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Aretxabala X, García del Caño G, Barrondo S, López de Jesús M, González-Burguera I, Saumell-Esnaola M, Goicolea MA, Sallés J. Endocannabinoid 2-Arachidonoylglycerol Synthesis and Metabolism at Neuronal Nuclear Matrix Fractions Derived from Adult Rat Brain Cortex. Int J Mol Sci 2023; 24:ijms24043165. [PMID: 36834575 PMCID: PMC9965625 DOI: 10.3390/ijms24043165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/27/2023] [Accepted: 02/02/2023] [Indexed: 02/08/2023] Open
Abstract
In this report, we describe the kinetics characteristics of the diacylglycerol lipase-α (DGLα) located at the nuclear matrix of nuclei derived from adult cortical neurons. Thus, using high-resolution fluorescence microscopy, classical biochemical subcellular fractionation, and Western blot techniques, we demonstrate that the DGLα enzyme is located in the matrix of neuronal nuclei. Furthermore, by quantifying the 2-arachidonoylglycerol (2-AG) level by liquid chromatography and mass spectrometry when 1-stearoyl-2-arachidonoyl-sn-glycerol (SAG) was exogenously added as substrate, we describe the presence of a mechanism for 2-AG production through DGLα dependent biosynthesis with an apparent Km (Kmapp) of 180 µM and a Vmax of 1.3 pmol min-1 µg-1 protein. We also examined the presence of enzymes with hydrolytic and oxygenase activities that are able to use 2-AG as substrate, and described the localization and compartmentalization of the major 2-AG degradation enzymes, namely monoacylglycerol lipase (MGL), fatty acid amide hydrolase (FAAH), α/β-hydrolase domain 12 protein (ABHD12) and cyclooxygenase-2 (COX2). Of these, only ABHD12 exhibited the same distribution with respect to chromatin, lamin B1, SC-35 and NeuN as that described for DGLα. When 2-AG was exogenously added, we observed the production of arachidonic acid (AA), which was prevented by inhibitors (but not specific MGL or ABHD6 inhibitors) of the ABHD family. Overall, our results expand knowledge about the subcellular distribution of neuronal DGLα, and provide biochemical and morphological evidence to ensure that 2-AG is produced in the neuronal nuclear matrix. Thus, this work paves the way for proposing a working hypothesis about the role of 2-AG produced in neuronal nuclei.
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Affiliation(s)
- Xabier Aretxabala
- Department of Neurosciences, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), 01006 Vitoria-Gasteiz, Spain
| | - Gontzal García del Caño
- Department of Neurosciences, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), 01006 Vitoria-Gasteiz, Spain
- Bioaraba, Neurofarmacología Celular y Molecular, 01008 Vitoria-Gasteiz, Spain
| | - Sergio Barrondo
- Bioaraba, Neurofarmacología Celular y Molecular, 01008 Vitoria-Gasteiz, Spain
- Department of Pharmacology, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), 01006 Vitoria-Gasteiz, Spain
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), 28029 Madrid, Spain
| | - Maider López de Jesús
- Bioaraba, Neurofarmacología Celular y Molecular, 01008 Vitoria-Gasteiz, Spain
- Department of Pharmacology, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), 01006 Vitoria-Gasteiz, Spain
| | - Imanol González-Burguera
- Department of Neurosciences, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), 01006 Vitoria-Gasteiz, Spain
- Bioaraba, Neurofarmacología Celular y Molecular, 01008 Vitoria-Gasteiz, Spain
| | - Miquel Saumell-Esnaola
- Bioaraba, Neurofarmacología Celular y Molecular, 01008 Vitoria-Gasteiz, Spain
- Department of Pharmacology, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), 01006 Vitoria-Gasteiz, Spain
| | - María Aranzazu Goicolea
- Department of Analytical Chemistry, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), 01006 Vitoria-Gasteiz, Spain
| | - Joan Sallés
- Bioaraba, Neurofarmacología Celular y Molecular, 01008 Vitoria-Gasteiz, Spain
- Department of Pharmacology, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), 01006 Vitoria-Gasteiz, Spain
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), 28029 Madrid, Spain
- Correspondence: ; Tel.: +34-945-013114
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Pathak RU, Bihani A, Sureka R, Varma P, Mishra RK. In situ nuclear matrix preparation in Drosophila melanogaster embryos/tissues and its use in studying the components of nuclear architecture. Nucleus 2022; 13:116-128. [PMID: 35239464 PMCID: PMC8896195 DOI: 10.1080/19491034.2022.2043608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The study of nuclear matrix (NuMat) over the last 40 years has been limited to either isolated nuclei from tissues or cells grown in culture. Here, we provide a protocol for NuMat preparation in intact Drosophila melanogaster embryos and its use in dissecting the components of nuclear architecture. The protocol does not require isolation of nuclei and therefore maintains the three-dimensional milieu of an intact embryo, which is biologically more relevant compared to cells in culture. One of the advantages of this protocol is that only a small number of embryos are required. The protocol has been extended to larval tissues like salivary glands with little modification. Taken together, it becomes possible to carry out such studies in parallel to genetic experiments using mutant/transgenic flies. This protocol, therefore, opens the powerful field of fly genetics to cell biology in the study of nuclear architecture. Summary: Nuclear Matrix is a biochemically defined entity and a basic component of the nuclear architecture. Here we present a protocol to isolate and visualize Nuclear Matrix in situ in the Drosophila melanogaster and its potential applications.
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Affiliation(s)
- Rashmi U Pathak
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | - Ashish Bihani
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | | | - Parul Varma
- Present Address: Department of Neuroscience, Development and Regenerative Biology, The University of Texas at San Antonio, Texas, USA
| | - Rakesh K Mishra
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India.,Tata Institute for Genetics and Society, Bangalore, India
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3
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The Long Linker Region of Telomere-Binding Protein TRF2 Is Responsible for Interactions with Lamins. Int J Mol Sci 2021; 22:ijms22073293. [PMID: 33804854 PMCID: PMC8036907 DOI: 10.3390/ijms22073293] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 12/15/2022] Open
Abstract
Telomere-binding factor 2 (TRF2) is part of the shelterin protein complex found at chromosome ends. Lamin A/C interacts with TRF2 and influences telomere position. TRF2 has an intrinsically disordered region between the ordered dimerization and DNA-binding domains. This domain is referred to as the long linker region of TRF2, or udTRF2. We suggest that udTRF2 might be involved in the interaction between TRF2 and lamins. The recombinant protein corresponding to the udTRF2 region along with polyclonal antibodies against this region were used in co-immunoprecipitation with purified lamina and nuclear extracts. Co-immunoprecipitation followed by Western blots and mass spectrometry indicated that udTRF2 interacts with lamins, preferably lamins A/C. The interaction did not involve any lamin-associated proteins, was not dependent on the post-translation modification of lamins, nor did it require their higher-order assembly. Besides lamins, a number of other udTRF2-interacting proteins were identified by mass spectrometry, including several heterogeneous nuclear ribonucleoproteins (hnRNP A2/B1, hnRNPA1, hnRNP A3, hnRNP K, hnRNP L, hnRNP M), splicing factors (SFPQ, NONO, SRSF1, and others), helicases (DDX5, DHX9, and Eif4a3l1), topoisomerase I, and heat shock protein 71, amongst others. Some of the identified interactors are known to be involved in telomere biology; the roles of the others remain to be investigated. Thus, the long linker region of TRF2 (udTRF2) is a regulatory domain responsible for the association between TRF2 and lamins and is involved in interactions with other proteins.
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4
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Razin SV, Borunova VV, Iarovaia OV, Vassetzky YS. Nuclear matrix and structural and functional compartmentalization of the eucaryotic cell nucleus. BIOCHEMISTRY (MOSCOW) 2015; 79:608-18. [PMID: 25108324 DOI: 10.1134/s0006297914070037] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Becoming popular at the end of the 20th century, the concept of the nuclear matrix implies the existence of a nuclear skeleton that organizes functional elements in the cell nucleus. This review presents a critical analysis of the results obtained in the study of nuclear matrix in the light of current views on the organization of the cell nucleus. Numerous studies of nuclear matrix have failed to provide evidence of the existence of such a structure. Moreover, the existence of a filamentous structure that supports the nuclear compartmentalization appears to be unnecessary, since this function is performed by the folded genome itself.
