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Keuper K, Bartek J, Maya-Mendoza A. The nexus of nuclear envelope dynamics, circular economy and cancer cell pathophysiology. Eur J Cell Biol 2024; 103:151394. [PMID: 38340500 DOI: 10.1016/j.ejcb.2024.151394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 02/12/2024] Open
Abstract
The nuclear envelope (NE) is a critical component in maintaining the function and structure of the eukaryotic nucleus. The NE and lamina are disassembled during each cell cycle to enable an open mitosis. Nuclear architecture construction and deconstruction is a prime example of a circular economy, as it fulfills a highly efficient recycling program bound to continuous assessment of the quality and functionality of the building blocks. Alterations in the nuclear dynamics and lamina structure have emerged as important contributors to both oncogenic transformation and cancer progression. However, the knowledge of the NE breakdown and reassembly is still limited to a fraction of participating proteins and complexes. As cancer cells contain highly diverse nuclei in terms of DNA content, but also in terms of nuclear number, size, and shape, it is of great interest to understand the intricate relationship between these nuclear features in cancer cell pathophysiology. In this review, we provide insights into how those NE dynamics are regulated, and how lamina destabilization processes may alter the NE circular economy. Moreover, we expand the knowledge of the lamina-associated domain region by using strategic algorithms, including Artificial Intelligence, to infer protein associations, assess their function and location, and predict cancer-type specificity with implications for the future of cancer diagnosis, prognosis and treatment. Using this approach we identified NUP98 and MECP2 as potential proteins that exhibit upregulation in Acute Myeloid Leukemia (LAML) patients with implications for early diagnosis.
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Affiliation(s)
- Kristina Keuper
- DNA Replication and Cancer Group, Danish Cancer Institute, Copenhagen, Denmark; Genome Integrity Group, Danish Cancer Institute, Copenhagen, Denmark
| | - Jiri Bartek
- Genome Integrity Group, Danish Cancer Institute, Copenhagen, Denmark; Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SciLifeLab, Stockholm, Sweden
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2
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Afanasyev AY, Kim Y, Tolokh IS, Sharakhov IV, Onufriev AV. The probability of chromatin to be at the nuclear lamina has no systematic effect on its transcription level in fruit flies. Epigenetics Chromatin 2024; 17:13. [PMID: 38705995 PMCID: PMC11071202 DOI: 10.1186/s13072-024-00528-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 02/08/2024] [Indexed: 05/07/2024] Open
Abstract
BACKGROUND Multiple studies have demonstrated a negative correlation between gene expression and positioning of genes at the nuclear envelope (NE) lined by nuclear lamina, but the exact relationship remains unclear, especially in light of the highly stochastic, transient nature of the gene association with the NE. RESULTS In this paper, we ask whether there is a causal, systematic, genome-wide relationship between the expression levels of the groups of genes in topologically associating domains (TADs) of Drosophila nuclei and the probabilities of TADs to be found at the NE. To investigate the nature of this possible relationship, we combine a coarse-grained dynamic model of the entire Drosophila nucleus with genome-wide gene expression data; we analyze the TAD averaged transcription levels of genes against the probabilities of individual TADs to be in contact with the NE in the control and lamins-depleted nuclei. Our findings demonstrate that, within the statistical error margin, the stochastic positioning of Drosophila melanogaster TADs at the NE does not, by itself, systematically affect the mean level of gene expression in these TADs, while the expected negative correlation is confirmed. The correlation is weak and disappears completely for TADs not containing lamina-associated domains (LADs) or TADs containing LADs, considered separately. Verifiable hypotheses regarding the underlying mechanism for the presence of the correlation without causality are discussed. These include the possibility that the epigenetic marks and affinity to the NE of a TAD are determined by various non-mutually exclusive mechanisms and remain relatively stable during interphase. CONCLUSIONS At the level of TADs, the probability of chromatin being in contact with the nuclear envelope has no systematic, causal effect on the transcription level in Drosophila. The conclusion is reached by combining model-derived time-evolution of TAD locations within the nucleus with their experimental gene expression levels.
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Affiliation(s)
- Alexander Y Afanasyev
- Department of Biomedical Engineering and Mechanics, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Yoonjin Kim
- Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Igor S Tolokh
- Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Igor V Sharakhov
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA.
| | - Alexey V Onufriev
- Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA.
- Department of Physics, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA.
- Center for Soft Matter and Biological Physics, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA.
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3
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Martino S, Carollo PS, Barra V. A Glimpse into Chromatin Organization and Nuclear Lamina Contribution in Neuronal Differentiation. Genes (Basel) 2023; 14:genes14051046. [PMID: 37239406 DOI: 10.3390/genes14051046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023] Open
Abstract
During embryonic development, stem cells undergo the differentiation process so that they can specialize for different functions within the organism. Complex programs of gene transcription are crucial for this process to happen. Epigenetic modifications and the architecture of chromatin in the nucleus, through the formation of specific regions of active as well as inactive chromatin, allow the coordinated regulation of the genes for each cell fate. In this mini-review, we discuss the current knowledge regarding the regulation of three-dimensional chromatin structure during neuronal differentiation. We also focus on the role the nuclear lamina plays in neurogenesis to ensure the tethering of the chromatin to the nuclear envelope.
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Affiliation(s)
- Salvatore Martino
- Department of Biological Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy
| | - Pietro Salvatore Carollo
- Department of Biological Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy
- Institute of Molecular Bioimaging and Physiology, National Research Council (IBFM-CNR), 90015 Cefalù, Italy
| | - Viviana Barra
- Department of Biological Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy
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4
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Tian W, Hao X, Nie R, Ling Y, Zhang B, Zhang H, Wu C. Comparative Transcriptome Analysis Reveals Regulatory Mechanism of Long Non-Coding RNAs during Abdominal Preadipocyte Adipogenic Differentiation in Chickens. Animals (Basel) 2022; 12:1099. [PMID: 35565526 PMCID: PMC9101879 DOI: 10.3390/ani12091099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/11/2022] [Accepted: 04/21/2022] [Indexed: 11/24/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are implicated in mammalian adipogenesis and obesity. However, their genome-wide distribution, expression profiles, and regulatory mechanisms during chicken adipogenesis remain rarely understood. In the present study, lncRNAs associated with adipogenesis were identified from chicken abdominal adipocytes at multiple differentiation stages using Ribo-Zero RNA-seq. A total of 15,179 lncRNAs were identified and characterized by stage-specific expression patterns. Of these, 840 differentially expressed lncRNAs were detected, and their cis- and trans-target genes were significantly enriched in multiple lipid-related pathways. Through weighted gene co-expression network analysis (WGCNA) and time-series expression profile clustering analysis, 14 key lncRNAs were identified as candidate regulatory lncRNAs in chicken adipogenic differentiation. The cis- and trans-regulatory interactions of key lncRNAs were constructed based on their differentially expressed cis- and trans-target genes, respectively. We also constructed a competing endogenous RNA (ceRNA) network based on the key lncRNAs, differentially expressed miRNAs, and differentially expressed mRNAs. MSTRG.25116.1 was identified as a potential regulator of chicken abdominal preadipocyte adipogenic differentiation by acting as a transcriptional trans-regulator of fatty acid amide hydrolase (FAAH) gene expression and/or a ceRNA that post-transcriptionally mediates FAAH gene expression by sponging gga-miR-1635.
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Affiliation(s)
| | | | | | | | - Bo Zhang
- National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (W.T.); (X.H.); (R.N.); (Y.L.); (C.W.)
| | - Hao Zhang
- National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (W.T.); (X.H.); (R.N.); (Y.L.); (C.W.)
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5
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Evangelisti C, Rusciano I, Mongiorgi S, Ramazzotti G, Lattanzi G, Manzoli L, Cocco L, Ratti S. The wide and growing range of lamin B-related diseases: from laminopathies to cancer. Cell Mol Life Sci 2022; 79:126. [PMID: 35132494 PMCID: PMC8821503 DOI: 10.1007/s00018-021-04084-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 12/03/2021] [Accepted: 12/08/2021] [Indexed: 12/18/2022]
Abstract
B-type lamins are fundamental components of the nuclear lamina, a complex structure that acts as a scaffold for organization and function of the nucleus. Lamin B1 and B2, the most represented isoforms, are encoded by LMNB1 and LMNB2 gene, respectively. All B-type lamins are synthesized as precursors and undergo sequential post-translational modifications to generate the mature protein. B-type lamins are involved in a wide range of nuclear functions, including DNA replication and repair, regulation of chromatin and nuclear stiffness. Moreover, lamins B1 and B2 regulate several cellular processes, such as tissue development, cell cycle, cellular proliferation, senescence, and DNA damage response. During embryogenesis, B-type lamins are essential for organogenesis, in particular for brain development. As expected from the numerous and pivotal functions of B-type lamins, mutations in their genes or fluctuations in their expression levels are critical for the onset of several diseases. Indeed, a growing range of human disorders have been linked to lamin B1 or B2, increasing the complexity of the group of diseases collectively known as laminopathies. This review highlights the recent findings on the biological role of B-type lamins under physiological or pathological conditions, with a particular emphasis on brain disorders and cancer.
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Affiliation(s)
- Camilla Evangelisti
- Cellular Signalling Laboratory, Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Isabella Rusciano
- Cellular Signalling Laboratory, Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Sara Mongiorgi
- Cellular Signalling Laboratory, Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Giulia Ramazzotti
- Cellular Signalling Laboratory, Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Giovanna Lattanzi
- CNR Institute of Molecular Genetics "Luigi Luca Cavalli-Sforza", Unit of Bologna, Bologna, Italy
- IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Lucia Manzoli
- Cellular Signalling Laboratory, Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy.
| | - Lucio Cocco
- Cellular Signalling Laboratory, Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy.
| | - Stefano Ratti
- Cellular Signalling Laboratory, Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
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Chromosomal Rearrangements and Altered Nuclear Organization: Recent Mechanistic Models in Cancer. Cancers (Basel) 2021; 13:cancers13225860. [PMID: 34831011 PMCID: PMC8616464 DOI: 10.3390/cancers13225860] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/09/2021] [Accepted: 11/19/2021] [Indexed: 01/07/2023] Open
Abstract
Simple Summary New methodologies and technologies developed in the last few decades have highlighted the precise spatial organization of the genome into the cell nucleus, with chromatin architecture playing a central role in controlling several genome functions. Genes are expressed in a well-defined way and at a well-defined time during cell differentiation, and alterations in genome organization can lead to genetic diseases, such as cancers. Here we review how the genome is organized in the cell nucleus and the evidence of genome misorganization leading to cancer diseases. Abstract The last decade has seen significant progress in understanding how the genome is organized spatially within interphase nuclei. Recent analyses have confirmed earlier molecular cytogenetic studies on chromosome positioning within interphase nuclei and provided new information about the topologically associated domains (TADs). Examining the nuances of how genomes are organized within interphase nuclei will provide information fundamental to understanding gene regulation and expression in health and disease. Indeed, the radial spatial positioning of individual gene loci within nuclei has been associated with up- and down-regulation of specific genes, and disruption of normal genome organization within nuclei will result in compromised cellular health. In cancer cells, where reorganization of the nuclear architecture may occur in the presence of chromosomal rearrangements such as translocations, inversions, or deletions, gene repositioning can change their expression. To date, very few studies have focused on radial gene positioning and the correlation to gene expression in cancers. Further investigations would improve our understanding of the biological mechanisms at the basis of cancer and, in particular, in leukemia initiation and progression, especially in those cases where the molecular consequences of chromosomal rearrangements are still unclear. In this review, we summarize the main milestones in the field of genome organization in the nucleus and the alterations to this organization that can lead to cancer diseases.
