-driven caging in sculpting nuclear shapes is investigated as cells spread on aligned single fibers, doublets, and multiple fibers of varying diameters. Cell contractility increases with fiber diameter due to increased focal adhesion clustering and density of actin stress fibers, which correlates with increased mechanosensitive transcription factor Yes-associated protein (YAP) translocation to the nucleus. Unexpectedly, large- and small-diameter fiber combinations lead to teardrop-shaped nuclei due to stress fiber anisotropy across the cell. As cells spread on fibers, diameter-dependent nuclear envelope invaginations that run the nucleus's length are formed at fiber contact sites. The sharpest invaginations enriched with heterochromatin clustering and sites of DNA repair are insufficient to trigger nucleus rupture. Overall, the authors quantitate the previously unknown sculpting and adaptability of nuclei to fibrous environments with pathophysiological implications.
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Affiliation(s)
- Aniket Jana
- Department of Mechanical EngineeringVirginia TechBlacksburgVA24061USA
| | - Avery Tran
- Department of Chemical and Biomolecular EngineeringJohns Hopkins UniversityBaltimoreMD21218USA
| | - Amritpal Gill
- Department of Mechanical EngineeringVirginia TechBlacksburgVA24061USA
| | - Alexander Kiepas
- Department of Chemical and Biomolecular EngineeringJohns Hopkins UniversityBaltimoreMD21218USA
| | - Rakesh K. Kapania
- Kevin T. Crofton Department of Aerospace EngineeringVirginia TechBlacksburgVA24061USA
| | | | - Amrinder S. Nain
- Department of Mechanical EngineeringVirginia TechBlacksburgVA24061USA
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90
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Jain N, Lord JM, Vogel V. Mechanoimmunology: Are inflammatory epigenetic states of macrophages tuned by biophysical factors? APL Bioeng 2022; 6:031502. [PMID: 36051106 PMCID: PMC9427154 DOI: 10.1063/5.0087699] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 07/26/2022] [Indexed: 11/17/2022] Open
Abstract
Many inflammatory diseases that are responsible for a majority of deaths are still uncurable, in part as the underpinning pathomechanisms and how to combat them is still poorly understood. Tissue-resident macrophages play pivotal roles in the maintenance of tissue homeostasis, but if they gradually convert to proinflammatory phenotypes, or if blood-born proinflammatory macrophages persist long-term after activation, they contribute to chronic inflammation and fibrosis. While biochemical factors and how they regulate the inflammatory transcriptional response of macrophages have been at the forefront of research to identify targets for therapeutic interventions, evidence is increasing that physical factors also tune the macrophage phenotype. Recently, several mechanisms have emerged as to how physical factors impact the mechanobiology of macrophages, from the nuclear translocation of transcription factors to epigenetic modifications, perhaps even DNA methylation. Insight into the mechanobiology of macrophages and associated epigenetic modifications will deliver novel therapeutic options going forward, particularly in the context of increased inflammation with advancing age and age-related diseases. We review here how biophysical factors can co-regulate pro-inflammatory gene expression and epigenetic modifications and identify knowledge gaps that require urgent attention if this therapeutic potential is to be realized.