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Affiliation(s)
- S V Razin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
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5
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García del Caño G, Aretxabala X, González-Burguera I, Montaña M, López de Jesús M, Barrondo S, Barrio RJ, Sampedro C, Goicolea MA, Sallés J. Nuclear diacylglycerol lipase-α in rat brain cortical neurons: evidence of 2-arachidonoylglycerol production in concert with phospholipase C-β activity. J Neurochem 2014; 132:489-503. [PMID: 25308538 DOI: 10.1111/jnc.12963] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 09/22/2014] [Accepted: 10/07/2014] [Indexed: 01/12/2023]
Abstract
In this report, we describe the localization of diacylglycerol lipase-α (DAGLα) in nuclei from adult cortical neurons, as assessed by double-immunofluorescence staining of rat brain cortical sections and purified intact nuclei and by western blot analysis of subnuclear fractions. Double-labeling assays using the anti-DAGLα antibody and NeuN combined with Hoechst staining showed that only nuclei of neuronal origin were DAGLα positive. At high resolution, DAGLα-signal displayed a punctate pattern in nuclear subdomains poor in Hoechst's chromatin and lamin B1 staining. In contrast, SC-35- and NeuN-signals (markers of the nuclear speckles) showed a high overlap with DAGLα within specific subdomains of the nuclear matrix. Among the members of the phospholipase C-β (PLCβ) family, PLCβ1, PLCβ2, and PLCβ4 exhibited the same distribution with respect to chromatin, lamin B1, SC-35, and NeuN as that described for DAGLα. Furthermore, by quantifying the basal levels of 2-arachidonoylglycerol (2-AG) by liquid chromatography and mass spectrometry (LC-MS), and by characterizing the pharmacology of its accumulation, we describe the presence of a mechanism for 2-AG production, and its PLCβ/DAGLα-dependent biosynthesis in isolated nuclei. These results extend our knowledge about subcellular distribution of neuronal DAGLα, providing biochemical grounds to hypothesize a role for 2-AG locally produced within the neuronal nucleus.
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Affiliation(s)
- Gontzal García del Caño
- Departamento de Neurociencias, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), 01006 Vitoria-Gasteiz (Araba), Spain
| | - Xabier Aretxabala
- Departamento de Neurociencias, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), 01006 Vitoria-Gasteiz (Araba), Spain
| | - Imanol González-Burguera
- Departamento de Farmacología, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), 01006 Vitoria-Gasteiz (Araba), Spain
| | - Mario Montaña
- Departamento de Farmacología, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), 01006 Vitoria-Gasteiz (Araba), Spain
| | - Maider López de Jesús
- Departamento de Farmacología, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), 01006 Vitoria-Gasteiz (Araba), Spain
| | - Sergio Barrondo
- Departamento de Farmacología, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), 01006 Vitoria-Gasteiz (Araba), Spain
| | - Ramón J Barrio
- Departamento de Química Analítica, Facultad de Farmacia, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), 01006 Vitoria-Gasteiz (Araba), Spain
| | - Carmen Sampedro
- Servicio General de Análisis, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), 01006 Vitoria-Gasteiz (Araba), Spain
| | - M Arantzazu Goicolea
- Departamento de Química Analítica, Facultad de Farmacia, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), 01006 Vitoria-Gasteiz (Araba), Spain
| | - Joan Sallés
- Departamento de Farmacología, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), 01006 Vitoria-Gasteiz (Araba), Spain
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6
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Razin SV, Iarovaia OV, Vassetzky YS. A requiem to the nuclear matrix: from a controversial concept to 3D organization of the nucleus. Chromosoma 2014; 123:217-24. [PMID: 24664318 DOI: 10.1007/s00412-014-0459-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 03/10/2014] [Accepted: 03/14/2014] [Indexed: 12/13/2022]
Abstract
The first papers coining the term "nuclear matrix" were published 40 years ago. Here, we review the data obtained during the nuclear matrix studies and discuss the contribution of this controversial concept to our current understanding of nuclear architecture and three-dimensional organization of genome.
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Affiliation(s)
- S V Razin
- Institute of Gene Biology of the Russian Academy of Sciences, 119334, Moscow, Russia
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7
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Henderson SC, Locke M. The development of branched silk gland nuclei. Tissue Cell 2012; 23:867-80. [PMID: 18621190 DOI: 10.1016/0040-8166(91)90036-s] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/1991] [Indexed: 11/16/2022]
Abstract
Nuclei in the giant polyploid silk gland cells of Calpodes ethlius grow by endomitosis and can develop hundreds of branches during larval life. The shape of the these nuclei is characteristic for each region of the gland. We have found shape to be correlated with arrangement of the nuclear matrix. Scanning electron microscopy showed nuclear matrices with shapes similar to those of feulgen stained nuclei. Profiles of isolated matrices seen by transmission electron microscopy had filaments aligned parallel to the long axis of nuclear branches. DNA stained by Hoechst had a similar parallel alignment within the branches. Nuclear shape may be maintained by a small number of components, since electrophoretic analysis showed only a few abundant polypeptides in the matrix fraction. Silk gland nuclei have some of the same nuclear matrix antigens found in smaller, more regularly shaped, eukaryote nuclei.
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Affiliation(s)
- S C Henderson
- Department of Zoology, University of Western Ontario, London, Ontario, Canada, N6A 5B7
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8
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Sjakste N, Bielskiene K, Bagdoniene L, Labeikyte D, Gutcaits A, Vassetzky Y, Sjakste T. Tightly bound to DNA proteins: Possible universal substrates for intranuclear processes. Gene 2012; 492:54-64. [PMID: 22001404 DOI: 10.1016/j.gene.2011.09.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Revised: 09/08/2011] [Accepted: 09/22/2011] [Indexed: 01/05/2023]
Affiliation(s)
- N Sjakste
- Faculty of Medicine, University of Latvia, Šarlotes 1a, LV1001, Riga, Latvia
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9
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Razin SV, Gavrilov AA, Pichugin A, Lipinski M, Iarovaia OV, Vassetzky YS. Transcription factories in the context of the nuclear and genome organization. Nucleic Acids Res 2011; 39:9085-92. [PMID: 21880598 PMCID: PMC3241665 DOI: 10.1093/nar/gkr683] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
In the eukaryotic nucleus, genes are transcribed in transcription factories. In the present review, we re-evaluate the models of transcription factories in the light of recent and older data. Based on this analysis, we propose that transcription factories result from the aggregation of RNA polymerase II-containing pre-initiation complexes assembled next to each other in the nuclear space. Such an aggregation can be triggered by the phosphorylation of the C-terminal domain of RNA polymerase II molecules and their interaction with various transcription factors. Individual transcription factories would thus incorporate tissue-specific, co-regulated as well as housekeeping genes based only on their initial proximity to each other in the nuclear space. Targeting genes to be transcribed to protein-dense factories that contain all factors necessary for transcription initiation and elongation through chromatin templates clearly favors a more economical utilization and better recycling of the transcription machinery.
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Affiliation(s)
- S V Razin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.
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10
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Razin SV, Gavrilov AA, Yarovaya OV. Transcription factories and spatial organization of eukaryotic genomes. BIOCHEMISTRY (MOSCOW) 2011; 75:1307-15. [PMID: 21314597 DOI: 10.1134/s0006297910110015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The phenomenon of association of transcribed genes into so-called transcription factories and also the role of these associations in spatial organization of the eukaryotic genome are actively discussed in the modern literature. Some authors think that the association of transcribed genes into transcription factories constitutes a major factor supporting the function-dependent three-dimensional organization of the interphase genome. In spite of the obvious interest in the problem of spatial organization of transcription in the eukaryotic cell nucleus, the number of experimental studies of transcriptional factories remains rather limited and the results of these studies are often contradictory. In the current review we have tried to critically re-evaluate the published experimental results that constitute the basis for current models and also the models themselves. We have especially analyzed the existing contradictions and attempted to explain them whenever possible. We also discuss new models that can explain the biological significance of clustering of transcribed genes and show possible mechanisms of the origin of transcription factories in the course of evolution.
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Affiliation(s)
- S V Razin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia.
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11
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Albrethsen J, Knol JC, Jimenez CR. Unravelling the nuclear matrix proteome. J Proteomics 2008; 72:71-81. [PMID: 18957335 DOI: 10.1016/j.jprot.2008.09.005] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2008] [Revised: 09/29/2008] [Accepted: 09/30/2008] [Indexed: 12/28/2022]
Abstract
The nuclear matrix (NM) model posits the presence of a protein/RNA scaffold that spans the mammalian nucleus. The NM proteins are involved in basic nuclear function and are a promising source of protein biomarkers for cancer. Importantly, the NM proteome is operationally defined as the proteins from cells and tissue that are extracted following a specific biochemical protocol; in brief, the soluble proteins and lipids, cytoskeleton, and chromatin elements are removed in a sequential fashion, leaving behind the proteins that compose the NM. So far, the NM has not been sufficiently verified as a biological entity and only preliminary at the molecular level. Here, we argue for a combined effort of proteomics, immunodetection and microscopy to unravel the composition and structure of the NM.