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Nuclear Dynamics and Chromatin Structure: Implications for Pancreatic Cancer. Cells 2021; 10:cells10102624. [PMID: 34685604 PMCID: PMC8534098 DOI: 10.3390/cells10102624] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 09/20/2021] [Accepted: 09/27/2021] [Indexed: 12/14/2022] Open
Abstract
Changes in nuclear shape have been extensively associated with the dynamics and functionality of cancer cells. In most normal cells, nuclei have a regular ellipsoid shape and minimal variation in nuclear size; however, an irregular nuclear contour and abnormal nuclear size is often observed in cancer, including pancreatic cancer. Furthermore, alterations in nuclear morphology have become the 'gold standard' for tumor staging and grading. Beyond the utility of altered nuclear morphology as a diagnostic tool in cancer, the implications of altered nuclear structure for the biology and behavior of cancer cells are profound as changes in nuclear morphology could impact cellular responses to physical strain, adaptation during migration, chromatin organization, and gene expression. Here, we aim to highlight and discuss the factors that regulate nuclear dynamics and their implications for pancreatic cancer biology.
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8
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Patil S, Sengupta K. Role of A- and B-type lamins in nuclear structure-function relationships. Biol Cell 2021; 113:295-310. [PMID: 33638183 DOI: 10.1111/boc.202000160] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 02/06/2021] [Accepted: 02/08/2021] [Indexed: 12/15/2022]
Abstract
Nuclear lamins are type V intermediate filament proteins that form a filamentous meshwork beneath the inner nuclear membrane. Additionally, a sub-population of A- and B-type lamins localizes in the nuclear interior. The nuclear lamina protects the nucleus from mechanical stress and mediates nucleo-cytoskeletal coupling. Lamins form a scaffold that partially tethers chromatin at the nuclear envelope. The nuclear lamina also stabilises protein-protein interactions involved in gene regulation and DNA repair. The lamin-based protein sub-complexes are implicated in both nuclear and cytoskeletal organisation, the mechanical stability of the nucleus, genome organisation, transcriptional regulation, genome stability and cellular differentiation. Here, we review recent research on nuclear lamins and unique roles of A- and B-type lamins in modulating various nuclear processes and their impact on cell function.
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Affiliation(s)
- Shalaka Patil
- Biology, Chromosome Biology Lab (CBL), Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pune, 411008, India
| | - Kundan Sengupta
- Biology, Chromosome Biology Lab (CBL), Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pune, 411008, India
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9
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Zhou R, Gao YQ. A DNA Sequence Based Polymer Model for Chromatin Folding. Int J Mol Sci 2021; 22:1328. [PMID: 33572740 PMCID: PMC7865792 DOI: 10.3390/ijms22031328] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 01/16/2021] [Accepted: 01/25/2021] [Indexed: 11/17/2022] Open
Abstract
The recent development of sequencing technology and imaging methods has provided an unprecedented understanding of the inter-phase chromatin folding in mammalian nuclei. It was found that chromatin folds into topological-associated domains (TADs) of hundreds of kilo base pairs (kbps), and is further divided into spatially segregated compartments (A and B). The compartment B tends to be located near to the periphery or the nuclear center and interacts with other domains of compartments B, while compartment A tends to be located between compartment B and interacts inside the domains. These spatial domains are found to highly correlate with the mosaic CpG island (CGI) density. High CGI density corresponds to compartments A and small TADs, and vice versa. The variation of contact probability as a function of sequential distance roughly follows a power-law decay. Different chromosomes tend to segregate to occupy different chromosome territories. A model that can integrate these properties at multiple length scales and match many aspects is highly desired. Here, we report a DNA-sequence based coarse-grained block copolymer model that considers different interactions between blocks of different CGI density, interactions of TAD formation, as well as interactions between chromatin and the nuclear envelope. This model captures the various single-chromosome properties and partially reproduces the formation of chromosome territories.
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Affiliation(s)
- Rui Zhou
- Biomedical Pioneering Innovation Center, Peking University, Beijing 100871, China;
| | - Yi Qin Gao
- Biomedical Pioneering Innovation Center, Peking University, Beijing 100871, China;
- Beijing Advanced Innovation Center for Genomics, Peking University, Beijing 100871, China
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
- Shenzhen Bay Laboratory, 5F, No.9 Duxue Rd., Nanshan District, Shenzhen 518055, China
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10
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Borini Etichetti CM, Arel Zalazar E, Cocordano N, Girardini J. Beyond the Mevalonate Pathway: Control of Post-Prenylation Processing by Mutant p53. Front Oncol 2020; 10:595034. [PMID: 33224889 PMCID: PMC7674641 DOI: 10.3389/fonc.2020.595034] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 10/08/2020] [Indexed: 12/21/2022] Open
Abstract
Missense mutations in the TP53 gene are among the most frequent alterations in human cancer. Consequently, many tumors show high expression of p53 point mutants, which may acquire novel activities that contribute to develop aggressive tumors. An unexpected aspect of mutant p53 function was uncovered by showing that some mutants can increase the malignant phenotype of tumor cells through alteration of the mevalonate pathway. Among metabolites generated through this pathway, isoprenoids are of particular interest, since they participate in a complex process of posttranslational modification known as prenylation. Recent evidence proposes that mutant p53 also enhances this process through transcriptional activation of ICMT, the gene encoding the methyl transferase responsible for the last step of protein prenylation. In this way, mutant p53 may act at different levels to promote prenylation of key proteins in tumorigenesis, including several members of the RAS and RHO families. Instead, wild type p53 acts in the opposite way, downregulating mevalonate pathway genes and ICMT. This oncogenic circuit also allows to establish potential connections with other metabolic pathways. The demand of acetyl-CoA for the mevalonate pathway may pose limitations in cell metabolism. Likewise, the dependence on S-adenosyl methionine for carboxymethylation, may expose cells to methionine stress. The involvement of protein prenylation in tumor progression offers a novel perspective to understand the antitumoral effects of mevalonate pathway inhibitors, such as statins, and to explore novel therapeutic strategies.
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Affiliation(s)
| | - Evelyn Arel Zalazar
- Instituto de Inmunología Clínica y Experimental de Rosario, IDICER, CONICET-UNR, Rosario, Argentina
| | - Nabila Cocordano
- Instituto de Inmunología Clínica y Experimental de Rosario, IDICER, CONICET-UNR, Rosario, Argentina
| | - Javier Girardini
- Instituto de Inmunología Clínica y Experimental de Rosario, IDICER, CONICET-UNR, Rosario, Argentina
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11
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Liu R, Ding J. Chromosomal Repositioning and Gene Regulation of Cells on a Micropillar Array. ACS APPLIED MATERIALS & INTERFACES 2020; 12:35799-35812. [PMID: 32667177 DOI: 10.1021/acsami.0c05883] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
While various cell responses on material surfaces have been examined, relatively few reports are focused on significant self-deformation of cell nuclei and corresponding chromosomal repositioning. Herein, we prepared a micropillar array of poly(lactide-co-glycolide) (PLGA) and observed significant nuclear deformation of HeLa cells on the polymeric micropillars. In particular, we detected the territory positioning of chromosomes 18 and 19 and gene expression profiles of HeLa cells on the micropillar array using fluorescence in situ hybridization and a DNA microarray. Chromosome 18 was found to be translocated closer to the nuclear periphery than chromosome 19 on the micropillar array. With the repositioning of chromosomal territories, HeLa cells changed their gene expressions on the micropillar array with 180 genes upregulated and 255 genes downregulated for all of the 23 pairs of chromosomes under the experimental conditions and the employed Bioinformatics criteria. Hence, this work deepens the understanding on cell-material interactions by revealing that material surface topography can probably influence chromosomal repositioning in the nuclei and gene expressions of cells.
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Affiliation(s)
- Ruili Liu
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200438, China
| | - Jiandong Ding
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200438, China
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12
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Dazzoni R, Grélard A, Morvan E, Bouter A, Applebee CJ, Loquet A, Larijani B, Dufourc EJ. The unprecedented membrane deformation of the human nuclear envelope, in a magnetic field, indicates formation of nuclear membrane invaginations. Sci Rep 2020; 10:5147. [PMID: 32198481 PMCID: PMC7083927 DOI: 10.1038/s41598-020-61746-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 01/14/2020] [Indexed: 12/04/2022] Open
Abstract
Human nuclear membrane (hNM) invaginations are thought to be crucial in fusion, fission and remodeling of cells and present in many human diseases. There is however little knowledge, if any, about their lipid composition and dynamics. We therefore isolated nuclear envelope lipids from human kidney cells, analyzed their composition and determined the membrane dynamics after resuspension in buffer. The hNM lipid extract was composed of a complex mixture of phospholipids, with high amounts of phosphatidylcholines, phosphatidylinositols (PI) and cholesterol. hNM dynamics was determined by solid-state NMR and revealed that the lamellar gel-to-fluid phase transition occurs below 0 °C, reflecting the presence of elevated amounts of unsaturated fatty acid chains. Fluidity was higher than the plasma membrane, illustrating the dual action of Cholesterol (ordering) and PI lipids (disordering). The most striking result was the large magnetic field-induced membrane deformation allowing to determine the membrane bending elasticity, a property related to hydrodynamics of cells and organelles. Human Nuclear Lipid Membranes were at least two orders of magnitude more elastic than the classical plasma membrane suggesting a physical explanation for the formation of nuclear membrane invaginations.
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Affiliation(s)
- Régine Dazzoni
- Institute of Chemistry & Biology of Membranes & Nanoobjects, UMR5248, CNRS, Université Bordeaux, INP-Bordeaux, F-33600, Pessac, France.,Cell Biophysics Laboratory, Ikerbasque Basque Foundation for Science, Instituto Biofísika (CSIC, UPV/EHU) and Research Centre for Experimental Marine Biology and Biotechnology (PiE), University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Axelle Grélard
- Institute of Chemistry & Biology of Membranes & Nanoobjects, UMR5248, CNRS, Université Bordeaux, INP-Bordeaux, F-33600, Pessac, France
| | - Estelle Morvan
- Institut Européen de Chimie et Biologie, UMS3033, CNRS, Université Bordeaux, INSERM (US001), 2 rue Escarpit, Pessac, 33600, France
| | - Anthony Bouter
- Institute of Chemistry & Biology of Membranes & Nanoobjects, UMR5248, CNRS, Université Bordeaux, INP-Bordeaux, F-33600, Pessac, France
| | - Christopher J Applebee
- Cell Biophysics Laboratory, Ikerbasque Basque Foundation for Science, Instituto Biofísika (CSIC, UPV/EHU) and Research Centre for Experimental Marine Biology and Biotechnology (PiE), University of the Basque Country (UPV/EHU), Leioa, Spain.,Cell Biophysics Laboratory, Centre for Therapeutic Innovation & Department of Pharmacy and Pharmacology, & Department of Physics, University of Bath, Bath, United Kingdom
| | - Antoine Loquet
- Institute of Chemistry & Biology of Membranes & Nanoobjects, UMR5248, CNRS, Université Bordeaux, INP-Bordeaux, F-33600, Pessac, France
| | - Banafshé Larijani
- Cell Biophysics Laboratory, Ikerbasque Basque Foundation for Science, Instituto Biofísika (CSIC, UPV/EHU) and Research Centre for Experimental Marine Biology and Biotechnology (PiE), University of the Basque Country (UPV/EHU), Leioa, Spain. .,Cell Biophysics Laboratory, Centre for Therapeutic Innovation & Department of Pharmacy and Pharmacology, & Department of Physics, University of Bath, Bath, United Kingdom.
| | - Erick J Dufourc
- Institute of Chemistry & Biology of Membranes & Nanoobjects, UMR5248, CNRS, Université Bordeaux, INP-Bordeaux, F-33600, Pessac, France.
