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Fenstermaker TK, Petruk S, Mazo A. An emerging paradigm in epigenetic marking: coordination of transcription and replication. Transcription 2024; 15:22-37. [PMID: 38378467 DOI: 10.1080/21541264.2024.2316965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 02/06/2024] [Indexed: 02/22/2024] Open
Abstract
DNA replication and RNA transcription both utilize DNA as a template and therefore need to coordinate their activities. The predominant theory in the field is that in order for the replication fork to proceed, transcription machinery has to be evicted from DNA until replication is complete. If that does not occur, these machineries collide, and these collisions elicit various repair mechanisms which require displacement of one of the enzymes, often RNA polymerase, in order for replication to proceed. This model is also at the heart of the epigenetic bookmarking theory, which implies that displacement of RNA polymerase during replication requires gradual re-building of chromatin structure, which guides recruitment of transcriptional proteins and resumption of transcription. We discuss these theories but also bring to light newer data that suggest that these two processes may not be as detrimental to one another as previously thought. This includes findings suggesting that these processes can occur without fork collapse and that RNA polymerase may only be transiently displaced during DNA replication. We discuss potential mechanisms by which RNA polymerase may be retained at the replication fork and quickly rebind to DNA post-replication. These discoveries are important, not only as new evidence as to how these two processes are able to occur harmoniously but also because they have implications on how transcriptional programs are maintained through DNA replication. To this end, we also discuss the coordination of replication and transcription in light of revising the current epigenetic bookmarking theory of how the active gene status can be transmitted through S phase.
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Affiliation(s)
- Tyler K Fenstermaker
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Svetlana Petruk
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Alexander Mazo
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
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Anachkova BB, Djeliova VL. Stability of proteins involved in initiation of DNA replication in UV damaged human cells. ACTA ACUST UNITED AC 2021; 77:113-123. [PMID: 34333892 DOI: 10.1515/znc-2020-0286] [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: 11/26/2020] [Accepted: 07/17/2021] [Indexed: 11/15/2022]
Abstract
The protein stability of the initiation factors Orc2, Orc3, Orc4, and Cdc6 was analyzed after UV light exposure in two human cell lines. In the cell line with higher repair capacity, HEK 293, no changes in the cell cycle distribution or in the protein levels of the investigated factors were detected. In HeLa cells that are characterized by lower repair capacity, UV irradiation caused a reduction of the levels of Cdc6, Orc2 and Orc3, but not of Orc4 or triggered apoptosis. The appearance of the truncated 49 kDa form of Cdc6 suggested the involvement of the caspase pathway in the degradation of the proteins. Reduced protein levels of Cdc6 were detected in UV damaged HeLa cells in which the apoptotic process was blocked with the caspase inhibitor Z-VAD-fmk, indicating that the degradation of Cdc6 is mediated by the proteasome pathway instead. In the presence of caffeine, an inhibitor of the cell cycle checkpoint kinases, Cdc6 was stabilized, demonstrating that its degradation is controlled by the DNA damage cell cycle checkpoint. We conclude that in response to DNA damage, the activation of origins of replication can be prevented by the degradation of Cdc6, most likely through the proteasome pathway.
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Affiliation(s)
- Boyka Borisova Anachkova
- Department of the Molecular Biology of the Cell Cycle, Institute of Molecular Biology "RoumenTsanev", Bulgarian Academy of Sciences, Akad. G. Bonchev Street, Bl. 21, Sofia1113, Bulgaria
| | - Vera Lyubchova Djeliova
- Department of the Molecular Biology of the Cell Cycle, Institute of Molecular Biology "RoumenTsanev", Bulgarian Academy of Sciences, Akad. G. Bonchev Street, Bl. 21, Sofia1113, Bulgaria
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Duer M, Cobb AM, Shanahan CM. DNA Damage Response: A Molecular Lynchpin in the Pathobiology of Arteriosclerotic Calcification. Arterioscler Thromb Vasc Biol 2020; 40:e193-e202. [PMID: 32404005 DOI: 10.1161/atvbaha.120.313792] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Vascular calcification is a ubiquitous pathology of aging. Oxidative stress, persistent DNA damage, and senescence are major pathways driving both cellular and tissue aging, and emerging evidence suggests that these pathways are activated, and even accelerated, in patients with vascular calcification. The DNA damage response-a complex signaling platform that maintains genomic integrity-is induced by oxidative stress and is intimately involved in regulating cell death and osteogenic differentiation in both bone and the vasculature. Unexpectedly, a posttranslational modification, PAR (poly[ADP-ribose]), which is a byproduct of the DNA damage response, initiates biomineralization by acting to concentrate calcium into spheroidal structures that can nucleate apatitic mineral on the ECM (extracellular matrix). As we start to dissect the molecular mechanisms driving aging-associated vascular calcification, novel treatment strategies to promote healthy aging and delay pathological change are being unmasked. Drugs targeting the DNA damage response and senolytics may provide new avenues to tackle this detrimental and intractable pathology.
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Affiliation(s)
- Melinda Duer
- From the Department of Chemistry, University of Cambridge, United Kingdom (M.D.)
| | - Andrew M Cobb
- British Heart Foundation Centre of Research Excellence, School of Cardiovascular Medicine and Sciences, King's College London, United Kingdom (A.M.C., C.M.S.)
| | - Catherine M Shanahan
- British Heart Foundation Centre of Research Excellence, School of Cardiovascular Medicine and Sciences, King's College London, United Kingdom (A.M.C., C.M.S.)
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Gil L, Niño SA, Chi-Ahumada E, Rodríguez-Leyva I, Guerrero C, Rebolledo AB, Arias JA, Jiménez-Capdeville ME. Perinuclear Lamin A and Nucleoplasmic Lamin B2 Characterize Two Types of Hippocampal Neurons through Alzheimer's Disease Progression. Int J Mol Sci 2020; 21:E1841. [PMID: 32155994 PMCID: PMC7084765 DOI: 10.3390/ijms21051841] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 02/28/2020] [Accepted: 03/03/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Recent reports point to a nuclear origin of Alzheimer's disease (AD). Aged postmitotic neurons try to repair their damaged DNA by entering the cell cycle. This aberrant cell cycle re-entry involves chromatin modifications where nuclear Tau and the nuclear lamin are involved. The purpose of this work was to elucidate their participation in the nuclear pathological transformation of neurons at early AD. METHODOLOGY The study was performed in hippocampal paraffin embedded sections of adult, senile, and AD brains at I-VI Braak stages. We analyzed phospho-Tau, lamins A, B1, B2, and C, nucleophosmin (B23) and the epigenetic marker H4K20me3 by immunohistochemistry. RESULTS Two neuronal populations were found across AD stages, one is characterized by a significant increase of Lamin A expression, reinforced perinuclear Lamin B2, elevated expression of H4K20me3 and nuclear Tau loss, while neurons with nucleoplasmic Lamin B2 constitute a second population. CONCLUSIONS The abnormal cell cycle reentry in early AD implies a fundamental neuronal transformation. This implies the reorganization of the nucleo-cytoskeleton through the expression of the highly regulated Lamin A, heterochromatin repression and building of toxic neuronal tangles. This work demonstrates that nuclear Tau and lamin modifications in hippocampal neurons are crucial events in age-related neurodegeneration.
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Affiliation(s)
- Laura Gil
- Departamento de Genética, Escuela de Medicina, Universidad “Alfonso X el Sabio”, 28691 Madrid, Spain; (L.G.)
| | - Sandra A. Niño
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí 78210, Mexico
| | - Erika Chi-Ahumada
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí 78210, Mexico
| | | | - Carmen Guerrero
- Banco de cerebros (Biobanco), Hospital Universitario Fundación Alcorcón, Alcorcón, 28922 Madrid, Spain
| | - Ana Belén Rebolledo
- Banco de cerebros (Biobanco), Hospital Universitario Fundación Alcorcón, Alcorcón, 28922 Madrid, Spain
| | - José A. Arias
- Departamento de Genética, Escuela de Medicina, Universidad “Alfonso X el Sabio”, 28691 Madrid, Spain; (L.G.)
| | - María E. Jiménez-Capdeville
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí 78210, Mexico
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Casanovas A, Ribas-Maynou J, Lara-Cerrillo S, Jimenez-Macedo AR, Hortal O, Benet J, Carrera J, García-Peiró A. Double-stranded sperm DNA damage is a cause of delay in embryo development and can impair implantation rates. Fertil Steril 2019; 111:699-707.e1. [PMID: 30826116 DOI: 10.1016/j.fertnstert.2018.11.035] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 11/26/2018] [Accepted: 11/26/2018] [Indexed: 12/16/2022]
Abstract
OBJECTIVE To analyze the effect of single- and double-stranded sperm DNA fragmentation (ssSDF and dsSDF) on human embryo kinetics monitored under a time-lapse system. DESIGN Observational, double blind, prospective cohort study. SETTING University spin-off and private center. PATIENT(S) One hundred ninety-six embryos from 43 infertile couples were included prospectively. INTERVENTION(S) None. MAIN OUTCOME MEASURE(S) SsSDF and dsSDF were analyzed in the same semen sample used for intracytoplasmic sperm injection. Embryo kinetics was then monitored using time-lapse technology, and the timing of each embryo division was obtained. RESULT(S) When comparing embryos obtained from semen samples with low dsSDF and high dsSDF, splitting data using a statistically significant delay in high dsSDF was observed in second polar body extrusion, T4, T8, morula, and starting blastocyst and embryo implantation rates were impaired. Embryo kinetics and implantation rates are not significantly affected when high values of ssSDF are present. Different patterns of delay in embryo kinetics were observed for these different types of DNA damage: dsSDF caused a delay along all stages of embryo development; however, its major effect was observed at the second polar body extrusion and morula stages, coinciding with embryo DNA damage checkpoint activation as described before; ssSDF had its major effect at the pronucleus stage, but embryo kinetics was then restored at all following stages. The results show that dsSDF could be the main type of DNA damage that affects embryo development in intracytoplasmic sperm injection cycles, probably due to motility-based sperm selection in this assisted reproduction procedure. CONCLUSION(S) Double-stranded sperm DNA damage caused a delay in embryo development and impaired implantation, while single-stranded DNA damage did not significantly affect embryo kinetics and implantation.
