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Hu R, Cao Y, Wang Y, Zhao T, Yang K, Fan M, Guan M, Hou Y, Ying J, Ma X, Deng N, Sun X, Zhang Y, Zhang X. TMEM120B strengthens breast cancer cell stemness and accelerates chemotherapy resistance via β1-integrin/FAK-TAZ-mTOR signaling axis by binding to MYH9. Breast Cancer Res 2024; 26:48. [PMID: 38504374 PMCID: PMC10949598 DOI: 10.1186/s13058-024-01802-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 02/29/2024] [Indexed: 03/21/2024] Open
Abstract
BACKGROUND Breast cancer stem cell (CSC) expansion results in tumor progression and chemoresistance; however, the modulation of CSC pluripotency remains unexplored. Transmembrane protein 120B (TMEM120B) is a newly discovered protein expressed in human tissues, especially in malignant tissues; however, its role in CSC expansion has not been studied. This study aimed to determine the role of TMEM120B in transcriptional coactivator with PDZ-binding motif (TAZ)-mediated CSC expansion and chemotherapy resistance. METHODS Both bioinformatics analysis and immunohistochemistry assays were performed to examine expression patterns of TMEM120B in lung, breast, gastric, colon, and ovarian cancers. Clinicopathological factors and overall survival were also evaluated. Next, colony formation assay, MTT assay, EdU assay, transwell assay, wound healing assay, flow cytometric analysis, sphere formation assay, western blotting analysis, mouse xenograft model analysis, RNA-sequencing assay, immunofluorescence assay, and reverse transcriptase-polymerase chain reaction were performed to investigate the effect of TMEM120B interaction on proliferation, invasion, stemness, chemotherapy sensitivity, and integrin/FAK/TAZ/mTOR activation. Further, liquid chromatography-tandem mass spectrometry analysis, GST pull-down assay, and immunoprecipitation assays were performed to evaluate the interactions between TMEM120B, myosin heavy chain 9 (MYH9), and CUL9. RESULTS TMEM120B expression was elevated in lung, breast, gastric, colon, and ovarian cancers. TMEM120B expression positively correlated with advanced TNM stage, lymph node metastasis, and poor prognosis. Overexpression of TMEM120B promoted breast cancer cell proliferation, invasion, and stemness by activating TAZ-mTOR signaling. TMEM120B directly bound to the coil-coil domain of MYH9, which accelerated the assembly of focal adhesions (FAs) and facilitated the translocation of TAZ. Furthermore, TMEM120B stabilized MYH9 by preventing its degradation by CUL9 in a ubiquitin-dependent manner. Overexpression of TMEM120B enhanced resistance to docetaxel and doxorubicin. Conversely, overexpression of TMEM120B-∆CCD delayed the formation of FAs, suppressed TAZ-mTOR signaling, and abrogated chemotherapy resistance. TMEM120B expression was elevated in breast cancer patients with poor treatment outcomes (Miller/Payne grades 1-2) than in those with better outcomes (Miller/Payne grades 3-5). CONCLUSIONS Our study reveals that TMEM120B bound to and stabilized MYH9 by preventing its degradation. This interaction activated the β1-integrin/FAK-TAZ-mTOR signaling axis, maintaining stemness and accelerating chemotherapy resistance.
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Affiliation(s)
- Ran Hu
- Department of Pathology, College of Basic Medical Sciences, First Affiliated Hospital of China Medical University, No.77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning Province, 110122, China
- Department of Pathology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yu Cao
- Department of Surgical Oncology and Breast Surgery, First Affiliated Hospital of China Medical University, Shenyang, China
| | - Yuanyuan Wang
- Department of Anesthesiology, The Fourth Affiliated Hospital, China Medical University, Shenyang, China
| | - Tingting Zhao
- Department of Surgical Oncology and Breast Surgery, First Affiliated Hospital of China Medical University, Shenyang, China
| | - Kaibo Yang
- Department of Ophthalmology, The First Hospital of China Medical University, Shenyang, China
- Department of Immunology, College of Basic Medical Sciences of China Medical University, Shenyang, China
| | - Mingwei Fan
- Department of Pathology, College of Basic Medical Sciences, First Affiliated Hospital of China Medical University, No.77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning Province, 110122, China
| | - Mengyao Guan
- Department of Pathology, College of Basic Medical Sciences, First Affiliated Hospital of China Medical University, No.77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning Province, 110122, China
| | - Yuekang Hou
- Department of Pathology, College of Basic Medical Sciences, First Affiliated Hospital of China Medical University, No.77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning Province, 110122, China
| | - Jiao Ying
- Department of Pathology, College of Basic Medical Sciences, First Affiliated Hospital of China Medical University, No.77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning Province, 110122, China
| | - Xiaowen Ma
- Second Department of Clinical Medicine, China Medical University, Shenyang, China
| | - Ning Deng
- Department of Breast Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, China
| | - Xun Sun
- Department of Immunology, College of Basic Medical Sciences of China Medical University, Shenyang, China.
| | - Yong Zhang
- Department of Pathology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, China.
| | - Xiupeng Zhang
- Department of Pathology, College of Basic Medical Sciences, First Affiliated Hospital of China Medical University, No.77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning Province, 110122, China.
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Shevelyov YY. Interactions of Chromatin with the Nuclear Lamina and Nuclear Pore Complexes. Int J Mol Sci 2023; 24:15771. [PMID: 37958755 PMCID: PMC10649103 DOI: 10.3390/ijms242115771] [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: 10/06/2023] [Revised: 10/26/2023] [Accepted: 10/29/2023] [Indexed: 11/15/2023] Open
Abstract
Heterochromatin and euchromatin form different spatial compartments in the interphase nucleus, with heterochromatin being localized mainly at the nuclear periphery. The mechanisms responsible for peripheral localization of heterochromatin are still not fully understood. The nuclear lamina and nuclear pore complexes were obvious candidates for the role of heterochromatin binders. This review is focused on recent studies showing that heterochromatin interactions with the nuclear lamina and nuclear pore complexes maintain its peripheral localization. Differences in chromatin interactions with the nuclear envelope in cell populations and in individual cells are also discussed.
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Affiliation(s)
- Yuri Y Shevelyov
- Laboratory of Analysis of Gene Regulation, National Research Centre "Kurchatov Institute", Kurchatov Sq. 2, 123182 Moscow, Russia
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Elzamzami FD, Samal A, Arun AS, Dharmaraj T, Prasad NR, Rendon-Jonguitud A, DeVine L, Walston JD, Cole RN, Wilson KL. Native lamin A/C proteomes and novel partners from heart and skeletal muscle in a mouse chronic inflammation model of human frailty. Front Cell Dev Biol 2023; 11:1240285. [PMID: 37936983 PMCID: PMC10626543 DOI: 10.3389/fcell.2023.1240285] [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: 06/14/2023] [Accepted: 10/05/2023] [Indexed: 11/09/2023] Open
Abstract
Clinical frailty affects ∼10% of people over age 65 and is studied in a chronically inflamed (Interleukin-10 knockout; "IL10-KO") mouse model. Frailty phenotypes overlap the spectrum of diseases ("laminopathies") caused by mutations in LMNA. LMNA encodes nuclear intermediate filament proteins lamin A and lamin C ("lamin A/C"), important for tissue-specific signaling, metabolism and chromatin regulation. We hypothesized that wildtype lamin A/C associations with tissue-specific partners are perturbed by chronic inflammation, potentially contributing to dysfunction in frailty. To test this idea we immunoprecipitated native lamin A/C and associated proteins from skeletal muscle, hearts and brains of old (21-22 months) IL10-KO versus control C57Bl/6 female mice, and labeled with Tandem Mass Tags for identification and quantitation by mass spectrometry. We identified 502 candidate lamin-binding proteins from skeletal muscle, and 340 from heart, including 62 proteins identified in both tissues. Candidates included frailty phenotype-relevant proteins Perm1 and Fam210a, and nuclear membrane protein Tmem38a, required for muscle-specific genome organization. These and most other candidates were unaffected by IL10-KO, but still important as potential lamin A/C-binding proteins in native heart or muscle. A subset of candidates (21 in skeletal muscle, 30 in heart) showed significantly different lamin A/C-association in an IL10-KO tissue (p < 0.05), including AldoA and Gins3 affected in heart, and Lmcd1 and Fabp4 affected in skeletal muscle. To screen for binding, eleven candidates plus prelamin A and emerin controls were arrayed as synthetic 20-mer peptides (7-residue stagger) and incubated with recombinant purified lamin A "tail" residues 385-646 under relatively stringent conditions. We detected strong lamin A binding to peptides solvent exposed in Lmcd1, AldoA, Perm1, and Tmem38a, and plausible binding to Csrp3 (muscle LIM protein). These results validated both proteomes as sources for native lamin A/C-binding proteins in heart and muscle, identified four candidate genes for Emery-Dreifuss muscular dystrophy (CSRP3, LMCD1, ALDOA, and PERM1), support a lamin A-interactive molecular role for Tmem38A, and supported the hypothesis that lamin A/C interactions with at least two partners (AldoA in heart, transcription factor Lmcd1 in muscle) are altered in the IL10-KO model of frailty.
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Affiliation(s)
- Fatima D. Elzamzami
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Arushi Samal
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Adith S. Arun
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Tejas Dharmaraj
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Neeti R. Prasad
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Alex Rendon-Jonguitud
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Lauren DeVine
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Jeremy D. Walston
- Division of Geriatric Medicine and Gerontology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Robert N. Cole
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Katherine L. Wilson
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
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de Las Heras JI, Todorow V, Krečinić-Balić L, Hintze S, Czapiewski R, Webb S, Schoser B, Meinke P, Schirmer EC. Metabolic, fibrotic and splicing pathways are all altered in Emery-Dreifuss muscular dystrophy spectrum patients to differing degrees. Hum Mol Genet 2023; 32:1010-1031. [PMID: 36282542 PMCID: PMC9991002 DOI: 10.1093/hmg/ddac264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/16/2022] [Accepted: 10/20/2022] [Indexed: 11/14/2022] Open
Abstract
Emery-Dreifuss muscular dystrophy (EDMD) is a genetically and clinically variable disorder. Previous attempts to use gene expression changes to find its pathomechanism were unavailing, so we engaged a functional pathway analysis. RNA-Seq was performed on cells from 10 patients diagnosed with an EDMD spectrum disease with different mutations in seven genes. Upon comparing to controls, the pathway analysis revealed that multiple genes involved in fibrosis, metabolism, myogenic signaling and splicing were affected in all patients. Splice variant analysis revealed alterations of muscle-specific variants for several important muscle genes. Deeper analysis of metabolic pathways revealed a reduction in glycolytic and oxidative metabolism and reduced numbers of mitochondria across a larger set of 14 EDMD spectrum patients and 7 controls. Intriguingly, the gene expression signatures segregated the patients into three subgroups whose distinctions could potentially relate to differences in clinical presentation. Finally, differential expression analysis of miRNAs changing in the patients similarly highlighted fibrosis, metabolism and myogenic signaling pathways. This pathway approach revealed a transcriptome profile that can both be used as a template for establishing a biomarker panel for EDMD and direct further investigation into its pathomechanism. Furthermore, the segregation of specific gene changes into distinct groups that appear to correlate with clinical presentation may template development of prognostic biomarkers, though this will first require their testing in a wider set of patients with more clinical information.