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Affiliation(s)
- Jakob Albrethsen
- OncoProteomics Laboratory, CCA 1-60, Department Medical Oncology, VUmc-Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
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12
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Bare DJ, Kettlun CS, Liang M, Bers DM, Mignery GA. Cardiac Type 2 Inositol 1,4,5-Trisphosphate Receptor. J Biol Chem 2005; 280:15912-20. [PMID: 15710625 DOI: 10.1074/jbc.m414212200] [Citation(s) in RCA: 141] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The type 2 inositol 1,4,5-trisphosphate receptor (InsP(3)R2) was identified previously as the predominant isoform in cardiac ventricular myocytes. Here we reported the subcellular localization of InsP(3)R2 to the cardiomyocyte nuclear envelope (NE). The other major known endo/sarcoplasmic reticulum calcium-release channel (ryanodine receptor) was not localized to the NE, indicating functional segregation of these channels and possibly a unique role for InsP(3)R2 in regulating nuclear calcium dynamics. Immunoprecipitation experiments revealed that the NE InsP(3)R2 associates with Ca(2+)/calmodulin-dependent protein kinase IIdelta (CaMKIIdelta), the major isoform expressed in cardiac myocytes. Recombinant InsP(3)R2 and CaMKIIdelta(B) also co-immunoprecipitated after co-expression in COS-1 cells. Additionally, the amino-terminal 1078 amino acids of the InsP(3)R2 were sufficient for interaction with CaMKIIdelta(B) and associated upon mixing following separate expression. CaMKII can also phosphorylate InsP(3)R2, as demonstrated by (32)P labeling. Incorporation of CaMKII-treated InsP(3)R2 into planar lipid bilayers revealed that InsP(3)-mediated channel open probability is significantly reduced ( approximately 11 times) by phosphorylation via CaMKII. We concluded that the InsP(3)R2 and CaMKIIdelta likely represent two central components of a multiprotein signaling complex, and this raises the possibility that calcium release via InsP(3)R2 in the myocyte NE may activate local CaMKII signaling, which may feedback on InsP(3)R2 function.
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Affiliation(s)
- Dan J Bare
- Department of Physiology and Cardiovascular Institute, Loyola University Chicago, Maywood, Illinois 60153, USA
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Barboro P, D'Arrigo C, Mormino M, Coradeghini R, Parodi S, Patrone E, Balbi C. An intranuclear frame for chromatin compartmentalization and higher-order folding. J Cell Biochem 2003; 88:113-20. [PMID: 12461780 DOI: 10.1002/jcb.10378] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Recent ultrastructural, immunoelectron, and confocal microscopy observations done in our laboratory [Barboro et al. [2002] Exp. Cell. Res. 279:202-218] have confirmed that lamins and the nuclear mitotic apparatus protein (NuMA) are localized inside the interphase nucleus in a polymerized form. This provided evidence of the existence of a RNA stabilized lamin/NuMA frame, consisting of a web of thin ( approximately 3 and approximately 5 nm) lamin filaments to which NuMA is anchored mainly in the form of discrete islands, which might correspond to the minilattices described by Harborth et al. [1999] (EMBO. J. 18:1689-1700). In this article we propose that this scaffold is involved in the compartmentalization of both chromatin and functional domains and further determines the higher-order nuclear organization. This hypothesis is strongly supported by the scrutiny of different structural transitions which occur inside the nucleus, such as chromatin displacement and rearrangements, the collapse of the internal nuclear matrix after RNA digestion and the disruption of chromosome territories induced by RNase A and high salt treatment. All of these destructive events directly depend on the loss of the stabilizing effect exerted on the different levels of structural organization by the interaction of RNA with lamins and/or NuMA. Therefore, the integrity of nuclear RNA must be safeguarded as far as possible to isolate the matrix in the native form. This material will allow for the first time the unambiguous ultrastructural localization inside the INM of the components of the functional domains, so opening new avenues of investigation on the mechanisms of gene expression in eukaryotes.
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Affiliation(s)
- Paola Barboro
- Istituto Nazionale per la Ricerca sul Cancro, I-16132 Genova, Italy
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14
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Humphrey GW, Wang Y, Russanova VR, Hirai T, Qin J, Nakatani Y, Howard BH. Stable histone deacetylase complexes distinguished by the presence of SANT domain proteins CoREST/kiaa0071 and Mta-L1. J Biol Chem 2001; 276:6817-24. [PMID: 11102443 DOI: 10.1074/jbc.m007372200] [Citation(s) in RCA: 257] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human histone deacetylases I (HDAC1) and II (HDAC2) are homologous proteins (84% identity) that catalyze release of acetyl groups from modified N-terminal lysines of core histones. Histone deacetylation is correlated with both transient and persistent states of transcriptional inactivity (i.e. silencing) in many eukaryotes. In this study, we analyzed complexes containing HDAC1 and HDAC2 to identify the proteins most stably associated with these deacetylases. Complex cI (9.5 S) contained transcriptional corepressor CoREST/kiaa0071 and a protein homologous to FAD-dependent oxidoreductases, kiaa0601. Complex cII (15 S) contained >/=15 proteins, including CHD3/4 (Mi-2), Mta-L1, RbAp48/46, and MBD3, characteristic of vertebrate nucleosome-remodeling complexes. Under native conditions, cI and cII may contain HDAC1, HDAC2 or both; these can be dissociated to cI and cII core complexes containing only HDAC1 or HDAC2. The (m)CpG-binding protein MBD2 was associated only with the HDAC1 cII core complex. A model is proposed in which HDAC1 core complexes can be targeted to methylated DNA via MBD2 with recruitment of HDAC2 occurring through formation of HDAC1/2 cII dimers. We note that the cI component CoREST/kiaa0071 and the cII component Mta-L1 share a region of homology that includes a SANT domain; this domain may play a role in complex assembly.
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Affiliation(s)
- G W Humphrey
- Laboratory of Molecular Growth Regulation, NICHD, National Institutes of Health, Bethesda, Maryland 20892-2753, USA
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Glazko GV, Rogozin IB, Glazkov MV. Comparative study and prediction of DNA fragments associated with various elements of the nuclear matrix. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1517:351-64. [PMID: 11342213 DOI: 10.1016/s0167-4781(00)00297-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Scaffold/matrix-associated region (S/MAR) sequences are DNA regions that are attached to the nuclear matrix, and participate in many cellular processes. The nuclear matrix is a complex structure consisting of various elements. In this paper we compared frequencies of simple nucleotide motifs in S/MAR sequences and in sequences extracted directly from various nuclear matrix elements, such as nuclear lamina, cores of rosette-like structures, synaptonemal complex. Multivariate linear discriminant analysis revealed significant differences between these sequences. Based on this result we have developed a program, ChrClass (Win/NT version, ftp.bionet.nsc.ru/pub/biology/chrclass/chrclass.zip), for the prediction of the regions associated with various elements of the nuclear matrix in a query sequence. Subsequently, several test samples were analyzed by using two S/MAR prediction programs (a ChrClass and MAR-Finder) and a simple MRS criterion (S/MAR recognition signature) indicating the presence of S/MARs. Some overlap between the predictions of all MAR prediction tools has been found. Simultaneous use of the ChrClass, MRS criterion and MAR-Finder programs may help to obtain a more clearcut picture of S/MAR distribution in a query sequence. In general, our results suggest that the proportion of missed S/MARs is lower for ChrClass, whereas the proportion of wrong S/MARs is lower for MAR-Finder and MRS.
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Affiliation(s)
- G V Glazko
- Institute of Cytology and Genetics, Novosibirsk, Russia.
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16
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Tan JH, Wooley JC, LeStourgeon WM. Nuclear matrix-like filaments and fibrogranular complexes form through the rearrangement of specific nuclear ribonucleoproteins. Mol Biol Cell 2000; 11:1547-54. [PMID: 10793134 PMCID: PMC14866 DOI: 10.1091/mbc.11.5.1547] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The behavior of nuclear pre-mRNA-binding proteins after their nuclease and/or salt-induced release from RNA was investigated. After RNase digestion or salt extraction, two proteins that initially exist as tetramers (A2)(3)B1 in isolated heterogeneous nuclear ribonucleoprotein (hnRNP) complexes quantitatively reassociated to form regular helical filaments ranging in length from 100 nm to >10 microm. In highly magnified preparations prepared for scanning transmission electron microscopy, single filaments have diameters near 18 nm. In conventional negatively stained preparations viewed at low magnification, the diameters of the thinnest filaments range from 7 to 10 nm. At protein concentrations of >0.1 mg/ml, the filaments rapidly aggregated to form thicker filamentous networks that look like the fibrogranular structures termed the "nuclear matrix." Like the residual material seen in nuclear matrix preparations, the hnRNP filaments were insoluble in 2 M NaCl. Filament formation is associated with, and may be dependent on, disulfide bridge formation between the hnRNP proteins. The reducing agent 2-mercaptoethanol significantly attenuates filament assembly, and the residual material that forms is ultrastructurally distinct from the 7- to 10-nm fibers. In addition to the protein rearrangement leading to filament formation, nearly one-third of the protein present in chromatin-clarified nuclear extracts was converted to salt-insoluble material within 1 min of digestion with RNase. These observations are consistent with the possibility that the residual material termed the nuclear matrix may be enriched in, if not formed by, denatured proteins that function in pre-mRNA packaging, processing, and transport.