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13
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Crosetto N, Bienko M. Radial Organization in the Mammalian Nucleus. Front Genet 2020; 11:33. [PMID: 32117447 PMCID: PMC7028756 DOI: 10.3389/fgene.2020.00033] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 01/10/2020] [Indexed: 11/13/2022] Open
Abstract
In eukaryotic cells, most of the genetic material is contained within a highly specialized organelle-the nucleus. A large body of evidence indicates that, within the nucleus, chromatinized DNA is spatially organized at multiple length scales. The higher-order organization of chromatin is crucial for proper execution of multiple genome functions, including DNA replication and transcription. Here, we review our current knowledge on the spatial organization of chromatin in the nucleus of mammalian cells, focusing in particular on how chromatin is radially arranged with respect to the nuclear lamina. We then discuss the possible mechanisms by which the radial organization of chromatin in the cell nucleus is established. Lastly, we propose a unifying model of nuclear spatial organization, and suggest novel approaches to test it.
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Affiliation(s)
| | - Magda Bienko
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
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14
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Hah J, Kim DH. Deciphering Nuclear Mechanobiology in Laminopathy. Cells 2019; 8:E231. [PMID: 30862117 PMCID: PMC6468464 DOI: 10.3390/cells8030231] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 02/23/2019] [Accepted: 03/05/2019] [Indexed: 12/13/2022] Open
Abstract
Extracellular mechanical stimuli are translated into biochemical signals inside the cell via mechanotransduction. The nucleus plays a critical role in mechanoregulation, which encompasses mechanosensing and mechanotransduction. The nuclear lamina underlying the inner nuclear membrane not only maintains the structural integrity, but also connects the cytoskeleton to the nuclear envelope. Lamin mutations, therefore, dysregulate the nuclear response, resulting in abnormal mechanoregulations, and ultimately, disease progression. Impaired mechanoregulations even induce malfunction in nuclear positioning, cell migration, mechanosensation, as well as differentiation. To know how to overcome laminopathies, we need to understand the mechanisms of laminopathies in a mechanobiological way. Recently, emerging studies have demonstrated the varying defects from lamin mutation in cellular homeostasis within mechanical surroundings. Therefore, this review summarizes recent findings highlighting the role of lamins, the architecture of nuclear lamina, and their disease relevance in the context of nuclear mechanobiology. We will also provide an overview of the differentiation of cellular mechanics in laminopathy.
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Affiliation(s)
- Jungwon Hah
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul 02841, Korea.
| | - Dong-Hwee Kim
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul 02841, Korea.
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15
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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: 62] [Impact Index Per Article: 12.4] [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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16
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Manley HR, Keightley MC, Lieschke GJ. The Neutrophil Nucleus: An Important Influence on Neutrophil Migration and Function. Front Immunol 2018; 9:2867. [PMID: 30564248 PMCID: PMC6288403 DOI: 10.3389/fimmu.2018.02867] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 11/21/2018] [Indexed: 11/13/2022] Open
Abstract
Neutrophil nuclear morphology has historically been used in haematology for neutrophil identification and characterisation, but its exact role in neutrophil function has remained enigmatic. During maturation, segmentation of the neutrophil nucleus into its mature, multi-lobulated shape is accompanied by distinct changes in nuclear envelope composition, resulting in a unique nucleus that is believed to be imbued with extraordinary nuclear flexibility. As a rate-limiting factor for cell migration, nuclear morphology and biomechanics are particularly important in the context of neutrophil migration during immune responses. Being an extremely plastic and fast migrating cell type, it is to be expected that neutrophils have an especially deformable nucleus. However, many questions still surround the dynamic capacities of the neutrophil nucleus, and which nuclear and cytoskeletal elements determine these dynamics. The biomechanics of the neutrophil nucleus should also be considered for their influences on the production of neutrophil extracellular traps (NETs), given this process sees the release of chromatin "nets" from nucleoplasm to extracellular space. Although past studies have investigated neutrophil nuclear composition and shape, in a new era of more sophisticated biomechanical and genetic techniques, 3D migration studies, and higher resolution microscopy we now have the ability to further investigate and understand neutrophil nuclear plasticity at an unprecedented level. This review addresses what is currently understood about neutrophil nuclear structure and its role in migration and the release of NETs, whilst highlighting open questions surrounding neutrophil nuclear dynamics.
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Affiliation(s)
- Harriet R Manley
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia
| | | | - Graham J Lieschke
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia
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17
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Pradhan R, Ranade D, Sengupta K. Emerin modulates spatial organization of chromosome territories in cells on softer matrices. Nucleic Acids Res 2018; 46:5561-5586. [PMID: 29684168 PMCID: PMC6009696 DOI: 10.1093/nar/gky288] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 04/04/2018] [Accepted: 04/06/2018] [Indexed: 02/06/2023] Open
Abstract
Cells perceive and relay external mechanical forces into the nucleus through the nuclear envelope. Here we examined the effect of lowering substrate stiffness as a paradigm to address the impact of altered mechanical forces on nuclear structure-function relationships. RNA sequencing of cells on softer matrices revealed significant transcriptional imbalances, predominantly in chromatin associated processes and transcriptional deregulation of human Chromosome 1. Furthermore, 3-Dimensional fluorescence in situ hybridization (3D-FISH) analyses showed a significant mislocalization of Chromosome 1 and 19 Territories (CT) into the nuclear interior, consistent with their transcriptional deregulation. However, CT18 with relatively lower transcriptional dysregulation, also mislocalized into the nuclear interior. Furthermore, nuclear Lamins that regulate chromosome positioning, were mislocalized into the nuclear interior in response to lowered matrix stiffness. Notably, Lamin B2 overexpression retained CT18 near the nuclear periphery in cells on softer matrices. While, cells on softer matrices also activated emerin phosphorylation at a novel Tyr99 residue, the inhibition of which in a phospho-deficient mutant (emerinY99F), selectively retained chromosome 18 and 19 but not chromosome 1 territories at their conserved nuclear locations. Taken together, emerin functions as a key mechanosensor, that modulates the spatial organization of chromosome territories in the interphase nucleus.
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Affiliation(s)
- Roopali Pradhan
- Biology, Main Building, First Floor, Room#B-216, Indian Institute of Science Education and Research (IISER), Pune, Dr Homi Bhabha Road, Pashan, Pune 411008, Maharashtra, India
| | - Devika Ranade
- Biology, Main Building, First Floor, Room#B-216, Indian Institute of Science Education and Research (IISER), Pune, Dr Homi Bhabha Road, Pashan, Pune 411008, Maharashtra, India
| | - Kundan Sengupta
- Biology, Main Building, First Floor, Room#B-216, Indian Institute of Science Education and Research (IISER), Pune, Dr Homi Bhabha Road, Pashan, Pune 411008, Maharashtra, India
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18
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Lukášová E, Kovařík A, Kozubek S. Consequences of Lamin B1 and Lamin B Receptor Downregulation in Senescence. Cells 2018; 7:cells7020011. [PMID: 29415520 PMCID: PMC5850099 DOI: 10.3390/cells7020011] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 01/24/2018] [Accepted: 01/31/2018] [Indexed: 01/28/2023] Open
Abstract
Anchoring of heterochromatin to the nuclear envelope appears to be an important process ensuring the spatial organization of the chromatin structure and genome function in eukaryotic nuclei. Proteins of the inner nuclear membrane (INM) mediating these interactions are able to recognize lamina-associated heterochromatin domains (termed LAD) and simultaneously bind either lamin A/C or lamin B1. One of these proteins is the lamin B receptor (LBR) that binds lamin B1 and tethers heterochromatin to the INM in embryonic and undifferentiated cells. It is replaced by lamin A/C with specific lamin A/C binding proteins at the beginning of cell differentiation and in differentiated cells. Our functional experiments in cancer cell lines show that heterochromatin in cancer cells is tethered to the INM by LBR, which is downregulated together with lamin B1 at the onset of cell transition to senescence. The downregulation of these proteins in senescent cells leads to the detachment of centromeric repetitive sequences from INM, their relocation to the nucleoplasm, and distension. In cells, the expression of LBR and LB1 is highly coordinated as evidenced by the reduction of both proteins in LBR shRNA lines. The loss of the constitutive heterochromatin structure containing LADs results in changes in chromatin architecture and genome function and can be the reason for the permanent loss of cell proliferation in senescence.
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Affiliation(s)
- Emilie Lukášová
- Department of Cell Biology and Radiobiology, Institute of Biophysics, Czech Academy of Sciences, Královopolská 135, Brno 61265, Czech Republic.
- Department of Molecular Epigenetics, Institute of Biophysics, Czech Academy of Sciences, Královopolská 135, Brno 61265, Czech Republic.
| | - Aleš Kovařík
- Department of Molecular Epigenetics, Institute of Biophysics, Czech Academy of Sciences, Královopolská 135, Brno 61265, Czech Republic.
| | - Stanislav Kozubek
- Department of Cell Biology and Radiobiology, Institute of Biophysics, Czech Academy of Sciences, Královopolská 135, Brno 61265, Czech Republic.
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19
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Klymenko T, Bloehdorn J, Bahlo J, Robrecht S, Akylzhanova G, Cox K, Estenfelder S, Wang J, Edelmann J, Strefford JC, Wojdacz TK, Fischer K, Hallek M, Stilgenbauer S, Cragg M, Gribben J, Braun A. Lamin B1 regulates somatic mutations and progression of B-cell malignancies. Leukemia 2018; 32:364-375. [PMID: 28804121 PMCID: PMC5808072 DOI: 10.1038/leu.2017.255] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 07/07/2017] [Accepted: 07/31/2017] [Indexed: 12/24/2022]
Abstract
Somatic hypermutation (SHM) is a pivotal process in adaptive immunity that occurs in the germinal centre and allows B cells to change their primary DNA sequence and diversify their antigen receptors. Here, we report that genome binding of Lamin B1, a component of the nuclear envelope involved in epigenetic chromatin regulation, is reduced during B-cell activation and formation of lymphoid germinal centres. Chromatin immunoprecipitation-Seq analysis showed that kappa and heavy variable immunoglobulin domains were released from the Lamin B1 suppressive environment when SHM was induced in B cells. RNA interference-mediated reduction of Lamin B1 resulted in spontaneous SHM as well as kappa-light chain aberrant surface expression. Finally, Lamin B1 expression level correlated with progression-free and overall survival in chronic lymphocytic leukaemia, and was strongly involved in the transformation of follicular lymphoma. In summary, here we report that Lamin B1 is a negative epigenetic regulator of SHM in normal B-cells and a 'mutational gatekeeper', suppressing the aberrant mutations that drive lymphoid malignancy.