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Affiliation(s)
| | - Vanessa Todorow
- Friedrich-Baur-Institute, Department of Neurology, LMU Clinic, Ludwig-Maximillians-University, Munich, Germany
| | - Lejla Krečinić-Balić
- Friedrich-Baur-Institute, Department of Neurology, LMU Clinic, Ludwig-Maximillians-University, Munich, Germany
| | - Stefan Hintze
- Friedrich-Baur-Institute, Department of Neurology, LMU Clinic, Ludwig-Maximillians-University, Munich, Germany
| | - Rafal Czapiewski
- Institute of Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Shaun Webb
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Benedikt Schoser
- Friedrich-Baur-Institute, Department of Neurology, LMU Clinic, Ludwig-Maximillians-University, Munich, Germany
| | - Peter Meinke
- Friedrich-Baur-Institute, Department of Neurology, LMU Clinic, Ludwig-Maximillians-University, Munich, Germany
| | - Eric C Schirmer
- Institute of Cell Biology, University of Edinburgh, Edinburgh, UK
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Todorow V, Hintze S, Schoser B, Meinke P. Nuclear envelope transmembrane proteins involved in genome organization are misregulated in myotonic dystrophy type 1 muscle. Front Cell Dev Biol 2023; 10:1007331. [PMID: 36699009 PMCID: PMC9868253 DOI: 10.3389/fcell.2022.1007331] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 12/27/2022] [Indexed: 01/11/2023] Open
Abstract
Myotonic dystrophy type 1 is a multisystemic disorder with predominant muscle and neurological involvement. Despite a well described pathomechanism, which is primarily a global missplicing due to sequestration of RNA-binding proteins, there are still many unsolved questions. One such question is the disease etiology in the different affected tissues. We observed alterations at the nuclear envelope in primary muscle cell cultures before. This led us to reanalyze a published RNA-sequencing dataset of DM1 and control muscle biopsies regarding the misregulation of NE proteins. We could identify several muscle NE protein encoding genes to be misregulated depending on the severity of the muscle phenotype. Among these misregulated genes were NE transmembrane proteins (NETs) involved in nuclear-cytoskeletal coupling as well as genome organization. For selected genes, we could confirm that observed gene-misregulation led to protein expression changes. Furthermore, we investigated if genes known to be under expression-regulation by genome organization NETs were also misregulated in DM1 biopsies, which revealed that misregulation of two NETs alone is likely responsible for differential expression of about 10% of all genes being differentially expressed in DM1. Notably, the majority of NETs identified here to be misregulated in DM1 muscle are mutated in Emery-Dreifuss muscular dystrophy or clinical similar muscular dystrophies, suggesting a broader similarity on the molecular level for muscular dystrophies than anticipated. This shows not only the importance of muscle NETs in muscle health and disease, but also highlights the importance of the NE in DM1 disease progression.
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Schirmer EC, Latonen L, Tollis S. Nuclear size rectification: A potential new therapeutic approach to reduce metastasis in cancer. Front Cell Dev Biol 2022; 10:1022723. [PMID: 36299481 PMCID: PMC9589484 DOI: 10.3389/fcell.2022.1022723] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 09/12/2022] [Indexed: 03/07/2024] Open
Abstract
Research on metastasis has recently regained considerable interest with the hope that single cell technologies might reveal the most critical changes that support tumor spread. However, it is possible that part of the answer has been visible through the microscope for close to 200 years. Changes in nuclear size characteristically occur in many cancer types when the cells metastasize. This was initially discarded as contributing to the metastatic spread because, depending on tumor types, both increases and decreases in nuclear size could correlate with increased metastasis. However, recent work on nuclear mechanics and the connectivity between chromatin, the nucleoskeleton, and the cytoskeleton indicate that changes in this connectivity can have profound impacts on cell mobility and invasiveness. Critically, a recent study found that reversing tumor type-dependent nuclear size changes correlated with reduced cell migration and invasion. Accordingly, it seems appropriate to now revisit possible contributory roles of nuclear size changes to metastasis.
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Affiliation(s)
- Eric C. Schirmer
- Institute of Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Leena Latonen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
- Foundation for the Finnish Cancer Institute, Helsinki, Finland
| | - Sylvain Tollis
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
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PfARID Regulates P. falciparum Malaria Parasite Male Gametogenesis and Female Fertility and Is Critical for Parasite Transmission to the Mosquito Vector. mBio 2022; 13:e0057822. [PMID: 35638735 PMCID: PMC9239086 DOI: 10.1128/mbio.00578-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sexual reproduction of Plasmodium falciparum parasites is critical to the spread of malaria in the human population. The factors that regulate gene expression underlying formation of fertilization-competent gametes, however, remain unknown. Here, we report that P. falciparum expresses a protein with an AT-rich interaction domain (ARID) which, in other organisms, is part of chromatin remodeling complexes. P. falciparum ARID (PfARID) localized to the parasite nucleus and is critical for the formation of male gametes and fertility of female gametes. PfARID gene deletion (Pfarid–) gametocytes showed downregulation of gene expression important for gametogenesis, antigenic variation, and cell signaling and for parasite development in the mosquito. Our study identifies PfARID as a critical nuclear protein involved in regulating the gene expression landscape of mature gametocytes. This establishes fertility and also prepares the parasite for postfertilization events that are essential for infection of the mosquito vector.
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To be or not be (in the LAD): emerging roles of lamin proteins in transcriptional regulation. Biochem Soc Trans 2022; 50:1035-1044. [PMID: 35437578 PMCID: PMC9162450 DOI: 10.1042/bst20210858] [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: 11/26/2021] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 12/21/2022]
Abstract
Lamins are components of the nuclear lamina, a protein meshwork that underlies the nuclear membrane. Lamins interact with chromatin in transcriptionally silent regions defined as lamina-associated-domains (LADs). However, recent studies have shown that lamins regulate active transcription inside LADs. In addition, ChIP-seq analysis has shown that lamins interact with lamin-dependent promoters and enhancers located in the interior of the nucleus. Moreover, functional studies suggest that lamins regulate transcription at associated-promoters and long-range chromatin interactions of key developmental gene programs. This review will discuss emerging, non-canonical functions of lamins in controlling non-silent genes located both inside and outside of LADs, focusing on transcriptional regulation and chromatin organization in Drosophila and mammals as metazoan model organisms.
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Qian N, Li S, Tan X. The curious case of TMEM120A: Mechanosensor, fat regulator, or antiviral defender? Bioessays 2022; 44:e2200045. [PMID: 35419854 DOI: 10.1002/bies.202200045] [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: 02/21/2022] [Revised: 03/17/2022] [Accepted: 03/23/2022] [Indexed: 11/06/2022]
Abstract
Mechanical pain sensing, adipogenesis, and STING-dependent innate immunity seem three distinct biological processes without substantial relationships. Intriguingly, TMEM120A, a transmembrane protein, has been shown to detect mechanical pain stimuli as a mechanosensitive channel, contribute to adipocyte differentiation/function by regulating genome organization and promote STING trafficking to active cellular innate immune response. However, the role of TMEM120A as a mechanosensitive channel was challenged by recent studies which cannot reproduce data supporting its role in mechanosensing. Furthermore, the molecular mechanism by which TMEM120A contributes to adipocyte differentiation/function and promotes STING trafficking remains elusive. In this review, we discuss these multiple proposed functions of TMEM120A and hypothesize the molecular mechanism underlying TMEM120A's role in fatty acid metabolism and STING signaling.
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Affiliation(s)
- Nianchao Qian
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Shuo Li
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Xu Tan
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China.,Tsinghua-Peking Center for Life Sciences, Beijing, China.,Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
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Czapiewski R, Batrakou DG, de Las Heras JI, Carter RN, Sivakumar A, Sliwinska M, Dixon CR, Webb S, Lattanzi G, Morton NM, Schirmer EC. Genomic loci mispositioning in Tmem120a knockout mice yields latent lipodystrophy. Nat Commun 2022; 13:321. [PMID: 35027552 PMCID: PMC8758788 DOI: 10.1038/s41467-021-27869-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 12/19/2021] [Indexed: 12/13/2022] Open
Abstract
Little is known about how the observed fat-specific pattern of 3D-spatial genome organisation is established. Here we report that adipocyte-specific knockout of the gene encoding nuclear envelope transmembrane protein Tmem120a disrupts fat genome organisation, thus causing a lipodystrophy syndrome. Tmem120a deficiency broadly suppresses lipid metabolism pathway gene expression and induces myogenic gene expression by repositioning genes, enhancers and miRNA-encoding loci between the nuclear periphery and interior. Tmem120a-/- mice, particularly females, exhibit a lipodystrophy syndrome similar to human familial partial lipodystrophy FPLD2, with profound insulin resistance and metabolic defects that manifest upon exposure to an obesogenic diet. Interestingly, similar genome organisation defects occurred in cells from FPLD2 patients that harbour nuclear envelope protein encoding LMNA mutations. Our data indicate TMEM120A genome organisation functions affect many adipose functions and its loss may yield adiposity spectrum disorders, including a miRNA-based mechanism that could explain muscle hypertrophy in human lipodystrophy.
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Affiliation(s)
- Rafal Czapiewski
- Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Dzmitry G Batrakou
- Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | | | - Roderick N Carter
- Molecular Metabolism Group, University/BHF Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, EH16 4TJ, UK
| | | | | | - Charles R Dixon
- Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Shaun Webb
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Giovanna Lattanzi
- CNR - National Research Council of Italy, Institute of Molecular Genetics "Luigi Luca Cavalli-Sforza", Unit of Bologna, Bologna, 40136, Italy
- IRCCS, Istituto Ortopedico Rizzoli, Bologna, 40136, Italy
| | - Nicholas M Morton
- Molecular Metabolism Group, University/BHF Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, EH16 4TJ, UK
| | - Eric C Schirmer
- Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK.
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Bridger JM, Pereira RT, Pina C, Tosi S, Lewis A. Alterations to Genome Organisation in Stem Cells, Their Differentiation and Associated Diseases. Results Probl Cell Differ 2022; 70:71-102. [PMID: 36348105 DOI: 10.1007/978-3-031-06573-6_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The organisation of the genome in its home, the cell nucleus, is reliant on a number of different aspects to establish, maintain and alter its functional non-random positioning. The genome is dispersed throughout a cell nucleus in specific chromosome territories which are further divided into topologically associated domains (TADs), where regions of the genome from different and the same chromosomes come together. This organisation is both controlled by DNA and chromatin epigenetic modification and the association of the genome with nuclear structures such as the nuclear lamina, the nucleolus and nuclear bodies and speckles. Indeed, sequences that are associated with the first two structures mentioned are termed lamina-associated domains (LADs) and nucleolar-associated domains (NADs), respectively. The modifications and nuclear structures that regulate genome function are altered through a cell's life from stem cell to differentiated cell through to reversible quiescence and irreversible senescence, and hence impacting on genome organisation, altering it to silence specific genes and permit others to be expressed in a controlled way in different cell types and cell cycle statuses. The structures and enzymes and thus the organisation of the genome can also be deleteriously affected, leading to disease and/or premature ageing.
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Affiliation(s)
- Joanna M Bridger
- Division of Biosciences, Department of Life Sciences, Centre for Genome Engineering and Maintenance (cenGEM), College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UK.
| | - Rita Torres Pereira
- Division of Biosciences, Department of Life Sciences, Centre for Genome Engineering and Maintenance (cenGEM), College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UK
| | - Cristina Pina
- Division of Biosciences, Department of Life Sciences, Centre for Genome Engineering and Maintenance (cenGEM), College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UK
| | - Sabrina Tosi
- Division of Biosciences, Department of Life Sciences, Centre for Genome Engineering and Maintenance (cenGEM), College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UK
| | - Annabelle Lewis
- Division of Biosciences, Department of Life Sciences, Centre for Genome Engineering and Maintenance (cenGEM), College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UK
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Padilla-Mejia NE, Makarov AA, Barlow LD, Butterfield ER, Field MC. Evolution and diversification of the nuclear envelope. Nucleus 2021; 12:21-41. [PMID: 33435791 PMCID: PMC7889174 DOI: 10.1080/19491034.2021.1874135] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/08/2020] [Accepted: 12/11/2020] [Indexed: 02/06/2023] Open
Abstract
Eukaryotic cells arose ~1.5 billion years ago, with the endomembrane system a central feature, facilitating evolution of intracellular compartments. Endomembranes include the nuclear envelope (NE) dividing the cytoplasm and nucleoplasm. The NE possesses universal features: a double lipid bilayer membrane, nuclear pore complexes (NPCs), and continuity with the endoplasmic reticulum, indicating common evolutionary origin. However, levels of specialization between lineages remains unclear, despite distinct mechanisms underpinning various nuclear activities. Several distinct modes of molecular evolution facilitate organellar diversification and to understand which apply to the NE, we exploited proteomic datasets of purified nuclear envelopes from model systems for comparative analysis. We find enrichment of core nuclear functions amongst the widely conserved proteins to be less numerous than lineage-specific cohorts, but enriched in core nuclear functions. This, together with consideration of additional evidence, suggests that, despite a common origin, the NE has evolved as a highly diverse organelle with significant lineage-specific functionality.
