1
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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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2
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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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3
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Ikegami K, Secchia S, Almakki O, Lieb JD, Moskowitz IP. Phosphorylated Lamin A/C in the Nuclear Interior Binds Active Enhancers Associated with Abnormal Transcription in Progeria. Dev Cell 2020; 52:699-713.e11. [PMID: 32208162 DOI: 10.1016/j.devcel.2020.02.011] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 12/13/2019] [Accepted: 02/13/2020] [Indexed: 02/06/2023]
Abstract
LMNA encodes nuclear Lamin A/C that tethers lamina-associated domains (LADs) to the nuclear periphery. Mutations in LMNA cause degenerative disorders including the premature aging disorder Hutchinson-Gilford progeria, but the mechanisms are unknown. We report that Ser22-phosphorylated (pS22) Lamin A/C was localized to the nuclear interior in human fibroblasts throughout the cell cycle. pS22-Lamin A/C interacted with a subset of putative active enhancers, not LADs, at locations co-bound by the transcriptional activator c-Jun. In progeria-patient fibroblasts, a subset of pS22-Lamin A/C-binding sites were lost, whereas new pS22-Lamin A/C-binding sites emerged in normally quiescent loci. New pS22-Lamin A/C binding was accompanied by increased histone acetylation, increased c-Jun binding, and upregulation of nearby genes implicated in progeria pathophysiology. These results suggest that Lamin A/C regulates gene expression by enhancer binding. Disruption of the gene regulatory rather than LAD tethering function of Lamin A/C may underlie the pathogenesis of disorders caused by LMNA mutations.
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Affiliation(s)
- Kohta Ikegami
- Department of Pediatrics, The University of Chicago, Chicago, IL 60637, USA; Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA.
| | - Stefano Secchia
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA; Department of Biology, Lunds University, Lund 22362, Sweden
| | - Omar Almakki
- Department of Pediatrics, The University of Chicago, Chicago, IL 60637, USA
| | - Jason D Lieb
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
| | - Ivan P Moskowitz
- Department of Pediatrics, The University of Chicago, Chicago, IL 60637, USA; Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA; Department of Pathology, The University of Chicago, Chicago, IL 60637, USA
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4
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Richardson A, Zentz ZA, Chambers AE, Sandwith SN, Reisinger MA, Saunders DW, Tompkins JD, Riggs AD, Routh ED, Rubenstein EM, Smaldino MA, Vaughn JP, Haney RA, Smaldino PJ. G-Quadruplex Helicase DHX36/G4R1 Engages Nuclear Lamina Proteins in Quiescent Breast Cancer Cells. ACS OMEGA 2020; 5:24916-24926. [PMID: 33015511 PMCID: PMC7528498 DOI: 10.1021/acsomega.0c03723] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 08/21/2020] [Indexed: 06/11/2023]
Abstract
G-quadruplexes (G4s) are nucleic acid structures found enriched within gene regulatory sequences. G4s control fundamental cellular processes, including replication, transcription, and translation. Proto-oncogenes are enriched with G4 sequences, while tumor-suppressor genes are depleted, suggesting roles for G4s in cell survival and proliferation. Specialized helicases participate in G4-mediated gene regulation via enzymatic unwinding activity. One such enzyme, DHX36/G4R1, is the major G4-helicase and is a master regulator of G4-DNAs and mRNAs. G4-resolution promotes the expression of proproliferative genes; as such, DHX36/G4R1 promotes cell proliferation. Little is known about how DHX36/G4R1 itself is regulated in nondividing cells. We hypothesized that DHX36/G4R1 protein binding partners are altered when a cell transitions from a dividing to a quiescent state. We found that DHX36/G4R1 co-purifies with a distinct set of proteins under quiescent conditions, which may represent a novel complex that regulates DHX36/G4R1 during cell cycle transitions and have implications for development and cancer.
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Affiliation(s)
- Adam.
E. Richardson
- Department
of Biology, Ball State University, Muncie, Indiana 47306, United States
| | - Zachary. A. Zentz
- Department
of Biology, Ball State University, Muncie, Indiana 47306, United States
| | - Antonio E. Chambers
- Department
of Biology, Ball State University, Muncie, Indiana 47306, United States
| | - Siara N. Sandwith
- Department
of Biology, Ball State University, Muncie, Indiana 47306, United States
| | - Michael A. Reisinger
- Department
of Biology, Ball State University, Muncie, Indiana 47306, United States
| | - Destinee W. Saunders
- Department
of Biology, Ball State University, Muncie, Indiana 47306, United States
| | - Joshua D. Tompkins
- Department
of Diabetes Complications and Metabolism, City of Hope, Duarte, California 91010, United States
| | - Arthur D. Riggs
- Department
of Diabetes Complications and Metabolism, City of Hope, Duarte, California 91010, United States
| | - Eric D. Routh
- Lineberger
Comprehensive Cancer Center, University
of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Eric M. Rubenstein
- Department
of Biology, Ball State University, Muncie, Indiana 47306, United States
| | - Melissa A. Smaldino
- Department
of Biology, Ball State University, Muncie, Indiana 47306, United States
| | - James P. Vaughn
- NanoMedica
LLC, Winston-Salem, North Carolina 27101, United States
| | - Robert A. Haney
- Department
of Biology, Ball State University, Muncie, Indiana 47306, United States
| | - Philip J. Smaldino
- Department
of Biology, Ball State University, Muncie, Indiana 47306, United States
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5
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Romero-Bueno R, de la Cruz Ruiz P, Artal-Sanz M, Askjaer P, Dobrzynska A. Nuclear Organization in Stress and Aging. Cells 2019; 8:cells8070664. [PMID: 31266244 PMCID: PMC6678840 DOI: 10.3390/cells8070664] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 06/23/2019] [Accepted: 06/25/2019] [Indexed: 12/18/2022] Open
Abstract
The eukaryotic nucleus controls most cellular processes. It is isolated from the cytoplasm by the nuclear envelope, which plays a prominent role in the structural organization of the cell, including nucleocytoplasmic communication, chromatin positioning, and gene expression. Alterations in nuclear composition and function are eminently pronounced upon stress and during premature and physiological aging. These alterations are often accompanied by epigenetic changes in histone modifications. We review, here, the role of nuclear envelope proteins and histone modifiers in the 3-dimensional organization of the genome and the implications for gene expression. In particular, we focus on the nuclear lamins and the chromatin-associated protein BAF, which are linked to Hutchinson–Gilford and Nestor–Guillermo progeria syndromes, respectively. We also discuss alterations in nuclear organization and the epigenetic landscapes during normal aging and various stress conditions, ranging from yeast to humans.