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Affiliation(s)
- J H Tan
- Department of Molecular Biology, Vanderbilt University, Nashville, Tennessee 37235, USA
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17
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Ma H, Siegel AJ, Berezney R. Association of chromosome territories with the nuclear matrix. Disruption of human chromosome territories correlates with the release of a subset of nuclear matrix proteins. J Cell Biol 1999; 146:531-42. [PMID: 10444063 PMCID: PMC2150557 DOI: 10.1083/jcb.146.3.531] [Citation(s) in RCA: 124] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/1998] [Accepted: 07/02/1999] [Indexed: 11/27/2022] Open
Abstract
To study the possible role of the nuclear matrix in chromosome territory organization, normal human fibroblast cells are treated in situ via classic isolation procedures for nuclear matrix in the absence of nuclease (e.g., DNase I) digestion, followed by chromosome painting. We report for the first time that chromosome territories are maintained intact on the nuclear matrix. In contrast, complete extraction of the internal nuclear matrix components with RNase treatment followed by 2 M NaCl results in the disruption of higher order chromosome territory architecture. Correlative with territorial disruption is the formation of a faint DNA halo surrounding the nuclear lamina and a dispersive effect on the characteristically discrete DNA replication sites in the nuclear interior. Identical results were obtained using eight different human chromosome paints. Based on these findings, we developed a fractionation strategy to release the bulk of nuclear matrix proteins under conditions where the chromosome territories are maintained intact. A second treatment results in disruption of the chromosome territories in conjunction with the release of a small subset of acidic proteins. These proteins are distinct from the major nuclear matrix proteins and may be involved in mediating chromosome territory organization.
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Affiliation(s)
- Hong Ma
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York 14260
| | - Alan J. Siegel
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York 14260
| | - Ronald Berezney
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York 14260
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18
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Neves D, Magalhães MM, Magalhães MC. Immunocytochemical detection of structural and regulatory proteins in rat adrenal nuclear matrix. Biotech Histochem 1999; 74:85-91. [PMID: 10333405 DOI: 10.3109/10520299909066482] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The nuclear matrix is a specific cell structure consisting of a residual nucleoskeleton that extends from the nucleoli to the nuclear envelope. The nuclear matrix of steroidogenic cells was isolated previously from a purified nuclear fraction. We present here an in situ extraction method, modified Lutz's method, for rat glandular adrenal cell nuclear matrix. This residual organelle was characterized and studied using immunocytochemical methods. The adrenal glands were removed, the cells prepared in suspension and deposited by cytospin onto Poly-L-lysine glass slides. The nuclear matrix was extracted with Nonidet P-40, DNase I and high and low ionic strength buffers. Structural proteins, nuclear lamins, coilin and fibrillarin were detected immunocytochemically. The adrenal fasciculata cells were easily identified by this method because of their large nuclei and abundant lipid droplets in the cytoplasm. After immunocytochemical detection by antibodies against lamins A and C, a marked brown layer at the periphery of the nucleus was observed. The intensity of the staining was lower using the antibody against nuclear lamin B. Immunocytochemical detection of the protein coilin revealed punctuated stained areas, 2-6 per nucleus, that probably correspond to the coiled bodies. The protein fibrillarin was detected at the nucleolus and coiled bodies. Our technique is simple, reveals well preserved adrenal nuclear matrices, and may be a useful method for immunocytochemical analysis and in situ hybridization.
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Affiliation(s)
- D Neves
- Institute of Histology and Embryology, Faculty of Medicine of Oporto, Porto, Portugal
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19
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Ragano-Caracciolo M, Berlin WK, Miller MW, Hanover JA. Nuclear glycogen and glycogen synthase kinase 3. Biochem Biophys Res Commun 1998; 249:422-7. [PMID: 9712712 DOI: 10.1006/bbrc.1998.9159] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Glycogen is the principal storage form of glucose in animal cells. It accumulates in electron-dense cytoplasmic granules and is synthesized by glycogen synthase (GS), the rate-limiting enzyme of glycogen deposition. Glycogen synthase kinase-3 (GSK-3) is a protein kinase that phosphorylates GS. Two nearly identical forms of GSK-3 exist: GSK-3 alpha and GSK-3 beta. Both are constitutively active in resting cells and their activity can be modulated by hormones and growth factors. GSK-3 is implicated in the regulation of many physiological responses in mammalian cells by phosphorylating substrates including neuronal cell adhesion molecule, neurofilaments, synapsin I, and tau. Recent observations point to functions for glycogen and glycogen metabolism in the nucleus. GSK-3 phosphorylates several transcription factors, and we have recently shown that it modifies the major nuclear pore protein p62. It also regulates PK1, a protein kinase required for maintaining the interphase state and for DNA replication in cycling Xenopus egg extracts. Recently, glycogen was shown to be required for nuclear reformation in vitro using ovulated Xenopus laevis egg lysates. Because neither glycogen nor GSK-3 has been localized to the nuclear envelope or intranuclear sites, glycogen and GSK-3 activites were measured in rat liver nuclei and nuclear reformation extracts. Significant quantities of glycogen-like material co-purified with the rat-liver nuclear envelope. GSK-3 is also highly enriched in the glycogen pellet of egg extracts of Xenopus that is required for nuclear assembly in vitro. Based on the finding that enzymes of glycogen metabolism copurify with glycogen, we propose that glycogen may serve a structural role as a scaffold for nuclear assembly and sequestration of critical kinases and phosphatases in the nucleus.
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Affiliation(s)
- M Ragano-Caracciolo
- Laboratory of Cell Biochemestry and Biology (LCBB), National Institute of Diabetes and Kidney and Digestive Disease, National institutes of Health, 8 Center Drive, Bethesda, Maryland, 20892-MSC-0851, USA.
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20
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Abstract
The possible existence in eukaryotic cells of an internal, non-chromatin nuclear structural framework that facilitates gene readout as a set of spatially concerted reactions has become a popular but controversial theater of investigation. This article endeavors to present a circumspect review of the nuclear matrix concept as we presently know it, framed around two contrasting hypotheses: (1) that an internal nuclear framework actively enhances gene expression (in much the same way the cytoskeleton mediates cell locomotion, mitosis and intracellular vesicular traffic) versus (2) that the interphase chromosomes have fixed, inherited positions and that the DNA replication, transcripton and RNA processing machinery diffusionally arrives at sites of gene readout, with some aspects of nuclear structure thus being more a result than a cause of gene expression. On balance, the available information suggests that interactions among various gene expression machines may contribute to isolated nuclear matrix preparations. Some components of isolated nuclear matrix preparations may also reflect induced or reconfigured protein-protein associations. The protein characterization and ultrastructural analysis of the isolated nuclear matrix has advanced significantly in recent years, although controversies remain. Important new clues are now coming in from promising contemporary lines of research that report on nuclear structure in living cells.
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Affiliation(s)
- T Pederson
- Worcester Foundation for Biomedical Research, Shrewsbury, MA 01545, USA.
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21
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Cossons N, Nielsen TO, Dini C, Tomilin N, Young DB, Riabowol KT, Rattner JB, Johnston RN, Zannis-Hadjopoulos M, Price GB. Circular YAC vectors containing a small mammalian origin sequence can associate with the nuclear matrix. J Cell Biochem 1997; 67:439-50. [PMID: 9383704 DOI: 10.1002/(sici)1097-4644(19971215)67:4<439::aid-jcb3>3.0.co;2-t] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Three different mammalian origins of DNA replication, 343, S3, and X24, have been cloned into a 15.8 kb circular yeast vector pYACneo. Subsequent transfection into HeLa cells resulted in the isolation of several stably maintained clones. Two cell lines, C343e2 and CS3e1, were found to have sequences maintained as episomes in long-term culture with a stability per generation of approximately 80%. Both episomes also contain matrix attachment region (MAR) sequences which mediate the binding of DNA to the nuclear skeleton and are thought to play a role in DNA replication. Using high salt extraction of the nucleus and fluorescent in situ hybridization, we were able to demonstrate an association of the 343 episome with the nuclear matrix, most probably through functional MAR sequences that allow an association with the nuclear matrix and associated regions containing essential replication proteins. The presence of functional MARs in small episomal sequences may facilitate the replication and maintenance of transfected DNA as an episome and improve their utility as small episomal constructs, potential microchromosomes.