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MESH Headings
- B-Lymphocytes/pathology
- Cell Line, Tumor
- Chromatin Immunoprecipitation/methods
- Disease Progression
- Humans
- Immunoglobulin Heavy Chains/genetics
- Immunoglobulin Variable Region/genetics
- Lamin Type B/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Lymphoma, Follicular/genetics
- Lymphoma, Follicular/pathology
- Somatic Hypermutation, Immunoglobulin/genetics
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Affiliation(s)
- T Klymenko
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University, London, UK
| | - J Bloehdorn
- Department of Internal Medicine III, University of Ulm, Ulm, Germany
| | - J Bahlo
- Department I of Internal Medicine, Center for Integrated Oncology Cologne, University Hospital of Cologne, Cologne, Germany
| | - S Robrecht
- Department I of Internal Medicine, Center for Integrated Oncology Cologne, University Hospital of Cologne, Cologne, Germany
| | - G Akylzhanova
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University, London, UK
| | - K Cox
- Academic Unit of Cancer Sciences, Faculty of Medicine, Cancer Research UK Centre and Experimental Cancer Medicine Centre, University of Southampton, Southampton, UK
| | - S Estenfelder
- Department of Internal Medicine III, University of Ulm, Ulm, Germany
| | - J Wang
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University, London, UK
| | - J Edelmann
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University, London, UK
| | - J C Strefford
- Academic Unit of Cancer Sciences, Faculty of Medicine, Cancer Research UK Centre and Experimental Cancer Medicine Centre, University of Southampton, Southampton, UK
| | - T K Wojdacz
- Academic Unit of Cancer Sciences, Faculty of Medicine, Cancer Research UK Centre and Experimental Cancer Medicine Centre, University of Southampton, Southampton, UK
- Aarhus Institute of Advanced Studies, Aarhus University, Aarhus, Denmark
| | - K Fischer
- Department I of Internal Medicine, Center for Integrated Oncology Cologne, University Hospital of Cologne, Cologne, Germany
| | - M Hallek
- Department I of Internal Medicine, Center for Integrated Oncology Cologne, University Hospital of Cologne, Cologne, Germany
| | - S Stilgenbauer
- Department of Internal Medicine III, University of Ulm, Ulm, Germany
| | - M Cragg
- Academic Unit of Cancer Sciences, Faculty of Medicine, Cancer Research UK Centre and Experimental Cancer Medicine Centre, University of Southampton, Southampton, UK
| | - J Gribben
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University, London, UK
| | - A Braun
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University, London, UK
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20
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Lee SH, Hadipour-Lakmehsari S, Miyake T, Gramolini AO. Three-dimensional imaging reveals endo(sarco)plasmic reticulum-containing invaginations within the nucleoplasm of muscle. Am J Physiol Cell Physiol 2017; 314:C257-C267. [PMID: 29167149 DOI: 10.1152/ajpcell.00141.2017] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The mammalian nucleus has invaginations from the cytoplasm, termed nucleoplasmic reticulum (NR). With increased resolution of cellular imaging, progress has been made in understanding the formation and function of NR. In fact, nucleoplasmic Ca2+ homeostasis has been implicated in the regulation of gene expression, DNA repair, and cell death. However, the majority of studies focus on cross-sectional or single-plane analyses of NR invaginations, providing an incomplete assessment of its distribution and content. Here, we provided advanced imaging and three-dimensional reconstructive analyses characterizing the molecular constituents of nuclear invaginations in the nucleoplasm in HEK293 cells, murine C2C12 muscle cells, and cardiac myocytes. We demonstrated the presence of critical Ca2+ regulatory channels, including sarco(endo)plasmic reticulum Ca2+-ATPase 2a (SERCA2a), stromal interaction molecule 1 (STIM1), and Ca2+ release-activated Ca2+ channel protein 1 (ORAI1), in the nucleoplasm in isolated primary mouse cardiomyocytes. We have shown for the first time the presence of STIM1 and ORAI1 in the nucleoplasm, suggesting the presence of store-operated calcium entry (SOCE) mechanism in nucleoplasmic Ca2+ regulation. These results show that nucleoplasmic invaginations contain continuous endoplasmic reticulum components, mitochondria, and intact nuclear membranes, highlighting the extremely detailed and complex nature of this organellar structure.
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Affiliation(s)
- Shin-Haw Lee
- Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research , Toronto, Ontario , Canada.,Faculty of Medicine, Department of Physiology, University of Toronto , Toronto, Ontario , Canada
| | - Sina Hadipour-Lakmehsari
- Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research , Toronto, Ontario , Canada.,Faculty of Medicine, Department of Physiology, University of Toronto , Toronto, Ontario , Canada
| | - Tetsuaki Miyake
- Faculty of Medicine, Department of Physiology, University of Toronto , Toronto, Ontario , Canada
| | - Anthony O Gramolini
- Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research , Toronto, Ontario , Canada.,Faculty of Medicine, Department of Physiology, University of Toronto , Toronto, Ontario , Canada
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21
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Bhattacharjee P, Dasgupta D, Sengupta K. DCM associated LMNA mutations cause distortions in lamina structure and assembly. Biochim Biophys Acta Gen Subj 2017; 1861:2598-2608. [PMID: 28844980 DOI: 10.1016/j.bbagen.2017.08.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 08/01/2017] [Accepted: 08/11/2017] [Indexed: 11/22/2022]
Abstract
BACKGROUND A and B-type lamins are integral scaffolding components of the nuclear lamina which impart rigidity and shape to all metazoan nuclei. Over 450 mutations in A-type lamins are associated with 16 human diseases including dilated cardiomyopathy (DCM). Here, we show that DCM mutants perturb the self-association of lamin A (LA) and it's binding with lamin B1 (LB1). METHODS We used confocal and superresolution microscopy (NSIM) to study the effect of LA mutants on the nuclear lamina. We further used circular dichroism, fluorescence spectroscopy and isothermal titration calorimetry (ITC) to probe the structural modulations, self-association and heteropolymeric association of mutant LA. RESULTS Transfection of mutants in cultured cell lines result in the formation of nuclear aggregates of varied size and distribution. Endogenous LB1 is sequestered into these aggregates. This is consistent with the ten-fold increase in association constant of the mutant proteins compared to the wild type. These mutants exhibit differential heterotypic interaction with LB1, along with significant secondary and tertiary structural alterations of the interacting proteins. Thermodynamic studies demonstrate that the mutants bind to LB1 with different stoichiometry, affinity and energetics. CONCLUSIONS In this report we show that increased self-association propensity of mutant LA modulates the LA-LB1 interaction and precludes the formation of an otherwise uniform laminar network. GENERAL SIGNIFICANCE Our results might highlight the role of homotypic and heterotypic interactions of LA in the pathogenesis of DCM and hence laminopathies in the broader sense.
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Affiliation(s)
- Pritha Bhattacharjee
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
| | - Dipak Dasgupta
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India.
| | - Kaushik Sengupta
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India.
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22
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Boubriak II, Malhas AN, Drozdz MM, Pytowski L, Vaux DJ. Stress-induced release of Oct-1 from the nuclear envelope is mediated by JNK phosphorylation of lamin B1. PLoS One 2017; 12:e0177990. [PMID: 28542436 PMCID: PMC5443517 DOI: 10.1371/journal.pone.0177990] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 05/06/2017] [Indexed: 02/08/2023] Open
Abstract
The nuclear lamina can bind and sequester transcription factors (TFs), a function lost if the lamina is abnormal, with missing or mutant lamin proteins. We now show that TF sequestration is not all-or-nothing, but a dynamic physiological response to external signals. We show that the binding of the ubiquitous TF, Oct-1, to lamin B1 was reversed under conditions of cellular stress caused, inter alia, by the chemical methylating agent methylmethanesulfonate (MMS). A search for lamin B1 post-translational modifications that might mediate changes in Oct-1 binding using kinase inhibitors uncovered a role for c-Jun N-terminal kinase (JNK). Phosphoproteomic and site-directed mutagenesis analyses of lamin B1 isolated from control and MMS-treated nuclei identified T575 as a JNK site phosphorylated after stress. A new phospho-T575 specific anti-peptide antibody confirmed increased interphase cellular T575 phosphorylation after cell exposure to certain stress conditions, enabling us to conclude that lamin B1 acts as an interphase kinase target, releasing Oct-1 to execute a protective response to stress.
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Affiliation(s)
- Ivan I. Boubriak
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Ashraf N. Malhas
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Marek M. Drozdz
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Lior Pytowski
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - David J. Vaux
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
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23
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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: 18] [Impact Index Per Article: 2.6] [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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24
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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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25
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Ranade D, Koul S, Thompson J, Prasad KB, Sengupta K. Chromosomal aneuploidies induced upon Lamin B2 depletion are mislocalized in the interphase nucleus. Chromosoma 2017; 126:223-244. [PMID: 26921073 PMCID: PMC5371638 DOI: 10.1007/s00412-016-0580-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 01/28/2016] [Accepted: 02/09/2016] [Indexed: 12/31/2022]
Abstract
Chromosome territories assume non-random positions in the interphase nucleus with gene-rich chromosomes localized toward the nuclear interior and gene-poor chromosome territories toward the nuclear periphery. Lamins are intermediate filament proteins of the inner nuclear membrane required for the maintenance of nuclear structure and function. Here, we show using whole-genome expression profiling that Lamin A/C or Lamin B2 depletion in an otherwise diploid colorectal cancer cell line (DLD1) deregulates transcript levels from specific chromosomes. Further, three-dimensional fluorescence in situ hybridization (3D-FISH) analyses of a subset of these transcriptionally deregulated chromosome territories revealed that the diploid chromosome territories in Lamin-depleted cells largely maintain conserved positions in the interphase nucleus in a gene-density-dependent manner. In addition, chromosomal aneuploidies were induced in ~25 % of Lamin A/C or Lamin B2-depleted cells. Sub-populations of these aneuploid cells consistently showed a mislocalization of the gene-rich aneuploid chromosome 19 territory toward the nuclear periphery, while gene-poor aneuploid chromosome 18 territory was mislocalized toward the nuclear interior predominantly upon Lamin B2 than Lamin A/C depletion. In addition, a candidate gene locus ZNF570 (Chr.19q13.12) significantly overexpressed upon Lamin B2 depletion was remarkably repositioned away from the nuclear lamina. Taken together, our studies strongly implicate an overarching role for Lamin B2 in the maintenance of nuclear architecture since loss of Lamin B2 relieves the spatial positional constraints required for maintaining conserved localization of aneuploid chromosome territories in the interphase nucleus.
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Affiliation(s)
- Devika Ranade
- Biology, Indian Institute of Science Education and Research, Pune, Main Building, Homi Bhabha Road, Pashan, Pune, Maharashtra, 411008, India
| | - Shivsmriti Koul
- Biology, Indian Institute of Science Education and Research, Pune, Main Building, Homi Bhabha Road, Pashan, Pune, Maharashtra, 411008, India
| | - Joyce Thompson
- Biology, Indian Institute of Science Education and Research, Pune, Main Building, Homi Bhabha Road, Pashan, Pune, Maharashtra, 411008, India
| | - Kumar Brajesh Prasad
- Biology, Indian Institute of Science Education and Research, Pune, Main Building, Homi Bhabha Road, Pashan, Pune, Maharashtra, 411008, India
| | - Kundan Sengupta
- Biology, Indian Institute of Science Education and Research, Pune, Main Building, Homi Bhabha Road, Pashan, Pune, Maharashtra, 411008, India.