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Affiliation(s)
- Norma E. Padilla-Mejia
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - Alexandr A. Makarov
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - Lael D. Barlow
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - Erin R. Butterfield
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - Mark C. Field
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České, Czech Republic
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Seelbinder B, Ghosh S, Schneider SE, Scott AK, Berman AG, Goergen CJ, Margulies KB, Bedi K, Casas E, Swearingen AR, Brumbaugh J, Calve S, Neu CP. Nuclear deformation guides chromatin reorganization in cardiac development and disease. Nat Biomed Eng 2021; 5:1500-1516. [PMID: 34857921 PMCID: PMC9300284 DOI: 10.1038/s41551-021-00823-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 10/20/2021] [Indexed: 01/31/2023]
Abstract
In cardiovascular tissues, changes in the mechanical properties of the extracellular matrix are associated with cellular de-differentiation and with subsequent functional declines. However, the underlying mechanoreceptive mechanisms are largely unclear. Here, by generating high-resolution, full-field strain maps of cardiomyocyte nuclei during contraction in vitro, complemented with evidence from tissues from patients with cardiomyopathy and from mice with reduced cardiac performance, we show that cardiomyocytes establish a distinct nuclear organization during maturation, characterized by the reorganization of H3K9me3-marked chromatin towards the nuclear border. Specifically, we show that intranuclear tension is spatially correlated with H3K9me3-marked chromatin, that reductions in nuclear deformation (through environmental stiffening or through the disruption of complexes of the linker of nucleoskeleton and cytoskeleton) abrogate chromatin reorganization and lead to the dissociation of H3K9me3-marked chromatin from the nuclear periphery, and that the suppression of H3K9 methylation induces chromatin reorganization and reduces the expression of cardiac developmental genes. Overall, our findings indicate that, by integrating environmental mechanical cues, the nuclei of cardiomyocytes guide and stabilize the fate of cells through the reorganization of epigenetically marked chromatin.
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Affiliation(s)
- Benjamin Seelbinder
- Department of Mechanical Engineering, University of Colorado Boulder, Boulder (CO)
| | - Soham Ghosh
- Department of Mechanical Engineering, University of Colorado Boulder, Boulder (CO)
| | | | - Adrienne K. Scott
- Department of Mechanical Engineering, University of Colorado Boulder, Boulder (CO)
| | - Alycia G. Berman
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette (IN)
| | - Craig J. Goergen
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette (IN)
| | | | - Kenneth Bedi
- Cardiovascular Institute, University of Pennsylvania, Philadelphia (PA)
| | - Eduard Casas
- Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder (CO)
| | - Alison R. Swearingen
- Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder (CO)
| | - Justin Brumbaugh
- Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder (CO)
| | - Sarah Calve
- Department of Mechanical Engineering, University of Colorado Boulder, Boulder (CO),Weldon School of Biomedical Engineering, Purdue University, West Lafayette (IN)
| | - Corey P. Neu
- Department of Mechanical Engineering, University of Colorado Boulder, Boulder (CO),Corresponding Author
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14
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Vogel P, Read RW, Hansen GM, Powell DR. Histopathology is required to identify and characterize myopathies in high-throughput phenotype screening of genetically engineered mice. Vet Pathol 2021; 58:1158-1171. [PMID: 34269122 DOI: 10.1177/03009858211030541] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The development of mouse models that replicate the genetic and pathological features of human disease is important in preclinical research because these types of models enable the completion of meaningful pharmacokinetic, safety, and efficacy studies. Numerous relevant mouse models of human disease have been discovered in high-throughput screening programs, but there are important specific phenotypes revealed by histopathology that are not reliably detected by any other physiological or behavioral screening tests. As part of comprehensive phenotypic analyses of over 4000 knockout (KO) mice, histopathology identified 12 lines of KO mice with lesions indicative of an autosomal recessive myopathy. This report includes a brief summary of histological and other findings in these 12 lines. Notably, the inverted screen test detected muscle weakness in only 4 of these 12 lines (Scyl1, Plpp7, Chkb, and Asnsd1), all 4 of which have been previously recognized and published. In contrast, 6 of 8 KO lines showing negative or inconclusive findings on the inverted screen test (Plppr2, Pnpla7, Tenm1, Srpk3, Sidt2, Yif1b, Mrs2, and Pnpla2) had not been previously identified as having myopathies. These findings support the need to include histopathology in phenotype screening protocols in order to identify novel genetic myopathies that are not clinically evident or not detected by the inverted screen test.
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Affiliation(s)
- Peter Vogel
- 5417St Jude Children's Research Hospital, Memphis, TN, USA
| | - Robert W Read
- 57636Lexicon Pharmaceuticals Inc, The Woodlands, TX, USA
| | | | - David R Powell
- 57636Lexicon Pharmaceuticals Inc, The Woodlands, TX, USA
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15
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Pawar S, Kutay U. The Diverse Cellular Functions of Inner Nuclear Membrane Proteins. Cold Spring Harb Perspect Biol 2021; 13:a040477. [PMID: 33753404 PMCID: PMC8411953 DOI: 10.1101/cshperspect.a040477] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The nuclear compartment is delimited by a specialized expanded sheet of the endoplasmic reticulum (ER) known as the nuclear envelope (NE). Compared to the outer nuclear membrane and the contiguous peripheral ER, the inner nuclear membrane (INM) houses a unique set of transmembrane proteins that serve a staggering range of functions. Many of these functions reflect the exceptional position of INM proteins at the membrane-chromatin interface. Recent research revealed that numerous INM proteins perform crucial roles in chromatin organization, regulation of gene expression, genome stability, and mediation of signaling pathways into the nucleus. Other INM proteins establish mechanical links between chromatin and the cytoskeleton, help NE remodeling, or contribute to the surveillance of NE integrity and homeostasis. As INM proteins continue to gain prominence, we review these advancements and give an overview on the functional versatility of the INM proteome.
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Affiliation(s)
- Sumit Pawar
- Institute of Biochemistry, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Ulrike Kutay
- Institute of Biochemistry, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
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16
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Record J, Saeed MB, Venit T, Percipalle P, Westerberg LS. Journey to the Center of the Cell: Cytoplasmic and Nuclear Actin in Immune Cell Functions. Front Cell Dev Biol 2021; 9:682294. [PMID: 34422807 PMCID: PMC8375500 DOI: 10.3389/fcell.2021.682294] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 07/06/2021] [Indexed: 12/12/2022] Open
Abstract
Actin cytoskeletal dynamics drive cellular shape changes, linking numerous cell functions to physiological and pathological cues. Mutations in actin regulators that are differentially expressed or enriched in immune cells cause severe human diseases known as primary immunodeficiencies underscoring the importance of efficienct actin remodeling in immune cell homeostasis. Here we discuss recent findings on how immune cells sense the mechanical properties of their environement. Moreover, while the organization and biochemical regulation of cytoplasmic actin have been extensively studied, nuclear actin reorganization is a rapidly emerging field that has only begun to be explored in immune cells. Based on the critical and multifaceted contributions of cytoplasmic actin in immune cell functionality, nuclear actin regulation is anticipated to have a large impact on our understanding of immune cell development and functionality.
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Affiliation(s)
- Julien Record
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Mezida B. Saeed
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Tomas Venit
- Science Division, Biology Program, New York University Abu Dhabi (NYUAD), Abu Dhabi, United Arab Emirates
| | - Piergiorgio Percipalle
- Science Division, Biology Program, New York University Abu Dhabi (NYUAD), Abu Dhabi, United Arab Emirates
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Lisa S. Westerberg
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
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17
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Biferali B, Bianconi V, Perez DF, Kronawitter SP, Marullo F, Maggio R, Santini T, Polverino F, Biagioni S, Summa V, Toniatti C, Pasini D, Stricker S, Di Fabio R, Chiacchiera F, Peruzzi G, Mozzetta C. Prdm16-mediated H3K9 methylation controls fibro-adipogenic progenitors identity during skeletal muscle repair. SCIENCE ADVANCES 2021; 7:7/23/eabd9371. [PMID: 34078594 PMCID: PMC8172132 DOI: 10.1126/sciadv.abd9371] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 04/06/2021] [Indexed: 05/15/2023]
Abstract
H3K9 methylation maintains cell identity orchestrating stable silencing and anchoring of alternate fate genes within the heterochromatic compartment underneath the nuclear lamina (NL). However, how cell type-specific genomic regions are specifically targeted to the NL is still elusive. Using fibro-adipogenic progenitors (FAPs) as a model, we identified Prdm16 as a nuclear envelope protein that anchors H3K9-methylated chromatin in a cell-specific manner. We show that Prdm16 mediates FAP developmental capacities by orchestrating lamina-associated domain organization and heterochromatin sequestration at the nuclear periphery. We found that Prdm16 localizes at the NL where it cooperates with the H3K9 methyltransferases G9a/GLP to mediate tethering and silencing of myogenic genes, thus repressing an alternative myogenic fate in FAPs. Genetic and pharmacological disruption of this repressive pathway confers to FAP myogenic competence, preventing fibro-adipogenic degeneration of dystrophic muscles. In summary, we reveal a druggable mechanism of heterochromatin perinuclear sequestration exploitable to reprogram FAPs in vivo.
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Affiliation(s)
- Beatrice Biferali
- Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR) of Italy c/o Department of Biology and Biotechnology "C. Darwin," Sapienza University, 00185 Rome, Italy
- Department of Biology and Biotechnology "C. Darwin," Sapienza University, 00185 Rome, Italy
| | - Valeria Bianconi
- Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR) of Italy c/o Department of Biology and Biotechnology "C. Darwin," Sapienza University, 00185 Rome, Italy
- Department of Biology and Biotechnology "C. Darwin," Sapienza University, 00185 Rome, Italy
| | - Daniel Fernandez Perez
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | | | - Fabrizia Marullo
- Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR) of Italy c/o Department of Biology and Biotechnology "C. Darwin," Sapienza University, 00185 Rome, Italy
- Department of Biology and Biotechnology "C. Darwin," Sapienza University, 00185 Rome, Italy
| | - Roberta Maggio
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Tiziana Santini
- Department of Biology and Biotechnology "C. Darwin," Sapienza University, 00185 Rome, Italy
- Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy
| | - Federica Polverino
- Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR) of Italy c/o Department of Biology and Biotechnology "C. Darwin," Sapienza University, 00185 Rome, Italy
| | - Stefano Biagioni
- Department of Biology and Biotechnology "C. Darwin," Sapienza University, 00185 Rome, Italy
| | - Vincenzo Summa
- IRBM Science Park, Via Pontina Km 30.600, 00070 Pomezia, Italy
| | - Carlo Toniatti
- IRBM Science Park, Via Pontina Km 30.600, 00070 Pomezia, Italy
| | - Diego Pasini
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
- Department of Health Sciences, University of Milan, Via A. di Rudini 8, 20142 Milan, Italy
| | - Sigmar Stricker
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
| | - Romano Di Fabio
- IRBM Science Park, Via Pontina Km 30.600, 00070 Pomezia, Italy
- Promidis, Via Olgettina 60, 20132 Milano, Italy
| | - Fulvio Chiacchiera
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Giovanna Peruzzi
- Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy
| | - Chiara Mozzetta
- Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR) of Italy c/o Department of Biology and Biotechnology "C. Darwin," Sapienza University, 00185 Rome, Italy.