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Affiliation(s)
- Nikhil Jain
- Authors to whom correspondence should be addressed: and
| | | | - Viola Vogel
- Department of Health Sciences and Technology, Institute of Translational Medicine, ETH Zurich, Zurich, Switzerland
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91
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van Schaik T, Liu NQ, Manzo SG, Peric-Hupkes D, de Wit E, van Steensel B. CTCF and cohesin promote focal detachment of DNA from the nuclear lamina. Genome Biol 2022; 23:185. [PMID: 36050765 PMCID: PMC9438259 DOI: 10.1186/s13059-022-02754-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 08/22/2022] [Indexed: 01/23/2023] Open
Abstract
Background Lamina-associated domains (LADs) are large genomic regions that are positioned at the nuclear lamina. It has remained largely unclear what drives the positioning and demarcation of LADs. Because the insulator protein CTCF is enriched at LAD borders, it was postulated that CTCF binding could position some LAD boundaries, possibly through its function in stalling cohesin and hence preventing cohesin invading into the LAD. To test this, we mapped genome–nuclear lamina interactions in mouse embryonic stem cells after rapid depletion of CTCF and other perturbations of cohesin dynamics. Results CTCF and cohesin contribute to a sharp transition in lamina interactions at LAD borders, while LADs are maintained after depletion of these proteins, also at borders marked by CTCF. CTCF and cohesin may thus reinforce LAD borders, but do not position these. CTCF binding sites within LADs are locally detached from the lamina and enriched for accessible DNA and active histone modifications. Remarkably, despite lamina positioning being strongly correlated with genome inactivity, this DNA remains accessible after the local detachment is lost following CTCF depletion. At a chromosomal scale, cohesin depletion and cohesin stabilization by depletion of the unloading factor WAPL quantitatively affect lamina interactions, indicative of perturbed chromosomal positioning in the nucleus. Finally, while H3K27me3 is locally enriched at CTCF-marked LAD borders, we find no evidence for an interplay between CTCF and H3K27me3 on lamina interactions. Conclusions These findings illustrate that CTCF and cohesin are not primary determinants of LAD patterns. Rather, these proteins locally modulate NL interactions. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02754-3.
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Affiliation(s)
- Tom van Schaik
- Oncode Institute and Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Ning Qing Liu
- Oncode Institute and Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Stefano G Manzo
- Oncode Institute and Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Daan Peric-Hupkes
- Oncode Institute and Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands.,Present address: Annogen, Amsterdam, the Netherlands
| | - Elzo de Wit
- Oncode Institute and Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Bas van Steensel
- Oncode Institute and Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands. .,Department of Cell Biology, Erasmus University Medical Center, Rotterdam, the Netherlands.
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92
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Shaw NM, Rios-Monterrosa JL, Fedorchak GR, Ketterer MR, Coombs GS, Lammerding J, Wallrath LL. Effects of mutant lamins on nucleo-cytoskeletal coupling in Drosophila models of LMNA muscular dystrophy. Front Cell Dev Biol 2022; 10:934586. [PMID: 36120560 PMCID: PMC9471154 DOI: 10.3389/fcell.2022.934586] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/20/2022] [Indexed: 11/13/2022] Open
Abstract
The nuclei of multinucleated skeletal muscles experience substantial external force during development and muscle contraction. Protection from such forces is partly provided by lamins, intermediate filaments that form a scaffold lining the inner nuclear membrane. Lamins play a myriad of roles, including maintenance of nuclear shape and stability, mediation of nuclear mechanoresponses, and nucleo-cytoskeletal coupling. Herein, we investigate how disease-causing mutant lamins alter myonuclear properties in response to mechanical force. This was accomplished via a novel application of a micropipette harpooning assay applied to larval body wall muscles of Drosophila models of lamin-associated muscular dystrophy. The assay enables the measurement of both nuclear deformability and intracellular force transmission between the cytoskeleton and nuclear interior in intact muscle fibers. Our studies revealed that specific mutant lamins increase nuclear deformability while other mutant lamins cause nucleo-cytoskeletal coupling defects, which were associated with loss of microtubular nuclear caging. We found that microtubule caging of the nucleus depended on Msp300, a KASH domain protein that is a component of the linker of nucleoskeleton and cytoskeleton (LINC) complex. Taken together, these findings identified residues in lamins required for connecting the nucleus to the cytoskeleton and suggest that not all muscle disease-causing mutant lamins produce similar defects in subcellular mechanics.