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26
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Lukášová E, Kovarˇík A, Bacˇíková A, Falk M, Kozubek S. Loss of lamin B receptor is necessary to induce cellular senescence. Biochem J 2017; 474:281-300. [PMID: 27760841 DOI: 10.1042/bcj20160459] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 10/17/2016] [Accepted: 10/19/2016] [Indexed: 12/16/2023]
Abstract
Cellular transition to senescence is associated with extensive chromatin reorganization and changes in gene expression. Recent studies appear to imply an association of lamin B1 (LB1) reduction with chromatin rearrangement in human fibroblasts promoted to senescence, while the mechanisms and structural features of these relationships have not yet been clarified. In this work, we examined the functions of LB1 and the lamin B receptor (LBR) in human cancer cells. We found that both LB1 and LBR tend to deplete during cancer cell transfer to senescence by γ-irradiation. A functional study employing silencing of LBR by small hairpin ribonucleic acid (shRNA) constructs revealed reduced LB1 levels suggesting that the regulation of both proteins is interrelated. The reduced expression of LBR resulted in the relocation of centromeric heterochromatin (CSH) from the inner nuclear membrane (INM) to the nucleoplasm and is associated with its unfolding. This indicates that LBR tethers heterochromatin to INM in cycling cancer cells and that LB1 is an integral part of this tethering. Down-regulation of LBR and LB1 at the onset of senescence are thus necessary for the release of heterochromatin binding to lamina, resulting in changes in chromatin architecture and gene expression. However, the senescence phenotype was not manifested in cell lines with reduced LBR and LB1 expression suggesting that other factors, such as deoxyribonucleic acid (DNA) damage, are needed to trigger senescence. We conclude that the primary response of cells to various stresses leading to senescence consists of the down-regulation of LBR and LB1 to attain reversal of the chromatin architecture.
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Affiliation(s)
- Emilie Lukášová
- Department of Cell Biology and Radiobiology, Institute of Biophysics, Czech Academy of Sciences, Královopolská 135, Brno 61265, Czech Republic
| | - Aleš Kovarˇík
- Department of Molecular Epigenetics, Institute of Biophysics, Czech Academy of Sciences, Královopolská 135, Brno 61265, Czech Republic
| | - Alena Bacˇíková
- Department of Cell Biology and Radiobiology, Institute of Biophysics, Czech Academy of Sciences, Královopolská 135, Brno 61265, Czech Republic
| | - Martin Falk
- Department of Cell Biology and Radiobiology, Institute of Biophysics, Czech Academy of Sciences, Královopolská 135, Brno 61265, Czech Republic
| | - Stanislav Kozubek
- Department of Cell Biology and Radiobiology, Institute of Biophysics, Czech Academy of Sciences, Královopolská 135, Brno 61265, Czech Republic
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27
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Meaburn KJ. Spatial Genome Organization and Its Emerging Role as a Potential Diagnosis Tool. Front Genet 2016; 7:134. [PMID: 27507988 PMCID: PMC4961005 DOI: 10.3389/fgene.2016.00134] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 07/13/2016] [Indexed: 12/12/2022] Open
Abstract
In eukaryotic cells the genome is highly spatially organized. Functional relevance of higher order genome organization is implied by the fact that specific genes, and even whole chromosomes, alter spatial position in concert with functional changes within the nucleus, for example with modifications to chromatin or transcription. The exact molecular pathways that regulate spatial genome organization and the full implication to the cell of such an organization remain to be determined. However, there is a growing realization that the spatial organization of the genome can be used as a marker of disease. While global genome organization patterns remain largely conserved in disease, some genes and chromosomes occupy distinct nuclear positions in diseased cells compared to their normal counterparts, with the patterns of reorganization differing between diseases. Importantly, mapping the spatial positioning patterns of specific genomic loci can distinguish cancerous tissue from benign with high accuracy. Genome positioning is an attractive novel biomarker since additional quantitative biomarkers are urgently required in many cancer types. Current diagnostic techniques are often subjective and generally lack the ability to identify aggressive cancer from indolent, which can lead to over- or under-treatment of patients. Proof-of-principle for the use of genome positioning as a diagnostic tool has been provided based on small scale retrospective studies. Future large-scale studies are required to assess the feasibility of bringing spatial genome organization-based diagnostics to the clinical setting and to determine if the positioning patterns of specific loci can be useful biomarkers for cancer prognosis. Since spatial reorganization of the genome has been identified in multiple human diseases, it is likely that spatial genome positioning patterns as a diagnostic biomarker may be applied to many diseases.
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Affiliation(s)
- Karen J. Meaburn
- Cell Biology of Genomes Group, National Cancer Institute, National Institutes of HealthBethesda, MD, USA
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28
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Irianto J, Pfeifer CR, Ivanovska IL, Swift J, Discher DE. Nuclear lamins in cancer. Cell Mol Bioeng 2016; 9:258-267. [PMID: 27570565 PMCID: PMC4999255 DOI: 10.1007/s12195-016-0437-8] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 04/12/2016] [Indexed: 01/25/2023] Open
Abstract
Dysmorphic nuclei are commonly seen in cancers and provide strong motivation for studying the main structural proteins of nuclei, the lamins, in cancer. Past studies have also demonstrated the significance of microenvironment mechanics to cancer progression, which is extremely interesting because the lamina was recently shown to be mechanosensitive. Here, we review current knowledge relating cancer progression to lamina biophysics. Lamin levels can constrain cancer cell migration in 3D and thereby impede tumor growth, and lamins can also protect a cancer cell's genome. In addition, lamins can influence transcriptional regulators (RAR, SRF, YAP/TAZ) and chromosome conformation in lamina associated domains. Further investigation of the roles for lamins in cancer and even DNA damage may lead to new therapies or at least to a clearer understanding of lamins as bio-markers in cancer progression.
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Affiliation(s)
- Jerome Irianto
- Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Charlotte R. Pfeifer
- Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Irena L. Ivanovska
- Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joe Swift
- Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Dennis E. Discher
- Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
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29
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Abstract
The nucleus is typically depicted as a sphere encircled by a smooth surface of nuclear envelope. For most cell types, this depiction is accurate. In other cell types and in some pathological conditions, however, the smooth nuclear exterior is interrupted by tubular invaginations of the nuclear envelope, often referred to as a “nucleoplasmic reticulum,” into the deep nuclear interior. We have recently reported a significant expansion of the nucleoplasmic reticulum in postmortem human Alzheimer's disease brain tissue. We found that dysfunction of the nucleoskeleton, a lamin-rich meshwork that coats the inner nuclear membrane and associated invaginations, is causal for Alzheimer's disease-related neurodegeneration in vivo. Additionally, we demonstrated that proper function of the nucleoskeleton is required for survival of adult neurons and maintaining genomic architecture. Here, we elaborate on the significance of these findings in regard to pathological states and physiological aging, and discuss cellular causes and consequences of nuclear envelope invagination.
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Affiliation(s)
- Bess Frost
- a Barshop Institute for Longevity and Aging Studies , Department of Cellular and Structural Biology , University of Texas Health Science Center San Antonio , San Antonio , Texas , USA
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30
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Czapiewski R, Robson MI, Schirmer EC. Anchoring a Leviathan: How the Nuclear Membrane Tethers the Genome. Front Genet 2016; 7:82. [PMID: 27200088 PMCID: PMC4859327 DOI: 10.3389/fgene.2016.00082] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 04/20/2016] [Indexed: 12/21/2022] Open
Abstract
It is well established that the nuclear envelope has many distinct direct connections to chromatin that contribute to genome organization. The functional consequences of genome organization on gene regulation are less clear. Even less understood is how interactions of lamins and nuclear envelope transmembrane proteins (NETs) with chromatin can produce anchoring tethers that can withstand the physical forces of and on the genome. Chromosomes are the largest molecules in the cell, making megadalton protein structures like the nuclear pore complexes and ribosomes seem small by comparison. Thus to withstand strong forces from chromosome dynamics an anchoring tether is likely to be much more complex than a single protein-protein or protein-DNA interaction. Here we will briefly review known NE-genome interactions that likely contribute to spatial genome organization, postulate in the context of experimental data how these anchoring tethers contribute to gene regulation, and posit several hypotheses for the physical nature of these tethers that need to be investigated experimentally. Significantly, disruption of these anchoring tethers and the subsequent consequences for gene regulation could explain how mutations in nuclear envelope proteins cause diseases ranging from muscular dystrophy to lipodystrophy to premature aging progeroid syndromes. The two favored hypotheses for nuclear envelope protein involvement in disease are (1) weakening nuclear and cellular mechanical stability, and (2) disrupting genome organization and gene regulation. Considerable experimental support has been obtained for both. The integration of both mechanical and gene expression defects in the disruption of anchoring tethers could provide a unifying hypothesis consistent with both.
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Affiliation(s)
| | | | - Eric C. Schirmer
- The Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of EdinburghEdinburgh, UK
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31
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Giacomini C, Mahajani S, Ruffilli R, Marotta R, Gasparini L. Lamin B1 protein is required for dendrite development in primary mouse cortical neurons. Mol Biol Cell 2016; 27:35-47. [PMID: 26510501 PMCID: PMC4694760 DOI: 10.1091/mbc.e15-05-0307] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 10/07/2015] [Accepted: 10/23/2015] [Indexed: 01/15/2023] Open
Abstract
Lamin B1, a key component of the nuclear lamina, plays an important role in brain development and function. A duplication of the human lamin B1 (LMNB1) gene has been linked to adult-onset autosomal dominant leukodystrophy, and mouse and human loss-of-function mutations in lamin B1 are susceptibility factors for neural tube defects. In the mouse, experimental ablation of endogenous lamin B1 (Lmnb1) severely impairs embryonic corticogenesis. Here we report that in primary mouse cortical neurons, LMNB1 overexpression reduces axonal outgrowth, whereas deficiency of endogenous Lmnb1 results in aberrant dendritic development. In the absence of Lmnb1, both the length and complexity of dendrites are reduced, and their growth is unresponsive to KCl stimulation. This defective dendritic outgrowth stems from impaired ERK signaling. In Lmnb1-null neurons, ERK is correctly phosphorylated, but phospho-ERK fails to translocate to the nucleus, possibly due to delocalization of nuclear pore complexes (NPCs) at the nuclear envelope. Taken together, these data highlight a previously unrecognized role of lamin B1 in dendrite development of mouse cortical neurons through regulation of nuclear shuttling of specific signaling molecules and NPC distribution.
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Affiliation(s)
- Caterina Giacomini
- Molecular Neurodegeneration Lab, Neuroscience and Brain Technologies Department, 16163 Genoa, Italy
| | - Sameehan Mahajani
- Molecular Neurodegeneration Lab, Neuroscience and Brain Technologies Department, 16163 Genoa, Italy
| | - Roberta Ruffilli
- Electron Microscopy Lab, Nanochemistry Department, Istituto Italiano di Tecnologia, 16163 Genoa, Italy
| | - Roberto Marotta
- Electron Microscopy Lab, Nanochemistry Department, Istituto Italiano di Tecnologia, 16163 Genoa, Italy
| | - Laura Gasparini
- Molecular Neurodegeneration Lab, Neuroscience and Brain Technologies Department, 16163 Genoa, Italy
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32
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Fu Y, Lv P, Yan G, Fan H, Cheng L, Zhang F, Dang Y, Wu H, Wen B. MacroH2A1 associates with nuclear lamina and maintains chromatin architecture in mouse liver cells. Sci Rep 2015; 5:17186. [PMID: 26603343 PMCID: PMC4658601 DOI: 10.1038/srep17186] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 10/26/2015] [Indexed: 12/26/2022] Open
Abstract
In the interphase nucleus, chromatin is organized into three-dimensional conformation to coordinate genome functions. The lamina-chromatin association is important to facilitate higher-order chromatin in mammalian cells, but its biological significances and molecular mechanisms remain poorly understood. One obstacle is that the list of lamina-associated proteins remains limited, presumably due to the inherent insolubility of lamina proteins. In this report, we identified 182 proteins associated with lamin B1 (a constitutive component of lamina) in mouse hepatocytes, by adopting virus-based proximity-dependent biotin identification. These proteins are functionally related to biological processes such as chromatin organization. As an example, we validated the association between lamin B1 and core histone macroH2A1, a histone associated with repressive chromatin. Furthermore, we mapped Lamina-associated domains (LADs) in mouse liver cells and found that boundaries of LADs are enriched for macroH2A. More interestingly, knocking-down of macroH2A1 resulted in the release of heterochromatin foci marked by histone lysine 9 trimethylation (H3K9me3) and the decondensation of global chromatin structure. However, down-regulation of lamin B1 led to redistribution of macroH2A1. Taken together, our data indicated that macroH2A1 is associated with lamina and is required to maintain chromatin architecture in mouse liver cells.