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Affiliation(s)
| | - Jordi Ribas-Maynou
- Centro de Infertilidad Masculina y Análisis de Barcelona, Barcelona, Spain
| | | | | | - Olga Hortal
- Unitat d'Endocrinologia Ginecològica, Barcelona, Spain
| | - Jordi Benet
- Unitat de Biologia Cellular i Genètica Mèdica, Departament de Biologia Cellular, Fisiologia i Immunologia, Facultat de Medicina, Universitat Autònoma de Barcelona, Campus de la UAB, Barcelona, Spain
| | - Joan Carrera
- Unitat d'Endocrinologia Ginecològica, Barcelona, Spain
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Courtot L, Hoffmann JS, Bergoglio V. The Protective Role of Dormant Origins in Response to Replicative Stress. Int J Mol Sci 2018; 19:ijms19113569. [PMID: 30424570 PMCID: PMC6274952 DOI: 10.3390/ijms19113569] [Citation(s) in RCA: 30] [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: 10/02/2018] [Revised: 11/05/2018] [Accepted: 11/07/2018] [Indexed: 02/07/2023] Open
Abstract
Genome stability requires tight regulation of DNA replication to ensure that the entire genome of the cell is duplicated once and only once per cell cycle. In mammalian cells, origin activation is controlled in space and time by a cell-specific and robust program called replication timing. About 100,000 potential replication origins form on the chromatin in the gap 1 (G1) phase but only 20⁻30% of them are active during the DNA replication of a given cell in the synthesis (S) phase. When the progress of replication forks is slowed by exogenous or endogenous impediments, the cell must activate some of the inactive or "dormant" origins to complete replication on time. Thus, the many origins that may be activated are probably key to protect the genome against replication stress. This review aims to discuss the role of these dormant origins as safeguards of the human genome during replicative stress.
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Affiliation(s)
- Lilas Courtot
- CRCT, Université de Toulouse, Inserm, CNRS, UPS; Equipe labellisée Ligue Contre le Cancer, Laboratoire d'excellence Toulouse Cancer, 2 Avenue Hubert Curien, 31037 Toulouse, France.
| | - Jean-Sébastien Hoffmann
- CRCT, Université de Toulouse, Inserm, CNRS, UPS; Equipe labellisée Ligue Contre le Cancer, Laboratoire d'excellence Toulouse Cancer, 2 Avenue Hubert Curien, 31037 Toulouse, France.
| | - Valérie Bergoglio
- CRCT, Université de Toulouse, Inserm, CNRS, UPS; Equipe labellisée Ligue Contre le Cancer, Laboratoire d'excellence Toulouse Cancer, 2 Avenue Hubert Curien, 31037 Toulouse, France.
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Champroux A, Damon-Soubeyrand C, Goubely C, Bravard S, Henry-Berger J, Guiton R, Saez F, Drevet J, Kocer A. Nuclear Integrity but Not Topology of Mouse Sperm Chromosome is Affected by Oxidative DNA Damage. Genes (Basel) 2018; 9:genes9100501. [PMID: 30336622 PMCID: PMC6210505 DOI: 10.3390/genes9100501] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 10/12/2018] [Accepted: 10/15/2018] [Indexed: 01/15/2023] Open
Abstract
Recent studies have revealed a well-defined higher order of chromosome architecture, named chromosome territories, in the human sperm nuclei. The purpose of this work was, first, to investigate the topology of a selected number of chromosomes in murine sperm; second, to evaluate whether sperm DNA damage has any consequence on chromosome architecture. Using fluorescence in situ hybridization, confocal microscopy, and 3D-reconstruction approaches we demonstrate that chromosome positioning in the mouse sperm nucleus is not random. Some chromosomes tend to occupy preferentially discrete positions, while others, such as chromosome 2 in the mouse sperm nucleus are less defined. Using a mouse transgenic model (Gpx5−/−) of sperm nuclear oxidation, we show that oxidative DNA damage does not disrupt chromosome organization. However, when looking at specific nuclear 3D-parameters, we observed that they were significantly affected in the transgenic sperm, compared to the wild-type. Mild reductive DNA challenge confirmed the fragility of the organization of the oxidized sperm nucleus, which may have unforeseen consequences during post-fertilization events. These data suggest that in addition to the sperm DNA fragmentation, which is already known to modify sperm nucleus organization, the more frequent and, to date, the less highly-regarded phenomenon of sperm DNA oxidation also affects sperm chromatin packaging.
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Affiliation(s)
- Alexandre Champroux
- GReD "Genetics, Reproduction & Development" Laboratory, UMR CNRS 6293, INSERM U1103, Université Clermont Auvergne, 28 Place Henri Dunant, 63000 Clermont-Ferrand, France.
| | - Christelle Damon-Soubeyrand
- GReD "Genetics, Reproduction & Development" Laboratory, UMR CNRS 6293, INSERM U1103, Université Clermont Auvergne, 28 Place Henri Dunant, 63000 Clermont-Ferrand, France.
| | - Chantal Goubely
- GReD "Genetics, Reproduction & Development" Laboratory, UMR CNRS 6293, INSERM U1103, Université Clermont Auvergne, 28 Place Henri Dunant, 63000 Clermont-Ferrand, France.
| | - Stephanie Bravard
- GReD "Genetics, Reproduction & Development" Laboratory, UMR CNRS 6293, INSERM U1103, Université Clermont Auvergne, 28 Place Henri Dunant, 63000 Clermont-Ferrand, France.
| | - Joelle Henry-Berger
- GReD "Genetics, Reproduction & Development" Laboratory, UMR CNRS 6293, INSERM U1103, Université Clermont Auvergne, 28 Place Henri Dunant, 63000 Clermont-Ferrand, France.
| | - Rachel Guiton
- GReD "Genetics, Reproduction & Development" Laboratory, UMR CNRS 6293, INSERM U1103, Université Clermont Auvergne, 28 Place Henri Dunant, 63000 Clermont-Ferrand, France.
| | - Fabrice Saez
- GReD "Genetics, Reproduction & Development" Laboratory, UMR CNRS 6293, INSERM U1103, Université Clermont Auvergne, 28 Place Henri Dunant, 63000 Clermont-Ferrand, France.
| | - Joel Drevet
- GReD "Genetics, Reproduction & Development" Laboratory, UMR CNRS 6293, INSERM U1103, Université Clermont Auvergne, 28 Place Henri Dunant, 63000 Clermont-Ferrand, France.
| | - Ayhan Kocer
- GReD "Genetics, Reproduction & Development" Laboratory, UMR CNRS 6293, INSERM U1103, Université Clermont Auvergne, 28 Place Henri Dunant, 63000 Clermont-Ferrand, France.
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Minina JM, Karamysheva TV, Rubtsov NB, Zhdanova NS. Replication timing of large Sorex granarius (Soricidae, Eulipotyphla) telomeres. PROTOPLASMA 2018; 255:1477-1486. [PMID: 29627866 DOI: 10.1007/s00709-018-1244-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 03/19/2018] [Indexed: 06/08/2023]
Abstract
Previously, we described the unique feature of telomeric regions in Iberian shrew Sorex granarius: its telomeres have two ranges of size, very small (3.8 kb of telomeric repeats on average) and very large discontinuous telomeres (213 kb) interrupted with 18S rDNA. In this study, we have demonstrated extraordinary replication pattern of S. granarius large telomeres that have not been shown before in other studied mammal. Using the ReD-FISH procedure, we observed prolonged, through S period, large telomere replication. Furthermore, revealed ReD-FISH asymmetric signals were probably caused by partial replication of telomeres within an hour of 5-bromodeoxyuridine treatment due to the large size and special organization. We also found that in contrast to the telomeric halo from primary fibroblasts of bovine, mink, and common shrew, telomere halo of S. granarius consists of multiple loops bundled together, some of which contain rDNA. Here, we suggested several replicons firing possibly stochastic in each large telomere. Finally, we performed the TIF assay to reveal DNA damage responses at the telomeres, and along with TIF in nuclei, we found large bodies of telomeric DNA and ɤ-H2AX in the cytoplasm and on the surface of fibroblasts. We discuss the possibility of additional origin activation together with recombination-dependent replication pathways, mainly homologous recombination including BIR for replication fork stagnation overcoming and further S. granarius large telomere replication.
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Affiliation(s)
- Julia M Minina
- The Federal Research Center Institute of Cytology and Genetics of SB RAS, Lavrentjeva av. 10, 630090, Novosibirsk, Russia.
| | - Tatjana V Karamysheva
- The Federal Research Center Institute of Cytology and Genetics of SB RAS, Lavrentjeva av. 10, 630090, Novosibirsk, Russia
| | - Nicolaj B Rubtsov
- The Federal Research Center Institute of Cytology and Genetics of SB RAS, Lavrentjeva av. 10, 630090, Novosibirsk, Russia
| | - Natalia S Zhdanova
- The Federal Research Center Institute of Cytology and Genetics of SB RAS, Lavrentjeva av. 10, 630090, Novosibirsk, Russia
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Silva-Santiago E, Rivera-Mulia JC, Aranda-Anzaldo A. The Set of Structural DNA-Nuclear Matrix Interactions in Neurons Is Cell-Type Specific and Rather Independent of Functional Constraints. J Cell Biochem 2017; 118:2151-2160. [DOI: 10.1002/jcb.25852] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 12/19/2016] [Indexed: 01/03/2023]
Affiliation(s)
- Evangelina Silva-Santiago
- Facultad de Medicina, Laboratorio de Biología Molecular y Neurociencias; Universidad Autónoma del Estado de México; Toluca 50180 Edo. Méx. Mexico
| | - Juan Carlos Rivera-Mulia
- Facultad de Medicina, Laboratorio de Biología Molecular y Neurociencias; Universidad Autónoma del Estado de México; Toluca 50180 Edo. Méx. Mexico
| | - Armando Aranda-Anzaldo
- Facultad de Medicina, Laboratorio de Biología Molecular y Neurociencias; Universidad Autónoma del Estado de México; Toluca 50180 Edo. Méx. Mexico
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10
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Silva-Santiago E, Pardo JP, Hernández-Muñoz R, Aranda-Anzaldo A. The nuclear higher-order structure defined by the set of topological relationships between DNA and the nuclear matrix is species-specific in hepatocytes. Gene 2017; 597:40-48. [PMID: 27771449 DOI: 10.1016/j.gene.2016.10.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 10/12/2016] [Accepted: 10/18/2016] [Indexed: 10/20/2022]
Abstract
During the interphase the nuclear DNA of metazoan cells is organized in supercoiled loops anchored to constituents of a nuclear substructure or compartment known as the nuclear matrix. The stable interactions between DNA and the nuclear matrix (NM) correspond to a set of topological relationships that define a nuclear higher-order structure (NHOS). Current evidence suggests that the NHOS is cell-type-specific. Biophysical evidence and theoretical models suggest that thermodynamic and structural constraints drive the actualization of DNA-NM interactions. However, if the topological relationships between DNA and the NM were the subject of any biological constraint with functional significance then they must be adaptive and thus be positively selected by natural selection and they should be reasonably conserved, at least within closely related species. We carried out a coarse-grained, comparative evaluation of the DNA-NM topological relationships in primary hepatocytes from two closely related mammals: rat and mouse, by determining the relative position to the NM of a limited set of target sequences corresponding to highly-conserved genomic regions that also represent a sample of distinct chromosome territories within the interphase nucleus. Our results indicate that the pattern of topological relationships between DNA and the NM is not conserved between the hepatocytes of the two closely related species, suggesting that the NHOS, like the karyotype, is species-specific.