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Affiliation(s)
- N Cossons
- McGill Cancer Centre, McGill University, Montreal, Quebec, Canada
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22
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Neri LM, Riederer BM, Valmori A, Capitani S, Martelli AM. Different concentrations of Mg++ ions affect nuclear matrix protein distribution during thermal stabilization of isolated nuclei. J Histochem Cytochem 1997; 45:1317-28. [PMID: 9313794 DOI: 10.1177/002215549704501001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The nuclear matrix, a proteinaceous network believed to be a scaffolding structure determining higher-order organization of chromatin, is usually prepared from intact nuclei by a series of extraction steps. In most cell types investigated the nuclear matrix does not spontaneously resist these treatments but must be stabilized before the application of extracting agents. Incubation of isolated nuclei at 37C or 42C in buffers containing Mg++ has been widely employed as stabilizing agent. We have previously demonstrated that heat treatment induces changes in the distribution of three nuclear scaffold proteins in nuclei prepared in the absence of Mg++ ions. We studied whether different concentrations of Mg++ (2.0-5 mM) affect the spatial distribution of nuclear matrix proteins in nuclei isolated from K562 erythroleukemia cells and stabilized by heat at either 37C or 42C. Five proteins were studied, two of which were RNA metabolism-related proteins (a 105-kD component of splicing complexes and an RNP component), one a 126-kD constituent of a class of nuclear bodies, and two were components of the inner matrix network. The localization of proteins was determined by immunofluorescent staining and confocal scanning laser microscope. Mg++ induced significant changes of antigen distribution even at the lowest concentration employed, and these modifications were enhanced in parallel with increase in the concentration of the divalent cation. The different sensitivity to heat stabilization and Mg++ of these nuclear proteins might reflect a different degree of association with the nuclear scaffold and can be closely related to their functional or structural role.
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Affiliation(s)
- L M Neri
- Istituto di Anatomia Umana Normale, Università di Ferrara, Italy
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23
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Mattagajasingh SN, Misra HP. Mechanisms of the carcinogenic chromium(VI)-induced DNA-protein cross-linking and their characterization in cultured intact human cells. J Biol Chem 1996; 271:33550-60. [PMID: 8969221 DOI: 10.1074/jbc.271.52.33550] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
DNA-protein complexes (DPCs) were induced in human leukemic T-lymphocyte MOLT4 cells by treatment with potassium chromate. DPCs were isolated by ultracentrifugal sedimentation in the presence of 2% SDS and 5 M urea. The complexes were analyzed by two-dimensional SDS-polyacrylamide gel electrophoresis. Three acidic proteins of 74, 44, and 42 kDa and a basic protein of 51 kDa were primarily complexed to DNA following 25 microM chromate treatment. Higher concentrations of chromate cross-linked many other proteins to DNA. Amino acid sequencing and immunoblotting studies indicated that the acidic 44-kDa protein could be nuclear beta-actin. Lectin and aminoglycoside nucleotidyltransferase were also found to cross-link with DNA by chromate treatment. The composition and stability of the DPCs were studied using nucleases, proteinase K, and disruptive chemicals. Pretreatment of cells with antioxidants inhibited the formation of DPCs, measured as K+-SDS precipitable DPCs, indicating the involvement of oxidative mechanisms. Because chromate causes certain nuclear proteins to form complexes with DNA and the complexes are resistant to treatments such as 2% SDS and 5 M urea, but disruptable under gel electrophoretic conditions, chromium could be used as a cross-linking agent for the identification of other proteins, such as transcription factors, that transiently interact with DNA.
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Affiliation(s)
- S N Mattagajasingh
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland Regional College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061-0442, USA.
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24
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Alberti I, Parodi S, Barboro P, Sanna P, Nicolò G, Allera C, Patrone E, Galli S, Balbi C. Differential nuclear matrix-intermediate filament expression in human prostate cancer in respect to benign prostatic hyperplasia. Cancer Lett 1996; 109:193-8. [PMID: 9020920 DOI: 10.1016/s0304-3835(96)04444-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We have characterized the changes in composition of the nuclear matrix-intermediate filament complex (NM-IF) isolated from prostate cancer (PCa), compared with benign prostatic hyperplasia (BPH). We prepared the NM-IF from ten patients undergoing radical retropubic prostectomy; the benign hyperplastic tissue was obtained from the prostate lobe contralateral to the cancer zone. Several quantitative and qualitative changes have been identified. Three new proteins of molecular weight 48, 47 and 29 kDa and isoelectric point 6.0, 4.9 and 6.4, respectively, were detected in PCa, referred to here as P8, P5 and NM-1, P8 was present in all ten of the tumors examined, P5 was expressed in 9/10 PCa; conversely, they were present in only one and two BPH, respectively; NM-1 was found in eight tumors out of nine and never in BPH. These proteins are expressed in moderately differentiated malignant cells, suggesting that the proteins of the NM-IF complex can be interesting biomarkers for prostate cancer. Immunoblot analysis shows that P8 and P5 proteins belong to the IF superfamily. This observation, taken together with previous data obtained by our and other groups, suggests that the characterization of NM-IF protein changes could also shed light on mechanistic aspects of cancer progression.
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Affiliation(s)
- I Alberti
- Istituto Nazionale per la Ricerea sul Cancro, Genova, Italy
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25
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26
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Mattern KA, Humbel BM, Muijsers AO, de Jong L, van Driel R. hnRNP proteins and B23 are the major proteins of the internal nuclear matrix of HeLa S3 cells. J Cell Biochem 1996; 62:275-89. [PMID: 8844407 DOI: 10.1002/(sici)1097-4644(199608)62:2<275::aid-jcb15>3.0.co;2-k] [Citation(s) in RCA: 93] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The nuclear matrix is the structure that persists after removal of chromatin and loosely bound components from the nucleus. It consists of a peripheral lamina-pore complex and an intricate internal fibrogranular structure. Little is known about the molecular structure of this proteinaceous internal network. Our aim is to identify the major proteins of the internal nuclear matrix of HeLa 53 cells. To this end, a cell fraction containing the internal fibrogranular structure was compared with one from which this structure had been selectively dissociated. Protein compositions were quantitatively analyzed after high-resolution two-dimensional gel electrophoresis. We have identified the 21 most abundant polypeptides that are present exclusively in the internal nuclear matrix. Sixteen of these proteins are heterogeneous nuclear ribonucleoprotein (hnRNP) proteins. B23 (numatrin) is another abundant protein of the internal nuclear matrix. Our results show that most of the quantitatively major polypeptides of the internal nuclear matrix are proteins involved in RNA metabolism, including packaging and transport of RNA.
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Affiliation(s)
- K A Mattern
- E.C. Slater Instituut, University of Amsterdam, The Netherlands
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27
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Abstract
Jacob and Brenner proposed a model for control of DNA replication in which a trans-acting initiator protein binds to a cis-acting replicator to effect initiation of nascent DNA chains at a fixed locus. Although replicators have been identified in prokaryotic and simple eukaryotic genomes, it has been much more difficult to demonstrate their presence in mammalian chromosomes. Owing to the lack of genetic approaches for identifying mammalian replicators, investigators have directed attention to localizing nascent strand start sites, which should lie close to replicators. Toward this end, a variety of clever techniques have been invented for analyzing replication intermediates, but only rarely have more than one of these techniques been applied to a single locus. However, virtually all have been used to analyze the dihydrofolate reductase locus in CHO cells. The picture that has developed in this locus is that initiation can occur at any of a large number of sites scattered throughout a broad zone, but somewhat more frequently near two sites that may correspond to true genetic replicators. Furthermore, it appears that local transcriptional activity, as well as appropriate torsional stress (as imparted by local attachment to the nuclear matrix), may have profound effects on origin activity.
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Affiliation(s)
- P A Dijkwel
- Department of Biochemistry, University of Virginia School of Medicine, Charlottesville 22908, USA
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28
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Hempel K, Strätling WH. The chicken lysozyme gene 5′ MAR and the Drosophila histone SAR are electroelutable from encapsulated and digested nuclei. J Cell Sci 1996; 109 ( Pt 6):1459-69. [PMID: 8799833 DOI: 10.1242/jcs.109.6.1459] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cultured chicken cells were encapsulated in agarose microbeads, lysed in a near-physiological buffer and resulting encapsulated nuclei were digested with a restriction enzyme and electroeluted. After removal of approximately 97% of the chromatin, the nuclear lamina, residual nucleoli and an internal nuclear network remained. The majority of nascent RNA was also recovered in digested and electroeluted nuclei. Surprisingly, however, the chicken lysozyme gene 5′ MAR was quantitatively electroeluted from digested nuclei of expressing and non-expressing cells, as well as the promoter region and the coding sequence. When encapsulated nuclei were digested partially, the proportion of elutable 5′ MAR chromatin was comparable to that of elutable bulk chromatin. Furthermore, after digestion of encapsulated nuclei from Drosophila Kc cells, the histone SAR was electroeluted to the same extent as bulk chromatin. We conclude that the lysozyme gene 5′ MAR and the histone SAR are not permanently attached to a nuclear matrix or scaffold.