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Affiliation(s)
- Raquel Romero-Bueno
- Andalusian Center for Developmental Biology (CABD), Consejo Superior de Investigaciones Científicas/Junta de Andalucia/Universidad Pablo de Olavide, 41013 Seville, Spain
| | - Patricia de la Cruz Ruiz
- Andalusian Center for Developmental Biology (CABD), Consejo Superior de Investigaciones Científicas/Junta de Andalucia/Universidad Pablo de Olavide, 41013 Seville, Spain
| | - Marta Artal-Sanz
- Andalusian Center for Developmental Biology (CABD), Consejo Superior de Investigaciones Científicas/Junta de Andalucia/Universidad Pablo de Olavide, 41013 Seville, Spain
| | - Peter Askjaer
- Andalusian Center for Developmental Biology (CABD), Consejo Superior de Investigaciones Científicas/Junta de Andalucia/Universidad Pablo de Olavide, 41013 Seville, Spain.
| | - Agnieszka Dobrzynska
- Andalusian Center for Developmental Biology (CABD), Consejo Superior de Investigaciones Científicas/Junta de Andalucia/Universidad Pablo de Olavide, 41013 Seville, Spain.
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6
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Leemans C, van der Zwalm MCH, Brueckner L, Comoglio F, van Schaik T, Pagie L, van Arensbergen J, van Steensel B. Promoter-Intrinsic and Local Chromatin Features Determine Gene Repression in LADs. Cell 2019; 177:852-864.e14. [PMID: 30982597 PMCID: PMC6506275 DOI: 10.1016/j.cell.2019.03.009] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 01/23/2019] [Accepted: 03/04/2019] [Indexed: 12/28/2022]
Abstract
It is largely unclear whether genes that are naturally embedded in lamina-associated domains (LADs) are inactive due to their chromatin environment or whether LADs are merely secondary to the lack of transcription. We show that hundreds of human promoters become active when moved from their native LAD position to a neutral context in the same cells, indicating that LADs form a repressive environment. Another set of promoters inside LADs is able to "escape" repression, although their transcription elongation is attenuated. By inserting reporters into thousands of genomic locations, we demonstrate that escaper promoters are intrinsically less sensitive to LAD repression. This is not simply explained by promoter strength but by the interplay between promoter sequence and local chromatin features that vary strongly across LADs. Enhancers also differ in their sensitivity to LAD chromatin. This work provides a general framework for the systematic understanding of gene regulation by repressive chromatin.
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Affiliation(s)
- Christ Leemans
- Division of Gene Regulation and Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Marloes C H van der Zwalm
- Division of Gene Regulation and Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Laura Brueckner
- Division of Gene Regulation and Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Federico Comoglio
- Division of Gene Regulation and Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Tom van Schaik
- Division of Gene Regulation and Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Ludo Pagie
- Division of Gene Regulation and Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Joris van Arensbergen
- Division of Gene Regulation and Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Bas van Steensel
- Division of Gene Regulation and Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands.
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7
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Sui T, Liu D, Liu T, Deng J, Chen M, Xu Y, Song Y, Ouyang H, Lai L, Li Z. LMNA-mutated Rabbits: A Model of Premature Aging Syndrome with Muscular Dystrophy and Dilated Cardiomyopathy. Aging Dis 2019; 10:102-115. [PMID: 30705772 PMCID: PMC6345340 DOI: 10.14336/ad.2018.0209] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 02/09/2018] [Indexed: 12/13/2022] Open
Abstract
Premature aging syndromes are rare genetic disorders mimicking clinical and molecular features of aging. Products of the LMNA gene, primarily lamin A and C, are major components of the nuclear lamina. A recently identified group of premature aging syndromes was related to mutations of the LMNA gene. Although LMNA disorders have been identified in premature aging syndromes, affect specifically the skeletal muscles, cardiac muscles, and lipodystrophy, understanding the pathogenic mechanisms still need to be elucidated. Here, to establish a rabbit knockout (KO) model of premature aging syndromes, we performed precise LMNA targeting in rabbits via co-injection of Cas9/sgRNA mRNA into zygotes. The LMNA-KO rabbits exhibited reduced locomotion activity with abnormal stiff walking posture and a shortened stature, all of them died within 22 days. In addition, cardiomyopathy, muscular dystrophy, bone and joint abnormalities, as well as lipodystrophy were observed in LMNA-KO rabbits. In conclusion, the novel rabbit LMNA-KO model, displayed typical features of histopathological defects that are observed in premature aging syndromes, and may be utilized as a valuable resource for understanding the pathophysiological mechanisms of premature aging syndromes and elucidating mysteries of the normal process of aging in humans.
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Affiliation(s)
- Tingting Sui
- 1Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun 130062, China
| | - Di Liu
- 1Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun 130062, China
| | - Tingjun Liu
- 1Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun 130062, China
| | - Jichao Deng
- 1Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun 130062, China
| | - Mao Chen
- 1Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun 130062, China
| | - Yuanyuan Xu
- 1Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun 130062, China
| | - Yuning Song
- 1Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun 130062, China
| | - Hongsheng Ouyang
- 1Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun 130062, China
| | - Liangxue Lai
- 1Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun 130062, China.,2Key Laboratory of Regenerative Biology, and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, China
| | - Zhanjun Li
- 1Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun 130062, China
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8
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Almonacid M, Terret ME, Verlhac MH. Nuclear positioning as an integrator of cell fate. Curr Opin Cell Biol 2018; 56:122-129. [PMID: 30594054 DOI: 10.1016/j.ceb.2018.12.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 08/21/2018] [Accepted: 12/01/2018] [Indexed: 11/28/2022]
Abstract
Cells are the building units of living organisms and consequently adapt to their environment by modulating their intracellular architecture, in particular the position of their nucleus. Important efforts have been made to decipher the molecular mechanisms involved in nuclear positioning. The LINC complex at the nuclear envelope is a very important part of the molecular connectivity between the cell outside and the intranuclear compartment, and thus emerged as a central player in nuclear mechanotransduction. More recent concepts in nuclear mechanotransduction came from studies involving nuclear confined migration, compression or swelling. Also, the effect of nuclear mechanosensitive properties in driving cell differentiation raises the question of nuclear mechanotransduction and gene expression and recent efforts have been done to tackle it, even though it remains difficult to address in a direct manner. Eventually, an original mechanism of nucleus positioning, mechanotransduction and regulation of gene expression in the non-adherent, non-polarized mouse oocyte, highlights the fact that nuclear positioning is an important developmental issue.