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Affiliation(s)
- Nicholas M. Shaw
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Jose L. Rios-Monterrosa
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Gregory R. Fedorchak
- The Nancy E. and Peter C. Meinig School of Biomedical Engineering, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, United States
| | - Margaret R. Ketterer
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Gary S. Coombs
- Biology Department, Waldorf University, Forest City, IA, United States
| | - Jan Lammerding
- The Nancy E. and Peter C. Meinig School of Biomedical Engineering, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, United States
| | - Lori L. Wallrath
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
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93
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West G, Turunen M, Aalto A, Virtanen L, Li SP, Heliö T, Meinander A, Taimen P. A heterozygous p.S143P mutation in LMNA associates with proteasome dysfunction and enhanced autophagy-mediated degradation of mutant lamins A and C. Front Cell Dev Biol 2022; 10:932983. [PMID: 36111332 PMCID: PMC9468711 DOI: 10.3389/fcell.2022.932983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 07/27/2022] [Indexed: 01/09/2023] Open
Abstract
Lamins A and C are nuclear intermediate filament proteins that form a proteinaceous meshwork called lamina beneath the inner nuclear membrane. Mutations in the LMNA gene encoding lamins A and C cause a heterogenous group of inherited degenerative diseases known as laminopathies. Previous studies have revealed altered cell signaling pathways in lamin-mutant patient cells, but little is known about the fate of mutant lamins A and C within the cells. Here, we analyzed the turnover of lamins A and C in cells derived from a dilated cardiomyopathy patient with a heterozygous p.S143P mutation in LMNA. We found that transcriptional activation and mRNA levels of LMNA are increased in the primary patient fibroblasts, but the protein levels of lamins A and C remain equal in control and patient cells because of a meticulous interplay between autophagy and the ubiquitin-proteasome system (UPS). Both endogenous and ectopic expression of p.S143P lamins A and C cause significantly reduced activity of UPS and an accumulation of K48-ubiquitin chains in the nucleus. Furthermore, K48-ubiquitinated lamins A and C are degraded by compensatory enhanced autophagy, as shown by increased autophagosome formation and binding of lamins A and C to microtubule-associated protein 1A/1B-light chain 3. Finally, chaperone 4-PBA augmented protein degradation by restoring UPS activity as well as autophagy in the patient cells. In summary, our results suggest that the p.S143P-mutant lamins A and C have overloading and deleterious effects on protein degradation machinery and pharmacological interventions with compounds enhancing protein degradation may be beneficial for cell homeostasis.
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Affiliation(s)
- Gun West
- Institute of Biomedicine and FICAN West Cancer Centre, University of Turku, Turku, Finland,InFLAMES Research Flagship Center, University of Turku and Åbo Akademi University, Turku, Finland
| | - Minttu Turunen
- Institute of Biomedicine and FICAN West Cancer Centre, University of Turku, Turku, Finland,InFLAMES Research Flagship Center, University of Turku and Åbo Akademi University, Turku, Finland
| | - Anna Aalto
- InFLAMES Research Flagship Center, University of Turku and Åbo Akademi University, Turku, Finland,Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Laura Virtanen
- Institute of Biomedicine and FICAN West Cancer Centre, University of Turku, Turku, Finland,InFLAMES Research Flagship Center, University of Turku and Åbo Akademi University, Turku, Finland
| | - Song-Ping Li
- Institute of Biomedicine and FICAN West Cancer Centre, University of Turku, Turku, Finland,InFLAMES Research Flagship Center, University of Turku and Åbo Akademi University, Turku, Finland
| | - Tiina Heliö
- Heart and Lung Center Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Annika Meinander
- InFLAMES Research Flagship Center, University of Turku and Åbo Akademi University, Turku, Finland,Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Pekka Taimen
- Institute of Biomedicine and FICAN West Cancer Centre, University of Turku, Turku, Finland,InFLAMES Research Flagship Center, University of Turku and Åbo Akademi University, Turku, Finland,Department of Pathology, Laboratory Division, Turku University Hospital, Turku, Finland,*Correspondence: Pekka Taimen,
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94
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Polyploidy and Myc Proto-Oncogenes Promote Stress Adaptation via Epigenetic Plasticity and Gene Regulatory Network Rewiring. Int J Mol Sci 2022; 23:ijms23179691. [PMID: 36077092 PMCID: PMC9456078 DOI: 10.3390/ijms23179691] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022] Open