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Affiliation(s)
- Evangelina Silva-Santiago
- Laboratorio de Biología Molecular y Neurociencias, Facultad de Medicina, Universidad Autónoma del Estado de México, Toluca, 50180, Edo. Méx., Mexico
| | - Juan Pablo Pardo
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacan, 04510, Ciudad de México, Mexico
| | - Rolando Hernández-Muñoz
- Departamento de Biología Celular y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacan, 04510, Ciudad de México, Mexico
| | - Armando Aranda-Anzaldo
- Laboratorio de Biología Molecular y Neurociencias, Facultad de Medicina, Universidad Autónoma del Estado de México, Toluca, 50180, Edo. Méx., Mexico.
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Champroux A, Torres-Carreira J, Gharagozloo P, Drevet JR, Kocer A. Mammalian sperm nuclear organization: resiliencies and vulnerabilities. Basic Clin Androl 2016; 26:17. [PMID: 28031843 PMCID: PMC5175393 DOI: 10.1186/s12610-016-0044-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 11/12/2016] [Indexed: 01/07/2023] Open
Abstract
Sperm cells are remarkably complex and highly specialized compared to somatic cells. Their function is to deliver to the oocyte the paternal genomic blueprint along with a pool of proteins and RNAs so a new generation can begin. Reproductive success, including optimal embryonic development and healthy offspring, greatly depends on the integrity of the sperm chromatin structure. It is now well documented that DNA damage in sperm is linked to reproductive failures both in natural and assisted conception (Assisted Reproductive Technologies [ART]). This manuscript reviews recent important findings concerning - the unusual organization of mammalian sperm chromatin and its impact on reproductive success when modified. This review is focused on sperm chromatin damage and their impact on embryonic development and transgenerational inheritance.
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Affiliation(s)
- A. Champroux
- GReD “Genetics, Reproduction & Development” Laboratory, UMR CNRS 6293, INSERM U1103, Clermont Université, BP60026 - TSA60026, 63178 Aubière cedex, France
| | - J. Torres-Carreira
- Centro Universitário Rio Preto, UNIRP, Rodovia Br153, Km 69, CEP15093-450 São José do Rio Preto, São Paulo Brazil
| | - P. Gharagozloo
- CellOxess LLC, 830 Bear Tavern Road, Ewing, NJ 08628 USA
| | - J. R. Drevet
- GReD “Genetics, Reproduction & Development” Laboratory, UMR CNRS 6293, INSERM U1103, Clermont Université, BP60026 - TSA60026, 63178 Aubière cedex, France
| | - A. Kocer
- GReD “Genetics, Reproduction & Development” Laboratory, UMR CNRS 6293, INSERM U1103, Clermont Université, BP60026 - TSA60026, 63178 Aubière cedex, France
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12
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Ohsaki E, Ueda K. A chimeric protein composed of NuMA fused to the DNA binding domain of LANA is sufficient for the ori-P-dependent DNA replication. Virology 2016; 500:190-197. [PMID: 27829174 DOI: 10.1016/j.virol.2016.10.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 10/20/2016] [Accepted: 10/31/2016] [Indexed: 01/25/2023]
Abstract
The Kaposi's sarcoma-associated herpesvirus (KSHV) genome is stably maintained in KSHV-infected PEL cell lines during cell division. We previously showed that accumulation of LANA in the nuclear matrix fraction could be important for the latent DNA replication, and that the functional significance of LANA should be its recruitment of ori-P to the nuclear matrix. Here, we investigated whether the forced localization of the LANA-DNA binding domain (DBD) to the nuclear matrix facilitated ori-P-containing plasmid replication. We demonstrated that chimeric proteins constructed by fusion of LANA DBD with the nuclear mitotic apparatus protein (NuMA), which is one of the components of the nuclear matrix, could bind with ori-P and enhance replication of an ori-P-containing plasmid, compared with that in the presence of DBD alone. These results further suggested that the ori-P recruitment to the nuclear matrix through the binding with DBD is important for latent viral DNA replication.
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Affiliation(s)
- Eriko Ohsaki
- Division of Virology, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Keiji Ueda
- Division of Virology, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Osaka, Japan.
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Aranda-Anzaldo A, Dent MAR. Why Cortical Neurons Cannot Divide, and Why Do They Usually Die in the Attempt? J Neurosci Res 2016; 95:921-929. [PMID: 27402311 DOI: 10.1002/jnr.23765] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 03/25/2016] [Accepted: 04/25/2016] [Indexed: 12/19/2022]
Abstract
Cortical neurons are prime examples of terminally differentiated, postmitotic cells. However, under experimental or pathological conditions, they can re-enter the cell cycle and replicate DNA but are unable to divide, dying by apoptosis or becoming either polyploid or aneuploid. Any cellular state that depends on the action of genes and their products can be reverted or bypassed by spontaneous or induced mutations, yet there are currently no reports of dividing cortical neurons. Thus, it seems unlikely that the remarkably stable postmitotic condition of cortical neurons depends on specific gene functions. This Review summarizes evidence that the postmitotic state of cortical neurons depends on the high stability of its underlying nuclear structure that results from an entropy-driven process aimed at dissipating the intrinsic structural stress present in chromosomal DNA in such a way that the structural stability of the neuronal nucleus becomes an insurmountable energy barrier for karyokinesis and mitosis. From this perspective, the integral properties of the nuclear higher order structure in neurons provide an explanation not only for why cortical neurons cannot divide but also for why they usually die if they happen to replicate their DNA. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Armando Aranda-Anzaldo
- Laboratorio de Biología Molecular y Neurociencias, Facultad de Medicina, Universidad Autónoma del Estado de México, Toluca, Estado México, México
| | - Myrna A R Dent
- Laboratorio de Biología Molecular y Neurociencias, Facultad de Medicina, Universidad Autónoma del Estado de México, Toluca, Estado México, México
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Copeland NA, Sercombe HE, Wilson RHC, Coverley D. Cyclin A/CDK2 phosphorylation of CIZ1 blocks replisome formation and initiation of mammalian DNA replication. J Cell Sci 2015; 128:1518-27. [DOI: 10.1242/jcs.161919] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 02/23/2015] [Indexed: 12/25/2022] Open
Abstract
CIZ1 is a nuclear matrix protein that cooperates with cyclin A/CDK2 to promote mammalian DNA replication. We show here that cyclin A/CDK2 also negatively regulates CIZ1 activity via phosphorylation at threonines 144, 192, and 293. Phosphomimetic mutants do not promote DNA replication in cell-free and cell-based assays, and also have a dominant negative effect on replisome formation at the level of PCNA recruitment. Phosphorylation blocks direct interaction with cyclin A/CDK2, and recruitment of endogenous cyclin A to the nuclear matrix. In contrast, phosphomimetic CIZ1 retains nuclear matrix binding capability, and interaction with CDC6 is not affected. Phospho-threonine 192-specific antibodies confirm that CIZ1 is phosphorylated during S-phase and G2, and show that phosphorylation at this site occurs at post-initiation concentrations of cyclin A/CDK2. Together the data suggest that CIZ1 is a kinase sensor that promotes initiation of DNA replication at low kinase levels, when in a hypophosphorylated state that is permissive for cyclin A-CDK2 interaction and delivery to licensed origins, but blocks delivery at higher kinase levels when it is itself phosphorylated.
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15
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Flickinger RA. Possible role of H1 histone in replication timing. Dev Growth Differ 2014; 57:1-9. [PMID: 25495214 DOI: 10.1111/dgd.12190] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 11/03/2014] [Accepted: 11/04/2014] [Indexed: 01/02/2023]
Abstract
AT-rich repetitive DNA sequences become late replicating during cell differentiation. Replication timing is not correlated with LINE density in human cells (Ryba et al. 2010). However, short and properly spaced runs of oligo dA or dT present in nuclear matrix attachment regions (MARs) of the genome are good candidates for elements of AT-rich repetitive late replicating DNA. MAR attachment to the nuclear matrix is negatively regulated by chromatin binding of H1 histone, but this is counteracted by H1 phosphorylation, high mobility group proteins or, indirectly, core histone acetylation. Fewer MAR attachments correlates positively with longer average DNA loop size, longer replicons and an increase of late replicating DNA.
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Affiliation(s)
- Reed A Flickinger
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, 14260, New York, USA
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16
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The higher-order structure in the cells nucleus as the structural basis of the post-mitotic state. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014; 114:137-45. [DOI: 10.1016/j.pbiomolbio.2014.02.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 02/09/2014] [Indexed: 11/19/2022]
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17
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Puglisi R, Maccari I, Pipolo S, Mangia F, Boitani C. The nuclear form of glutathione peroxidase 4 colocalizes and directly interacts with protamines in the nuclear matrix during mouse sperm chromatin assembly. SPERMATOGENESIS 2014; 4:e28460. [PMID: 25225625 PMCID: PMC4160342 DOI: 10.4161/spmg.28460] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 03/04/2014] [Accepted: 03/06/2014] [Indexed: 11/19/2022]
Abstract
The testis-specific nuclear form of Phospholipid Hydroperoxide Glutathione Peroxidase (nGPx4) is associated with the nuclear matrix during spermiogenesis and is implicated in sperm chromatin condensation. In this study, we have addressed the question whether nGPx4 directly interacts with protamines by transiently sharing a nuclear matrix localization. We first expressed tagged protamine 1-myc and protamine 2-V5 in HeLa and COS-1 cells and showed by both confocal microscopy and immunoblotting analyses that protamines were produced in vitro and colocalized correctly to the nucleus. Co-transfection experiments demonstrated that protamine 1 was physically associated with flag-nGPx4 specifically at the level of nuclear matrix. The peculiar presence of protamines together with nGPx4 in this subnuclear compartment was also confirmed in mouse elongated spermatids by immunofluorescence, suggesting that nGPx4 is a physiological component of a novel protein complex relevant to chromatin assembly in condensing haploid cells. Also, in epididymal sperm, nGPx4 and protamine 1 co-immunoprecipitated, indicating that nGPx4, although localized to a subnuclear compartment different from that of protamines, represents a constant link between nuclear matrix and chromatin in mammalian male gamete.