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18
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Bitman-Lotan E, Orian A. Nuclear organization and regulation of the differentiated state. Cell Mol Life Sci 2021; 78:3141-3158. [PMID: 33507327 PMCID: PMC8038961 DOI: 10.1007/s00018-020-03731-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 12/01/2020] [Accepted: 12/04/2020] [Indexed: 12/22/2022]
Abstract
Regulation of the differentiated identity requires active and continued supervision. Inability to maintain the differentiated state is a hallmark of aging and aging-related disease. To maintain cellular identity, a network of nuclear regulators is devoted to silencing previous and non-relevant gene programs. This network involves transcription factors, epigenetic regulators, and the localization of silent genes to heterochromatin. Together, identity supervisors mold and maintain the unique nuclear environment of the differentiated cell. This review describes recent discoveries regarding mechanisms and regulators that supervise the differentiated identity and protect from de-differentiation, tumorigenesis, and attenuate forced somatic cell reprograming. The review focuses on mechanisms involved in H3K9me3-decorated heterochromatin and the importance of nuclear lamins in cell identity. We outline how the biophysical properties of these factors are involved in self-compartmentalization of heterochromatin and cell identity. Finally, we discuss the relevance of these regulators to aging and age-related disease.
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Affiliation(s)
- Eliya Bitman-Lotan
- Rappaport Research Institute and Faculty of Medicine, The Rappaport Faculty of Medicine Technion-IIT, Technion Integrative Cancer Center (TICC), Technion-Israel Institute of Technology, Bat-Galim, 3109610, Haifa, Israel
| | - Amir Orian
- Rappaport Research Institute and Faculty of Medicine, The Rappaport Faculty of Medicine Technion-IIT, Technion Integrative Cancer Center (TICC), Technion-Israel Institute of Technology, Bat-Galim, 3109610, Haifa, Israel.
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19
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Brunet A, Destainville N, Collas P. Physical constraints in polymer modeling of chromatin associations with the nuclear periphery at kilobase scale. Nucleus 2021; 12:6-20. [PMID: 33435761 PMCID: PMC7808377 DOI: 10.1080/19491034.2020.1868105] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Interactions of chromatin with the nuclear lamina imposes a radial genome distribution important for nuclear functions. How physical properties of chromatin affect these interactions is unclear. We used polymer simulations to model how physical parameters of chromatin affect its interaction with the lamina. Impact of polymer stiffness is greater than stretching on its configurations at the lamina; these are manifested as trains describing extended interactions, and loops describing desorbed regions . Conferring an attraction potential leads to persistent interaction and adsorption-desorption regimes manifested by fluctuations between trains and loops. These are modulated by polymer stiffness and stretching, with a dominant impact of stiffness on resulting structural configurations. We infer that flexible euchromatin is more prone to stochastic interactions with lamins than rigid heterochromatin characterizing constitutive LADs. Our models provide insights on the physical properties of chromatin as a polymer which affect the dynamics and patterns of interactions with the nuclear lamina.
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Affiliation(s)
- Annaël Brunet
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo , Oslo, Norway
| | - Nicolas Destainville
- Laboratoire De Physique Théorique, IRSAMC, Université De Toulouse (UPS) , CNRS, Toulouse, France
| | - Philippe Collas
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo , Oslo, Norway.,Department of Immunology and Transfusion Medicine, Oslo University Hospital , Oslo, Norway
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20
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Gatticchi L, de Las Heras JI, Sivakumar A, Zuleger N, Roberti R, Schirmer EC. Tm7sf2 Disruption Alters Radial Gene Positioning in Mouse Liver Leading to Metabolic Defects and Diabetes Characteristics. Front Cell Dev Biol 2020; 8:592573. [PMID: 33330474 PMCID: PMC7719783 DOI: 10.3389/fcell.2020.592573] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 10/26/2020] [Indexed: 01/23/2023] Open
Abstract
Tissue-specific patterns of radial genome organization contribute to genome regulation and can be established by nuclear envelope proteins. Studies in this area often use cancer cell lines, and it is unclear how well such systems recapitulate genome organization of primary cells or animal tissues; so, we sought to investigate radial genome organization in primary liver tissue hepatocytes. Here, we have used a NET47/Tm7sf2–/– liver model to show that manipulating one of these nuclear membrane proteins is sufficient to alter tissue-specific gene positioning and expression. Dam-LaminB1 global profiling in primary liver cells shows that nearly all the genes under such positional regulation are related to/important for liver function. Interestingly, Tm7sf2 is a paralog of the HP1-binding nuclear membrane protein LBR that, like Tm7sf2, also has an enzymatic function in sterol reduction. Fmo3 gene/locus radial mislocalization could be rescued with human wild-type, but not TM7SF2 mutants lacking the sterol reductase function. One central pathway affected is the cholesterol synthesis pathway. Within this pathway, both Cyp51 and Msmo1 are under Tm7sf2 positional and expression regulation. Other consequences of the loss of Tm7sf2 included weight gain, insulin sensitivity, and reduced levels of active Akt kinase indicating additional pathways under its regulation, several of which are highlighted by mispositioning genes. This study emphasizes the importance for tissue-specific radial genome organization in tissue function and the value of studying genome organization in animal tissues and primary cells over cell lines.
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Affiliation(s)
- Leonardo Gatticchi
- Department of Experimental Medicine, University of Perugia, Perugia, Italy
| | - Jose I de Las Heras
- Institute of Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Aishwarya Sivakumar
- Institute of Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Nikolaj Zuleger
- Institute of Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Rita Roberti
- Department of Experimental Medicine, University of Perugia, Perugia, Italy
| | - Eric C Schirmer
- Institute of Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
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21
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Burla R, La Torre M, Maccaroni K, Verni F, Giunta S, Saggio I. Interplay of the nuclear envelope with chromatin in physiology and pathology. Nucleus 2020; 11:205-218. [PMID: 32835589 PMCID: PMC7529417 DOI: 10.1080/19491034.2020.1806661] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 07/30/2020] [Accepted: 08/03/2020] [Indexed: 12/21/2022] Open
Abstract
The nuclear envelope compartmentalizes chromatin in eukaryotic cells. The main nuclear envelope components are lamins that associate with a panoply of factors, including the LEM domain proteins. The nuclear envelope of mammalian cells opens up during cell division. It is reassembled and associated with chromatin at the end of mitosis when telomeres tether to the nuclear periphery. Lamins, LEM domain proteins, and DNA binding factors, as BAF, contribute to the reorganization of chromatin. In this context, an emerging role is that of the ESCRT complex, a machinery operating in multiple membrane assembly pathways, including nuclear envelope reformation. Research in this area is unraveling how, mechanistically, ESCRTs link to nuclear envelope associated factors as LEM domain proteins. Importantly, ESCRTs work also during interphase for repairing nuclear envelope ruptures. Altogether the advances in this field are giving new clues for the interpretation of diseases implicating nuclear envelope fragility, as laminopathies and cancer. ABBREVIATIONS na, not analyzed; ko, knockout; kd, knockdown; NE, nuclear envelope; LEM, LAP2-emerin-MAN1 (LEM)-domain containing proteins; LINC, linker of nucleoskeleton and cytoskeleton complexes; Cyt, cytoplasm; Chr, chromatin; MB, midbody; End, endosomes; Tel, telomeres; INM, inner nuclear membrane; NP, nucleoplasm; NPC, Nuclear Pore Complex; ER, Endoplasmic Reticulum; SPB, spindle pole body.
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Affiliation(s)
- Romina Burla
- Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
- CNR Institute of Molecular Biology and Pathology, Italy
| | - Mattia La Torre
- Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
| | - Klizia Maccaroni
- Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
| | - Fiammetta Verni
- Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
| | - Simona Giunta
- Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
- Rockefeller University, New York, NY, USA
| | - Isabella Saggio
- Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
- CNR Institute of Molecular Biology and Pathology, Italy
- Institute of Structural Biology, School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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22
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Gatticchi L, Petricciuolo M, Scarpelli P, Macchioni L, Corazzi L, Roberti R. Tm7sf2 gene promotes adipocyte differentiation of mouse embryonic fibroblasts and improves insulin sensitivity. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1868:118897. [PMID: 33121932 DOI: 10.1016/j.bbamcr.2020.118897] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 10/14/2020] [Accepted: 10/16/2020] [Indexed: 12/13/2022]
Abstract
Adipogenesis is a finely orchestrated program involving a transcriptional cascade coordinated by CEBP and PPAR family members and by hormonally induced signaling pathways. Alterations in any of these factors result into impaired formation of fully differentiated adipocytes. Tm7sf2 gene encodes for a Δ(14)-sterol reductase primarily involved in cholesterol biosynthesis. Furthermore, TM7SF2 modulates the expression of the master gene of adipogenesis PPARγ, suggesting a role in the regulation of adipose tissue homeostasis. We investigated the differentiation of Tm7sf2-/- MEFs into adipocytes, compared to Tm7sf2+/+ MEFs. Tm7sf2 expression was increased at late stage of differentiation in wild type cells, while Tm7sf2-/- MEFs exhibited a reduced capacity to differentiate into mature adipocytes. Indeed, Tm7sf2-/- MEFs had lower neutral lipid accumulation and reduced expression of adipogenic regulators. At early stage, the reduction in C/EBPβ expression impaired mitotic clonal expansion, which is needed by preadipocytes for adipogenesis induction. At late stage, the expression and activity of C/EBPα and PPARγ were inhibited in Tm7sf2-/- cells, leading to the reduced expression of adipocyte genes like Srebp-1c, Fasn, Scd-1, Adipoq, Fabp4, and Glut4. Loss of the acquisition of adipocyte phenotype was accompanied by a reduction in the levels of Irs1, and phosphorylated Akt and ERK1/2, indicating a blunted insulin signaling in differentiating Tm7sf2-/- cells. Moreover, throughout the differentiation process, increased expression of the antiadipogenic Mmp3 was observed in MEFs lacking Tm7sf2. These findings indicate Tm7sf2 as a novel factor influencing adipocyte differentiation that could be relevant to adipose tissue development and maintenance of metabolic health.
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Affiliation(s)
- Leonardo Gatticchi
- Department of Experimental Medicine, Section of Physiology and Biochemistry, University of Perugia, 06132 Perugia, Italy.
| | - Maya Petricciuolo
- Department of Experimental Medicine, Section of Physiology and Biochemistry, University of Perugia, 06132 Perugia, Italy
| | - Paolo Scarpelli
- Department of Experimental Medicine, Section of Physiology and Biochemistry, University of Perugia, 06132 Perugia, Italy
| | - Lara Macchioni
- Department of Experimental Medicine, Section of Physiology and Biochemistry, University of Perugia, 06132 Perugia, Italy.
| | - Lanfranco Corazzi
- Department of Experimental Medicine, Section of Physiology and Biochemistry, University of Perugia, 06132 Perugia, Italy.
| | - Rita Roberti
- Department of Experimental Medicine, Section of Physiology and Biochemistry, University of Perugia, 06132 Perugia, Italy.