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Affiliation(s)
- K Hempel
- Institut für Physiologische Chemie, Universitäts-Krankenhaus Eppendorf, Hamburg, FR Germany
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29
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Nickerson JA, Blencowe BJ, Penman S. The architectural organization of nuclear metabolism. INTERNATIONAL REVIEW OF CYTOLOGY 1996; 162A:67-123. [PMID: 8575888 DOI: 10.1016/s0074-7696(08)61229-2] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Nucleic acid metabolism is structurally organized in the nucleus. DNA replication and transcription have been localized to particular nuclear domains. Additional domains have been identified by their morphology or by their composition; for example, by their high concentration of factors involved in RNA splicing. The domain organization of the nucleus is maintained by the nuclear matrix, a nonchromatin nuclear scaffolding that holds most nuclear RNA and organizes chromatin into loops. The nuclear matrix is built on a network of highly branched core filaments that have an average diameter of 10 nm. Many of the intermediates and the regulatory and catalytic factors of nucleic acid metabolism are retained in nuclear matrix preparations, suggesting that nucleic acid synthesis and processing are structure-bound processes in cells. Tissue-specific and malignancy-induced variations in nuclear structure and metabolism may result from altered matrix architecture and composition.
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Affiliation(s)
- J A Nickerson
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139, USA
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30
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Berezney R, Mortillaro MJ, Ma H, Wei X, Samarabandu J. The nuclear matrix: a structural milieu for genomic function. INTERNATIONAL REVIEW OF CYTOLOGY 1996; 162A:1-65. [PMID: 8575878 DOI: 10.1016/s0074-7696(08)61228-0] [Citation(s) in RCA: 103] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
While significant progress has been made in elucidating molecular properties of specific genes and their regulation, our understanding of how the whole genome is coordinated has lagged behind. To understand how the genome functions as a coordinated whole, we must understand how the nucleus is put together and functions as a whole. An important step in that direction occurred with the isolation and characterization of the nuclear matrix. Aside from the plethora of functional properties associated with these isolated nuclear structures, they have enabled the first direct examination and molecular cloning of specific nuclear matrix proteins. The isolated nuclear matrix can be used for providing an in vitro model for understanding nuclear matrix organization in whole cells. Recent development of high-resolution and three-dimensional approaches for visualizing domains of genomic organization and function in situ has provided corroborative evidence for the nuclear matrix as the site of organization for replication, transcription, and post-transcriptional processing. As more is learned about these in situ functional sites, appropriate experiments could be designed to test molecular mechanisms with the in vitro nuclear matrix systems. This is illustrated in this chapter by the studies of nuclear matrix-associated DNA replication which have evolved from biochemical studies of in vitro nuclear matrix systems toward three-dimensional computer image analysis of replication sites for individual genes.
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Affiliation(s)
- R Berezney
- Department of Biological Sciences, State University of New York at Buffalo 14260, USA
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31
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Moreno Díaz de la Espina SM. Nuclear matrix isolated from plant cells. INTERNATIONAL REVIEW OF CYTOLOGY 1996; 162B:75-139. [PMID: 8557494 DOI: 10.1016/s0074-7696(08)62615-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Residual nuclear matrices can be successfully obtained from isolated nuclei of different monocot and dicot plant species using either high ionic or low ionic extraction protocols. The protein composition of isolated nuclear matrices depends on the details of isolation protocols. They are stable and present in all cases, a tripartite organization with a lamina, nucleolar matrix, and internal matrix network, and also maintain some of the basic architectural features of intact nuclei. In situ preparations demonstrate the continuity between the nuclear matrix and the plant cytoskeleton. Two-dimensional separation of isolated plant nuclear matrix proteins reveals a heterogeneous polypeptide composition corresponding rather to a complex multicomponent matrix than to a simple nucleoskeletal structure. Immunological identification of some plant nuclear matrix components such as A and B type lamins, topoisomerase II, and some components of the transcription and splicing machineries, internal intermediate filament proteins, and also specific nucleolar proteins like fibrillarin and nucleolin, which associate to specific matrix domains, establish a model of organization for the plant nuclear matrix similar to that of other eukaryotes. Components of the transcription, processing, and DNA-anchoring complexes are associated with a very stable nucleoskeleton. The plant matrix-attached regions share structural and functional characteristics with those of insects, vertebrates, and yeast, and some of them are active in animal cells. In conclusion, the available data support the view that the plant nuclear matrix is basically similar in animal and plant systems, and has been evolutionarily conserved in eukaryotes.
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32
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Dijkwel PA, Hamlin JL. Origins of replication and the nuclear matrix: the DHFR domain as a paradigm. INTERNATIONAL REVIEW OF CYTOLOGY 1996; 162A:455-84. [PMID: 8575885 DOI: 10.1016/s0074-7696(08)61236-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The eukaryotic genome appears to be organized in a loopwise fashion by periodic attachment to the nuclear matrix. The proposal that a chromatin loop corresponds to a functional domain has stirred interest in the properties of the DNA sequences at the bases of these loops, the matrix-attached regions (MARs). Evidence has been presented suggesting that certain MARs act as boundary elements isolating domains from their chromosomal context. MARs have also been found in the vicinity of promoters and enhancers and they could act by displacing these cis-regulatory elements into the proper nuclear subcompartment. Attachment to the matrix might also play a role in DNA replication. A large body of evidence indicates that replication occurs on the nuclear matrix. This implies that any DNA sequence will be attached to the matrix at a certain time during the cell cycle. This transient mode of attachment contrasts with the proposed permanent attachment of origins of DNA replication with the nuclear matrix. While some data exist that support this suggestion, the current lack of understanding of the mammalian replication origin precludes definitive conclusions regarding the role of MARs in the initiation process.
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Affiliation(s)
- P A Dijkwel
- Department of Biochemistry, University of Virginia, School of Medicine, Charlottesville 22908, USA
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33
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Neri LM, Riederer BM, Marugg RA, Capitani S, Martelli AM. The effect of sodium tetrathionate stabilization on the distribution of three nuclear matrix proteins in human K562 erythroleukemia cells. Histochem Cell Biol 1995; 104:29-36. [PMID: 7584557 DOI: 10.1007/bf01464783] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Using both conventional fluorescence and confocal laser scanning microscopy we have investigated whether or not stabilization of isolated human erythroleukemic nuclei with sodium tetrathionate can maintain in the nuclear matrix the same spatial distribution of three polypeptides (M(r) 160 kDa and 125 kDa, previously shown to be components of the internal nuclear matrix plus the 180-kDa nucleolar isoform of DNA topoisomerase II) as seen in permeabilized cells. The incubation of isolated nuclei in the presence of 2 mM sodium tetrathionate was performed at 0 degrees C or 37 degrees C. The matrix fraction retained 20-40% of nuclear protein, depending on the temperature at which the chemical stabilization was executed. Western blot analysis revealed that the proteins studied were completely retained in the high-salt resistant matrix. Indirect immunofluorescence experiments showed that the distribution of the three antigens in the final matrix closely resembled that detected in permeabilized cells, particularly when the stabilization was performed at 37 degrees C. This conclusion was also strengthened by analysis of cells, isolated nuclei and the nuclear matrix by means of confocal laser scanning microscopy. We conclude that sodium tetrathionate stabilization of isolated nuclei does not alter the spatial distribution of some nuclear matrix proteins.
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Affiliation(s)
- L M Neri
- Istituto di Anatomia Umana Normale, Università di Ferrara, Italy
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34
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Smith A, Benavente R. An Mr 51,000 protein of mammalian spermatogenic cells that is common to the whole XY body and centromeric heterochromatin of autosomes. Chromosoma 1995; 103:591-6. [PMID: 7587581 DOI: 10.1007/bf00357685] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
During mammalian male meiotic prophase the sex chromosomes form a structure called the XY body or sex vesicle. This structure is characterized by differential condensation of chromatin and transcriptional inactivity. The reasons and mechanisms for the allocyclic behaviour of sex chromosomes with respect to autosomes are largely unknown. In order to gain insight into the process of XY-body formation we are involved in the characterization of proteins associated with meiotic sex chromosomes by immunological approaches. Here we report on the identification of an Mr 51,000 protein (p51) that is homogeneously distributed in the XY body of rodents as shown by immunocytochemistry with the novel monoclonal antibody 4EC. Interestingly, in germ line cells the antibody also labelled the centromeric heterochromatin of autosomes. We speculate that p51 may be a component of the mechanisms that lead to wide chromosome regions becoming inaccessible for transcription and/or recombination events.
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Affiliation(s)
- A Smith
- Department of Cell and Developmental Biology, Theodor-Boveri-Institute (Biocenter), University of Würzburg, Germany
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35
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van Steensel B, Jenster G, Damm K, Brinkmann AO, van Driel R. Domains of the human androgen receptor and glucocorticoid receptor involved in binding to the nuclear matrix. J Cell Biochem 1995; 57:465-78. [PMID: 7768981 DOI: 10.1002/jcb.240570312] [Citation(s) in RCA: 80] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Steroid receptors have been reported to bind to the nuclear matrix. The nuclear matrix is operationally defined as the residual nuclear structure that remains after extraction of most of the chromatin and all soluble and loosely bound components. To obtain insight in the molecular mechanism of the interaction of steroid receptors with the nuclear matrix, we studied the binding of several deletion mutants of the human androgen receptor (hAR) and the human glucocorticoid receptor (hGR) to the nuclear matrix. Receptor binding was tested for two different nuclear matrix preparations: complete matrices, in which most matrix proteins are retained during the isolation procedure, and depleted matrices, which consist of only a subset of these proteins. The results show that the C-terminal domain of the hAR binds tightly to both depleted and complete matrices. In addition, at least one other domain of the hAR binds to complete matrices but not to depleted matrices. In contrast to the hAR, the hGR binds only to complete matrices. For this interaction both the DNA-binding domain and the C-terminal domain of the hGR are required, whereas the N-terminal domain is not. We conclude that specific protein domains of the hAR and the hGR are involved in binding to the nuclear matrix. In addition, our results indicate that the hAR and the hGR are attached to the nuclear matrix through different molecular interactions.