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Affiliation(s)
- Rossella Puglisi
- DAHFMO; Section of Histology & Medical Embryology; University of Rome "La Sapienza;" Rome, Italy
| | - Irene Maccari
- DAHFMO; Section of Histology & Medical Embryology; University of Rome "La Sapienza;" Rome, Italy
| | - Simona Pipolo
- DAHFMO; Section of Histology & Medical Embryology; University of Rome "La Sapienza;" Rome, Italy
| | - Franco Mangia
- Dept Psychology; Section of Neuroscience; University of Rome"La Sapienza;" Rome, Italy
| | - Carla Boitani
- DAHFMO; Section of Histology & Medical Embryology; University of Rome "La Sapienza;" Rome, Italy
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18
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Noblanc A, Kocer A, Drevet JR. Recent knowledge concerning mammalian sperm chromatin organization and its potential weaknesses when facing oxidative challenge. Basic Clin Androl 2014; 24:6. [PMID: 26779341 PMCID: PMC4715350 DOI: 10.1186/2051-4190-24-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2014] [Accepted: 02/26/2014] [Indexed: 01/08/2023] Open
Abstract
Spermatozoa are the smallest and most cyto-differentiated mammalian cells. From a somatic cell-like appearance at the beginning of spermatogenesis, the male germ cell goes through a highly sophisticated process to reach its final organization entirely devoted to its mission which is to deliver the paternal genome to the oocyte. In order to fit the paternal DNA into the tiny spermatozoa head, complete chromatin remodeling is necessary. This review essentially focuses on present knowledge of this mammalian sperm nucleus compaction program. Particular attention is given to most recent advances that concern the specific organization of mammalian sperm chromatin and its potential weaknesses. Emphasis is placed on sperm DNA oxidative damage that may have dramatic consequences including infertility, abnormal embryonic development and the risk of transmission to descendants of an altered paternal genome.
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Affiliation(s)
- Anais Noblanc
- GReD Laboratory, CNRS UMR 6293 - INSERM U1103 - Clermont Université, Aubière, France
| | - Ayhan Kocer
- GReD Laboratory, CNRS UMR 6293 - INSERM U1103 - Clermont Université, Aubière, France
| | - Joël R Drevet
- GReD Laboratory, CNRS UMR 6293 - INSERM U1103 - Clermont Université, Aubière, France
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19
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Sukackaite R, Jensen MR, Mas PJ, Blackledge M, Buonomo SB, Hart DJ. Structural and biophysical characterization of murine rif1 C terminus reveals high specificity for DNA cruciform structures. J Biol Chem 2014; 289:13903-11. [PMID: 24634216 DOI: 10.1074/jbc.m114.557843] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Mammalian Rif1 is a key regulator of DNA replication timing, double-stranded DNA break repair, and replication fork restart. Dissecting the molecular functions of Rif1 is essential to understand how it regulates such diverse processes. However, Rif1 is a large protein that lacks well defined functional domains and is predicted to be largely intrinsically disordered; these features have hampered recombinant expression of Rif1 and subsequent functional characterization. Here we applied ESPRIT (expression of soluble proteins by random incremental truncation), an in vitro evolution-like approach, to identify high yielding soluble fragments encompassing conserved regions I and II (CRI and CRII) at the C-terminal region of murine Rif1. NMR analysis showed CRI to be intrinsically disordered, whereas CRII is partially folded. CRII binds cruciform DNA with high selectivity and micromolar affinity and thus represents a functional DNA binding domain. Mutational analysis revealed an α-helical region of CRII to be important for cruciform DNA binding and identified critical residues. Thus, we present the first structural study of the mammalian Rif1, identifying a domain that directly links its function to DNA binding. The high specificity of Rif1 for cruciform structures is significant given the role of this key protein in regulating origin firing and DNA repair.
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Affiliation(s)
- Rasa Sukackaite
- From the European Molecular Biology Laboratory (EMBL), Grenoble Outstation, 6 rue Jules Horowitz, 38042 France, the Unit for Virus Host-Cell Interactions, University of Grenoble Alpes-EMBL-CNRS, 6 rue Jules Horowitz, 38042 France, the European Molecular Biology Laboratory, Monterotondo Outstation, Adriano Buzzati-Traverso Campus, Via Ramarini 32, 00015 Monterotondo, Italy
| | - Malene Ringkjøbing Jensen
- the University of Grenoble Alpes, Institut de Biologie Structurale (IBS), 6 rue Jules Horowitz, F-38027 Grenoble, France, CEA, DSV, IBS, 6 rue Jules Horowitz, F-38027 Grenoble, France, CNRS, IBS, 6 rue Jules Horowitz, F-38027 Grenoble, France, and
| | - Philippe J Mas
- From the European Molecular Biology Laboratory (EMBL), Grenoble Outstation, 6 rue Jules Horowitz, 38042 France, the Unit for Virus Host-Cell Interactions, University of Grenoble Alpes-EMBL-CNRS, 6 rue Jules Horowitz, 38042 France
| | - Martin Blackledge
- the University of Grenoble Alpes, Institut de Biologie Structurale (IBS), 6 rue Jules Horowitz, F-38027 Grenoble, France, CEA, DSV, IBS, 6 rue Jules Horowitz, F-38027 Grenoble, France, CNRS, IBS, 6 rue Jules Horowitz, F-38027 Grenoble, France, and
| | - Sara B Buonomo
- the European Molecular Biology Laboratory, Monterotondo Outstation, Adriano Buzzati-Traverso Campus, Via Ramarini 32, 00015 Monterotondo, Italy
| | - Darren J Hart
- From the European Molecular Biology Laboratory (EMBL), Grenoble Outstation, 6 rue Jules Horowitz, 38042 France, the Unit for Virus Host-Cell Interactions, University of Grenoble Alpes-EMBL-CNRS, 6 rue Jules Horowitz, 38042 France,
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20
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Lima Neto QA, Rando FS, Freitas DVB, Rodrigues LF, Rosado FR, Fiorini A, Gimenes F, Tavares J, Fernandez MA. Straight core structure of DNA replication origins in the mammalian AMPD2 locus. BIOCHEMISTRY (MOSCOW) 2014; 79:37-43. [PMID: 24512662 DOI: 10.1134/s0006297914010064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Identification of the nucleotide consensus sequence in mammalian replication origins is a difficult and controversial problem. The hypothesis that local DNA topology could be involved in recognition by replication proteins is an exciting possibility. Secondary DNA structures, including intrinsically bent DNA, can be easily detected, and they may indicate a specific pattern in or near mammalian replication origins. This work presents the entire mapping of the intrinsically bent DNA sites (IBDSs), using in silico analysis and a circular permutation assay, of the DNA replication origins oriGNAI3, oriC, oriB, and oriA in the mammalian amplified AMPD2 gene domain. The results show that each origin presents an IBDS that flanks the straight core of these DNA replication sites. In addition, the in silico prediction of the nucleosome positioning reveals a strong indication that the center of an IBDS is localized in a nucleosome-free region (NFR). The structure of each of these curved sites is presented together with their helical parameters and topology. Together, the data that we present here indicate that the oriGNAI3 origin where preferential firing to the replication initiation events in the amplified AMPD2 domain occurs is the only origin that presents a straight, narrow region that is flanked on both sides by two intrinsically bent DNA sites within a short distance (~300 bp); however, all of the origins present at least one IBDS, which is localized in the NFR region. These results indicate that structural features could be implicated in the mammalian DNA replication origin and support the possibility of detecting and characterizing these segments.
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Affiliation(s)
- Q A Lima Neto
- Departamento de Biotecnologia, Genética e Biologia Celular, Universidade Estadual de Maringá, UEM, Maringá, Paraná, 87020-900, Brasil.
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21
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Abstract
The Mediator complex is a multi-subunit assembly that appears to be required for regulating expression of most RNA polymerase II (pol II) transcripts, which include protein-coding and most non-coding RNA genes. Mediator and pol II function within the pre-initiation complex (PIC), which consists of Mediator, pol II, TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH and is approximately 4.0 MDa in size. Mediator serves as a central scaffold within the PIC and helps regulate pol II activity in ways that remain poorly understood. Mediator is also generally targeted by sequence-specific, DNA-binding transcription factors (TFs) that work to control gene expression programs in response to developmental or environmental cues. At a basic level, Mediator functions by relaying signals from TFs directly to the pol II enzyme, thereby facilitating TF-dependent regulation of gene expression. Thus, Mediator is essential for converting biological inputs (communicated by TFs) to physiological responses (via changes in gene expression). In this review, we summarize an expansive body of research on the Mediator complex, with an emphasis on yeast and mammalian complexes. We focus on the basics that underlie Mediator function, such as its structure and subunit composition, and describe its broad regulatory influence on gene expression, ranging from chromatin architecture to transcription initiation and elongation, to mRNA processing. We also describe factors that influence Mediator structure and activity, including TFs, non-coding RNAs and the CDK8 module.
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Affiliation(s)
- Zachary C Poss
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, CO , USA
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22
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Shima H, Suzuki H, Sun J, Kono K, Shi L, Kinomura A, Horikoshi Y, Ikura T, Ikura M, Kanaar R, Igarashi K, Saitoh H, Kurumizaka H, Tashiro S. Activation of the SUMO modification system is required for the accumulation of RAD51 at sites of DNA damage. J Cell Sci 2013; 126:5284-92. [PMID: 24046452 DOI: 10.1242/jcs.133744] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Genetic information encoded in chromosomal DNA is challenged by intrinsic and exogenous sources of DNA damage. DNA double-strand breaks (DSBs) are extremely dangerous DNA lesions. RAD51 plays a central role in homologous DSB repair, by facilitating the recombination of damaged DNA with intact DNA in eukaryotes. RAD51 accumulates at sites containing DNA damage to form nuclear foci. However, the mechanism of RAD51 accumulation at sites of DNA damage is still unclear. Post-translational modifications of proteins, such as phosphorylation, acetylation and ubiquitylation play a role in the regulation of protein localization and dynamics. Recently, the covalent binding of small ubiquitin-like modifier (SUMO) proteins to target proteins, termed SUMOylation, at sites containing DNA damage has been shown to play a role in the regulation of the DNA-damage response. Here, we show that the SUMOylation E2 ligase UBC9, and E3 ligases PIAS1 and PIAS4, are required for RAD51 accretion at sites containing DNA damage in human cells. Moreover, we identified a SUMO-interacting motif (SIM) in RAD51, which is necessary for accumulation of RAD51 at sites of DNA damage. These findings suggest that the SUMO-SIM system plays an important role in DNA repair, through the regulation of RAD51 dynamics.
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Affiliation(s)
- Hiroki Shima
- Department of Cellular Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima 734-8553, Japan
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23
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Abstract
Although distinct chromatin types have been long known to replicate at different timepoints of S phase, fine replication control has only recently become considered as an epigenetic phenomenon. It is now clear that in course of differentiation significant changes in genome replication timing occur, and these changes are intimately linked with the changes in transcriptional activity and nuclear architecture. Temporally coordinate replication is organized spatially into discrete units having specific chromosomal organization and function. Even though the functional aspects of such tight control of replication timing remain to be explored, one can confidently consider the replication program as yet another fundamental feature characteristic of the given differentiation state. The present review touches upon the molecular mechanisms of spatial and temporal control of replication timing, involving individual replication origins as well as large chromatin domains.