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Affiliation(s)
- Maria Almonacid
- CIRB, Collège de France, and CNRS-UMR7241 and INSERM-U1050, Equipe Labellisée FRM, Paris F-75005, France.
| | - Marie-Emilie Terret
- CIRB, Collège de France, and CNRS-UMR7241 and INSERM-U1050, Equipe Labellisée FRM, Paris F-75005, France
| | - Marie-Hélène Verlhac
- CIRB, Collège de France, and CNRS-UMR7241 and INSERM-U1050, Equipe Labellisée FRM, Paris F-75005, France
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9
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Mattioli E, Andrenacci D, Garofalo C, Prencipe S, Scotlandi K, Remondini D, Gentilini D, Di Blasio AM, Valente S, Scarano E, Cicchilitti L, Piaggio G, Mai A, Lattanzi G. Altered modulation of lamin A/C-HDAC2 interaction and p21 expression during oxidative stress response in HGPS. Aging Cell 2018; 17:e12824. [PMID: 30109767 PMCID: PMC6156291 DOI: 10.1111/acel.12824] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 05/22/2018] [Accepted: 06/26/2018] [Indexed: 02/01/2023] Open
Abstract
Defects in stress response are main determinants of cellular senescence and organism aging. In fibroblasts from patients affected by Hutchinson-Gilford progeria, a severe LMNA-linked syndrome associated with bone resorption, cardiovascular disorders, and premature aging, we found altered modulation of CDKN1A, encoding p21, upon oxidative stress induction, and accumulation of senescence markers during stress recovery. In this context, we unraveled a dynamic interaction of lamin A/C with HDAC2, an histone deacetylase that regulates CDKN1A expression. In control skin fibroblasts, lamin A/C is part of a protein complex including HDAC2 and its histone substrates; protein interaction is reduced at the onset of DNA damage response and recovered after completion of DNA repair. This interplay parallels modulation of p21 expression and global histone acetylation, and it is disrupted by LMNAmutations leading to progeroid phenotypes. In fact, HGPS cells show impaired lamin A/C-HDAC2 interplay and accumulation of p21 upon stress recovery. Collectively, these results link altered physical interaction between lamin A/C and HDAC2 to cellular and organism aging. The lamin A/C-HDAC2 complex may be a novel therapeutic target to slow down progression of progeria symptoms.
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Affiliation(s)
- Elisabetta Mattioli
- CNR Institute of Molecular Genetics, Unit of Bologna; Bologna Italy
- Rizzoli Orthopedic Institute; IRCCS; Bologna Italy
| | - Davide Andrenacci
- CNR Institute of Molecular Genetics, Unit of Bologna; Bologna Italy
- Rizzoli Orthopedic Institute; IRCCS; Bologna Italy
| | - Cecilia Garofalo
- Rizzoli Orthopedic Institute; IRCCS; Bologna Italy
- CRS Development of Biomolecular Therapies, Experimental Oncology Lab; Rizzoli Institute; Bologna Italy
| | - Sabino Prencipe
- CNR Institute of Molecular Genetics, Unit of Bologna; Bologna Italy
- Rizzoli Orthopedic Institute; IRCCS; Bologna Italy
| | - Katia Scotlandi
- Rizzoli Orthopedic Institute; IRCCS; Bologna Italy
- CRS Development of Biomolecular Therapies, Experimental Oncology Lab; Rizzoli Institute; Bologna Italy
| | - Daniel Remondini
- Department of Physics and Astronomy; University of Bologna; Bologna Italy
| | - Davide Gentilini
- Centre for Biomedical Research and Technologies; Italian Auxologic Institute, IRCCS; Milan Italy
| | - Anna Maria Di Blasio
- Centre for Biomedical Research and Technologies; Italian Auxologic Institute, IRCCS; Milan Italy
| | - Sergio Valente
- Department of Drug Chemistry and Technologies; Pasteur Institute Italy; Cenci-Bolognetti Foundation; Sapienza University of Rome; Rome Italy
| | - Emanuela Scarano
- Pediatric Endocrinology and Rare Diseases Unit; University of Bologna; Bologna Italy
| | - Lucia Cicchilitti
- UOSD SAFU, Department of Research, Diagnosis and Innovative Technologies; IRCCS - Regina Elena National Cancer Institute; Rome Italy
| | - Giulia Piaggio
- UOSD SAFU, Department of Research, Diagnosis and Innovative Technologies; IRCCS - Regina Elena National Cancer Institute; Rome Italy
| | - Antonello Mai
- Department of Drug Chemistry and Technologies; Pasteur Institute Italy; Cenci-Bolognetti Foundation; Sapienza University of Rome; Rome Italy
| | - Giovanna Lattanzi
- CNR Institute of Molecular Genetics, Unit of Bologna; Bologna Italy
- Rizzoli Orthopedic Institute; IRCCS; Bologna Italy
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10
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de Leeuw R, Gruenbaum Y, Medalia O. Nuclear Lamins: Thin Filaments with Major Functions. Trends Cell Biol 2017; 28:34-45. [PMID: 28893461 DOI: 10.1016/j.tcb.2017.08.004] [Citation(s) in RCA: 191] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 08/08/2017] [Accepted: 08/14/2017] [Indexed: 10/18/2022]
Abstract
The nuclear lamina is a nuclear peripheral meshwork that is mainly composed of nuclear lamins, although a small fraction of lamins also localizes throughout the nucleoplasm. Lamins are classified as type V intermediate filament (IF) proteins. Mutations in lamin genes cause at least 15 distinct human diseases, collectively termed laminopathies, including muscle, metabolic, and neuronal diseases, and can cause accelerated aging. Most of these mutations are in the LMNA gene encoding A-type lamins. A growing number of nuclear proteins are known to bind lamins and are implicated in both nuclear and cytoskeletal organization, mechanical stability, chromatin organization, signaling, gene regulation, genome stability, and cell differentiation. Recent studies reveal the organization of the lamin filament meshwork in somatic cells where they assemble as tetramers in cross-section of the filaments.
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Affiliation(s)
- Rebecca de Leeuw
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Yosef Gruenbaum
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University, Beer-Sheva 84105, Israel.