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Affiliation(s)
- B van Steensel
- E.C. Slater Institute, University of Amsterdam, The Netherlands
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36
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Sevaljević L, Petrović M, Bogojević D. Inflammation of the dam has different effects on the binding of maternal and fetal rat liver nucleoproteins to the rat haptoglobin gene promoter. EXPERIENTIA 1994; 50:947-52. [PMID: 7957771 DOI: 10.1007/bf01923485] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Transcriptional regulation of binding interactions between nucleoproteins and the hormone response element (RE) of the rat haptoglobin (Hp) gene was investigated in adult and fetal livers of rats exposed to inflammation on day 19 of pregnancy. Nuclear extracts from the embryonal liver displayed a barely detectable binding-affinity for hormone RE, but in extracts from the adult liver it was noticeable. The acute phase reaction of the mother promoted an increase of Hp gene expression in both adult and fetal livers, relying on stage-specific changes in hormone RE binding activities of nucleoplasmic proteins. The results indicated that the elevation of Hp gene expression in fetal liver to the steady basal level found in adults required the induction of new trans-acting proteins, whereas an overexpression of this gene in adult acute phase liver relied essentially on an increase in the binding-affinity of the preexisting hormone RE binding proteins.
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Affiliation(s)
- L Sevaljević
- Institute for Biological Research, Belgrade, Yugoslavia
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37
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38
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York J, Majerus P. Nuclear phosphatidylinositols decrease during S-phase of the cell cycle in HeLa cells. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)37126-0] [Citation(s) in RCA: 101] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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39
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Jeong S, Stein A. Micrococcal nuclease digestion of nuclei reveals extended nucleosome ladders having anomalous DNA lengths for chromatin assembled on non-replicating plasmids in transfected cells. Nucleic Acids Res 1994; 22:370-5. [PMID: 7510391 PMCID: PMC523591 DOI: 10.1093/nar/22.3.370] [Citation(s) in RCA: 104] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The chromatin structures of a variety of plasmids and plasmid constructions, transiently transfected into mouse Ltk- cells using the DEAE-dextran procedure, were studied by micrococcal nuclease digestion of nuclei and Southern hybridization. Although regularly arranged nucleosome-like particles clearly were formed on the transfected DNA, the nucleosome ladders, in some cases with 13-14 bands, were anomalous. Most often, a ladder of DNA fragments with lengths of approximately 300, 500, 700, 900 bp, etc. was generated. In contrast, typical 180-190 bp multiples were generated from bulk cellular or endogenous beta-actin gene chromatin. Very similar results were obtained with all DNA's transfected, and in a variety of cell lines, provided that plasmid replication did not occur. Additionally, after digestion of nuclei, about 90% of the chromatin fragments that contained transfected DNA sequences could not be solubilized at low ionic strength, in contrast with bulk cellular chromatin, suggesting association with nuclear structures or nuclear matrix. The remaining 10% of transfected DNA sequences, arising from soluble chromatin fragments, generated a typical nucleosome ladder. These results are consistent with the idea that assembly of atypical chromatin structures might be induced by proximity to elements of the nuclear pore complex or by nuclear compartmentalization.
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Affiliation(s)
- S Jeong
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907
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40
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Martelli AM, Neri LM, Zamai L, Bareggi R, Manzoli L, Cocco L. 6-Iodoacetamidofluorescein labelling to assess the state of sulphhydril groups after thermal stabilization of isolated nuclei. THE HISTOCHEMICAL JOURNAL 1994; 26:179-88. [PMID: 8150664 DOI: 10.1007/bf00157967] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Isolated nuclei and nuclear matrices, prepared from mouse erythroleukaemia cells, were reacted with the sulphhydryl-specific dye 6-iodoacetamidofluorescein. To determine whether in vitro formation of disulphide bonds might play a role in the nuclear matrix stabilization triggered by exposure of isolated nuclei to the physiological temperature of 37 degrees C, a variety of techniques were employed to assess the state of cysteinyl residues after such an incubation. Both flow cytometry and confocal microscopy quantitative analysis did not reveal major differences in the fluorescence intensity of nuclei incubated at 37 degrees C in comparison with those maintained at 0 degrees C. Confocal scanning laser microscopy revealed that 6-iodoacetamidofluorescein labelled a fibrogranular network in isolated nuclei. The fluorescent pattern of the network was not affected by a 37 degrees C exposure of nuclei. However, such a network was not detectable in isolated nuclear matrices, thus suggesting a possible protein re-arrangement during matrix preparation. Sodium dodecyl sulphate-polyacrylamide gel electrophoresis of fluorescent-labelled nuclear proteins showed no difference between heat-exposed and control samples. We conclude that oxidation of cysteinyl residues is not a major factor leading to the stabilization of nuclei incubated at 37 degrees C.
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Affiliation(s)
- A M Martelli
- Dipartimento di Morfologia Umana Normale, Trieste, Italy
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41
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Stephanova E, Stancheva R, Avramova Z. Binding of sequences from the 5'- and 3'-nontranscribed spacers of the rat rDNA locus to the nucleolar matrix. Chromosoma 1993; 102:287-95. [PMID: 8486080 DOI: 10.1007/bf00352403] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Nucleolar matrix structures were obtained under different extraction conditions from highly purified isolated nucleoli. Their ultrastructural appearance, protein composition and capacity to bind rDNA preferentially were studied in a model binding system. A region spanning approximately 25 kb in the rat ribosomal gene locus was screened for DNA sites capable of specifically interacting with the proteins of the nucleolar matrix (MARs). Two such sites were identified: one is located on an EcoRV-KpnI fragment in the 5'-nontranscribed spacer region, between two repetitive elements and close to the transcription initiation site; the other MAR is on a PvuII-BamHI fragment located in the 3'-nontranscribed region, encompassing an element 85% homologous to a B2-sequence. The two MARs are located in regions rich in polypyrimidine/polypurine tracks and contain a few elements homologous to the consensus sequence for topoisomerase II. This indicates that the "attachment sites" for the ribosomal genes belong to the same class of sequences as the MARs attaching the chromosomal DNA to the nuclear matrix.
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Affiliation(s)
- E Stephanova
- Department of Cytology, University of Sofia, Bulgaria
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42
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Eckhert CD, Lockwood MK, Hsu MH, Ho J, Kang R. Microvascular changes in rat glomeruli as a consequence of small differences in selenium exposure. Exp Mol Pathol 1992; 57:222-34. [PMID: 1286673 DOI: 10.1016/0014-4800(92)90013-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
This paper evaluates the effect of small differences in selenium exposure, within the safe range, on the glomerular vascular tufts of rats fed high-sucrose diets. In the first experiment male Wistar rats were housed in galvanized cages and were provided sucrose-based diets to induce a mild chronic insult to the microcirculation. One group of rats received the diet prepared to contain 0.10 mg Se/kg and another group 0.21 mg Se/kg. To assure that the galvanized metal cages were not influencing the results of the experiment this protocol was repeated in a second experiment wherein rats were housed in stainless steel cages. The levels of Se used supported normal activity of the long-term indicator of Se sufficiency, erythrocyte glutathione peroxidase. In both experiments rats fed diets containing 0.21 mg Se/kg had larger Bowman's capsules (P < 0.01) and vascular tufts (P < 0.01). Vascular tufts from these rats also contained a higher proportion of open capillary lumen (P < 0.01), contained less cytoplasmic and extracellular material (P < 0.001), and had larger nuclei (P < 0.001) than those fed 0.10 mg Se/kg. A third study was designed to determine if the selenium-dependent differences in nuclear size were indicative of this being a site of incorporation. Year-old rats subjected to the same protocol as those in the second experiment were given 75Se, by injection into the femoral vein, to label the sites of incorporation. Glomeruli were purified and subjected to subcellular fractionation. Ninety percent of the radioactivity was associated with the crude nuclear fraction. Purification of the crude nuclear fraction demonstrated that the radioactivity was associated with the nuclei.
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Affiliation(s)
- C D Eckhert
- Department of Environmental Health Sciences, University of California, Los Angeles 90024-1772
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Abstract
The structure of the interphase nucleus is a major area of current interest in cell biology. It is thought likely that the nucleus is organised around some form of structural matrix and that this matrix will play a role in processes as diverse as chromosome replication and the integration of gene expression. However, the structure of the matrix within the nucleus has remained elusive, largely because attempts to define it have been dogged by technical problems arising from the great complexity of this organelle. This situation is now being changed by the application of in situ analysis and of molecular genetic methodologies which are opening up this hitherto intractable field.