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Ueda K, Xu ZJ, Miyagi N, Ono M, Wabiko H, Masuda K, Inoue M. Isolation and characterization of a carrot nucleolar protein with structural and sequence similarity to the vertebrate PESCADILLO protein. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2013; 208:83-92. [PMID: 23683933 DOI: 10.1016/j.plantsci.2013.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2013] [Revised: 03/29/2013] [Accepted: 04/03/2013] [Indexed: 06/02/2023]
Abstract
The nuclear matrix is involved in many nuclear events, but its protein architecture in plants is still not fully understood. A cDNA clone was isolated by immunoscreening with a monoclonal antibody raised against nuclear matrix proteins of Daucus carota L. Its deduced amino acid sequence showed about 40% identity with the PESCADILLO protein of zebrafish and humans. Primary structure analysis of the protein revealed a Pescadillo N-terminus domain, a single breast cancer C-terminal domain, two nuclear localization signals, and a potential coiled-coil region as also found in animal PESCADILLO proteins. Therefore, we designated this gene DcPES1. Although DcPES1 mRNA was detected in all tissues examined, its levels were highest in tissues with proliferating cells. Immunofluorescence using specific antiserum against the recombinant protein revealed that DcPES1 localized exclusively in the nucleolus. Examination of fusion proteins with green fluorescent protein revealed that the N-terminal portion was important for localization to the nucleoli of tobacco and onion cells. Moreover, when the nuclear matrix of carrot cells was immunostained with an anti-DcPES1 serum, the signal was detected in the nucleolus. Therefore, the DcPES1 protein appears to be a component of or tightly bound to components of the nuclear matrix.
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Affiliation(s)
- Kenji Ueda
- Faculty of Bioresource Sciences, Akita Prefectural University, Akita 010-0195, Japan.
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25
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Cha S, Seo T. Viral genome maintenance and latent replication of human gammaherpesviruses. Future Virol 2013. [DOI: 10.2217/fvl.13.37] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
During gammaherpesvirus latency, only a few genes are expressed and required for maintenance of viral latency over a long period. While the expressed latent viral proteins play functional roles in viral latent DNA replication, they do not have replication-associated enzymatic activity such as polymerase or helicase activity. Viral genomes are detected in a similar copy number per infected cell, suggesting that the viral genome is replicated and segregated using host replication machinery. Kaposi’s sarcoma-associated herpesvirus and EBV have trans-acting elements required for viral genome maintenance during latency; LANA1 and EBNA1, respectively. The proteins recruit host replication-associated proteins at their latent origins, leading to initiation of viral replication and segregation with host chromosomes once per cell cycle. In addition, viral latent origins (cis-elements) provide trans-element-binding sites as well as a sufficient space for recruitment of cellular factors. In this review, we describe the molecular mechanisms required for replication of the viral genome during latency, including interactions with cellular factors and the interplay between viral trans- and cis-elements.
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Affiliation(s)
- Seho Cha
- Department of Life Science, Dongguk University-Seoul, 26, 3 Pil-dong, Jung-gu, Seoul, 100-715, Republic of Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, 26, 3 Pil-dong, Jung-gu, Seoul, 100-715, Republic of Korea.
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26
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Castillo-Mora RC, Aranda-Anzaldo A. Reorganization of the DNA-nuclear matrix interactions in a 210 kb genomic region centered on c-myc after DNA replication in vivo. J Cell Biochem 2012; 113:2451-63. [PMID: 22396210 DOI: 10.1002/jcb.24123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
In the interphase nucleus of metazoan cells DNA is organized in supercoiled loops anchored to a nuclear matrix (NM). DNA loops are operationally classified in structural and facultative. Varied evidence indicates that DNA replication occurs in replication foci organized upon the NM and that structural DNA loops may correspond to the replicons in vivo. In normal rat liver the hepatocytes are arrested in G0 but synchronously re-enter the cell cycle after partial-hepatectomy leading to liver regeneration. Using this model we have previously determined that the DNA loops corresponding to a gene-rich genomic region move in a sequential fashion towards the NM during replication and then return to their original configuration in newly quiescent cells, once liver regeneration has been achieved. In the present work we determined the organization into structural DNA loops of a gene-poor region centered on c-myc and tracked-down its movement at the peak of S phase and after the return to cellular quiescence during and after liver regeneration. The results confirmed that looped DNA moves towards the NM during replication but in this case the configuration of the gene-poor region into DNA loops becomes reorganized and after replication only the loop containing c-myc resembles the original in the control G0 hepatocytes. Our results suggest that the local chromatin configuration around potentially active genes constraints the formation of specific structural DNA loops after DNA replication, while in non-coding regions the structural DNA loops are only loosely determined after DNA replication by structural constraints that modulate the DNA-NM interactions.
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Affiliation(s)
- Rebeca C Castillo-Mora
- Facultad de Medicina, Universidad Autónoma del Estado de México, Paseo Tollocan y Jesús Carranza s/n, Toluca, Edo. México, Mexico
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Moindrot B, Audit B, Klous P, Baker A, Thermes C, de Laat W, Bouvet P, Mongelard F, Arneodo A. 3D chromatin conformation correlates with replication timing and is conserved in resting cells. Nucleic Acids Res 2012; 40:9470-81. [PMID: 22879376 PMCID: PMC3479194 DOI: 10.1093/nar/gks736] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Although chromatin folding is known to be of functional importance to control the gene expression program, less is known regarding its interplay with DNA replication. Here, using Circular Chromatin Conformation Capture combined with high-throughput sequencing, we identified megabase-sized self-interacting domains in the nucleus of a human lymphoblastoid cell line, as well as in cycling and resting peripheral blood mononuclear cells (PBMC). Strikingly, the boundaries of those domains coincide with early-initiation zones in every cell types. Preferential interactions have been observed between the consecutive early-initiation zones, but also between those separated by several tens of megabases. Thus, the 3D conformation of chromatin is strongly correlated with the replication timing along the whole chromosome. We furthermore provide direct clues that, in addition to the timing value per se, the shape of the timing profile at a given locus defines its set of genomic contacts. As this timing-related scheme of chromatin organization exists in lymphoblastoid cells, resting and cycling PBMC, this indicates that it is maintained several weeks or months after the previous S-phase. Lastly, our work highlights that the major chromatin changes accompanying PBMC entry into cell cycle occur while keeping largely unchanged the long-range chromatin contacts.
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Affiliation(s)
- Benoit Moindrot
- Laboratoire Joliot-Curie, Ecole Normale Supérieure de Lyon, CNRS, F-69007 Lyon, France
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28
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Efficient recombinant production in mammalian cells using a novel IR/MAR gene amplification method. PLoS One 2012; 7:e41787. [PMID: 22844523 PMCID: PMC3402416 DOI: 10.1371/journal.pone.0041787] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 06/25/2012] [Indexed: 01/21/2023] Open
Abstract
We previously found that plasmids bearing a mammalian replication initiation region (IR) and a nuclear matrix attachment region (MAR) efficiently initiate gene amplification and spontaneously increase their copy numbers in animal cells. In this study, this novel method was applied to the establishment of cells with high recombinant antibody production. The level of recombinant antibody expression was tightly correlated with the efficiency of plasmid amplification and the cytogenetic appearance of the amplified genes, and was strongly dependent on cell type. By using a widely used cell line for industrial protein production, CHO DG44, clones expressing very high levels of antibody were easily obtained. High-producer clones stably expressed the antibody over several months without eliciting changes in both the protein expression level and the cytogenetic appearance of the amplified genes. The integrity and reactivity of the protein produced by this method was fine. In serum-free suspension culture, the specific protein production rate in high-density cultures was 29.4 pg/cell/day. In conclusion, the IR/MAR gene amplification method is a novel and efficient platform for recombinant antibody production in mammalian cells, which rapidly and easily enables the establishment of stable high-producer cell clone.
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29
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Shimizu Y, Luk H, Horio D, Miron P, Griswold M, Iglehart D, Hernandez B, Killeen J, ElShamy WM. BRCA1-IRIS overexpression promotes formation of aggressive breast cancers. PLoS One 2012; 7:e34102. [PMID: 22511931 PMCID: PMC3325250 DOI: 10.1371/journal.pone.0034102] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Accepted: 02/21/2012] [Indexed: 12/31/2022] Open
Abstract
Introduction Women with HER2+ or triple negative/basal-like (TN/BL) breast cancers succumb to their cancer rapidly due, in part to acquired Herceptin resistance and lack of TN/BL-targeted therapies. BRCA1-IRIS is a recently discovered, 1399 residue, BRCA1 locus alternative product, which while sharing 1365 residues with the full-length product of this tumor suppressor gene, BRCA1/p220, it has oncoprotein-like properties. Here, we examine whether BRCA1-IRIS is a valuable treatment target for HER2+ and/or TN/BL tumors. Methodology/Principal Findings Immunohistochemical staining of large cohort of human breast tumor samples using new monoclonal anti-BRCA1-IRIS antibody, followed by correlation of BRCA1-IRIS expression with that of AKT1, AKT2, p-AKT, survivin and BRCA1/p220, tumor status and age at diagnosis. Generation of subcutaneous tumors in SCID mice using human mammary epithelial (HME) cells overexpressing TERT/LT/BRCA1-IRIS, followed by comparing AKT, survivin, and BRCA1/p220 expression, tumor status and aggressiveness in these tumors to that in tumors developed using TERT/LT/RasV12-overexpressing HME cells. Induction of primary and invasive rat mammary tumors using the carcinogen N-methyl-N-nitrosourea (NMU), followed by analysis of rat BRCA1-IRIS and ERα mRNA levels in these tumors. High BRCA1-IRIS expression was detected in the majority of human breast tumors analyzed, which was positively correlated with that of AKT1-, AKT2-, p-AKT-, survivin, but negatively with BRCA1/p220 expression. BRCA1-IRIS-positivity induced high-grade, early onset and metastatic HER2+ or TN/BL tumors. TERT/LT/BRCA1-IRIS overexpressing HME cells formed invasive subcutaneous tumors that express high AKT1, AKT2, p-AKT and vimentin, but no CK19, p63 or BRCA1/p220. NMU-induced primary and invasive rat breast cancers expressed high levels of rat BRCA1-IRIS mRNA but low levels of rat ERα mRNA. Conclusion/Significance BRCA1-IRIS overexpression triggers aggressive breast tumor formation, especially in patients with HER2+ or TN/BL subtypes. We propose that BRCA1-IRIS inhibition may be pursued as a novel therapeutic option to treat these aggressive breast tumor subtypes.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Wael M. ElShamy
- Cancer Institute and Department of Biochemistry, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
- * E-mail:
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Ranneberg-Nilsen T, Rollag H, Slettebakk R, Backe PH, Olsen Ø, Luna L, Bjørås M. The chromatin remodeling factor SMARCB1 forms a complex with human cytomegalovirus proteins UL114 and UL44. PLoS One 2012; 7:e34119. [PMID: 22479537 PMCID: PMC3313996 DOI: 10.1371/journal.pone.0034119] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Accepted: 02/22/2012] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Human cytomegalovirus (HCMV) uracil DNA glycosylase, UL114, is required for efficient viral DNA replication. Presumably, UL114 functions as a structural partner to other factors of the DNA-replication machinery and not as a DNA repair protein. UL114 binds UL44 (HCMV processivity factor) and UL54 (HCMV-DNA-polymerase). In the present study we have searched for cellular partners of UL114. METHODOLOGY/PRINCIPAL FINDINGS In a yeast two-hybrid screen SMARCB1, a factor of the SWI/SNF chromatin remodeling complex, was found to be an interacting partner of UL114. This interaction was confirmed in vitro by co-immunoprecipitation and pull-down. Immunofluorescence microscopy revealed that SMARCB1 along with BRG-1, BAF170 and BAF155, which are the core SWI/SNF components required for efficient chromatin remodeling, were present in virus replication foci 24-48 hours post infection (hpi). Furthermore a direct interaction was also demonstrated for SMARCB1 and UL44. CONCLUSIONS/SIGNIFICANCE The core SWI/SNF factors required for efficient chromatin remodeling are present in the HCMV replication foci throughout infection. The proteins UL44 and UL114 interact with SMARCB1 and may participate in the recruitment of the SWI/SNF complex to the chromatinized virus DNA. Thus, the presence of the SWI/SNF chromatin remodeling complex in replication foci and its association with UL114 and with UL44 might imply its involvement in different DNA transactions.