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11
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Bell ES, Lammerding J. Causes and consequences of nuclear envelope alterations in tumour progression. Eur J Cell Biol 2016; 95:449-464. [PMID: 27397692 DOI: 10.1016/j.ejcb.2016.06.007] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 06/22/2016] [Accepted: 06/22/2016] [Indexed: 12/31/2022] Open
Abstract
Morphological changes in the size and shape of the nucleus are highly prevalent in cancer, but the underlying molecular mechanisms and the functional relevance remain poorly understood. Nuclear envelope proteins, which can modulate nuclear shape and organization, have emerged as key components in a variety of signalling pathways long implicated in tumourigenesis and metastasis. The expression of nuclear envelope proteins is altered in many cancers, and changes in levels of nuclear envelope proteins lamins A and C are associated with poor prognosis in multiple human cancers. In this review we highlight the role of the nuclear envelope in different processes important for tumour initiation and cancer progression, with a focus on lamins A and C. Lamin A/C controls many cellular processes with key roles in cancer, including cell invasion, stemness, genomic stability, signal transduction, transcriptional regulation, and resistance to mechanical stress. In addition, we discuss potential mechanisms mediating the changes in lamin levels observed in many cancers. A better understanding of cause-and-effect relationships between lamin expression and tumour progression could reveal important mechanisms for coordinated regulation of oncogenic processes, and indicate therapeutic vulnerabilities that could be exploited for improved patient outcome.
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Affiliation(s)
- Emily S Bell
- Meinig School of Biomedical Engineering & Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, United States
| | - Jan Lammerding
- Meinig School of Biomedical Engineering & Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, United States.
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12
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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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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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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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15
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Kind J, van Steensel B. Stochastic genome-nuclear lamina interactions: modulating roles of Lamin A and BAF. Nucleus 2014; 5:124-30. [PMID: 24717229 PMCID: PMC4049918 DOI: 10.4161/nucl.28825] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The nuclear lamina (NL) is thought to aid in the spatial organization of interphase chromosomes by providing an anchoring platform for hundreds of large genomic regions named lamina associated domains (LADs). Recently, a new live-cell imaging approach demonstrated directly that LAD-NL interactions are dynamic and in part stochastic. Here we discuss implications of these new findings and introduce Lamin A and BAF as potential modulators of stochastic LAD positioning.
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Affiliation(s)
- Jop Kind
- 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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16
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Dittmer TA, Sahni N, Kubben N, Hill DE, Vidal M, Burgess RC, Roukos V, Misteli T. Systematic identification of pathological lamin A interactors. Mol Biol Cell 2014; 25:1493-510. [PMID: 24623722 PMCID: PMC4004598 DOI: 10.1091/mbc.e14-02-0733] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Laminopathies are a collection of phenotypically diverse diseases that include muscular dystrophies, cardiomyopathies, lipodystrophies, and premature aging syndromes. Laminopathies are caused by >300 distinct mutations in the LMNA gene, which encodes the nuclear intermediate filament proteins lamin A and C, two major architectural elements of the mammalian cell nucleus. The genotype-phenotype relationship and the basis for the pronounced tissue specificity of laminopathies are poorly understood. Here we seek to identify on a global scale lamin A-binding partners whose interaction is affected by disease-relevant LMNA mutations. In a screen of a human genome-wide ORFeome library, we identified and validated 337 lamin A-binding proteins. Testing them against 89 known lamin A disease mutations identified 50 disease-associated interactors. Association of progerin, the lamin A isoform responsible for the premature aging disorder Hutchinson-Gilford progeria syndrome, with its partners was largely mediated by farnesylation. Mapping of the interaction sites on lamin A identified the immunoglobulin G (IgG)-like domain as an interaction hotspot and demonstrated that lamin A variants, which destabilize the Ig-like domain, affect protein-protein interactions more globally than mutations of surface residues. Analysis of a set of LMNA mutations in a single residue, which result in three phenotypically distinct diseases, identified disease-specific interactors. The results represent a systematic map of disease-relevant lamin A interactors and suggest loss of tissue-specific lamin A interactions as a mechanism for the tissue-specific appearance of laminopathic phenotypes.
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Affiliation(s)
- Travis A Dittmer
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215 Department of Genetics, Harvard Medical School, Boston, MA 02215
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17
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Brachner A, Foisner R. Lamina-associated polypeptide (LAP)2α and other LEM proteins in cancer biology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 773:143-63. [PMID: 24563347 DOI: 10.1007/978-1-4899-8032-8_7] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The LEM proteins comprise a heterogeneous family of chromatin-associated proteins that share the LEM domain, a structural motif mediating interaction with the DNA associated protein, Barrier-to-Autointegration Factor (BAF). Most of the LEM proteins are integral proteins of the inner nuclear membrane and associate with the nuclear lamina, a structural scaffold of lamin intermediate filament proteins at the nuclear periphery, which is involved in nuclear mechanical functions and (hetero-)chromatin organization. A few LEM proteins, such as Lamina-associated polypeptide (LAP)2α and Ankyrin and LEM domain-containing protein (Ankle)1 lack transmembrane domains and localize throughout the nucleoplasm and cytoplasm, respectively. LAP2α has been reported to regulate cell proliferation by affecting the activity of retinoblastoma protein in tissue progenitor cells and numerous studies showed upregulation of LAP2α in cancer. Ankle1 is a nuclease likely involved in DNA damage repair pathways and single nucleotide polymorphisms in the Ankle1 gene have been linked to increased breast and ovarian cancer risk. In this review we describe potential mechanisms of the involvement of LEM proteins, particularly of LAP2α and Ankle1 in tumorigenesis and we provide evidence that LAP2α expression may be a valuable diagnostic and prognostic marker for tumor analyses.
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Affiliation(s)
- Andreas Brachner
- Max F. Perutz Laboratories, Medical University Vienna, Dr. Bohr-Gasse 9, 1030, Vienna, Austria,
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Mahen R, Hattori H, Lee M, Sharma P, Jeyasekharan AD, Venkitaraman AR. A-type lamins maintain the positional stability of DNA damage repair foci in mammalian nuclei. PLoS One 2013; 8:e61893. [PMID: 23658700 PMCID: PMC3642183 DOI: 10.1371/journal.pone.0061893] [Citation(s) in RCA: 40] [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: 11/28/2012] [Accepted: 03/14/2013] [Indexed: 02/02/2023] Open
Abstract
A-type lamins encoded by LMNA form a structural fibrillar meshwork within the mammalian nucleus. How this nuclear organization may influence the execution of biological processes involving DNA transactions remains unclear. Here, we characterize changes in the dynamics and biochemical interactions of lamin A/C after DNA damage. We find that DNA breakage reduces the mobility of nucleoplasmic GFP-lamin A throughout the nucleus as measured by dynamic fluorescence imaging and spectroscopy in living cells, suggestive of incorporation into stable macromolecular complexes, but does not induce the focal accumulation of GFP-lamin A at damage sites. Using a proximity ligation assay and biochemical analyses, we show that lamin A engages chromatin via histone H2AX and its phosphorylated form (γH2AX) induced by DNA damage, and that these interactions are enhanced after DNA damage. Finally, we use three-dimensional time-lapse imaging to show that LMNA inactivation significantly reduces the positional stability of DNA repair foci in living cells. This defect is partially rescued by the stable expression of GFP-lamin A. Thus collectively, our findings suggest that the dynamic structural meshwork formed by A-type lamins anchors sites of DNA repair in mammalian nuclei, providing fresh insight into the control of DNA transactions by nuclear structural organization.