Abstract
Polyploid cells demonstrate biological plasticity and stress adaptation in evolution; development; and pathologies, including cardiovascular diseases, neurodegeneration, and cancer. The nature of ploidy-related advantages is still not completely understood. Here, we summarize the literature on molecular mechanisms underlying ploidy-related adaptive features. Polyploidy can regulate gene expression via chromatin opening, reawakening ancient evolutionary programs of embryonality. Chromatin opening switches on genes with bivalent chromatin domains that promote adaptation via rapid induction in response to signals of stress or morphogenesis. Therefore, stress-associated polyploidy can activate Myc proto-oncogenes, which further promote chromatin opening. Moreover, Myc proto-oncogenes can trigger polyploidization de novo and accelerate genome accumulation in already polyploid cells. As a result of these cooperative effects, polyploidy can increase the ability of cells to search for adaptive states of cellular programs through gene regulatory network rewiring. This ability is manifested in epigenetic plasticity associated with traits of stemness, unicellularity, flexible energy metabolism, and a complex system of DNA damage protection, combining primitive error-prone unicellular repair pathways, advanced error-free multicellular repair pathways, and DNA damage-buffering ability. These three features can be considered important components of the increased adaptability of polyploid cells. The evidence presented here contribute to the understanding of the nature of stress resistance associated with ploidy and may be useful in the development of new methods for the prevention and treatment of cardiovascular and oncological diseases.
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95
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Abstract
The human genome is arranged in the cell nucleus nonrandomly, and phase separation has been proposed as an important driving force for genome organization. However, the cell nucleus is an active system, and the contribution of nonequilibrium activities to phase separation and genome structure and dynamics remains to be explored. We simulated the genome using an energy function parametrized with chromosome conformation capture (Hi-C) data with the presence of active, nondirectional forces that break the detailed balance. We found that active forces that may arise from transcription and chromatin remodeling can dramatically impact the spatial localization of heterochromatin. When applied to euchromatin, active forces can drive heterochromatin to the nuclear envelope and compete with passive interactions among heterochromatin that tend to pull them in opposite directions. Furthermore, active forces induce long-range spatial correlations among genomic loci beyond single chromosome territories. We further showed that the impact of active forces could be understood from the effective temperature defined as the fluctuation-dissipation ratio. Our study suggests that nonequilibrium activities can significantly impact genome structure and dynamics, producing unexpected collective phenomena.
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Affiliation(s)
- Zhongling Jiang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, United States
| | - Yifeng Qi
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, United States
| | - Kartik Kamat
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, United States
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, United States
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96
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Sikder S, Arunkumar G, Melters DP, Dalal Y. Breaking the aging epigenetic barrier. Front Cell Dev Biol 2022; 10:943519. [PMID: 35966762 PMCID: PMC9366916 DOI: 10.3389/fcell.2022.943519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
Aging is an inexorable event occurring universally for all organisms characterized by the progressive loss of cell function. However, less is known about the key events occurring inside the nucleus in the process of aging. The advent of chromosome capture techniques and extensive modern sequencing technologies have illuminated a rather dynamic structure of chromatin inside the nucleus. As cells advance along their life cycle, chromatin condensation states alter which leads to a different epigenetic landscape, correlated with modified gene expression. The exact factors mediating these changes in the chromatin structure and function remain elusive in the context of aging cells. The accumulation of DNA damage, reactive oxygen species and loss of genomic integrity as cells cease to divide can contribute to a tumor stimulating environment. In this review, we focus on genomic and epigenomic changes occurring in an aged cell which can contribute to age-related tumor formation.