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Affiliation(s)
- Yuhua Fu
- Key Laboratory of Molecular Medicine of Ministry of Education and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Pin Lv
- Key Laboratory of Molecular Medicine of Ministry of Education and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Guoquan Yan
- Key Laboratory of Molecular Medicine of Ministry of Education and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Department of Chemistry, Fudan University, Shanghai, 200433
| | - Hui Fan
- Key Laboratory of Molecular Medicine of Ministry of Education and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Lu Cheng
- Key Laboratory of Molecular Medicine of Ministry of Education and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Feng Zhang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yongjun Dang
- Key Laboratory of Molecular Medicine of Ministry of Education and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Hao Wu
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA 30322, USA
| | - Bo Wen
- Key Laboratory of Molecular Medicine of Ministry of Education and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
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33
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Bhattacharjee P, Dasgupta D, Sengupta K. Molecular Events in Lamin B1 Homopolymerization: A Biophysical Characterization. J Phys Chem B 2015; 119:14014-21. [PMID: 26465373 DOI: 10.1021/acs.jpcb.5b07320] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Lamin B1 is one of the major constituents of the nuclear lamina, a filamentous network underlying the nucleoplasmic side of the inner nuclear membrane. Homopolymerization of lamin B1, coupled to the homotypic and heterotypic association of other lamin types, is central to building the higher order network pattern inside the nucleus. This in turn maintains the mechanical and functional integrity of the lamina. We have characterized the molecular basis of the self-association of lamin B1 using spectroscopic and calorimetric methods. We report that concentration dependent lamin B1 oligomerization involves significant alterations in secondary and tertiary structures of the protein resulting in fairly observable compaction in size. Comparison of the energetics of the homotypic association of lamin B1 with that of lamin A reported earlier led to the finding that lamin A oligomers had higher thermodynamic stability. This leads us to conjecture that lamin B1 has less stress bearing ability compared to lamin A.
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Affiliation(s)
- Pritha Bhattacharjee
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics , 1/AF Bidhannagar, Kolkata-700064, India
| | - Dipak Dasgupta
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics , 1/AF Bidhannagar, Kolkata-700064, India
| | - Kaushik Sengupta
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics , 1/AF Bidhannagar, Kolkata-700064, India
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34
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Chromatin at the nuclear periphery and the regulation of genome functions. Histochem Cell Biol 2015; 144:111-22. [PMID: 26170147 DOI: 10.1007/s00418-015-1346-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/28/2015] [Indexed: 01/01/2023]
Abstract
Chromatin is not randomly organized in the nucleus, and its spatial organization participates in the regulation of genome functions. However, this spatial organization is also not entirely fixed and modifications of chromatin architecture are implicated in physiological processes such as differentiation or senescence. One of the most striking features of chromatin architecture is the concentration of heterochromatin at the nuclear periphery. A closer examination of the association of chromatin at the nuclear periphery reveals that heterochromatin accumulates at the nuclear lamina, whereas nuclear pores are usually devoid of heterochromatin. After summarizing the current techniques used to study the attachment of chromatin at the nuclear lamina or the nuclear pores, we review the mechanisms underlying these attachments, their plasticity and their consequences on the regulation of gene expression, DNA repair and replication.
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35
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Giorgio E, Robyr D, Spielmann M, Ferrero E, Di Gregorio E, Imperiale D, Vaula G, Stamoulis G, Santoni F, Atzori C, Gasparini L, Ferrera D, Canale C, Guipponi M, Pennacchio LA, Antonarakis SE, Brussino A, Brusco A. A large genomic deletion leads to enhancer adoption by the lamin B1 gene: a second path to autosomal dominant adult-onset demyelinating leukodystrophy (ADLD). Hum Mol Genet 2015; 24:3143-54. [PMID: 25701871 PMCID: PMC4424952 DOI: 10.1093/hmg/ddv065] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 02/13/2015] [Indexed: 01/23/2023] Open
Abstract
Chromosomal rearrangements with duplication of the lamin B1 (LMNB1) gene underlie autosomal dominant adult-onset demyelinating leukodystrophy (ADLD), a rare neurological disorder in which overexpression of LMNB1 causes progressive central nervous system demyelination. However, we previously reported an ADLD family (ADLD-1-TO) without evidence of duplication or other mutation in LMNB1 despite linkage to the LMNB1 locus and lamin B1 overexpression. By custom array-CGH, we further investigated this family and report here that patients carry a large (∼660 kb) heterozygous deletion that begins 66 kb upstream of the LMNB1 promoter. Lamin B1 overexpression was confirmed in further ADLD-1-TO tissues and in a postmortem brain sample, where lamin B1 was increased in the frontal lobe. Through parallel studies, we investigated both loss of genetic material and chromosomal rearrangement as possible causes of LMNB1 overexpression, and found that ADLD-1-TO plausibly results from an enhancer adoption mechanism. The deletion eliminates a genome topological domain boundary, allowing normally forbidden interactions between at least three forebrain-directed enhancers and the LMNB1 promoter, in line with the observed mainly cerebral localization of lamin B1 overexpression and myelin degeneration. This second route to LMNB1 overexpression and ADLD is a new example of the relevance of regulatory landscape modifications in determining Mendelian phenotypes.
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Affiliation(s)
- Elisa Giorgio
- Department of Medical Sciences, University of Torino, via Santena, 19, Torino 10126, Italy
| | - Daniel Robyr
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva 1211, Switzerland
| | - Malte Spielmann
- Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, Berlin 14195, Germany
| | - Enza Ferrero
- Department of Medical Sciences, University of Torino, via Santena, 19, Torino 10126, Italy
| | - Eleonora Di Gregorio
- Department of Medical Sciences, University of Torino, via Santena, 19, Torino 10126, Italy Medical Genetics Unit and
| | - Daniele Imperiale
- Centro Regionale Malattie Da Prioni - Domp (ASLTO2), Torino 10144, Italy
| | - Giovanna Vaula
- Department of Neurology, Città della Salute e della Scienza University Hospital, Torino 10126, Italy
| | - Georgios Stamoulis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva 1211, Switzerland
| | - Federico Santoni
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva 1211, Switzerland
| | - Cristiana Atzori
- Centro Regionale Malattie Da Prioni - Domp (ASLTO2), Torino 10144, Italy
| | | | | | - Claudio Canale
- Department of Nanophysics, Istituto Italiano di Tecnologia, Genoa 16163, Italy and
| | - Michel Guipponi
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva 1211, Switzerland
| | - Len A Pennacchio
- Genomics Division, Lawrence Berkeley National Laboratory, MS 84-171, Berkeley, CA 9472, USA
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva 1211, Switzerland
| | - Alessandro Brussino
- Department of Medical Sciences, University of Torino, via Santena, 19, Torino 10126, Italy
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, via Santena, 19, Torino 10126, Italy Medical Genetics Unit and
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36
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Bartoletti-Stella A, Gasparini L, Giacomini C, Corrado P, Terlizzi R, Giorgio E, Magini P, Seri M, Baruzzi A, Parchi P, Brusco A, Cortelli P, Capellari S. Messenger RNA processing is altered in autosomal dominant leukodystrophy. Hum Mol Genet 2015; 24:2746-56. [PMID: 25637521 PMCID: PMC4406291 DOI: 10.1093/hmg/ddv034] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Accepted: 01/27/2015] [Indexed: 02/06/2023] Open
Abstract
Adult-onset autosomal dominant leukodystrophy (ADLD) is a slowly progressive neurological disorder characterized by autonomic dysfunction, followed by cerebellar and pyramidal features. ADLD is caused by duplication of the lamin B1 gene (LMNB1), which leads to its increased expression. The molecular pathways involved in the disease are still poorly understood. Hence, we analyzed global gene expression in fibroblasts and whole blood of LMNB1 duplication carriers and used Gene Set Enrichment Analysis to explore their gene signatures. We found that LMNB1 duplication is associated with dysregulation of genes involved in the immune system, neuronal and skeletal development. Genes with an altered transcriptional profile clustered in specific genomic regions. Among the dysregulated genes, we further studied the role of RAVER2, which we found to be overexpressed at mRNA and protein level. RAVER2 encodes a putative trans regulator of the splicing repressor polypyrimidine tract binding protein (PTB) and is likely implicated in alternative splicing regulation. Functional studies demonstrated an abnormal splicing pattern of several PTB-target genes and of the myelin protein gene PLP1, previously demonstrated to be involved in ADLD. Mutant mice with different lamin B1 expression levels confirmed that Raver2 expression is dependent on lamin B1 in neural tissue and determines an altered splicing pattern of PTB-target genes and Plp1. Overall our results demonstrate that deregulation of lamin B1 expression induces modified splicing of several genes, likely driven by raver-2 overexpression, and suggest that an alteration of mRNA processing could be a pathogenic mechanism in ADLD.
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Affiliation(s)
- Anna Bartoletti-Stella
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna 40123, Italy
| | - Laura Gasparini
- Department of Neuroscience and Brain Techonologies, Istituto Italiano di Tecnologia, Genova 16163, Italy
| | - Caterina Giacomini
- Department of Neuroscience and Brain Techonologies, Istituto Italiano di Tecnologia, Genova 16163, Italy
| | - Patrizia Corrado
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna 40123, Italy
| | - Rossana Terlizzi
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna 40123, Italy, IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Ospedale Bellaria, Bologna 40139, Italy
| | - Elisa Giorgio
- Department of Medical Sciences, University of Torino, Torino 10126, Italy
| | - Pamela Magini
- Medical Genetics Unit, Department of Medical and Surgical Sciences, University of Bologna 40138, Italy and
| | - Marco Seri
- Medical Genetics Unit, Department of Medical and Surgical Sciences, University of Bologna 40138, Italy and
| | - Agostino Baruzzi
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Ospedale Bellaria, Bologna 40139, Italy
| | - Piero Parchi
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna 40123, Italy, IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Ospedale Bellaria, Bologna 40139, Italy
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, Torino 10126, Italy, Città della Salute e della Scienza, University Hospital, Medical Genetics Unit, Torino 10126, Italy
| | - Pietro Cortelli
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna 40123, Italy, IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Ospedale Bellaria, Bologna 40139, Italy
| | - Sabina Capellari
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna 40123, Italy, IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Ospedale Bellaria, Bologna 40139, Italy,
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37
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Amendola M, van Steensel B. Nuclear lamins are not required for lamina-associated domain organization in mouse embryonic stem cells. EMBO Rep 2015; 16:610-7. [PMID: 25784758 DOI: 10.15252/embr.201439789] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 02/16/2015] [Indexed: 11/09/2022] Open
Abstract
In mammals, the nuclear lamina interacts with hundreds of large genomic regions, termed lamina-associated domains (LADs) that are generally in a transcriptionally repressed state. Lamins form the major structural component of the lamina and have been reported to bind DNA and chromatin. Here, we systematically evaluate whether lamins are necessary for the LAD organization in murine embryonic stem cells. Surprisingly, removal of essentially all lamins does not have any detectable effect on the genome-wide interaction pattern of chromatin with emerin, a marker of the inner nuclear membrane. This suggests that other components of the lamina mediate these interactions.