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Affiliation(s)
- Robert Mahen
- The Medical Research Council Cancer Cell Unit, Hutchison/MRC Research Centre, Cambridge, United Kingdom
| | - Hiroyoshi Hattori
- The Medical Research Council Cancer Cell Unit, Hutchison/MRC Research Centre, Cambridge, United Kingdom
| | - Miyoung Lee
- The Medical Research Council Cancer Cell Unit, Hutchison/MRC Research Centre, Cambridge, United Kingdom
| | - Pooja Sharma
- The Medical Research Council Cancer Cell Unit, Hutchison/MRC Research Centre, Cambridge, United Kingdom
| | - Anand D. Jeyasekharan
- The Medical Research Council Cancer Cell Unit, Hutchison/MRC Research Centre, Cambridge, United Kingdom
| | - Ashok R. Venkitaraman
- The Medical Research Council Cancer Cell Unit, Hutchison/MRC Research Centre, Cambridge, United Kingdom
- * E-mail:
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19
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Abstract
Faithful execution of developmental gene expression programs occurs at multiple levels and involves many different components such as transcription factors, histone-modification enzymes, and mRNA processing proteins. Recent evidence suggests that nucleoporins, well known components that control nucleo-cytoplasmic trafficking, have wide-ranging functions in developmental gene regulation that potentially extend beyond their role in nuclear transport. Whether the unexpected role of nuclear pore proteins in transcription regulation, which initially has been described in fungi and flies, also applies to human cells is unknown. Here we show at a genome-wide level that the nuclear pore protein NUP98 associates with developmentally regulated genes active during human embryonic stem cell differentiation. Overexpression of a dominant negative fragment of NUP98 levels decreases expression levels of NUP98-bound genes. In addition, we identify two modes of developmental gene regulation by NUP98 that are differentiated by the spatial localization of NUP98 target genes. Genes in the initial stage of developmental induction can associate with NUP98 that is embedded in the nuclear pores at the nuclear periphery. Alternatively, genes that are highly induced can interact with NUP98 in the nuclear interior, away from the nuclear pores. This work demonstrates for the first time that NUP98 dynamically associates with the human genome during differentiation, revealing a role of a nuclear pore protein in regulating developmental gene expression programs.
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20
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Frock RL, Chen SC, Da DF, Frett E, Lau C, Brown C, Pak DN, Wang Y, Muchir A, Worman HJ, Santana LF, Ladiges WC, Rabinovitch PS, Kennedy BK. Cardiomyocyte-specific expression of lamin a improves cardiac function in Lmna-/- mice. PLoS One 2012; 7:e42918. [PMID: 22905185 PMCID: PMC3419749 DOI: 10.1371/journal.pone.0042918] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Accepted: 07/16/2012] [Indexed: 11/18/2022] Open
Abstract
Lmna(-/-) mice display multiple tissue defects and die by 6-8 weeks of age reportedly from dilated cardiomyopathy with associated conduction defects. We sought to determine whether restoration of lamin A in cardiomyocytes improves cardiac function and extends the survival of Lmna(-/-) mice. We observed increased total desmin protein levels and disorganization of the cytoplasmic desmin network in ~20% of Lmna(-/-) ventricular myocytes, rescued in a cell-autonomous manner in Lmna(-/-) mice expressing a cardiac-specific lamin A transgene (Lmna(-/-); Tg). Lmna(-/-); Tg mice displayed significantly increased contractility and preservation of myocardial performance compared to Lmna(-/-) mice. Lmna(-/-); Tg mice attenuated ERK1/2 phosphorylation relative to Lmna(-/-) mice, potentially underlying the improved localization of connexin43 to the intercalated disc. Electrocardiographic recordings from Lmna(-/-) mice revealed arrhythmic events and increased frequency of PR interval prolongation, which is partially rescued in Lmna(-/-); Tg mice. These findings support our observation that Lmna(-/-); Tg mice have a 12% median extension in lifespan compared to Lmna(-/-) mice. While significant, Lmna(-/-); Tg mice only have modest improvement in cardiac function and survival likely stemming from the observation that only 40% of Lmna(-/-); Tg cardiomyocytes have detectable lamin A expression. Cardiomyocyte-specific restoration of lamin A in Lmna(-/-) mice improves heart-specific pathology and extends lifespan, demonstrating that the cardiac pathology of Lmna(-/-) mice limits survival. The expression of lamin A is sufficient to rescue certain cellular defects associated with loss of A-type lamins in cardiomyocytes in a cell-autonomous fashion.
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Affiliation(s)
- Richard L. Frock
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Steven C. Chen
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Dao-Fu Da
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | - Ellie Frett
- Department of Pharmacology and Physiology, University of Rochester, Rochester, New York, United States of America
| | - Carmen Lau
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Christina Brown
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Diana N. Pak
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Yuexia Wang
- Department of Medicine and Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, New York, United States of America
| | - Antoine Muchir
- Department of Medicine and Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, New York, United States of America
| | - Howard J. Worman
- Department of Medicine and Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, New York, United States of America
| | - Luis F. Santana
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington, United States of America
| | - Warren C. Ladiges
- Department of Comparative Medicine, University of Washington, Seattle, Washington, United States of America
| | - Peter S. Rabinovitch
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | - Brian K. Kennedy
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- Buck Institute for Age Research, Novato, California, United States of America
- * E-mail:
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21
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Gotic I, Foisner R. Multiple novel functions of lamina associated polypeptide 2α in striated muscle. Nucleus 2012; 1:397-401. [PMID: 21326822 DOI: 10.4161/nucl.1.5.12394] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2010] [Accepted: 05/18/2010] [Indexed: 01/19/2023] Open
Abstract
Lamina-associated polypeptide 2α (LAP2α) is a nucleoplasmic protein that interacts with A-type lamins and the retinoblastoma protein (pRb) and affects pRb-mediated cell cycle regulation and chromatin organization. Mutations in lamin A/C and LAP2α cause late onset striated muscle diseases, but the molecular mechanisms are poorly understood. We have recently reported on the striated muscle phenotype of LAP2α-deficient mice, revealing new unexpected roles of LAP2α. Loss of LAP2α in skeletal muscle caused an upregulated stem cell-type gene expression in muscle satellite cell progeny and their delayed myogenic differentiation in vitro. In vivo, the myofiber-associated muscle stem cell pool was increased. In addition, absence of LAP2α promoted muscle remodeling towards fast myofiber types in the soleus muscle of old animals. In cardiac tissue, deletion of LAP2α caused systolic dysfunction in young mice with an increased susceptibility for fibrosis in old animals. The functional impairment in the heart was accompanied by a deregulation of major cardiac transcription factors, GATA4 and MEF2c and activation of compensatory pathways, including the downregulation of β-adrenergic receptor signaling.Here we discuss potential functions of LAP2α in striated muscle at molecular level and how loss of these functions may cause the diverse muscle phenotypes. We propose that LAP2α serves as a transcriptional co-regulator, which controls muscle specific gene expression during muscle regeneration, muscle remodeling and stress response.