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Affiliation(s)
| | | | | | - Yamini Dalal
- Chromatin Structure and Epigenetic Mechanisms, Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, NCI, NIH, Bethesda, MD, United States
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97
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Perepelina K, Zaytseva A, Khudiakov A, Neganova I, Vasichkina E, Malashicheva A, Kostareva A. LMNA mutation leads to cardiac sodium channel dysfunction in the Emery-Dreifuss muscular dystrophy patient. Front Cardiovasc Med 2022; 9:932956. [PMID: 35935653 PMCID: PMC9355377 DOI: 10.3389/fcvm.2022.932956] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 06/27/2022] [Indexed: 11/18/2022] Open
Abstract
Pathogenic variants in the LMNA gene are known to cause laminopathies, a broad range of disorders with different clinical phenotypes. LMNA genetic variants lead to tissue-specific pathologies affecting various tissues and organs. Common manifestations of laminopathies include cardiovascular system abnormalities, in particular, cardiomyopathies and conduction disorders. In the present study, we used induced pluripotent stem cells from a patient carrying LMNA p.R249Q genetic variant to create an in vitro cardiac model of laminopathy. Induced pluripotent stem cell-derived cardiomyocytes with LMNA p.R249Q genetic variant showed a decreased sodium current density and an impaired sodium current kinetics alongside with changes in transcription levels of cardiac-specific genes. Thus, we obtained compelling in vitro evidence of an association between LMNA p.R249Q genetic variant and cardiac-related abnormalities.
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Affiliation(s)
- Kseniya Perepelina
- World-Class Research Centre for Personalized Medicine, Almazov National Medical Research Centre, Saint-Petersburg, Russia
- Department of Embryology, Faculty of Biology, St Petersburg State University, Saint-Petersburg, Russia
| | - Anastasia Zaytseva
- World-Class Research Centre for Personalized Medicine, Almazov National Medical Research Centre, Saint-Petersburg, Russia
- Laboratory of Biophysics of Synaptics Processes, Sechenov Institute of Evolutionary Physiology and Biochemistry RAS, Saint-Petersburg, Russia
| | - Aleksandr Khudiakov
- World-Class Research Centre for Personalized Medicine, Almazov National Medical Research Centre, Saint-Petersburg, Russia
| | - Irina Neganova
- Institute of Cytology, Russian Academy of Sciences, Saint-Petersburg, Russia
| | - Elena Vasichkina
- World-Class Research Centre for Personalized Medicine, Almazov National Medical Research Centre, Saint-Petersburg, Russia
| | - Anna Malashicheva
- World-Class Research Centre for Personalized Medicine, Almazov National Medical Research Centre, Saint-Petersburg, Russia
- Institute of Cytology, Russian Academy of Sciences, Saint-Petersburg, Russia
| | - Anna Kostareva
- World-Class Research Centre for Personalized Medicine, Almazov National Medical Research Centre, Saint-Petersburg, Russia
- Department of Women's and Children's Health and Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
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98
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Urciuoli E, Peruzzi B. The Paradox of Nuclear Lamins in Pathologies: Apparently Controversial Roles Explained by Tissue-Specific Mechanobiology. Cells 2022; 11:cells11142194. [PMID: 35883635 PMCID: PMC9318957 DOI: 10.3390/cells11142194] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/06/2022] [Accepted: 07/08/2022] [Indexed: 11/24/2022] Open
Abstract
The nuclear lamina is a complex meshwork of intermediate filaments (lamins) that is located beneath the inner nuclear membrane and the surrounding nucleoplasm. The lamins exert both structural and functional roles in the nucleus and, by interacting with several nuclear proteins, are involved in a wide range of nuclear and cellular activities. Due their pivotal roles in basic cellular processes, lamin gene mutations, or modulations in lamin expression, are often associated with pathological conditions, ranging from rare genetic diseases, such as laminopathies, to cancer. Although a substantial amount of literature describes the effects that are mediated by the deregulation of nuclear lamins, some apparently controversial results have been reported, which may appear to conflict with each other. In this context, we herein provide our explanation of such “controversy”, which, in our opinion, derives from the tissue-specific expression of nuclear lamins and their close correlation with mechanotransduction processes, which could be very different, or even opposite, depending on the specific mechanical conditions that should not be compared (a tissue vs. another tissue, in vivo studies vs. cell cultures on glass/plastic supports, etc.). Moreover, we have stressed the relevance of considering and reproducing the “mechano-environment” in in vitro experimentation. Indeed, when primary cells that are collected from patients or donors are maintained in a culture, the mechanical signals deriving from canonical experimental procedures of cell culturing could alter the lamin expression, thereby profoundly modifying the assessed cell type, in some cases even too much, compared to the cell of origin.