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Affiliation(s)
- Mario Amendola
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Bas van Steensel
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands
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38
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Gruenbaum Y, Foisner R. Lamins: nuclear intermediate filament proteins with fundamental functions in nuclear mechanics and genome regulation. Annu Rev Biochem 2015; 84:131-64. [PMID: 25747401 DOI: 10.1146/annurev-biochem-060614-034115] [Citation(s) in RCA: 368] [Impact Index Per Article: 40.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Lamins are intermediate filament proteins that form a scaffold, termed nuclear lamina, at the nuclear periphery. A small fraction of lamins also localize throughout the nucleoplasm. Lamins bind to a growing number of nuclear protein complexes and are implicated in both nuclear and cytoskeletal organization, mechanical stability, chromatin organization, gene regulation, genome stability, differentiation, and tissue-specific functions. The lamin-based complexes and their specific functions also provide insights into possible disease mechanisms for human laminopathies, ranging from muscular dystrophy to accelerated aging, as observed in Hutchinson-Gilford progeria and atypical Werner syndromes.
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Affiliation(s)
- Yosef Gruenbaum
- Department of Genetics, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel;
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39
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Ma Y, Kanakousaki K, Buttitta L. How the cell cycle impacts chromatin architecture and influences cell fate. Front Genet 2015; 6:19. [PMID: 25691891 PMCID: PMC4315090 DOI: 10.3389/fgene.2015.00019] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 01/14/2015] [Indexed: 01/17/2023] Open
Abstract
Since the earliest observations of cells undergoing mitosis, it has been clear that there is an intimate relationship between the cell cycle and nuclear chromatin architecture. The nuclear envelope and chromatin undergo robust assembly and disassembly during the cell cycle, and transcriptional and post-transcriptional regulation of histone biogenesis and chromatin modification is controlled in a cell cycle-dependent manner. Chromatin binding proteins and chromatin modifications in turn influence the expression of critical cell cycle regulators, the accessibility of origins for DNA replication, DNA repair, and cell fate. In this review we aim to provide an integrated discussion of how the cell cycle machinery impacts nuclear architecture and vice-versa. We highlight recent advances in understanding cell cycle-dependent histone biogenesis and histone modification deposition, how cell cycle regulators control histone modifier activities, the contribution of chromatin modifications to origin firing for DNA replication, and newly identified roles for nucleoporins in regulating cell cycle gene expression, gene expression memory and differentiation. We close with a discussion of how cell cycle status may impact chromatin to influence cell fate decisions, under normal contexts of differentiation as well as in instances of cell fate reprogramming.
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Affiliation(s)
- Yiqin Ma
- Department of Molecular, Cellular and Developmental Biology, University of Michigan , Ann Arbor, MI, USA
| | - Kiriaki Kanakousaki
- Department of Molecular, Cellular and Developmental Biology, University of Michigan , Ann Arbor, MI, USA
| | - Laura Buttitta
- Department of Molecular, Cellular and Developmental Biology, University of Michigan , Ann Arbor, MI, USA
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Camps J, Erdos MR, Ried T. The role of lamin B1 for the maintenance of nuclear structure and function. Nucleus 2015; 6:8-14. [PMID: 25602590 PMCID: PMC4615282 DOI: 10.1080/19491034.2014.1003510] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 11/24/2014] [Accepted: 11/25/2014] [Indexed: 12/22/2022] Open
Abstract
Lamins constitute an integral structural component of the nuclear lamina. However, their impact on the structure and stability of chromosome territories, and on the regulation of gene expression is explored to a lesser extent. By 3D-FISH, Camps and colleagues showed that lamin B1 (LMNB1) is required for proper chromosome condensation in interphase nuclei, and deficiency of LMNB1 triggers the relocation of the epigenetic mark of facultative heterochromatin, H3K27me3, toward the interior of the nucleus. Additionally, LMNB1 repression slowed cellular growth due to S-phase delays and increased genomic instability. Finally, silencing of LMNB1 resulted in enlarged nuclear speckles and in extensive changes in alternative splicing of multiple genes. Altogether, the data suggest a central role of LMNB1 for the condensation of chromosome territories, for the distribution of heterochromatin, and for the regulation of gene expression and splicing.
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Affiliation(s)
- Jordi Camps
- Laboratory of Gastrointestinal and Pancreatic Oncology; Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS); Hospital Clínic of Barcelona, CIBERehd; Barcelona, Spain
| | - Michael R Erdos
- Genome Technology Branch; National Human Genome Research Institute; National Institutes of Health; Bethesda, MD USA
| | - Thomas Ried
- Section of Cancer Genomics, Genetics Branch; National Cancer Institute; National Institutes of Health; Bethesda, MD USA
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41
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Ramdas NM, Shivashankar GV. Cytoskeletal control of nuclear morphology and chromatin organization. J Mol Biol 2014; 427:695-706. [PMID: 25281900 DOI: 10.1016/j.jmb.2014.09.008] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 09/03/2014] [Accepted: 09/06/2014] [Indexed: 02/06/2023]
Abstract
The nucleus is sculpted toward various morphologies during cellular differentiation and development. Alterations in nuclear shape often result in changes to chromatin organization and genome function. This is thought to be reflective of its role as a cellular mechanotransducer. Recent evidence has highlighted the importance of cytoskeletal organization in defining how nuclear morphology regulates chromatin dynamics. However, the mechanisms underlying cytoskeletal control of chromatin remodeling are not well understood. We demonstrate here the differential influence of perinuclear actin- and microtubule-driven assemblies on nuclear architecture using pharmacological inhibitors and targeted RNA interference knockdown of cytoskeleton components in Drosophila cells. We find evidence that the loss of perinuclear actin assembly results in basolateral enhancement of microtubule organization and this is reflected functionally by enhanced nuclear dynamics. Cytoskeleton reorganization leads to nuclear lamina deformation that influences heterochromatin localization and core histone protein mobility. We also show that modulations in actin-microtubule assembly result in differential gene expression patterns. Taken together, we suggest that perinuclear actin and basolateral microtubule organization exerts mechanical control on nuclear morphology and chromatin dynamics.
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Affiliation(s)
- Nisha M Ramdas
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560 065, India
| | - G V Shivashankar
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, 21 Lower Kent Ridge Road 119077, Singapore.
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42
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Camps J, Wangsa D, Falke M, Brown M, Case CM, Erdos MR, Ried T. Loss of lamin B1 results in prolongation of S phase and decondensation of chromosome territories. FASEB J 2014; 28:3423-34. [PMID: 24732130 PMCID: PMC4101663 DOI: 10.1096/fj.14-250456] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 04/07/2014] [Indexed: 01/04/2023]
Abstract
Nuclear lamin B1 (LMNB1) constitutes one of the major structural proteins in the lamina mesh. We silenced the expression of LMNB1 by RNA interference in the colon cancer cell line DLD-1 and showed a dramatic redistribution of H3K27me3 from the periphery to a more homogeneous nuclear dispersion. In addition, we observed telomere attrition and an increased frequency of micronuclei and nuclear blebs. By 3D-FISH analyses, we demonstrated that the volume and surface of chromosome territories were significantly larger in LMNB1-depleted cells, suggesting that LMNB1 is required to maintain chromatin condensation in interphase nuclei. These changes led to a prolonged S phase due to activation of Chk1. Finally, silencing of LMNB1 resulted in extensive changes in alternative splicing of multiple genes and in a higher number of enlarged nuclear speckles. Taken together, our results suggest a mechanistic role of the nuclear lamina in the organization of chromosome territories, maintenance of genome integrity and proper gene splicing.
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Affiliation(s)
- Jordi Camps
- Section of Cancer Genomics, Genetics Branch, National Cancer Institute, and
| | - Darawalee Wangsa
- Section of Cancer Genomics, Genetics Branch, National Cancer Institute, and
| | - Martin Falke
- Section of Cancer Genomics, Genetics Branch, National Cancer Institute, and
| | - Markus Brown
- Section of Cancer Genomics, Genetics Branch, National Cancer Institute, and
| | - Chanelle M Case
- Section of Cancer Genomics, Genetics Branch, National Cancer Institute, and
| | - Michael R Erdos
- Genome Technology Branch, National Human Genome Research Institute, U.S. National Institutes of Health, Bethesda, Maryland, USA
| | - Thomas Ried
- Section of Cancer Genomics, Genetics Branch, National Cancer Institute, and
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43
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Amendola M, van Steensel B. Mechanisms and dynamics of nuclear lamina–genome interactions. Curr Opin Cell Biol 2014; 28:61-8. [DOI: 10.1016/j.ceb.2014.03.003] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 03/06/2014] [Accepted: 03/08/2014] [Indexed: 12/21/2022]
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44
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Lee JM, Tu Y, Tatar A, Wu D, Nobumori C, Jung HJ, Yoshinaga Y, Coffinier C, de Jong PJ, Fong LG, Young SG. Reciprocal knock-in mice to investigate the functional redundancy of lamin B1 and lamin B2. Mol Biol Cell 2014; 25:1666-75. [PMID: 24672053 PMCID: PMC4019497 DOI: 10.1091/mbc.e14-01-0683] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 03/14/2014] [Accepted: 03/14/2014] [Indexed: 11/17/2022] Open
Abstract
Lamins B1 and B2 (B-type lamins) have very similar sequences and are expressed ubiquitously. In addition, both Lmnb1- and Lmnb2-deficient mice die soon after birth with neuronal layering abnormalities in the cerebral cortex, a consequence of defective neuronal migration. The similarities in amino acid sequences, expression patterns, and knockout phenotypes raise the question of whether the two proteins have redundant functions. To investigate this topic, we generated "reciprocal knock-in mice"-mice that make lamin B2 from the Lmnb1 locus (Lmnb1(B2/B2)) and mice that make lamin B1 from the Lmnb2 locus (Lmnb2(B1/B1)). Lmnb1(B2/B2) mice produced increased amounts of lamin B2 but no lamin B1; they died soon after birth with neuronal layering abnormalities in the cerebral cortex. However, the defects in Lmnb1(B2/B2) mice were less severe than those in Lmnb1-knockout mice, indicating that increased amounts of lamin B2 partially ameliorate the abnormalities associated with lamin B1 deficiency. Similarly, increased amounts of lamin B1 in Lmnb2(B1/B1) mice did not prevent the neurodevelopmental defects elicited by lamin B2 deficiency. We conclude that lamins B1 and B2 have unique roles in the developing brain and that increased production of one B-type lamin does not fully complement loss of the other.
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Affiliation(s)
- John M Lee
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095
| | - Yiping Tu
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095
| | - Angelica Tatar
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095
| | - Daniel Wu
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095
| | - Chika Nobumori
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095
| | - Hea-Jin Jung
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095
| | - Yuko Yoshinaga
- Children's Hospital Oakland Research Institute, Oakland, CA 94609
| | - Catherine Coffinier
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095
| | - Pieter J de Jong
- Children's Hospital Oakland Research Institute, Oakland, CA 94609
| | - Loren G Fong
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095
| | - Stephen G Young
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095
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45
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Malhas AN, Vaux DJ. Nuclear envelope invaginations and cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 773:523-35. [PMID: 24563364 DOI: 10.1007/978-1-4899-8032-8_24] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The nuclear envelope (NE) surrounds the nucleus and separates it from the cytoplasm. The NE is not a passive structural component, but rather contributes to various cellular processes such as genome organization, transcription, signaling, and stress responses. Although the NE is mostly a smooth surface, it also forms invaginations that can reach deep into the nucleoplasm and may even traverse the nucleus completely. Cancer cells are generally characterized by irregularities and invaginations of the NE that are of diagnostic and prognostic significance. In the current chapter, we describe the link between nuclear invaginations and irregularities with cancer and explore possible mechanistic roles they might have in tumorigenesis.