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Affiliation(s)
- Ivana Gotic
- Department of Medical Biochemistry, Max F. Perutz Laboratories, Medical University of Vienna, Vienna, Austria
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22
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Martins RP, Finan JD, Guilak F, Lee DA. Mechanical regulation of nuclear structure and function. Annu Rev Biomed Eng 2012; 14:431-55. [PMID: 22655599 DOI: 10.1146/annurev-bioeng-071910-124638] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Mechanical loading induces both nuclear distortion and alterations in gene expression in a variety of cell types. Mechanotransduction is the process by which extracellular mechanical forces can activate a number of well-studied cytoplasmic signaling cascades. Inevitably, such signals are transduced to the nucleus and induce transcription factor-mediated changes in gene expression. However, gene expression also can be regulated through alterations in nuclear architecture, providing direct control of genome function. One putative transduction mechanism for this phenomenon involves alterations in nuclear architecture that result from the mechanical perturbation of the cell. This perturbation is associated with direct mechanical strain or osmotic stress, which is transferred to the nucleus. This review describes the current state of knowledge relating the nuclear architecture and the transfer of mechanical forces to the nucleus mediated by the cytoskeleton, the nucleoskeleton, and the LINC (linker of the nucleoskeleton and cytoskeleton) complex. Moreover, remodeling of the nucleus induces alterations in nuclear stiffness, which may be associated with cell differentiation. These phenomena are discussed in relation to the potential influence of nuclear architecture-mediated mechanoregulation of transcription and cell fate.
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Affiliation(s)
- Rui P Martins
- Institute of Bioengineering, School of Engineering and Materials Science, Queen Mary University of London, London E1 4NS, United Kingdom
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23
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Kim Y, McDole K, Zheng Y. The function of lamins in the context of tissue building and maintenance. Nucleus 2012; 3:256-62. [PMID: 22614537 PMCID: PMC3414402 DOI: 10.4161/nucl.20392] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Lamins are the major structural components of the nuclear lamina found in metazoan organisms. Extensive studies using tissue culture cells have shown that lamins are involved in a wide range of basic cell functions. This has led to the prevailing idea that a given animal cell needs at least one lamin protein for its basic proliferation and survival. However, recent studies have shown that lamins are dispensable for the proliferation and survival of mouse embryonic stem cells (ESC). In contrast to a lack of essential functions in ESCs, certain differentiated cells lacking B-type lamins exhibit increased cell cycle exit rates and enhanced senescence. In this Extra View, we discuss how studies using animal models and cell cultures have begun to reveal cell-type specific functions of lamins in tissue building and homeostasis.
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Affiliation(s)
- Youngjo Kim
- Department of Embryology, Carnegie Institution for Science and Howard Hughes Medical Institute, Baltimore, MD, USA
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24
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Ohsaki E, Ueda K. Kaposi's Sarcoma-Associated Herpesvirus Genome Replication, Partitioning, and Maintenance in Latency. Front Microbiol 2012; 3:7. [PMID: 22291692 PMCID: PMC3264903 DOI: 10.3389/fmicb.2012.00007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Accepted: 01/05/2012] [Indexed: 02/03/2023] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) is thought to be an oncogenic member of the γ-herpesvirus subfamily. The virus usually establishes latency upon infection as a default infection pattern. The viral genome replicates according to the host cell cycle by recruiting the host cellular replication machinery. Among the latently expressing viral factors, LANA plays pivotal roles in viral genome replication, partitioning, and maintenance. LANA binds with two LANA-binding sites (LBS1/2) within a terminal repeat (TR) sequence and is indispensable for viral genome replication in latency. The nuclear matrix region seems to be important as a replication site, since LANA as well as cellular replication factors accumulate there and recruit the viral replication origin in latency (ori-P) by its binding activity to LBS. KSHV ori-P consists of LBS followed by a 32-bp GC-rich segment (32GC). Although it has been reported that LANA recruits cellular pre-replication complexes (pre-RC) such as origin recognition complexes (ORCs) to the ori-P through its interaction with ORCs, this mechanism does not account completely for the requirement of the 32GC. On the other hand, there are few reports about the partitioning and maintenance of the viral genome. LANA interacts with many kinds of chromosomal proteins, including Brd2/RING3, core histones, such as H2A/H2B and histone H1, and so on. The detailed molecular mechanisms by which LANA enables KSHV genome partitioning and maintenance still remain obscure. By integrating the findings reported thus far on KSHV genome replication, partitioning, and maintenance in latency, we will summarize what we know now, discuss what questions remain to be answered, and determine what needs to be done next to understand the mechanisms underlying viral replication, partitioning, and maintenance strategy.
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Affiliation(s)
- Eriko Ohsaki
- Division of Virology, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine Suita, Osaka, Japan
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25
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Herpesviruses and intermediate filaments: close encounters with the third type. Viruses 2011; 3:1015-40. [PMID: 21994768 PMCID: PMC3185793 DOI: 10.3390/v3071015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Revised: 06/07/2011] [Accepted: 06/24/2011] [Indexed: 01/29/2023] Open
Abstract
Intermediate filaments (IF) are essential to maintain cellular and nuclear integrity and shape, to manage organelle distribution and motility, to control the trafficking and pH of intracellular vesicles, to prevent stress-induced cell death, and to support the correct distribution of specific proteins. Because of this, IF are likely to be targeted by a variety of pathogens, and may act in favor or against infection progress. As many IF functions remain to be identified, however, little is currently known about these interactions. Herpesviruses can infect a wide variety of cell types, and are thus bound to encounter the different types of IF expressed in each tissue. The analysis of these interrelationships can yield precious insights into how IF proteins work, and into how viruses have evolved to exploit these functions. These interactions, either known or potential, will be the focus of this review.