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Affiliation(s)
- Toril Ranneberg-Nilsen
- Department of Microbiology, University of Oslo and Oslo University Hospital HF, Oslo, Norway
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Proteomic and protein interaction network analysis of human T lymphocytes during cell-cycle entry. Mol Syst Biol 2012; 8:573. [PMID: 22415777 PMCID: PMC3321526 DOI: 10.1038/msb.2012.5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Accepted: 01/30/2012] [Indexed: 12/23/2022] Open
Abstract
Proteomic analysis of T cells emerging from quiescence identifies dynamic network-level changes in key cellular processes. Disruption of two such processes, ribosome biogenesis and RNA splicing, reveals that the programs controlling cell growth and cell-cycle entry are separable. ![]()
The authors conduct a proteomic and protein interaction network analysis of human T lymphocytes during entry into the first cell cycle. Inhibiting the induction of eIF6 (60S ribosome biogenesis) causes T cells to enter the cell cycle without growing in size. Inhibiting the induction of SF3B2/SF3B4 (U2/U12-dependent RNA splicing) allows an increase in cell size without entering the cell cycle. These results provide proof of principle that blastogenesis and proliferation programs are separable in primary human T cells.
Regulating the transition of cells such as T lymphocytes from quiescence (G0) into an activated, proliferating state involves initiation of cellular programs resulting in entry into the cell cycle (proliferation), the growth cycle (blastogenesis, cell size) and effector (functional) activation. We show the first proteomic analysis of protein interaction networks activated during entry into the first cell cycle from G0. We also provide proof of principle that blastogenesis and proliferation programs are separable in primary human T cells. We employed a proteomic profiling method to identify large-scale changes in chromatin/nuclear matrix-bound and unbound proteins in human T lymphocytes during the transition from G0 into the first cell cycle and mapped them to form functionally annotated, dynamic protein interaction networks. Inhibiting the induction of two proteins involved in two of the most significantly upregulated cellular processes, ribosome biogenesis (eIF6) and hnRNA splicing (SF3B2/SF3B4), showed, respectively, that human T cells can enter the cell cycle without growing in size, or increase in size without entering the cell cycle.
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Aranda-Anzaldo A. The post-mitotic state in neurons correlates with a stable nuclear higher-order structure. Commun Integr Biol 2012; 5:134-9. [PMID: 22808316 PMCID: PMC3376047 DOI: 10.4161/cib.18761] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Neurons become terminally differentiated (TD) post-mitotic cells very early during development yet they may remain alive and functional for decades. TD neurons preserve the molecular machinery necessary for DNA synthesis that may be reactivated by different stimuli but they never complete a successful mitosis. The non-reversible nature of the post-mitotic state in neurons suggests a non-genetic basis for it since no set of mutations has been able to revert it. Comparative studies of the nuclear higher-order structure in neurons and cells with proliferating potential suggest that the non-reversible nature of the post-mitotic state in neurons has a structural basis in the stability of the nuclear higher-order structure.
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Affiliation(s)
- Armando Aranda-Anzaldo
- Laboratorio de Biología Molecular; Facultad de Medicina; Universidad Autónoma del Estado de México; Toluca, México
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The organization of a large transcriptional unit (Fyn) into structural DNA loops is cell-type specific and independent of transcription. Gene 2012; 493:1-8. [DOI: 10.1016/j.gene.2011.11.050] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Revised: 10/21/2011] [Accepted: 11/14/2011] [Indexed: 11/19/2022]
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Chun Y, Park B, Koh W, Lee S, Cheon Y, Kim R, Che L, Lee S. New centromeric component CENP-W is an RNA-associated nuclear matrix protein that interacts with nucleophosmin/B23 protein. J Biol Chem 2011; 286:42758-42769. [PMID: 22002061 DOI: 10.1074/jbc.m111.228411] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
CENP-W was originally identified as a putative oncogene, cancer-upregulated gene 2 (CUG2) that was commonly up-regulated in many cancer tissues. Recently, CENP-W has also been identified as a new centromeric component that interacts with CENP-T. As a complex with CENP-T, CENP-W plays crucial roles in assembly of the functional kinetochore complex. In this study, the subnuclear localization of CENP-W was extensively analyzed using various approaches. We found that ectopically expressed CENP-W primarily accumulated in the nucleolus and remained substantially associated with the nucleolus in stable cells. The following fractionation study also showed that CENP-W is associated with RNA as well as DNA. Moreover, a considerable amount of CENP-W was found in the nuclear mesh-like structure, nuclear matrix, possibly indicating that CENP-W participates in diverse subnuclear activities. Finally, biochemical affinity binding analysis revealed that CENP-W specifically interacts with the nucleolar phosphoprotein, nucleophosmin (B23). Depletion of cellular B23 by siRNA treatment induced a dramatic decrease of CENP-W stability and severe mislocalization during prophase. Our data proposed that B23 may function in the assembly of the kinetochore complex by interacting with CENP-W during interphase.
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Affiliation(s)
- Younghwa Chun
- Department of Microbiology and Molecular Biology, Chungnam National University, 305-764, Daejeon, Republic of Korea
| | - Byoungwoo Park
- Department of Microbiology and Molecular Biology, Chungnam National University, 305-764, Daejeon, Republic of Korea
| | - Wansoo Koh
- Department of Microbiology and Molecular Biology, Chungnam National University, 305-764, Daejeon, Republic of Korea
| | - Sunhee Lee
- Department of Microbiology and Molecular Biology, Chungnam National University, 305-764, Daejeon, Republic of Korea
| | - Yeongmi Cheon
- Department of Microbiology and Molecular Biology, Chungnam National University, 305-764, Daejeon, Republic of Korea
| | - Raehyung Kim
- Department of Microbiology and Molecular Biology, Chungnam National University, 305-764, Daejeon, Republic of Korea
| | - Lihua Che
- Department of Microbiology and Molecular Biology, Chungnam National University, 305-764, Daejeon, Republic of Korea
| | - Soojin Lee
- Department of Microbiology and Molecular Biology, Chungnam National University, 305-764, Daejeon, Republic of Korea.
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Dynamics of nuclear matrix proteome during embryonic development in Drosophila melanogaster. J Biosci 2011; 36:439-59. [DOI: 10.1007/s12038-011-9081-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Alva-Medina J, Maya-Mendoza A, Dent MAR, Aranda-Anzaldo A. Continued stabilization of the nuclear higher-order structure of post-mitotic neurons in vivo. PLoS One 2011; 6:e21360. [PMID: 21731716 PMCID: PMC3121788 DOI: 10.1371/journal.pone.0021360] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2011] [Accepted: 05/26/2011] [Indexed: 11/19/2022] Open
Abstract
Background Cellular terminal differentiation (TD) correlates with a permanent exit from the cell cycle and so TD cells become stably post-mitotic. However, TD cells express the molecular machinery necessary for cell proliferation that can be reactivated by experimental manipulation, yet it has not been reported the stable proliferation of any type of reactivated TD cells. Neurons become post-mitotic after leaving the ventricular zone. When neurons are forced to reenter the cell cycle they invariably undergo cell death. Wider evidence indicates that the post-mitotic state cannot solely depend on gene products acting in trans, otherwise mutations in the corresponding genes may lead to reentry and completion of the cell cycle in TD cells, but this has not been observed. In the interphase, nuclear DNA of metazoan cells is organized in supercoiled loops anchored to a nuclear nuclear matrix (NM). The DNA-NM interactions define a higher-order structure in the cell nucleus (NHOS). We have previously compared the NHOS of aged rat hepatocytes with that of early post-mitotic rat neurons and our results indicated that a very stable NHOS is a common feature of both senescent and post-mitotic cells in vivo. Principal Findings In the present work we compared the NHOS in rat neurons from different post-natal ages. Our results show that the trend towards further stabilization of the NHOS in neurons continues throughout post-natal life. This phenomenon occurs in absence of overt changes in the post-mitotic state and transcriptional activity of neurons, suggesting that it is independent of functional constraints. Conclusions Apparently the continued stabilization of the NHOS as a function of time is basically determined by thermodynamic and structural constraints. We discuss how the resulting highly stable NHOS of neurons may be the structural, non-genetic basis of their permanent and irreversible post-mitotic state.