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99
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Mora A, Huang X, Jauhari S, Jiang Q, Li X. Chromatin Hubs: A biological and computational outlook. Comput Struct Biotechnol J 2022; 20:3796-3813. [PMID: 35891791 PMCID: PMC9304431 DOI: 10.1016/j.csbj.2022.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/02/2022] [Accepted: 07/02/2022] [Indexed: 11/20/2022] Open
Abstract
This review discusses our current understanding of chromatin biology and bioinformatics under the unifying concept of “chromatin hubs.” The first part reviews the biology of chromatin hubs, including chromatin–chromatin interaction hubs, chromatin hubs at the nuclear periphery, hubs around macromolecules such as RNA polymerase or lncRNAs, and hubs around nuclear bodies such as the nucleolus or nuclear speckles. The second part reviews existing computational methods, including enhancer–promoter interaction prediction, network analysis, chromatin domain callers, transcription factory predictors, and multi-way interaction analysis. We introduce an integrated model that makes sense of the existing evidence. Understanding chromatin hubs may allow us (i) to explain long-unsolved biological questions such as interaction specificity and redundancy of mechanisms, (ii) to develop more realistic kinetic and functional predictions, and (iii) to explain the etiology of genomic disease.
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Affiliation(s)
- Antonio Mora
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health (Chinese Academy of Sciences), Guangzhou 511436, PR China
- Corresponding authors.
| | - Xiaowei Huang
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health (Chinese Academy of Sciences), Guangzhou 511436, PR China
| | - Shaurya Jauhari
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health (Chinese Academy of Sciences), Guangzhou 511436, PR China
| | - Qin Jiang
- Affiliated Eye Hospital of Nanjing Medical University, Nanjing 210000, PR China
| | - Xuri Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, and Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, PR China
- Corresponding authors.
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100
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Belmont AS. Nuclear Compartments: An Incomplete Primer to Nuclear Compartments, Bodies, and Genome Organization Relative to Nuclear Architecture. Cold Spring Harb Perspect Biol 2022; 14:a041268. [PMID: 34400557 PMCID: PMC9248822 DOI: 10.1101/cshperspect.a041268] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
This work reviews nuclear compartments, defined broadly to include distinct nuclear structures, bodies, and chromosome domains. It first summarizes original cytological observations before comparing concepts of nuclear compartments emerging from microscopy versus genomic approaches and then introducing new multiplexed imaging approaches that promise in the future to meld both approaches. I discuss how previous models of radial distribution of chromosomes or the binary division of the genome into A and B compartments are now being refined by the recognition of more complex nuclear compartmentalization. The poorly understood question of how these nuclear compartments are established and maintained is then discussed, including through the modern perspective of phase separation, before moving on to address possible functions of nuclear compartments, using the possible role of nuclear speckles in modulating gene expression as an example. Finally, the review concludes with a discussion of future questions for this field.
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Affiliation(s)
- Andrew S Belmont
- Department of Cell and Developmental Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801, USA
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