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Affiliation(s)
- Kris Noel Dahl
- Department of Biomedical Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA.
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Abstract
Now is an opportune moment to address the confluence of cell biological form and function that is the nucleus. Its arrival is especially timely because the recognition that the nucleus is extremely dynamic has now been solidly established as a paradigm shift over the past two decades, and also because we now see on the horizon numerous ways in which organization itself, including gene location and possibly self-organizing bodies, underlies nuclear functions.
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Affiliation(s)
- Thoru Pederson
- Program in Cell and Developmental Dynamics, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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Egecioglu D, Brickner JH. Gene positioning and expression. Curr Opin Cell Biol 2011; 23:338-45. [PMID: 21292462 DOI: 10.1016/j.ceb.2011.01.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Revised: 12/23/2010] [Accepted: 01/07/2011] [Indexed: 01/19/2023]
Abstract
Within the nucleus, the genome is spatially organized. Individual chromosomes are non-randomly positioned with respect to each other and with respect to nuclear landmarks [1,2]. Furthermore, the position of individual genes can reflect their expression. Here we discuss two well-characterized examples of gene relocalization associated with transcriptional activation: 1) developmentally regulated genes that move from the nuclear periphery to transcription factories in the nucleoplasm upon induction and 2) genes that are targeted from the nucleoplasm to the nuclear periphery, through interactions with the nuclear pore complex (NPC), upon activation. Finally, we speculate as to the mechanistic and functional commonalities of these phenomena.
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Affiliation(s)
- Defne Egecioglu
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
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Rodríguez J, Calvo F, González JM, Casar B, Andrés V, Crespo P. ERK1/2 MAP kinases promote cell cycle entry by rapid, kinase-independent disruption of retinoblastoma-lamin A complexes. ACTA ACUST UNITED AC 2011; 191:967-79. [PMID: 21115804 PMCID: PMC2995174 DOI: 10.1083/jcb.201004067] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
When in the nucleus, ERK1/2 dislodges the retinoblastoma protein from lamin A, facilitating its rapid phosphorylation. As orchestrators of essential cellular processes like proliferation, ERK1/2 mitogen-activated protein kinase signals impact on cell cycle regulation. A-type lamins are major constituents of the nuclear matrix that also control the cell cycle machinery by largely unknown mechanisms. In this paper, we disclose a functional liaison between ERK1/2 and lamin A whereby cell cycle progression is regulated. We demonstrate that lamin A serves as a mutually exclusive dock for ERK1/2 and the retinoblastoma (Rb) protein. Our results reveal that, immediately after their postactivation entrance in the nucleus, ERK1/2 dislodge Rb from its interaction with lamin A, thereby facilitating its rapid phosphorylation and consequently promoting E2F activation and cell cycle entry. Interestingly, these effects are independent of ERK1/2 kinase activity. We also show that cellular transformation and tumor cell proliferation are dependent on the balance between lamin A and nuclear ERK1/2 levels, which determines Rb accessibility for phosphorylation/inactivation.
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Affiliation(s)
- Javier Rodríguez
- Instituto de Biomedicina y Biotecnología de Cantabria, Consejo Superior de Investigaciones Científicas, Investigación Desarrollo e Innovación Cantabria, Departamento de Biología Molecular, Facultad de Medicina, Universidad de Cantabria, 39011 Santander, Spain
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30
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Abstract
The nuclear lamins are type V intermediate filament proteins that are critically important for the structural properties of the nucleus. In addition, they are involved in the regulation of numerous nuclear processes, including DNA replication, transcription and chromatin organization. The developmentally regulated expression of lamins suggests that they are involved in cellular differentiation. Their assembly dynamic properties throughout the cell cycle, particularly in mitosis, are influenced by posttranslational modifications. Lamins may regulate nuclear functions by direct interactions with chromatin and determining the spatial organization of chromosomes within the nuclear space. They may also regulate chromatin functions by interacting with factors that epigenetically modify the chromatin or directly regulate replication or transcription.
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Affiliation(s)
- Thomas Dechat
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
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31
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Mergui X, Puiffe ML, Valteau-Couanet D, Lipinski M, Bénard J, Amor-Guéret M. p21Waf1 expression is regulated by nuclear intermediate filament vimentin in neuroblastoma. BMC Cancer 2010; 10:473. [PMID: 20813048 PMCID: PMC2939553 DOI: 10.1186/1471-2407-10-473] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Accepted: 09/02/2010] [Indexed: 01/26/2023] Open
Abstract
Background Human neuroblastoma (NB) cell lines may present with either one of the so-called S-and N-subtypes. We have previously reported a strong correlation between protein expression levels of vimentin, an S-subtype marker, and the p21Waf1 cyclin-dependent kinase inhibitor. We here investigated whether this correlation extend to the mRNA level in NB cell lines as well as in patients' tumors. We also further explored the relationship between expression of vimentin and p21, by asking whether vimentin could regulate p21 expression. Methods Vimentin and p21 mRNA levels in NB cell lines as well as in patients' tumors (n = 77) were quantified using Q-PCR. Q-PCR data obtained from tumors of high risk NB patients (n = 40) were analyzed in relation with the overall survival using the Log-rank Kaplan-Meier estimation. siRNA-mediated depletion or overexpression of vimentin in highly or low expressing vimentin cell lines, respectively, followed by protein expression and promoter activation assays were used to assess the role of vimentin in modulating p21 expression. Results We extend the significant correlation between vimentin and p21 expression to the mRNA level in NB cell lines as well as in patients' tumors. Overall survival analysis from Q-PCR data obtained from tumors of high risk patients suggests that lower levels of p21 expression could be associated with a poorer outcome. Our data additionally indicate that the correlation observed between p21 and vimentin expression levels results from p21 transcriptional activity being regulated by vimentin. Indeed, downregulating vimentin resulted in a significant decrease in p21 mRNA and protein expression as well as in p21 promoter activity. Conversely, overexpressing vimentin triggered an increase in p21 promoter activity in cells with a nuclear expression of vimentin. Conclusion Our results suggest that p21 mRNA tumor expression level could represent a refined prognostic factor for high risk NB patients. Our data also show that vimentin regulates p21 transcription; this is the first demonstration of a gene regulating function for this type III-intermediate filament.
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Affiliation(s)
- Xénia Mergui
- Université Paris Sud-11, CNRS, UMR 8126, Institut de Cancérologie Gustave Roussy, 114 rue Edouard Vaillant, Villejuif F-94805, France.