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23
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Ghosh S, Seelbinder B, Henderson JT, Watts RD, Scott AK, Veress AI, Neu CP. Deformation Microscopy for Dynamic Intracellular and Intranuclear Mapping of Mechanics with High Spatiotemporal Resolution. Cell Rep 2020; 27:1607-1620.e4. [PMID: 31042484 PMCID: PMC8769958 DOI: 10.1016/j.celrep.2019.04.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 01/10/2019] [Accepted: 04/01/2019] [Indexed: 12/14/2022] Open
Abstract
Structural heterogeneity is a hallmark of living cells that drives local mechanical properties and dynamic cellular responses. However, the robust quantification of intracellular mechanics is lacking from conventional methods. Here, we describe the development of deformation microscopy, which leverages conventional imaging and an automated hyperelastic warping algorithm to investigate strain history, deformation dynamics, and changes in structural heterogeneity within the interior of cells and cell nuclei. Using deformation microscopy, we found that partial or complete disruption of LINC complexes in cardiomyocytes in vitro and lamin A/C deficiency in myocytes in vivo abrogate dominant tensile loading in the nuclear interior. We also found that cells cultured on stiff substrates or in hyperosmotic conditions displayed abnormal strain burden and asymmetries at interchromatin regions, which are associated with active transcription. Deformation microscopy represents a foundational approach toward intracellular elastography, with the potential utility to provide mechanistic and quantitative insights in diverse mechanobiological applications. Ghosh et al. show that deformation microscopy, a technique based on image analysis and mechanics, reveals deformation dynamics and structural heterogeneity changes for several applications and at multiple scales, including tissues, cells, and nuclei. They reveal how the disruption of nuclear proteins and pathological conditions abrogate mechanical strain in the nuclear interior.
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Affiliation(s)
- Soham Ghosh
- Department of Mechanical Engineering, University of Colorado Boulder, Boulder, CO, USA
| | - Benjamin Seelbinder
- Department of Mechanical Engineering, University of Colorado Boulder, Boulder, CO, USA
| | - Jonathan T Henderson
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Ryan D Watts
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Adrienne K Scott
- Department of Mechanical Engineering, University of Colorado Boulder, Boulder, CO, USA
| | - Alexander I Veress
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | - Corey P Neu
- Department of Mechanical Engineering, University of Colorado Boulder, Boulder, CO, USA; Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA.
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24
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Abstract
At the nuclear periphery, associations of chromatin with the nuclear lamina through lamina-associated domains (LADs) aid functional organization of the genome. We review the organization of LADs and provide evidence of LAD heterogeneity from cell ensemble and single-cell data. LADs are typically repressive environments in the genome; nonetheless, we discuss findings of lamin interactions with regulatory elements of active genes, and the role lamins may play in genome regulation. We address the relationship between LADs and other genome organizers, and the involvement of LADs in laminopathies. The current data lay the basis for future studies on the significance of lamin-chromatin interactions in health and disease.
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Affiliation(s)
- Nolwenn Briand
- Department of Molecular Medicine, Faculty of Medicine, University of Oslo, PO Box 1112 Blindern, 0317, Oslo, Norway
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, 0424, Oslo, Norway
| | - Philippe Collas
- Department of Molecular Medicine, Faculty of Medicine, University of Oslo, PO Box 1112 Blindern, 0317, Oslo, Norway.
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, 0424, Oslo, Norway.
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25
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Canat A, Veillet A, Bonnet A, Therizols P. Genome anchoring to nuclear landmarks drives functional compartmentalization of the nuclear space. Brief Funct Genomics 2020; 19:101-110. [DOI: 10.1093/bfgp/elz034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 11/04/2019] [Accepted: 11/05/2019] [Indexed: 01/18/2023] Open
Abstract
Abstract
The spatial organization of the genome contributes to essential functions such as transcription and chromosome integrity maintenance. The principles governing nuclear compartmentalization have been the focus of considerable research over the last decade. In these studies, the genome–nuclear structure interactions emerged as a main driver of this particular 3D genome organization. In this review, we describe the interactions between the genome and four major landmarks of the nucleus: the nuclear lamina, the nuclear pores, the pericentromeric heterochromatin and the nucleolus. We present the recent studies that identify sequences bound to these different locations and address the tethering mechanisms. We give an overview of the relevance of this organization in development and disease. Finally, we discuss the dynamic aspects and self-organizing properties that allow this complex architecture to be inherited.
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Affiliation(s)
- Antoine Canat
- Université de Paris, Laboratoire Génomes, Biologie Cellulaire et Thérapeutiques, CNRS UMR7212, INSERM U944, Institut de Recherche St Louis, F-75010 Paris, France
| | - Adeline Veillet
- Université de Paris, Laboratoire Génomes, Biologie Cellulaire et Thérapeutiques, CNRS UMR7212, INSERM U944, Institut de Recherche St Louis, F-75010 Paris, France
| | - Amandine Bonnet
- Université de Paris, Laboratoire Génomes, Biologie Cellulaire et Thérapeutiques, CNRS UMR7212, INSERM U944, Institut de Recherche St Louis, F-75010 Paris, France
| | - Pierre Therizols
- Université de Paris, Laboratoire Génomes, Biologie Cellulaire et Thérapeutiques, CNRS UMR7212, INSERM U944, Institut de Recherche St Louis, F-75010 Paris, France
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Feodorova Y, Falk M, Mirny LA, Solovei I. Viewing Nuclear Architecture through the Eyes of Nocturnal Mammals. Trends Cell Biol 2020; 30:276-289. [PMID: 31980345 DOI: 10.1016/j.tcb.2019.12.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 12/10/2019] [Accepted: 12/19/2019] [Indexed: 01/09/2023]
Abstract
The cell nucleus is a remarkably well-organized organelle with membraneless but distinct compartments of various functions. The largest of them, euchromatin and heterochromatin, are spatially segregated in such a way that the transcriptionally active genome occupies the nuclear interior, whereas silent genomic loci are preferentially associated with the nuclear envelope. This rule is broken by rod photoreceptor cells of nocturnal mammals, in which the two major compartments have inverted positions. The inversion and dense compaction of heterochromatin converts these nuclei into microlenses that focus light and facilitate nocturnal vision. As is often the case in biology, when a mutation helps to understand normal processes and structures, inverted nuclei have served as a tool to unravel general principles of nuclear organization, including mechanisms of heterochromatin tethering to the nuclear envelope, autonomous behavior of small genomic segments, and euchromatin-heterochromatin segregation.
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Affiliation(s)
- Yana Feodorova
- Biozentrum, Ludwig-Maximilians University Munich, Grosshadernerstrasse 2, 82152 Planegg-Martinsried, Germany; Department of Medical Biology, Medical University-Plovdiv, Boulevard Vasil Aprilov 15A, Plovdiv 4000, Bulgaria
| | - Martin Falk
- Institute for Medical Engineering and Science, and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Physics, University of Chicago, 929 E 57th St, Chicago, IL 60637, USA
| | - Leonid A Mirny
- Institute for Medical Engineering and Science, and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Irina Solovei
- Biozentrum, Ludwig-Maximilians University Munich, Grosshadernerstrasse 2, 82152 Planegg-Martinsried, Germany.
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Meinke P, Kerr ARW, Czapiewski R, de Las Heras JI, Dixon CR, Harris E, Kölbel H, Muntoni F, Schara U, Straub V, Schoser B, Wehnert M, Schirmer EC. A multistage sequencing strategy pinpoints novel candidate alleles for Emery-Dreifuss muscular dystrophy and supports gene misregulation as its pathomechanism. EBioMedicine 2019; 51:102587. [PMID: 31862442 PMCID: PMC7000448 DOI: 10.1016/j.ebiom.2019.11.048] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/18/2019] [Accepted: 11/26/2019] [Indexed: 12/27/2022] Open
Abstract
Background As genome-wide approaches prove difficult with genetically heterogeneous orphan diseases, we developed a new approach to identify candidate genes. We applied this to Emery-Dreifuss muscular dystrophy (EDMD), characterised by early onset contractures, slowly progressive muscular wasting, and life-threatening heart conduction disturbances with wide intra- and inter-familial clinical variability. Roughly half of EDMD patients are linked to six genes encoding nuclear envelope proteins, but the disease mechanism remains unclear because the affected proteins function in both cell mechanics and genome regulation. Methods A primer library was generated to test for mutations in 301 genes from four categories: (I) all known EDMD-linked genes; (II) genes mutated in related muscular dystrophies; (III) candidates generated by exome sequencing in five families; (IV) functional candidates — other muscle nuclear envelope proteins functioning in mechanical/genome processes affected in EDMD. This was used to sequence 56 unlinked patients with EDMD-like phenotype. Findings Twenty-one patients could be clearly assigned: 18 with mutations in genes of similar muscular dystrophies; 3 with previously missed mutations in EDMD-linked genes. The other categories yielded novel candidate genes, most encoding nuclear envelope proteins with functions in gene regulation. Interpretation Our multi-pronged approach identified new disease alleles and many new candidate EDMD genes. Their known functions strongly argue the EDMD pathomechanism is from altered gene regulation and mechanotransduction due to connectivity of candidates from the nuclear envelope to the plasma membrane. This approach highlights the value of testing for related diseases using primer libraries and may be applied for other genetically heterogeneous orphan diseases. Funding The Wellcome Trust, Muscular Dystrophy UK, Medical Research Council, European Community's Seventh Framework Programme “Integrated European –omics research project for diagnosis and therapy in rare neuromuscular and neurodegenerative diseases (NEUROMICS)”.
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Affiliation(s)
- Peter Meinke
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK; Friedrich Baur Institute at the Department of Neurology, University Hospital, LMU Munich, Germany
| | - Alastair R W Kerr
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Rafal Czapiewski
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | | | - Charles R Dixon
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Elizabeth Harris
- John Walton Muscular Dystrophy Research Centre, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Heike Kölbel
- Department of Pediatric Neurology, Developmental Neurology and Social Pediatrics, University of Essen, Germany
| | - Francesco Muntoni
- Dubowitz Neuromuscular Centre, University College London Great Ormond Street Institute of Child Health, London, UK; 1 NIHR Great Ormond Street Hospital Biomedical Research Centre, Great Ormond Street Institute of Child Health, University College London, & Great Ormond Street Hospital Trust, London, UK
| | - Ulrike Schara
- Department of Pediatric Neurology, Developmental Neurology and Social Pediatrics, University of Essen, Germany
| | - Volker Straub
- John Walton Muscular Dystrophy Research Centre, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Benedikt Schoser
- Friedrich Baur Institute at the Department of Neurology, University Hospital, LMU Munich, Germany
| | - Manfred Wehnert
- Institute of Human Genetics, University of Greifswald (retired), Greifswald, Germany
| | - Eric C Schirmer
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK.
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28
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Bergqvist C, Niss F, Figueroa RA, Beckman M, Maksel D, Jafferali MH, Kulyté A, Ström AL, Hallberg E. Monitoring of chromatin organization in live cells by FRIC. Effects of the inner nuclear membrane protein Samp1. Nucleic Acids Res 2019; 47:e49. [PMID: 30793190 PMCID: PMC6511872 DOI: 10.1093/nar/gkz123] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 01/17/2019] [Accepted: 02/19/2019] [Indexed: 12/24/2022] Open
Abstract
In most cells, transcriptionally inactive heterochromatin is preferentially localized in the nuclear periphery and transcriptionally active euchromatin is localized in the nuclear interior. Different cell types display characteristic chromatin distribution patterns, which change dramatically during cell differentiation, proliferation, senescence and different pathological conditions. Chromatin organization has been extensively studied on a cell population level, but there is a need to understand dynamic reorganization of chromatin at the single cell level, especially in live cells. We have developed a novel image analysis tool that we term Fluorescence Ratiometric Imaging of Chromatin (FRIC) to quantitatively monitor dynamic spatiotemporal distribution of euchromatin and total chromatin in live cells. A vector (pTandemH) assures stoichiometrically constant expression of the histone variants Histone 3.3 and Histone 2B, fused to EGFP and mCherry, respectively. Quantitative ratiometric (H3.3/H2B) imaging displayed a concentrated distribution of heterochromatin in the periphery of U2OS cell nuclei. As proof of concept, peripheral heterochromatin responded to experimental manipulation of histone acetylation. We also found that peripheral heterochromatin depended on the levels of the inner nuclear membrane protein Samp1, suggesting an important role in promoting peripheral heterochromatin. Taken together, FRIC is a powerful and robust new tool to study dynamic chromatin redistribution in live cells.