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Affiliation(s)
- Janeth Alva-Medina
- Laboratorio de Biología Molecular y Neurociencias, Facultad de Medicina, Universidad Autónoma del Estado de México, Toluca, Estado de México, México
| | - Apolinar Maya-Mendoza
- Laboratorio de Biología Molecular y Neurociencias, Facultad de Medicina, Universidad Autónoma del Estado de México, Toluca, Estado de México, México
| | - Myrna A. R. Dent
- Laboratorio de Biología Molecular y Neurociencias, Facultad de Medicina, Universidad Autónoma del Estado de México, Toluca, Estado de México, México
| | - Armando Aranda-Anzaldo
- Laboratorio de Biología Molecular y Neurociencias, Facultad de Medicina, Universidad Autónoma del Estado de México, Toluca, Estado de México, México
- * E-mail:
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Trego KS, Chernikova SB, Davalos AR, Perry JJP, Finger LD, Ng C, Tsai MS, Yannone SM, Tainer JA, Campisi J, Cooper PK. The DNA repair endonuclease XPG interacts directly and functionally with the WRN helicase defective in Werner syndrome. Cell Cycle 2011; 10:1998-2007. [PMID: 21558802 DOI: 10.4161/cc.10.12.15878] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
XPG is a structure-specific endonuclease required for nucleotide excision repair (NER). XPG incision defects result in the cancer-prone syndrome xeroderma pigmentosum, whereas truncating mutations of XPG cause the severe postnatal progeroid developmental disorder Cockayne syndrome. We show that XPG interacts directly with WRN protein, which is defective in the premature aging disorder Werner syndrome, and that the two proteins undergo similar subnuclear redistribution in S phase and colocalize in nuclear foci. The co-localization was observed in mid- to late S phase, when WRN moves from nucleoli to nuclear foci that have been shown to contain both protein markers of stalled replication forks and telomeric proteins. We mapped the interaction between XPG and WRN to the C-terminal domains of each, and show that interaction with the C-terminal domain of XPG strongly stimulates WRN helicase activity. WRN also possesses a competing DNA single-strand annealing activity that, combined with unwinding, has been shown to coordinate regression of model replication forks to form Holliday junction/chicken foot intermediate structures. We tested whether XPG stimulated WRN annealing activity, and found that XPG itself has intrinsic strand annealing activity that requires the unstructured R- and C-terminal domains but not the conserved catalytic core or endonuclease activity. Annealing by XPG is cooperative, rather than additive, with WRN annealing. Taken together, our results suggest a novel function for XPG in S phase that is, at least in part, performed coordinately with WRN, and which may contribute to the severity of the phenotypes that occur upon loss of XPG.
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Affiliation(s)
- Kelly S Trego
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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Trevilla-García C, Aranda-Anzaldo A. Cell-type-specific organization of nuclear DNA into structural looped domains. J Cell Biochem 2011; 112:531-40. [PMID: 21268074 DOI: 10.1002/jcb.22943] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
In the interphase nucleus of metazoan cells the DNA is organized in supercoiled loops anchored to a proteinaceous substructure known as the nuclear matrix (NM). The DNA is anchored to the NM by means of non-coding sequences of variable length known as matrix attachment regions or MARs operationally classified in structural-constitutive, resistant to high-salt extraction and transient-functional, non-resistant to high-salt extraction. The former are also known as true loop attachment regions or LARs that determine structural DNA loops. The DNA-NM interactions define a higher order structure within the cell nucleus (NHOS). We studied in a comparative fashion the NHOS in two primary cell types from the rat: hepatocytes and naive B lymphocytes, by analyzing the topological relationships between the NM and a set of eight short gene sequences located in six separate chromosomes and as such representing a coarse-grained, large-scale sample of the actual organization of nuclear DNA into structural loop domains. Our results indicate that such an organization is cell-type specific since most of the gene sequences studied showed significant differences in their relative position to the NM according to cell type. Such cell-type specific differences in the NHOS have no obvious correlation with the tissue-specific transcriptional activity of the corresponding genes, supporting the notion that permanent, structural DNA loops are different from transient, functional DNA loops that may be associated with transcription.
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Keaton MA, Taylor CM, Layer RM, Dutta A. Nuclear scaffold attachment sites within ENCODE regions associate with actively transcribed genes. PLoS One 2011; 6:e17912. [PMID: 21423757 PMCID: PMC3056778 DOI: 10.1371/journal.pone.0017912] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2011] [Accepted: 02/14/2011] [Indexed: 01/30/2023] Open
Abstract
The human genome must be packaged and organized in a functional manner for the regulation of DNA replication and transcription. The nuclear scaffold/matrix, consisting of structural and functional nuclear proteins, remains after extraction of nuclei and anchors loops of DNA. In the search for cis-elements functioning as chromatin domain boundaries, we identified 453 nuclear scaffold attachment sites purified by lithium-3,5-iodosalicylate extraction of HeLa nuclei across 30 Mb of the human genome studied by the ENCODE pilot project. The scaffold attachment sites mapped predominately near expressed genes and localized near transcription start sites and the ends of genes but not to boundary elements. In addition, these regions were enriched for RNA polymerase II and transcription factor binding sites and were located in early replicating regions of the genome. We believe these sites correspond to genome-interactions mediated by transcription factors and transcriptional machinery immobilized on a nuclear substructure.
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Affiliation(s)
- Mignon A. Keaton
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Christopher M. Taylor
- Department of Computer Science, University of New Orleans, New Orleans, Louisiana, United States of America
| | - Ryan M. Layer
- Department of Computer Science, University of Virginia, Charlottesville, Virginia, United States of America
| | - Anindya Dutta
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, United States of America
- * E-mail:
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Rivera-Mulia JC, Hernández-Muñoz R, Martínez F, Aranda-Anzaldo A. DNA moves sequentially towards the nuclear matrix during DNA replication in vivo. BMC Cell Biol 2011; 12:3. [PMID: 21244708 PMCID: PMC3037911 DOI: 10.1186/1471-2121-12-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Accepted: 01/19/2011] [Indexed: 11/21/2022] Open
Abstract
Background In the interphase nucleus of metazoan cells DNA is organized in supercoiled loops anchored to a nuclear matrix (NM). There is varied evidence indicating that DNA replication occurs in replication factories organized upon the NM and that DNA loops may correspond to the actual replicons in vivo. In normal rat liver the hepatocytes are arrested in G0 but they synchronously re-enter the cell cycle after partial-hepatectomy leading to liver regeneration in vivo. We have previously determined in quiescent rat hepatocytes that a 162 kbp genomic region containing members of the albumin gene family is organized into five structural DNA loops. Results In the present work we tracked down the movement relative to the NM of DNA sequences located at different points within such five structural DNA loops during the S phase and after the return to cellular quiescence during liver regeneration. Our results indicate that looped DNA moves sequentially towards the NM during replication and then returns to its original position in newly quiescent cells, once the liver regeneration has been achieved. Conclusions Looped DNA moves in a sequential fashion, as if reeled in, towards the NM during DNA replication in vivo thus supporting the notion that the DNA template is pulled progressively towards the replication factories on the NM so as to be replicated. These results provide further evidence that the structural DNA loops correspond to the actual replicons in vivo.
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Affiliation(s)
- Juan Carlos Rivera-Mulia
- Laboratorio de Biología Molecular, Facultad de Medicina, Universidad Autónoma del Estado de México, Apartado Postal 428, CP 50000 Toluca, Edo Méx, México
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Johnson GD, Lalancette C, Linnemann AK, Leduc F, Boissonneault G, Krawetz SA. The sperm nucleus: chromatin, RNA, and the nuclear matrix. Reproduction 2011; 141:21-36. [PMID: 20876223 PMCID: PMC5358669 DOI: 10.1530/rep-10-0322] [Citation(s) in RCA: 123] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Within the sperm nucleus, the paternal genome remains functionally inert and protected following protamination. This is marked by a structural morphogenesis that is heralded by a striking reduction in nuclear volume. Despite these changes, both human and mouse spermatozoa maintain low levels of nucleosomes that appear non-randomly distributed throughout the genome. These regions may be necessary for organizing higher order genomic structure through interactions with the nuclear matrix. The promoters of this transcriptionally quiescent genome are differentially marked by modified histones that may poise downstream epigenetic effects. This notion is supported by increasing evidence that the embryo inherits these differing levels of chromatin organization. In concert with the suite of RNAs retained in the mature sperm, they may synergistically interact to direct early embryonic gene expression. Irrespective, these features reflect the transcriptional history of spermatogenic differentiation. As such, they may soon be utilized as clinical markers of male fertility. In this review, we explore and discuss how this may be orchestrated.
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Affiliation(s)
- Graham D. Johnson
- The Center for Molecular Medicine and Genetics, Wayne State University of Medicine, C.S. Mott Center, 275 E. Hancock, Detroit, MI 48201
| | - Claudia Lalancette
- The Center for Molecular Medicine and Genetics, Wayne State University of Medicine, C.S. Mott Center, 275 E. Hancock, Detroit, MI 48201
- Department of Obstetrics and Gynecology, Wayne State University of Medicine, C.S. Mott Center, 275 E. Hancock, Detroit, MI 48201
| | - Amelia K. Linnemann
- The Center for Molecular Medicine and Genetics, Wayne State University of Medicine, C.S. Mott Center, 275 E. Hancock, Detroit, MI 48201
| | - Frédéric Leduc
- Department of Biochemistry, Faculty of Medicine, Université de Sherbrooke, Sherbrooke, Québec, Canada J1H 5N4
| | - Guylain Boissonneault
- Department of Biochemistry, Faculty of Medicine, Université de Sherbrooke, Sherbrooke, Québec, Canada J1H 5N4
| | - Stephen A. Krawetz
- The Center for Molecular Medicine and Genetics, Wayne State University of Medicine, C.S. Mott Center, 275 E. Hancock, Detroit, MI 48201
- Department of Obstetrics and Gynecology, Wayne State University of Medicine, C.S. Mott Center, 275 E. Hancock, Detroit, MI 48201
- Institute for Scientific Computing, Wayne State University of Medicine, C.S. Mott Center, 275 E. Hancock, Detroit, MI 48201
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The alphaherpesvirus US3/ORF66 protein kinases direct phosphorylation of the nuclear matrix protein matrin 3. J Virol 2010; 85:568-81. [PMID: 20962082 DOI: 10.1128/jvi.01611-10] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The protein kinase found in the short region of alphaherpesviruses, termed US3 in herpes simplex virus type 1 (HSV-1) and pseudorabies virus (PRV) and ORF66 in varicella-zoster virus (VZV), affects several viral and host cell processes, and its specific targets remain an area of active investigation. Reports suggesting that HSV-1 US3 substrates overlap with those of cellular protein kinase A (PKA) prompted the use of an antibody specific for phosphorylated PKA substrates to identify US3/ORF66 targets. HSV-1, VZV, and PRV induced very different substrate profiles that were US3/ORF66 kinase dependent. The predominant VZV-phosphorylated 125-kDa species was identified as matrin 3, one of the major nuclear matrix proteins. Matrin 3 was also phosphorylated by HSV-1 and PRV in a US3 kinase-dependent manner and by VZV ORF66 kinase at a novel residue (KRRRT150EE). Since VZV-directed T150 phosphorylation was not blocked by PKA inhibitors and was not induced by PKA activation, and since PKA predominantly targeted matrin 3 S188, it was concluded that phosphorylation by VZV was PKA independent. However, purified VZV ORF66 kinase did not phosphorylate matrin 3 in vitro, suggesting that additional cellular factors were required. In VZV-infected cells in the absence of the ORF66 kinase, matrin 3 displayed intranuclear changes, while matrin 3 showed a pronounced cytoplasmic distribution in late-stage cells infected with US3-negative HSV-1 or PRV. This work identifies phosphorylation of the nuclear matrix protein matrin 3 as a new conserved target of this kinase group.