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Affiliation(s)
- Ashraf N Malhas
- Sir William Dunn School of Pathology, South Parks Road, Oxford, OX1 3RE, UK,
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46
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Wazir U, Ahmed MH, Bridger JM, Harvey A, Jiang WG, Sharma AK, Mokbel K. The clinicopathological significance of lamin A/C, lamin B1 and lamin B receptor mRNA expression in human breast cancer. Cell Mol Biol Lett 2013; 18:595-611. [PMID: 24293108 PMCID: PMC6275779 DOI: 10.2478/s11658-013-0109-9] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2013] [Accepted: 11/25/2013] [Indexed: 12/26/2022] Open
Abstract
Lamin A/C (LMNA), lamin B1 (LMNB1) and lamin B receptor (LBR) have key roles in nuclear structural integrity and chromosomal stability. In this study, we have studied the relationships between the mRNA expressions of A-type lamins, LMNB1 and LBR and the clinicopathological parameters in human breast cancer. Samples of breast cancer tissues (n = 115) and associated non-cancerous tissue (ANCT; n = 30) were assessed using reverse transcription and quantitative PCR. Transcript levels were correlated with clinicopathological data. Higher levels of A-type lamins and LMNB1 mRNA expression were seen in ANCT. Higher lamin A/C expression was associated with the early clinical stage (TNM1 vs. TNM3 - 13 vs. 0.21; p = 0.0515), with better clinical outcomes (disease-free survival vs. mortality - 11 vs. 1; p = 0.0326), and with better overall (p = 0.004) and disease-free survival (p = 0.062). The expression of LMNB1 declined with worsening clinical outcome (disease-free vs. mortalities - 0.0011 vs. 0.000; p = 0.0177). LBR mRNA expression was directly associated with tumor grade (grade 1 vs. grade 3 - 0.00 vs. 0.00; p = 0.0479) and Nottingham Prognostic Index (NPI1 vs. NPI3 - 0.00 vs. 0.00; p = 0.0551). To the best of our knowledge, this is the first study to suggest such a role for A-type lamins, lamin B1 and LBR in human breast cancer, identifying an important area for further research.
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Affiliation(s)
- Umar Wazir
- The London Breast Institute, Princess Grace Hospital, London, UK
- Department of Breast Surgery, St. George’s Hospital and Medical School, University of London, London, UK
| | - Mai Hassan Ahmed
- Centre for Cell & Chromosome Biology, Uxbridge, London, UK
- Brunel Institute for Cancer Genetics and Pharmacogenomics, School of Health Sciences and Social Care, Brunel University, Uxbridge, London, UK
| | | | - Amanda Harvey
- Brunel Institute for Cancer Genetics and Pharmacogenomics, School of Health Sciences and Social Care, Brunel University, Uxbridge, London, UK
| | - Wen G. Jiang
- Metastasis and Angiogenesis Research Group, University Department of Surgery, Cardiff University School of Medicine, Cardiff University, Cardiff, Wales, UK
| | - Anup K. Sharma
- The London Breast Institute, Princess Grace Hospital, London, UK
| | - Kefah Mokbel
- London Breast Institute, the Princess Grace Hospital, 45 Nottingham Place, London, W1U 5NY UK
- The London Breast Institute, Princess Grace Hospital, London, UK
- Department of Breast Surgery, St. George’s Hospital and Medical School, University of London, London, UK
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47
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Sadaie M, Salama R, Carroll T, Tomimatsu K, Chandra T, Young AR, Narita M, Pérez-Mancera PA, Bennett DC, Chong H, Kimura H, Narita M. Redistribution of the Lamin B1 genomic binding profile affects rearrangement of heterochromatic domains and SAHF formation during senescence. Genes Dev 2013; 27:1800-8. [PMID: 23964094 PMCID: PMC3759696 DOI: 10.1101/gad.217281.113] [Citation(s) in RCA: 213] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 07/22/2013] [Indexed: 12/14/2022]
Abstract
Senescence is a stress-responsive form of stable cell cycle exit. Senescent cells have a distinct gene expression profile, which is often accompanied by the spatial redistribution of heterochromatin into senescence-associated heterochromatic foci (SAHFs). Studying a key component of the nuclear lamina lamin B1 (LMNB1), we report dynamic alterations in its genomic profile and their implications for SAHF formation and gene regulation during senescence. Genome-wide mapping reveals that LMNB1 is depleted during senescence, preferentially from the central regions of lamina-associated domains (LADs), which are enriched for Lys9 trimethylation on histone H3 (H3K9me3). LMNB1 knockdown facilitates the spatial relocalization of perinuclear H3K9me3-positive heterochromatin, thus promoting SAHF formation, which could be inhibited by ectopic LMNB1 expression. Furthermore, despite the global reduction in LMNB1 protein levels, LMNB1 binding increases during senescence in a small subset of gene-rich regions where H3K27me3 also increases and gene expression becomes repressed. These results suggest that LMNB1 may contribute to senescence in at least two ways due to its uneven genome-wide redistribution: first, through the spatial reorganization of chromatin and, second, through gene repression.
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Affiliation(s)
- Mahito Sadaie
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Rafik Salama
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Thomas Carroll
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Kosuke Tomimatsu
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
- Research Centre for Bioscience and Technology, Tottori University, Tottori 683-8503, Japan
| | - Tamir Chandra
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Andrew R.J. Young
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Masako Narita
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Pedro A. Pérez-Mancera
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Dorothy C. Bennett
- Biomedical Sciences Research Centre, St. George's, University of London, London SW17 0RE, United Kingdom
| | - Heung Chong
- Cellular Pathology, Division of Biomedical Sciences, St. George's, University of London, London SW17 0RE, United Kingdom
| | - Hiroshi Kimura
- Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan
| | - Masashi Narita
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
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48
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Wong JJL, Ritchie W, Ebner OA, Selbach M, Wong JWH, Huang Y, Gao D, Pinello N, Gonzalez M, Baidya K, Thoeng A, Khoo TL, Bailey CG, Holst J, Rasko JEJ. Orchestrated intron retention regulates normal granulocyte differentiation. Cell 2013; 154:583-95. [PMID: 23911323 DOI: 10.1016/j.cell.2013.06.052] [Citation(s) in RCA: 334] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 05/01/2013] [Accepted: 06/28/2013] [Indexed: 12/11/2022]
Abstract
Intron retention (IR) is widely recognized as a consequence of mis-splicing that leads to failed excision of intronic sequences from pre-messenger RNAs. Our bioinformatic analyses of transcriptomic and proteomic data of normal white blood cell differentiation reveal IR as a physiological mechanism of gene expression control. IR regulates the expression of 86 functionally related genes, including those that determine the nuclear shape that is unique to granulocytes. Retention of introns in specific genes is associated with downregulation of splicing factors and higher GC content. IR, conserved between human and mouse, led to reduced mRNA and protein levels by triggering the nonsense-mediated decay (NMD) pathway. In contrast to the prevalent view that NMD is limited to mRNAs encoding aberrant proteins, our data establish that IR coupled with NMD is a conserved mechanism in normal granulopoiesis. Physiological IR may provide an energetically favorable level of dynamic gene expression control prior to sustained gene translation.
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Affiliation(s)
- Justin J-L Wong
- Gene and Stem Cell Therapy Program, Centenary Institute, Camperdown 2050, Australia
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49
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Wei Z, Huang D, Gao F, Chang WH, An W, Coetzee GA, Wang K, Lu W. Biological implications and regulatory mechanisms of long-range chromosomal interactions. J Biol Chem 2013; 288:22369-77. [PMID: 23779110 DOI: 10.1074/jbc.r113.485292] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Development of high-throughput sequencing-based methods has enabled us to examine nuclear architecture at unprecedented resolution, allowing further examination of the function of long-range chromosomal interactions. Here, we review methods used to investigate novel long-range chromosomal interactions and genome-wide organization of chromatin. We further discuss transcriptional activation and silencing in relation to organization and positioning of gene loci and regulation of chromatin organization through protein complexes and noncoding RNAs.
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Affiliation(s)
- Zong Wei
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA
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50
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Robinson A, Partridge D, Malhas A, De Castro SCP, Gustavsson P, Thompson DN, Vaux DJ, Copp AJ, Stanier P, Bassuk AG, Greene NDE. Is LMNB1 a susceptibility gene for neural tube defects in humans? BIRTH DEFECTS RESEARCH. PART A, CLINICAL AND MOLECULAR TERATOLOGY 2013; 97:398-402. [PMID: 23733478 PMCID: PMC3738925 DOI: 10.1002/bdra.23141] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 03/13/2013] [Accepted: 03/27/2013] [Indexed: 01/09/2023]
Abstract
BACKGROUND Lamins are intermediate filament proteins that form a major component of the nuclear lamina, a protein complex at the surface of the inner nuclear membrane. Numerous clinically diverse conditions, termed laminopathies, have been found to result from mutation of LMNA. In contrast, coding or loss of function mutations of LMNB1, encoding lamin B1, have not been identified in human disease. In mice, polymorphism in Lmnb1 has been shown to modify risk of neural tube defects (NTDs), malformations of the central nervous system that result from incomplete closure of the neural folds. METHODS Mutation analysis by DNA sequencing was performed on all exons of LMNB1 in 239 samples from patients with NTDs from the United Kingdom, Sweden, and United States. Possible functional effects of missense variants were analyzed by bioinformatics prediction and fluorescence in photobleaching. RESULTS In NTD patients, we identified two unique missense variants that were predicted to disrupt protein structure/function and represent putative contributory mutations. Fluorescence loss in photobleaching analysis showed that the A436T variant compromised stability of lamin B1 interaction within the lamina. CONCLUSION The genetic basis of human NTDs appears highly heterogenous with possible involvement of multiple predisposing genes. We hypothesize that rare variants of LMNB1 may contribute to susceptibility to NTDs.
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Affiliation(s)
- Alexis Robinson
- Neural Development Unit and Newlife Birth Defects Research Centre, Institute of Child Health, University College LondonUnited Kingdom
| | - Darren Partridge
- Neural Development Unit and Newlife Birth Defects Research Centre, Institute of Child Health, University College LondonUnited Kingdom
| | - Ashraf Malhas
- Sir William Dunn School of Pathology, University of OxfordUnited Kingdom
| | - Sandra CP De Castro
- Neural Development Unit and Newlife Birth Defects Research Centre, Institute of Child Health, University College LondonUnited Kingdom
| | - Peter Gustavsson
- Department of Molecular Medicine and Surgery, Karolinska InstitutetStockholm, Sweden
| | - Dominic N Thompson
- Department of Neurosurgery, Great Ormond Street Hospital for Children NHS TrustLondon, United Kingdom
| | - David J Vaux
- Sir William Dunn School of Pathology, University of OxfordUnited Kingdom
| | - Andrew J Copp
- Neural Development Unit and Newlife Birth Defects Research Centre, Institute of Child Health, University College LondonUnited Kingdom
| | - Philip Stanier
- Neural Development Unit and Newlife Birth Defects Research Centre, Institute of Child Health, University College LondonUnited Kingdom
| | | | - Nicholas DE Greene
- Neural Development Unit and Newlife Birth Defects Research Centre, Institute of Child Health, University College LondonUnited Kingdom
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