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Affiliation(s)
- Cecilia Bergqvist
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16B, SE-106 91 Stockholm, Sweden
| | - Frida Niss
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16B, SE-106 91 Stockholm, Sweden
| | - Ricardo A Figueroa
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16B, SE-106 91 Stockholm, Sweden
| | - Marie Beckman
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16B, SE-106 91 Stockholm, Sweden.,Institute of Environmental Medicine, Karolinska Institutet SE-171 77 Sweden
| | - Danuta Maksel
- Monash Molecular Crystallisation Facility (MMCF), Monash University, VIC 3800, Australia
| | - Mohammed H Jafferali
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16B, SE-106 91 Stockholm, Sweden
| | - Agné Kulyté
- Lipid laboratory, Department of Medicine, Karolinska Institutet, SE-141 57 Huddinge, Sweden
| | - Anna-Lena Ström
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16B, SE-106 91 Stockholm, Sweden
| | - Einar Hallberg
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16B, SE-106 91 Stockholm, Sweden
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29
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Meaburn KJ, Misteli T. Assessment of the Utility of Gene Positioning Biomarkers in the Stratification of Prostate Cancers. Front Genet 2019; 10:1029. [PMID: 31681438 PMCID: PMC6812139 DOI: 10.3389/fgene.2019.01029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 09/25/2019] [Indexed: 12/24/2022] Open
Abstract
There is a pressing need for additional clinical biomarkers to predict the aggressiveness of individual cancers. Here, we examine the potential usefulness of spatial genome organization as a prognostic tool for prostate cancer. Using fluorescence in situ hybridization on formalin-fixed, paraffin embedded human prostate tissue specimens, we compared the nuclear positions of four genes between clinically relevant subgroups of prostate tissues. We find that directional repositioning of SP100 and TGFB3 gene loci stratifies prostate cancers of differing Gleason scores. A more peripheral position of SP100 and TGFB3 in the nucleus, compared to benign tissues, is associated with low Gleason score cancers, whereas more internal positioning correlates with higher Gleason scores. Conversely, LMNA is more internally positioned in many non-metastatic prostate cancers, while its position is indistinguishable from benign tissue in metastatic cancer. The false positive rates were relatively low, whereas, the false negative rates of single or combinations of genes were high, limiting the clinical utility of this assay in its current form. Nevertheless, our findings of subtype-specific gene positioning patterns in prostate cancer provides proof-of-concept for the potential usefulness of spatial gene positioning for prognostic applications, and encourage further exploration of spatial gene positioning patterns to identify novel clinically relevant molecular biomarkers, which may aid treatment decisions for cancer patients.
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Affiliation(s)
- Karen J Meaburn
- Cell Biology of Genomes Group, National Cancer Institute, NIH, Bethesda, MD, United States
| | - Tom Misteli
- Cell Biology of Genomes Group, National Cancer Institute, NIH, Bethesda, MD, United States
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30
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Collas P, Liyakat Ali TM, Brunet A, Germier T. Finding Friends in the Crowd: Three-Dimensional Cliques of Topological Genomic Domains. Front Genet 2019; 10:602. [PMID: 31275364 PMCID: PMC6593077 DOI: 10.3389/fgene.2019.00602] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 06/05/2019] [Indexed: 12/31/2022] Open
Abstract
The mammalian genome is intricately folded in a three-dimensional topology believed to be important for the orchestration of gene expression regulating development, differentiation and tissue homeostasis. Important features of spatial genome conformation in the nucleus are promoter-enhancer contacts regulating gene expression within topologically-associated domains (TADs), short- and long-range interactions between TADs and associations of chromatin with nucleoli and nuclear speckles. In addition, anchoring of chromosomes to the nuclear lamina via lamina-associated domains (LADs) at the nuclear periphery is a key regulator of the radial distribution of chromatin. To what extent TADs and LADs act in concert as genomic organizers to shape the three-dimensional topology of chromatin has long remained unknown. A new study addressing this key question provides evidence of (i) preferred long-range associations between TADs forming TAD “cliques” which organize large heterochromatin domains, and (ii) stabilization of TAD cliques by LADs at the nuclear periphery after induction of terminal differentiation. Here, we review these findings, address the issue of whether TAD cliques exist in single cells and discuss the extent of cell-to-cell heterogeneity in higher-order chromatin conformation. The recent observations provide a first appreciation of changes in 4-dimensional higher-order genome topologies during differentiation.
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Affiliation(s)
- Philippe Collas
- Department of Molecular Medicine, Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.,Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway
| | - Tharvesh M Liyakat Ali
- Department of Molecular Medicine, Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Annaël Brunet
- Department of Molecular Medicine, Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Thomas Germier
- Department of Molecular Medicine, Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
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31
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Alvarado-Kristensson M, Rosselló CA. The Biology of the Nuclear Envelope and Its Implications in Cancer Biology. Int J Mol Sci 2019; 20:E2586. [PMID: 31137762 PMCID: PMC6566445 DOI: 10.3390/ijms20102586] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Revised: 05/07/2019] [Accepted: 05/25/2019] [Indexed: 12/18/2022] Open
Abstract
The formation of the nuclear envelope and the subsequent compartmentalization of the genome is a defining feature of eukaryotes. Traditionally, the nuclear envelope was purely viewed as a physical barrier to preserve genetic material in eukaryotic cells. However, in the last few decades, it has been revealed to be a critical cellular component in controlling gene expression and has been implicated in several human diseases. In cancer, the relevance of the cell nucleus was first reported in the mid-1800s when an altered nuclear morphology was observed in tumor cells. This review aims to give a current and comprehensive view of the role of the nuclear envelope on cancer first by recapitulating the changes of the nuclear envelope during cell division, second, by reviewing the role of the nuclear envelope in cell cycle regulation, signaling, and the regulation of the genome, and finally, by addressing the nuclear envelope link to cell migration and metastasis and its use in cancer prognosis.
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Affiliation(s)
- Maria Alvarado-Kristensson
- Molecular Pathology, Department of Translational Medicine, Lund University, Skåne University Hospital, 20502 Malmö, Sweden.
| | - Catalina Ana Rosselló
- Laboratory of Molecular Cell Biomedicine, University of the Balearic Islands, 07121 Palma de Mallorca, Spain.
- Lipopharma Therapeutics, Isaac Newton, 07121 Palma de Mallorca, Spain.
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32
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Guerreiro I, Kind J. Spatial chromatin organization and gene regulation at the nuclear lamina. Curr Opin Genet Dev 2019; 55:19-25. [PMID: 31112905 DOI: 10.1016/j.gde.2019.04.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 03/13/2019] [Accepted: 04/15/2019] [Indexed: 12/31/2022]
Abstract
The nuclear lamina (NL) consists of a thin meshwork of lamins and associated proteins that lines the inner nuclear membrane (INM). In metazoan nuclei, a large proportion of the genome contacts the NL in broad lamina-associated domains (LADs). Contacts of the NL with the genome are believed to aid the spatial organization of chromosomes and contribute to the regulation of transcription. Here, we will focus on recent insights in the structural organization of the genome at the NL and the role of this organization in the regulation of gene expression.
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Affiliation(s)
- Isabel Guerreiro
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jop Kind
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands.
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33
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Sivakumar A, de Las Heras JI, Schirmer EC. Spatial Genome Organization: From Development to Disease. Front Cell Dev Biol 2019; 7:18. [PMID: 30949476 PMCID: PMC6437099 DOI: 10.3389/fcell.2019.00018] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 02/01/2019] [Indexed: 12/29/2022] Open
Abstract
Every living organism, from bacteria to humans, contains DNA encoding anything from a few hundred genes in intracellular parasites such as Mycoplasma, up to several tens of thousands in many higher organisms. The first observations indicating that the nucleus had some kind of organization were made over a hundred years ago. Understanding of its significance is both limited and aided by the development of techniques, in particular electron microscopy, fluorescence in situ hybridization, DamID and most recently HiC. As our knowledge about genome organization grows, it becomes apparent that the mechanisms are conserved in evolution, even if the individual players may vary. These mechanisms involve DNA binding proteins such as histones, and a number of architectural proteins, some of which are very much conserved, with some others having diversified and multiplied, acquiring specific regulatory functions. In this review we will look at the principles of genome organization in a hierarchical manner, from DNA packaging to higher order genome associations such as TADs, and the significance of radial positioning of genomic loci. We will then elaborate on the dynamics of genome organization during development, and how genome architecture plays an important role in cell fate determination. Finally, we will discuss how misregulation can be a factor in human disease.
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Affiliation(s)
- Aishwarya Sivakumar
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Jose I de Las Heras
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Eric C Schirmer
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
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34
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Shevelyov YY, Ulianov SV. The Nuclear Lamina as an Organizer of Chromosome Architecture. Cells 2019; 8:E136. [PMID: 30744037 PMCID: PMC6406483 DOI: 10.3390/cells8020136] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 02/04/2019] [Accepted: 02/06/2019] [Indexed: 01/20/2023] Open
Abstract
The nuclear lamina (NL) is a meshwork of lamins and lamin-associated proteins adjoining the inner side of the nuclear envelope. In early embryonic cells, the NL mainly suppresses background transcription, whereas, in differentiated cell types, its disruption affects gene expression more severely. Normally, the NL serves as a backbone for multiple chromatin anchoring sites, thus shaping the spatial organization of chromosomes in the interphase nucleus. However, upon cell senescence, aging, or in some types of terminally differentiated cells and lamin-associated diseases, the loss of NL-chromatin tethering causes drastic alterations in chromosome architecture. Here, we provide an overview of the recent advances in the field of NL-chromatin interactions, focusing on their impact on chromatin positioning, compaction, repression, and spatial organization.
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Affiliation(s)
- Yuri Y. Shevelyov
- Department of Molecular Genetics of Cell, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia;
| | - Sergey V. Ulianov
- Division of the Regulation of Transcription and Chromatin Dynamics, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia;
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35
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Perovanovic J, Hoffman EP. Mechanisms of allelic and clinical heterogeneity of lamin A/C phenotypes. Physiol Genomics 2018; 50:694-704. [PMID: 29750601 PMCID: PMC6335092 DOI: 10.1152/physiolgenomics.00128.2017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Mutations in the lamin A/C (LMNA) gene cause a broad range of clinical syndromes that show tissue-restricted abnormalities of post mitotic tissues, such as muscle, nerve, heart, and adipose tissue. Mutations in other nuclear envelope proteins cause clinically overlapping disorders. The majority of mutations are dominant single amino acid changes (toxic protein produced by the single mutant gene), and patients are heterozygous with both normal and abnormal proteins. Experimental support has been provided for different models of cellular pathogenesis in nuclear envelope diseases, including changes in heterochromatin formation at the nuclear membrane (epigenomics), changes in the timing of steps during terminal differentiation of cells, and structural abnormalities of the nuclear membrane. These models are not mutually exclusive and may be important in different cells at different times of development. Recent experiments using fusion proteins of normal and mutant lamin A/C proteins fused to a bacterial adenine methyltransferase (DamID) provided compelling evidence of mutation-specific perturbation of epigenomic imprinting during terminal differentiation. These gain-of-function properties include lineage-specific ineffective genomic silencing during exit from the cell cycle (heterochromatinization), as well as promiscuous initiation of silencing at incorrect places in the genome. To date, these findings have been limited to a few muscular dystrophy and lipodystrophy LMNA mutations but seem shared with a distinct nuclear envelope disease, emerin-deficient muscular dystrophy. The dominant-negative structural model and gain-of-function epigenomic models for distinct LMNA mutations are not mutually exclusive, and it is likely that both models contribute to aspects of the many complex clinical phenotypes observed.