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Hale JS, Frock RL, Mamman SA, Fink PJ, Kennedy BK. Cell-extrinsic defective lymphocyte development in Lmna(-/-) mice. PLoS One 2010; 5:e10127. [PMID: 20405040 PMCID: PMC2853576 DOI: 10.1371/journal.pone.0010127] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2010] [Accepted: 02/23/2010] [Indexed: 01/14/2023] Open
Abstract
Background Mutations in the LMNA gene, which encodes all A-type lamins, result in a variety of human diseases termed laminopathies. Lmna-/- mice appear normal at birth but become runted as early as 2 weeks of age and develop multiple tissue defects that mimic some aspects of human laminopathies. Lmna-/- mice also display smaller spleens and thymuses. In this study, we investigated whether altered lymphoid organ sizes are correlated with specific defects in lymphocyte development. Principal Findings Lmna-/- mice displayed severe age-dependent defects in T and B cell development which coincided with runting. Lmna-/- bone marrow reconstituted normal T and B cell development in irradiated wild-type recipients, driving generation of functional and self-MHC restricted CD4+ and CD8+ T cells. Transplantation of Lmna-/- neonatal thymus lobes into syngeneic wild-type recipients resulted in good engraftment of thymic tissue and normal thymocyte development. Conclusions Collectively, these data demonstrate that the severe defects in lymphocyte development that characterize Lmna-/- mice do not result directly from the loss of A-type lamin function in lymphocytes or thymic stroma. Instead, the immune defects in Lmna-/- mice likely reflect indirect damage, perhaps resulting from prolonged stress due to the striated muscle dystrophies that occur in these mice.
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Affiliation(s)
- J. Scott Hale
- Department of Immunology, University of Washington, Seattle, Washington, United States of America
| | - Richard L. Frock
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Sara A. Mamman
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Pamela J. Fink
- Department of Immunology, University of Washington, Seattle, Washington, United States of America
| | - Brian K. Kennedy
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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Andrés V, González JM. Role of A-type lamins in signaling, transcription, and chromatin organization. ACTA ACUST UNITED AC 2010; 187:945-57. [PMID: 20038676 PMCID: PMC2806284 DOI: 10.1083/jcb.200904124] [Citation(s) in RCA: 214] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A-type lamins (lamins A and C), encoded by the LMNA gene, are major protein constituents of the mammalian nuclear lamina, a complex structure that acts as a scaffold for protein complexes that regulate nuclear structure and functions. Interest in these proteins has increased in recent years with the discovery that LMNA mutations cause a variety of human diseases termed laminopathies, including progeroid syndromes and disorders that primarily affect striated muscle, adipose, bone, and neuronal tissues. In this review, we discuss recent research supporting the concept that lamin A/C and associated nuclear envelope proteins regulate gene expression in health and disease through interplay with signal transduction pathways, transcription factors, and chromatin-associated proteins.
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Affiliation(s)
- Vicente Andrés
- Department of Atherothrombosis and Cardiovascular Imaging, Fundación Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain.
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Albrethsen J, Knol JC, Piersma SR, Pham TV, de Wit M, Mongera S, Carvalho B, Verheul HMW, Fijneman RJA, Meijer GA, Jimenez CR. Subnuclear proteomics in colorectal cancer: identification of proteins enriched in the nuclear matrix fraction and regulation in adenoma to carcinoma progression. Mol Cell Proteomics 2010; 9:988-1005. [PMID: 20089989 DOI: 10.1074/mcp.m900546-mcp200] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Abnormalities in nuclear phenotype and chromosome structure are key features of cancer cells. Investigation of the protein determinants of nuclear subfractions in cancer may yield molecular insights into aberrant chromosome function and chromatin organization and in addition may yield biomarkers for early cancer detection. Here we evaluate a proteomics work flow for profiling protein constituents in subnuclear domains in colorectal cancer tissues and apply this work flow to a comparative analysis of the nuclear matrix fraction in colorectal adenoma and carcinoma tissue samples. First, we established the reproducibility of the entire work flow. In a reproducibility analysis of three nuclear matrix fractions independently isolated from the same colon tumor homogenate, 889 of 1,047 proteins (85%) were reproducibly identified at high confidence (minimally two peptides per protein at 99% confidence interval at the protein level) with an average coefficient of variance for the number of normalized spectral counts per protein of 30%. This indicates a good reproducibility of the entire work flow from biochemical isolation to nano-LC-MS/MS analysis. Second, using spectral counting combined with statistics, we identified proteins that are significantly enriched in the nuclear matrix fraction relative to two earlier fractions (the chromatin-binding and intermediate filament fractions) isolated from six colorectal tissue samples. The total data set contained 2,059 non-redundant proteins. Gene ontology mining and protein network analysis of nuclear matrix-enriched proteins revealed enrichment for proteins implicated in "RNA processing" and "mRNA metabolic process." Finally, an explorative comparison of the nuclear matrix proteome in colorectal adenoma and carcinoma tissues revealed many proteins previously implicated in oncogenesis as well as new candidates. A subset of these differentially expressed proteins also exhibited a corresponding change at the mRNA level. Together, the results show that subnuclear proteomics of tumor tissue is feasible and a promising avenue for exploring oncogenesis.
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Affiliation(s)
- Jakob Albrethsen
- OncoProteomics Laboratory, Department of Medical Oncology, VU University Medical Center (VUmc)-Cancer Center Amsterdam, The Netherlands
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Linnemann AK, Krawetz SA. Maintenance of a functional higher order chromatin structure: The role of the nuclear matrix in normal and disease states. GENE THERAPY & MOLECULAR BIOLOGY 2009; 13:231-243. [PMID: 20948980 PMCID: PMC2952954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The ordered packaging of DNA within the nucleus of somatic cells reflects a dynamic supportive structure that facilitates stable transcription interrupted by intermittent cycles of extreme condensation. This dynamic mode of packing and unpacking chromatin is intimately linked to the ability of the genome to specifically complex with both histones and non-histone proteins. Understanding the underlying mechanism that governs the formation of higher order chromatin structures is a key to understanding how local architecture modulates transcription. In part, the formation of these structures appears to be regulated through genomic looping that is dynamically mediated by attachment to the nuclear scaffold/matrix at S/MARs, i.e., Scaffold/Matrix Attachment Regions. Although the mechanism guiding the formation and use of these higher-ordered structures remains unknown, S/MARs continue to reveal a multitude of roles in development and the pathogenesis of disease.
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Affiliation(s)
| | - Stephen A. Krawetz
- The Center for Molecular Medicine and Genetics
- Department of Obstetrics and Gynecology
- Institute for Scientific Computing, Wayne State University School of Medicine
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