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Brewster AS, Chen XS. Insights into the MCM functional mechanism: lessons learned from the archaeal MCM complex. Crit Rev Biochem Mol Biol 2010; 45:243-56. [PMID: 20441442 DOI: 10.3109/10409238.2010.484836] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The helicase function of the minichromosome maintenance protein (MCM) is essential for genomic DNA replication in archaea and eukaryotes. There has been rapid progress in studies of the structure and function of MCM proteins from different organisms, leading to better understanding of the MCM helicase mechanism. Because there are a number of excellent reviews on this topic, we will use this review to summarize some of the recent progress, with particular focus on the structural aspects of MCM and their implications for helicase function. Given the hexameric and double hexameric architecture observed by X-ray crystallography and electron microscopy of MCMs from archaeal and eukaryotic cells, we summarize and discuss possible unwinding modes by either a hexameric or a double hexameric helicase. Additionally, our recent crystal structure of a full length archaeal MCM has provided structural information on an intact, multi-domain MCM protein, which includes the salient features of four unusual beta-hairpins from each monomer, and the side channels of a hexamer/double hexamer. These new structural data enable a closer examination of the structural basis of the unwinding mechanisms by MCM.
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Affiliation(s)
- Aaron S Brewster
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
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Mitsui J, Takahashi Y, Goto J, Tomiyama H, Ishikawa S, Yoshino H, Minami N, Smith DI, Lesage S, Aburatani H, Nishino I, Brice A, Hattori N, Tsuji S. Mechanisms of genomic instabilities underlying two common fragile-site-associated loci, PARK2 and DMD, in germ cell and cancer cell lines. Am J Hum Genet 2010; 87:75-89. [PMID: 20598272 DOI: 10.1016/j.ajhg.2010.06.006] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2010] [Revised: 05/05/2010] [Accepted: 06/13/2010] [Indexed: 11/17/2022] Open
Abstract
Common fragile sites (CFSs) are specific chromosome regions that exhibit an increased frequency of breaks when cells are exposed to a DNA-replication inhibitor such as aphidicolin. PARK2 and DMD, the causative genes for autosomal-recessive juvenile Parkinsonism and Duchenne and Becker muscular dystrophy, respectively, are two very large genes that are located within aphidicolin-induced CFSs. Gross rearrangements within these two genes are frequently observed as the causative mutations for these diseases, and similar alterations within the large fragile sites that surround these genes are frequently observed in cancer cells. To elucidate the molecular mechanisms underlying this fragility, we performed a custom-designed high-density comparative genomic hybridization analysis to determine the junction sequences of approximately 500 breakpoints in germ cell lines and cancer cell lines involving PARK2 or DMD. The sequence signatures where these breakpoints occur share some similar features both in germ cell lines and in cancer cell lines. Detailed analyses of these structures revealed that microhomologies are predominantly involved in rearrangement processes. Furthermore, breakpoint-clustering regions coincide with the latest-replicating region and with large nuclear-lamina-associated domains and are flanked by the highest-flexibility peaks and R/G band boundaries, suggesting that factors affecting replication timing collectively contribute to the vulnerability for rearrangement in both germ cell and somatic cell lines.
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Affiliation(s)
- Jun Mitsui
- Department of Neurology, Graduate School of Medicine, University of Tokyo, Tokyo 113-8655, Japan
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Kallappagoudar S, Varma P, Pathak RU, Senthilkumar R, Mishra RK. Nuclear matrix proteome analysis of Drosophila melanogaster. Mol Cell Proteomics 2010; 9:2005-18. [PMID: 20530634 DOI: 10.1074/mcp.m110.001362] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The nucleus is a highly structured organelle and contains many functional compartments. Although the structural basis for this complex spatial organization of compartments is unknown, a major component of this organization is likely to be the non-chromatin scaffolding called nuclear matrix (NuMat). Experimental evidence over the past decades indicates that most of the nuclear functions are at least transiently associated with the NuMat, although the components of NuMat itself are poorly known. Here, we report NuMat proteome analysis from Drosophila melanogaster embryos and discuss its links with nuclear architecture and functions. In the NuMat proteome, we found structural proteins, chaperones, DNA/RNA-binding proteins, chromatin remodeling and transcription factors. This complexity of NuMat proteome is an indicator of its structural and functional significance. Comparison of the two-dimensional profile of NuMat proteome from different developmental stages of Drosophila embryos showed that less than half of the NuMat proteome is constant, and the rest of the proteins are stage-specific dynamic components. These NuMat dynamics suggest a possible functional link between NuMat and embryonic development. Finally, we also showed that a subset of NuMat proteins remains associated with the mitotic chromosomes, implicating their role in mitosis and possibly the epigenetic cellular memory. NuMat proteome analysis provides tools and opens up ways to understand nuclear organization and function.
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Affiliation(s)
- Satish Kallappagoudar
- Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Hyderabad, India
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NeuN/Fox-3 is an intrinsic component of the neuronal nuclear matrix. FEBS Lett 2010; 584:2767-71. [DOI: 10.1016/j.febslet.2010.04.073] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Revised: 03/31/2010] [Accepted: 04/28/2010] [Indexed: 11/17/2022]
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Rivera-Mulia JC, Aranda-Anzaldo A. Determination of the in vivo structural DNA loop organization in the genomic region of the rat albumin locus by means of a topological approach. DNA Res 2010; 17:23-35. [PMID: 20047947 PMCID: PMC2818189 DOI: 10.1093/dnares/dsp027] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Nuclear DNA of metazoans is organized in supercoiled loops anchored to a proteinaceous substructure known as the nuclear matrix (NM). DNA is anchored to the NM by non-coding sequences known as matrix attachment regions (MARs). There are no consensus sequences for identification of MARs and not all potential MARs are actually bound to the NM constituting loop attachment regions (LARs). Fundamental processes of nuclear physiology occur at macromolecular complexes organized on the NM; thus, the topological organization of DNA loops must be important. Here, we describe a general method for determining the structural DNA loop organization in any large genomic region with a known sequence. The method exploits the topological properties of loop DNA attached to the NM and elementary topological principles such as that points in a deformable string (DNA) can be positionally mapped relative to a position-reference invariant (NM), and from such mapping, the configuration of the string in third dimension can be deduced. Therefore, it is possible to determine the specific DNA loop configuration without previous characterization of the LARs involved. We determined in hepatocytes and B-lymphocytes of the rat the DNA loop organization of a genomic region that contains four members of the albumin gene family.
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Affiliation(s)
- Juan Carlos Rivera-Mulia
- Laboratorio de Biología Molecular, Facultad de Medicina, Universidad Autónoma del Estado de México, Apartado Postal 428, Toluca, Edo. Méx., México
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de Boer P, Ramos L, de Vries M, Gochhait S. Memoirs of an insult: sperm as a possible source of transgenerational epimutations and genetic instability. Mol Hum Reprod 2009; 16:48-56. [PMID: 19897543 DOI: 10.1093/molehr/gap098] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Male transgenerational epigenetic effects have been discovered in the discipline of mouse radiation genetics, using genetic and non-genetic readouts. The mechanism to explain the origin of the transmission of epigenetic and genetic instability is still unknown. In a search for a hypothesis that could satisfy the data, we propose that regulation of chromosome structure in the germline, by the occupancy of matrix/scaffold associated regions, contains molecular memory function. The male germline is strikingly dynamic as to chromatin organization. This could explain why experience of irradiation stress leaves a persistent mark in the male germline only. To be installed, such memory requires both S-phase and chromatin reorganization during spermatogenesis and in the zygote, that likely also involves reorganization of loop domains. By this reorganization, another layer of information is added, needed to accommodate early embryonic development. Observations point at the involvement of DNA repair as inducer of transgenerational epigenetic modulation. Nuclear structure, chromatin composition and loop domain organization are aspects of human sperm variability that in many cases of assisted reproduction is increased due to inclusion of more incompletely differentiated/maturated sperm nuclei. Adjustment of loop domains in early embryo development can be anticipated and zygotic and cleavage stage S-phase repair activity will have to deal with potential paternal DNA lesions. Therefore, by changing male nucleus structure due to reproduction from impaired spermatogenesis, the transgenerational information content could be changed as well. We discuss aspects of male reproductive performance in the context of this hypothesis.
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Affiliation(s)
- P de Boer
- Department of Obstetrics and Gynaecology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands.
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Aranda-Anzaldo A. A structural basis for cellular senescence. Aging (Albany NY) 2009; 1:598-607. [PMID: 20157542 PMCID: PMC2806039 DOI: 10.18632/aging.100074] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2009] [Accepted: 07/28/2009] [Indexed: 12/18/2022]
Abstract
Replicative
senescence (RS) that limits the proliferating potential of normal
eukaryotic cells occurs either by a cell-division counting mechanism linked
to telomere erosion or prematurely through induction by cell stressors such
as oncogene hyper-activation. However, there is evidence that RS also
occurs by a stochastic process that is independent of number of cell
divisions or cellular stress and yet it leads to a highly-stable,
non-reversible post-mitotic state that may be long-lasting and that such a
process is widely represented among higher eukaryotes. Here I present and
discuss evidence that the interactions between DNA and the nuclear
substructure, commonly known as the nuclear matrix, define a higher-order
structure within the cell nucleus that following thermodynamic constraints,
stochastically evolves towards maximum stability, thus becoming limiting
for mitosis to occur. It is suggested that this process is responsible for
ultimate replicative senescence and yet it is compatible with long-term
cell survival.
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Affiliation(s)
- Armando Aranda-Anzaldo
- Laboratorio de Biología Molecular, Facultad de Medicina, Universidad Autónoma del Estado de México, Paseo Tollocan y Jesús Carranza, Toluca, Edo. Méx., México.
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Wang CJ, Lam W, Bussom S, Chang HM, Cheng YC. TREX1 acts in degrading damaged DNA from drug-treated tumor cells. DNA Repair (Amst) 2009; 8:1179-89. [PMID: 19617005 DOI: 10.1016/j.dnarep.2009.06.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2009] [Revised: 06/03/2009] [Accepted: 06/05/2009] [Indexed: 12/15/2022]
Abstract
The major mammalian exonuclease TREX1 has been proposed to play a role in DNA repair and drug resistance. However, no cellular evidence substantiates this claim. Recent reports indicate TREX1's involvement in autoimmunity. To further understand its role, we studied TREX1 expression and functionality in anticancer drug-treated tumor cells. We report that the expression and localization of TREX1 are cell-type dependent. Camptothecin and other DNA damaging agents induced both TREX1 protein and its mRNA in a dose- and time-dependent manner. Using a TREX1-inducible cell line, we performed clonogenic assays and found no change in sensitivity of the cells to the agents upon TREX1 induction, suggesting that TREX1 may not play a role in DNA repair or drug sensitivity. Nevertheless, TREX1 serves as a key enzyme in the degradation of DNA from dying cells leading to less cellular DNA. Ubiquitously expressed in normal tissues, TREX1 may act in degrading DNA in all cell types undergoing a dying process before phagocytosis occurs.
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Affiliation(s)
- Chuan-Jen Wang
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
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