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Affiliation(s)
- Jelena Perovanovic
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis, Musculoskeletal, and Skin Diseases, National Institutes of Health , Bethesda, Maryland
| | - Eric P Hoffman
- School of Pharmacy and Pharmaceutical Sciences, Binghamton University, State University of New York , Binghamton New York
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36
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Maraldi NM. The lamin code. Biosystems 2018; 164:68-75. [DOI: 10.1016/j.biosystems.2017.07.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 07/10/2017] [Accepted: 07/14/2017] [Indexed: 12/24/2022]
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Abstract
PURPOSE OF REVIEW Nuclear envelope links to a wide range of disorders, including several myopathies and neuropathies over the past 2 decades, has spurred research leading to a completely changed view of this important cellular structure and its functions. However, the many functions now assigned to the nuclear envelope make it increasingly hard to determine which functions underlie these disorders. RECENT FINDINGS New nuclear envelope functions in genome organization, regulation and repair, signaling, and nuclear and cellular mechanics have been added to its classical barrier function. Arguments can be made for any of these functions mediating abnormality in nuclear envelope disorders and data exist supporting many. Moreover, transient and/or distal nuclear envelope connections to other cellular proteins and structures may increase the complexity of these disorders. SUMMARY Although the increased understanding of nuclear envelope functions has made it harder to distinguish specific causes of nuclear envelope disorders, this is because it has greatly expanded the spectrum of possible mechanisms underlying them. This change in perspective applies well beyond the known nuclear envelope disorders, potentially implicating the nuclear envelope in a much wider range of myopathies and neuropathies.
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38
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Breaking the scale: how disrupting the karyoplasmic ratio gives cancer cells an advantage for metastatic invasion. Biochem Soc Trans 2017; 45:1333-1344. [PMID: 29150524 DOI: 10.1042/bst20170153] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 09/28/2017] [Accepted: 10/16/2017] [Indexed: 01/03/2023]
Abstract
Nuclear size normally scales with the size of the cell, but in cancer this 'karyoplasmic ratio' is disrupted. This is particularly so in more metastatic tumors where changes in the karyoplasmic ratio are used in both diagnosis and prognosis for several tumor types. However, the direction of nuclear size changes differs for particular tumor types: for example in breast cancer, larger nuclear size correlates with increased metastasis, while for lung cancer smaller nuclear size correlates with increased metastasis. Thus, there must be tissue-specific drivers of the nuclear size changes, but proteins thus far linked to nuclear size regulation are widely expressed. Notably, for these tumor types, ploidy changes have been excluded as the basis for nuclear size changes, and so, the increased metastasis is more likely to have a basis in the nuclear morphology change itself. We review what is known about nuclear size regulation and postulate how such nuclear size changes can increase metastasis and why the directionality can differ for particular tumor types.
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39
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Liu Y, Ma S, Chang J, Zhang T, Wang X, Shi R, Zhang J, Lu W, Liu Y, Xia Q. Tissue-specific genome editing of laminA/C in the posterior silk glands of Bombyx mori. J Genet Genomics 2017; 44:451-459. [DOI: 10.1016/j.jgg.2017.09.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Revised: 09/07/2017] [Accepted: 09/13/2017] [Indexed: 12/22/2022]
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40
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Nikolakaki E, Mylonis I, Giannakouros T. Lamin B Receptor: Interplay between Structure, Function and Localization. Cells 2017; 6:cells6030028. [PMID: 28858257 PMCID: PMC5617974 DOI: 10.3390/cells6030028] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 08/28/2017] [Accepted: 08/30/2017] [Indexed: 12/15/2022] Open
Abstract
Lamin B receptor (LBR) is an integral protein of the inner nuclear membrane, containing a hydrophilic N-terminal end protruding into the nucleoplasm, eight hydrophobic segments that span the membrane and a short, nucleoplasmic C-terminal tail. Two seemingly unrelated functions have been attributed to LBR. Its N-terminal domain tethers heterochromatin to the nuclear periphery, thus contributing to the shape of interphase nuclear architecture, while its transmembrane domains exhibit sterol reductase activity. Mutations within the transmembrane segments result in defects in cholesterol synthesis and are associated with diseases such as the Pelger–Huët anomaly and Greenberg skeletal dysplasia, whereas no such harmful mutations related to the anchoring properties of LBR have been reported so far. Recent evidence suggests a dynamic regulation of LBR expression levels, structural organization, localization and function, in response to various signals. The molecular mechanisms underlying this dynamic behavior have not yet been fully unraveled. Here, we provide an overview of the current knowledge of the interplay between the structure, function and localization of LBR, and hint at the interconnection of the two distinct functions of LBR.
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Affiliation(s)
- Eleni Nikolakaki
- Laboratory of Biochemistry, Department of Chemistry, Aristotelian University, Thessaloniki 54124, Greece.
| | - Ilias Mylonis
- Laboratory of Biochemistry, Faculty of Medicine, University of Thessaly, Panepistimiou 3 BIOPOLIS, Larissa 41500, Greece.
| | - Thomas Giannakouros
- Laboratory of Biochemistry, Department of Chemistry, Aristotelian University, Thessaloniki 54124, Greece.
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Lamina-Associated Domains: Links with Chromosome Architecture, Heterochromatin, and Gene Repression. Cell 2017; 169:780-791. [PMID: 28525751 DOI: 10.1016/j.cell.2017.04.022] [Citation(s) in RCA: 628] [Impact Index Per Article: 89.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 04/11/2017] [Accepted: 04/14/2017] [Indexed: 01/06/2023]
Abstract
In metazoan cell nuclei, hundreds of large chromatin domains are in close contact with the nuclear lamina. Such lamina-associated domains (LADs) are thought to help organize chromosomes inside the nucleus and have been associated with gene repression. Here, we discuss the properties of LADs, the molecular mechanisms that determine their association with the nuclear lamina, their dynamic links with other nuclear compartments, and their proposed roles in gene regulation.
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42
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Robson MI, de Las Heras JI, Czapiewski R, Sivakumar A, Kerr ARW, Schirmer EC. Constrained release of lamina-associated enhancers and genes from the nuclear envelope during T-cell activation facilitates their association in chromosome compartments. Genome Res 2017; 27:1126-1138. [PMID: 28424353 PMCID: PMC5495065 DOI: 10.1101/gr.212308.116] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 04/12/2017] [Indexed: 01/15/2023]
Abstract
The 3D organization of the genome changes concomitantly with expression changes during hematopoiesis and immune activation. Studies have focused either on lamina-associated domains (LADs) or on topologically associated domains (TADs), defined by preferential local chromatin interactions, and chromosome compartments, defined as higher-order interactions between TADs sharing functionally similar states. However, few studies have investigated how these affect one another. To address this, we mapped LADs using Lamin B1-DamID during Jurkat T-cell activation, finding significant genome reorganization at the nuclear periphery dominated by release of loci frequently important for T-cell function. To assess how these changes at the nuclear periphery influence wider genome organization, our DamID data sets were contrasted with TADs and compartments. Features of specific repositioning events were then tested by fluorescence in situ hybridization during T-cell activation. First, considerable overlap between TADs and LADs was observed with the TAD repositioning as a unit. Second, A1 and A2 subcompartments are segregated in 3D space through differences in proximity to LADs along chromosomes. Third, genes and a putative enhancer in LADs that were released from the periphery during T-cell activation became preferentially associated with A2 subcompartments and were constrained to the relative proximity of the lamina. Thus, lamina associations influence internal nuclear organization, and changes in LADs during T-cell activation may provide an important additional mode of gene regulation.
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Affiliation(s)
- Michael I Robson
- The Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Jose I de Las Heras
- The Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Rafal Czapiewski
- The Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Aishwarya Sivakumar
- The Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Alastair R W Kerr
- The Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Eric C Schirmer
- The Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
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43
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Abstract
Nuclear lamins are components of the peripheral lamina that define the mechanical properties of nuclei and tether heterochromatin to the periphery. A-type lamins localize also to the nuclear interior, but the regulation and specific functions of this nucleoplasmic lamin pool are poorly understood. In this Commentary, we summarize known pathways that are potentially involved in the localization and dynamic behavior of intranuclear lamins, including their post-translational modifications and interactions with nucleoplasmic proteins, such as lamina-associated polypeptide 2α (LAP2α; encoded by TMPO). In addition, new data suggest that lamins in the nuclear interior have an important role in chromatin regulation and gene expression through dynamic binding to both hetero- and euchromatic genomic regions and promoter subdomains, thereby affecting epigenetic pathways and chromatin accessibility. Nucleoplasmic lamins also have a role in spatial chromatin organization and may be involved in mechanosignaling. In view of this newly emerging concept, we propose that the previously reported cellular phenotypes in lamin-linked diseases are, at least in part, rooted in an impaired regulation and/or function of the nucleoplasmic lamin A/C pool.
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Affiliation(s)
- Nana Naetar
- Center of Medical Biochemistry, Max F. Perutz Laboratories (MFPL), Medical University of Vienna, Vienna Biocenter (VBC), Dr.-Bohr-Gasse 9, Vienna A-1030, Austria
| | - Simona Ferraioli
- Center of Medical Biochemistry, Max F. Perutz Laboratories (MFPL), Medical University of Vienna, Vienna Biocenter (VBC), Dr.-Bohr-Gasse 9, Vienna A-1030, Austria
| | - Roland Foisner
- Center of Medical Biochemistry, Max F. Perutz Laboratories (MFPL), Medical University of Vienna, Vienna Biocenter (VBC), Dr.-Bohr-Gasse 9, Vienna A-1030, Austria
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Charó NL, Rodríguez Ceschan MI, Galigniana NM, Toneatto J, Piwien-Pilipuk G. Organization of nuclear architecture during adipocyte differentiation. Nucleus 2017; 7:249-69. [PMID: 27416359 DOI: 10.1080/19491034.2016.1197442] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Obesity is a serious health problem worldwide since it is a major risk factor for chronic diseases such as type II diabetes. Obesity is the result of hyperplasia (associated with increased adipogenesis) and hypertrophy (associated with decreased adipogenesis) of the adipose tissue. Therefore, understanding the molecular mechanisms underlying the process of adipocyte differentiation is relevant to delineate new therapeutic strategies for treatment of obesity. As in all differentiation processes, temporal patterns of transcription are exquisitely controlled, allowing the acquisition and maintenance of the adipocyte phenotype. The genome is spatially organized; therefore decoding local features of the chromatin language alone does not suffice to understand how cell type-specific gene expression patterns are generated. Elucidating how nuclear architecture is built during the process of adipogenesis is thus an indispensable step to gain insight in how gene expression is regulated to achieve the adipocyte phenotype. Here we will summarize the recent advances in our understanding of the organization of nuclear architecture as progenitor cells differentiate in adipocytes, and the questions that still remained to be answered.
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Affiliation(s)
- Nancy L Charó
- a Laboratory of Nuclear Architecture, Instituto de Biología y Medicina Experimental (IByME) - CONICET , Buenos Aires , Argentina
| | - María I Rodríguez Ceschan
- a Laboratory of Nuclear Architecture, Instituto de Biología y Medicina Experimental (IByME) - CONICET , Buenos Aires , Argentina
| | - Natalia M Galigniana
- a Laboratory of Nuclear Architecture, Instituto de Biología y Medicina Experimental (IByME) - CONICET , Buenos Aires , Argentina
| | - Judith Toneatto
- a Laboratory of Nuclear Architecture, Instituto de Biología y Medicina Experimental (IByME) - CONICET , Buenos Aires , Argentina
| | - Graciela Piwien-Pilipuk
- a Laboratory of Nuclear Architecture, Instituto de Biología y Medicina Experimental (IByME) - CONICET , Buenos Aires , Argentina
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45
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Cabianca DS, Gasser SM. Spatial segregation of heterochromatin: Uncovering functionality in a multicellular organism. Nucleus 2017; 7:301-7. [PMID: 27187571 DOI: 10.1080/19491034.2016.1187354] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Multiple layers of regulation are required to ensure appropriate patterns of gene expression for accurate cell differentiation. Interphase chromatin is non-randomly distributed within the nucleus, with highly compacted, transcriptionally silent heterochromatin enriched at the nuclear and nucleolar periphery. Whether this spatial organization serves a function in organismal physiology, rather than simply being a byproduct of chromatin metabolism, is a fundamental question. Recent work performed in C. elegans embryos characterized the molecular mechanisms that drive the perinuclear anchoring of heterochromatin. Moreover, for the first time it was shown that heterochromatin sequestration helps to restrict cell differentiation programs, while sustaining commitment to a specified fate. Here, we describe and comment on these findings, placing them in a broader context.
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Affiliation(s)
- Daphne S Cabianca
- a Friedrich Miescher Institute for Biomedical Research , Basel , Switzerland
| | - Susan M Gasser
- a Friedrich Miescher Institute for Biomedical Research , Basel , Switzerland.,b Faculty of Natural Sciences , University of Basel , Basel , Switzerland
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46
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Dixon CR, Platani M, Makarov AA, Schirmer EC. Microinjection of Antibodies Targeting the Lamin A/C Histone-Binding Site Blocks Mitotic Entry and Reveals Separate Chromatin Interactions with HP1, CenpB and PML. Cells 2017; 6:cells6020009. [PMID: 28346356 PMCID: PMC5492013 DOI: 10.3390/cells6020009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 02/24/2017] [Accepted: 03/14/2017] [Indexed: 02/07/2023] Open
Abstract
Lamins form a scaffold lining the nucleus that binds chromatin and contributes to spatial genome organization; however, due to the many other functions of lamins, studies knocking out or altering the lamin polymer cannot clearly distinguish between direct and indirect effects. To overcome this obstacle, we specifically targeted the mapped histone-binding site of A/C lamins by microinjecting antibodies specific to this region predicting that this would make the genome more mobile. No increase in chromatin mobility was observed; however, interestingly, injected cells failed to go through mitosis, while control antibody-injected cells did. This effect was not due to crosslinking of the lamin polymer, as Fab fragments also blocked mitosis. The lack of genome mobility suggested other lamin-chromatin interactions. To determine what these might be, mini-lamin A constructs were expressed with or without the histone-binding site that assembled into independent intranuclear structures. HP1, CenpB and PML proteins accumulated at these structures for both constructs, indicating that other sites supporting chromatin interactions exist on lamin A. Together, these results indicate that lamin A-chromatin interactions are highly redundant and more diverse than generally acknowledged and highlight the importance of trying to experimentally separate their individual functions.
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Affiliation(s)
- Charles R Dixon
- The Wellcome Trust Centre for Cell Biology, University of Edinburgh, Kings Buildings, Swann 5.22, Max Born Crescent, Edinburgh EH9 3BF, UK.
| | - Melpomeni Platani
- The Wellcome Trust Centre for Cell Biology, University of Edinburgh, Kings Buildings, Swann 5.22, Max Born Crescent, Edinburgh EH9 3BF, UK.
| | - Alexandr A Makarov
- The Wellcome Trust Centre for Cell Biology, University of Edinburgh, Kings Buildings, Swann 5.22, Max Born Crescent, Edinburgh EH9 3BF, UK.
| | - Eric C Schirmer
- The Wellcome Trust Centre for Cell Biology, University of Edinburgh, Kings Buildings, Swann 5.22, Max Born Crescent, Edinburgh EH9 3BF, UK.
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47
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Abstract
As a compartment border, the nuclear envelope (NE) needs to serve as both a protective membrane shell for the genome and a versatile communication interface between the nucleus and the cytoplasm. Despite its important structural role in sheltering the genome, the NE is a dynamic and highly adaptable boundary that changes composition during differentiation, deforms in response to mechanical challenges, can be repaired upon rupture and even rapidly disassembles and reforms during open mitosis. NE remodelling is fundamentally involved in cell growth, division and differentiation, and if perturbed can lead to devastating diseases such as muscular dystrophies or premature ageing.
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48
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de Las Heras JI, Zuleger N, Batrakou DG, Czapiewski R, Kerr ARW, Schirmer EC. Tissue-specific NETs alter genome organization and regulation even in a heterologous system. Nucleus 2017; 8:81-97. [PMID: 28045568 PMCID: PMC5287206 DOI: 10.1080/19491034.2016.1261230] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Different cell types exhibit distinct patterns of 3D genome organization that correlate with changes in gene expression in tissue and differentiation systems. Several tissue-specific nuclear envelope transmembrane proteins (NETs) have been found to influence the spatial positioning of genes and chromosomes that normally occurs during tissue differentiation. Here we study 3 such NETs: NET29, NET39, and NET47, which are expressed preferentially in fat, muscle and liver, respectively. We found that even when exogenously expressed in a heterologous system they can specify particular genome organization patterns and alter gene expression. Each NET affected largely different subsets of genes. Notably, the liver-specific NET47 upregulated many genes in HT1080 fibroblast cells that are normally upregulated in hepatogenesis, showing that tissue-specific NETs can favor expression patterns associated with the tissue where the NET is normally expressed. Similarly, global profiling of peripheral chromatin after exogenous expression of these NETs using lamin B1 DamID revealed that each NET affected the nuclear positioning of distinct sets of genomic regions with a significant tissue-specific component. Thus NET influences on genome organization can contribute to gene expression changes associated with differentiation even in the absence of other factors and overt cellular differentiation changes.
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Affiliation(s)
- Jose I de Las Heras
- a The Wellcome Trust Centre for Cell Biology , University of Edinburgh , Edinburgh , UK
| | - Nikolaj Zuleger
- a The Wellcome Trust Centre for Cell Biology , University of Edinburgh , Edinburgh , UK
| | - Dzmitry G Batrakou
- a The Wellcome Trust Centre for Cell Biology , University of Edinburgh , Edinburgh , UK
| | - Rafal Czapiewski
- a The Wellcome Trust Centre for Cell Biology , University of Edinburgh , Edinburgh , UK
| | - Alastair R W Kerr
- a The Wellcome Trust Centre for Cell Biology , University of Edinburgh , Edinburgh , UK
| | - Eric C Schirmer
- a The Wellcome Trust Centre for Cell Biology , University of Edinburgh , Edinburgh , UK
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49
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Le Thanh P, Meinke P, Korfali N, Srsen V, Robson MI, Wehnert M, Schoser B, Sewry CA, Schirmer EC. Immunohistochemistry on a panel of Emery-Dreifuss muscular dystrophy samples reveals nuclear envelope proteins as inconsistent markers for pathology. Neuromuscul Disord 2016; 27:338-351. [PMID: 28214269 PMCID: PMC5380655 DOI: 10.1016/j.nmd.2016.12.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 11/22/2016] [Accepted: 12/09/2016] [Indexed: 11/08/2022]
Abstract
Altered distribution of EDMD-linked proteins is not a general characteristic of EDMD. Tissue-specific proteins exhibit altered distributions in some EDMD patients. Variation in redistributed proteins in EDMD may underlie its clinical variability.
Reports of aberrant distribution for some nuclear envelope proteins in cells expressing a few Emery–Dreifuss muscular dystrophy mutations raised the possibility that such protein redistribution could underlie pathology and/or be diagnostic. However, this disorder is linked to 8 different genes encoding nuclear envelope proteins, raising the question of whether a particular protein is most relevant. Therefore, myoblast/fibroblast cultures from biopsy and tissue sections from a panel of nine Emery–Dreifuss muscular dystrophy patients (4 male, 5 female) including those carrying emerin and FHL1 (X-linked) and several lamin A (autosomal dominant) mutations were stained for the proteins linked to the disorder. As tissue-specific nuclear envelope proteins have been postulated to mediate the tissue-specific pathologies of different nuclear envelopathies, patient samples were also stained for several muscle-specific nuclear membrane proteins. Although linked proteins nesprin 1 and SUN2 and muscle-specific proteins NET5/Samp1 and Tmem214 yielded aberrant distributions in individual patient cells, none exhibited defects through the larger patient panel. Muscle-specific Tmem38A normally appeared in both the nuclear envelope and sarcoplasmic reticulum, but most patient samples exhibited a moderate redistribution favouring the sarcoplasmic reticulum. The absence of striking uniform defects in nuclear envelope protein distribution indicates that such staining will be unavailing for general diagnostics, though it remains possible that specific mutations exhibiting protein distribution defects might reflect a particular clinical variant. These findings further argue that multiple pathways can lead to the generally similar pathologies of this disorder while at the same time the different cellular phenotypes observed possibly may help explain the considerable clinical variation of EDMD.
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Affiliation(s)
- Phu Le Thanh
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Peter Meinke
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK; Friedrich-Baur-Institute, Ludwig Maximilian University, Munich, Germany
| | - Nadia Korfali
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Vlastimil Srsen
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Michael I Robson
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Manfred Wehnert
- Institute of Human Genetics, University of Greifswald, Greifswald, Germany
| | - Benedikt Schoser
- Friedrich-Baur-Institute, Ludwig Maximilian University, Munich, Germany
| | - Caroline A Sewry
- Dubowitz Neuromuscular Centre, Great Ormond Street Hospital for Children NHS Trust, London, UK
| | - Eric C Schirmer
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK.
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50
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Snyder MJ, Lau AC, Brouhard EA, Davis MB, Jiang J, Sifuentes MH, Csankovszki G. Anchoring of Heterochromatin to the Nuclear Lamina Reinforces Dosage Compensation-Mediated Gene Repression. PLoS Genet 2016; 12:e1006341. [PMID: 27690361 PMCID: PMC5045178 DOI: 10.1371/journal.pgen.1006341] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 09/06/2016] [Indexed: 12/21/2022] Open
Abstract
Higher order chromosome structure and nuclear architecture can have profound effects on gene regulation. We analyzed how compartmentalizing the genome by tethering heterochromatic regions to the nuclear lamina affects dosage compensation in the nematode C. elegans. In this organism, the dosage compensation complex (DCC) binds both X chromosomes of hermaphrodites to repress transcription two-fold, thus balancing gene expression between XX hermaphrodites and XO males. X chromosome structure is disrupted by mutations in DCC subunits. Using X chromosome paint fluorescence microscopy, we found that X chromosome structure and subnuclear localization are also disrupted when the mechanisms that anchor heterochromatin to the nuclear lamina are defective. Strikingly, the heterochromatic left end of the X chromosome is less affected than the gene-rich middle region, which lacks heterochromatic anchors. These changes in X chromosome structure and subnuclear localization are accompanied by small, but significant levels of derepression of X-linked genes as measured by RNA-seq, without any observable defects in DCC localization and DCC-mediated changes in histone modifications. We propose a model in which heterochromatic tethers on the left arm of the X cooperate with the DCC to compact and peripherally relocate the X chromosomes, contributing to gene repression.
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Affiliation(s)
- Martha J. Snyder
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Alyssa C. Lau
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Elizabeth A. Brouhard
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Michael B. Davis
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Jianhao Jiang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Margarita H. Sifuentes
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Györgyi Csankovszki
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
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