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Affiliation(s)
- R S Jack
- Institut für Genetik, Universität zu Köln, Federal Republic of Germany
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44
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Bartjeliotou AJ, Dimitriadis GJ. The association of the human epsilon-globin gene with the nuclear matrix: a reconsideration. Mol Cell Biochem 1992; 115:105-15. [PMID: 1435759 DOI: 10.1007/bf00229102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The association of the human epsilon-globin gene with the nuclear matrix was studied in erythroid and non-erythroid cell lines. Using a high salt method to prepare histone depleted nuclei we studied the association of variety of fragments covering a 7.8 kb region which contains the human epsilon-globin gene. We furthermore studied the association of a set of DNA fragments covering the 13 kb human G gamma/A gamma-globin gene domain, the 16 kb psi beta/delta-globin gene domain and the 10 kb beta-globin gene domain with the nuclear matrix of K562 and Raji cells. The results show that all fragments studied are easily released from the nuclear matrix, indicating no specific association. Summarizing our results we could say that a region starting 5.7 kb 5' to the human epsilon-globin gene and ending 4 kb 3' to the human beta-globin gene seems to contain no attachment sites with the nuclear matrix of both erythroid and non-erythroid cells.
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Falcieri E, Gobbi P, Sabatelli P, Santi S, Farabegoli F, Rana R, Cataldi A, Maraldi NM, Martelli AM. A combined ultrastructural approach to the study of nuclear matrix thermal stabilization. HISTOCHEMISTRY 1992; 98:121-9. [PMID: 1385369 DOI: 10.1007/bf00717003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Using mouse erythroleukaemia cells and different ultrastructural techniques, the morphology was investigated of the nuclear matrix obtained after incubation at 37 degrees C of isolated nuclei. If purified nuclei were heated for 45 min at 37 degrees C, the final matrix exhibited well-recognizable nucleolar remnants, an inner network and a peripheral lamina. Without such incubation only the peripheral lamina was seen surrounding homogeneous, finely granular material. Similar results were obtained with both araldite-embedded and freeze-fractured nuclear matrices, although in the latter case the loose granular material was not evident. Observations of araldite-embedded, heat-treated nuclei revealed clumping of heterochromatin in small, very electron-dense masses with large interchromatin spaces. These ultrastructural aspects were even more striking in freeze-fractured nuclei. Cytochemical matrix analysis by osmium-amine staining for nucleic acids and DNase-gold labelling for DNA localization demonstrated that also matrix residual nucleic acids, mostly RNA, are stabilized by heat exposure of isolated nuclei. The results demonstrate that the morphology of heat-stabilized nuclear matrix is not artefactually affected during the preparation for conventional electron microscopy and suggest a possible involvement of nucleic acids in the heat-induced stabilization of the nuclear matrix.
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Affiliation(s)
- E Falcieri
- Istituto di Anatomia Umana Normale, Università di Bologna, Italy
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46
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Andreeva M, Markova D, Loidl P, Djondjurov L. Intranuclear compartmentalization of transcribed and nontranscribed c-myc sequences in Namalva-S cells. EUROPEAN JOURNAL OF BIOCHEMISTRY 1992; 207:887-94. [PMID: 1379916 DOI: 10.1111/j.1432-1033.1992.tb17121.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
This investigation is centered on the intranuclear localization of transcribed and nontranscribed c-myc sequences in human Namalva-S cells bearing t(8;14) translocation. Southern hybridization showed that the breakpoint in the truncated allele of c-myc lies outside the characteristic 12.8-kbp EcoRI fragment: as Northern analysis indicated, this reorganization induces a high level of c-myc transcription. Following high-salt treatment, EcoRI digestion and centrifugation, isolated nuclei from the same cells are separated into two residual fractions: a heavier P fraction including nuclear matrix structures and a light S fraction representing dehistonized chromatin fibres. Comparative hybridization experiments revealed that the above procedure separates the c-myc sequences between the two fractions. To locate the site of intranuclear c-myc transcription, we performed run-on experiments with two fractions, topologically analogous to the residual P and S fractions but maintaining the original chromatin organization. These experiments indicated that chromatin P fraction harbours actively transcribed c-myc sequences while chromatin S harbours nontranscribed ones. Further experiments have clarified that the transcribed c-myc sequences are firmly bound to the matrix by multiple attachment sites, arranged throughout the entire gene locus. It was found, moreover, that at the site of attachment the interaction between DNA and the matrix components is realized via proteins. Controls with the beta-globin gene, which is constitutively nonexpressed in Namalva-S cells but upon induction is highly expressed in murine erythroleukemia cells, completely confirmed the conclusion we had made for the intranuclear localization of c-myc. Thus the experiments presented here support the more common idea that the transcribed and nontranscribed sequences are precisely compartmentalized.
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MESH Headings
- Animals
- Blotting, Northern
- Blotting, Southern
- Cell Fractionation
- Cells, Cultured
- Chromatin
- Chromosomes, Human, Pair 14
- Chromosomes, Human, Pair 8
- DNA/analysis
- Genes, myc
- Globins/genetics
- Humans
- Mice
- RNA/analysis
- Restriction Mapping
- Transcription, Genetic
- Translocation, Genetic
- Tumor Cells, Cultured
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Affiliation(s)
- M Andreeva
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia
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47
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Martelli AM, Gilmour RS, Bareggi R, Cocco L. The effect of in vitro heat exposure on the recovery of nuclear matrix-bound DNA polymerase alpha activity during the different phases of the cell cycle in synchronized HeLa S3 cells. Exp Cell Res 1992; 201:470-6. [PMID: 1639141 DOI: 10.1016/0014-4827(92)90296-k] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
HeLa S3 cells were synchronized by a double thymidine block or aphidicolin treatment and the levels of nuclear matrix-bound DNA polymerase alpha activity were then measured using activated calf thymus DNA as template. The nuclear matrix was obtained by 2 M NaCl extraction and DNase I digestion of isolated nuclei incubated at 37 degrees C for 45 min prior to subfractionation. In all phases of the cell cycle 25-30% of nuclear DNA polymerase alpha activity remained matrix-bound, even when cells were in the G1 phase. No dynamic association of DNA polymerase alpha activity with the matrix was seen, at variance with previous results obtained in regenerating rat liver. The variations measured in matrix-bound activity closely followed those detected in isolated nuclei throughout the cell cycle. If nuclei were not heat-stabilized very low levels of DNA polymerase alpha activity were measured in the matrix (1-2% of total nuclear activity). Heat incubation of nuclei failed to produce any enrichment in matrix-associated newly replicated DNA, whereas the sulfhydryl cross-linking chemical sodium tetrathionate did. Therefore the results obtained after the heat stabilization procedure do not completely fit with the model that envisions the nuclear matrix as the active site where eucaryotic DNA replication takes place.
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Affiliation(s)
- A M Martelli
- Istituto di Anatomia Umana Normale, Bologna, Italy
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48
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Cai S, Zeng C, Li J, Zhai Z. Identification of the nuclear matrix and chromosome scaffold in dinoflagellate Crypthecodinium cohnii. Cell Res 1992. [DOI: 10.1038/cr.1992.16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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49
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Stuurman N, Floore A, Colen A, de Jong L, van Driel R. Stabilization of the nuclear matrix by disulfide bridges: identification of matrix polypeptides that form disulfides. Exp Cell Res 1992; 200:285-94. [PMID: 1572396 DOI: 10.1016/0014-4827(92)90174-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The molecular structure of the nuclear matrix is still poorly understood. We have tried to assess which proteins are important structural elements by examining the process of stabilization of the nuclear matrix by sodium tetrathionate. Sodium tetrathionate stabilizes the nuclear matrix by oxidizing sulfhydryl groups to disulfides. We show that tetrathionate-stabilized matrices are disassembled in buffers containing SDS, indicating that the stabilized nuclear matrix is not a continuous network of cross-linked proteins. Using monobromobimane, a thiol-specific fluorescent reagent, we show that many protein thiols in the stabilized matrix are oxidized. By chromatography on activated thiol-Sepharose we estimated that about 50% of the matrix proteins had oxidized sulfhydryl groups. The protein composition of the material bound to activated thiol-Sepharose was similar to that of the not-bound material. A few proteins are highly enriched in the fraction that was bound to the column. This indicates that many matrix protein species are partially oxidized and that some proteins are completely oxidized. The oxidized protein thiols are found in relatively large complexes as determined by SDS gel-electrophoresis under nonreducing conditions. These results are interpreted in terms of protein-protein interactions in the matrix. The possible role of thiols and disulfides in the in vivo organization of the nucleus is discussed.
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Affiliation(s)
- N Stuurman
- E. C. Slater Institute for Biochemical Research, University of Amsterdam, The Netherlands
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50
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Siddiqui R, Exton J. Phospholipid base exchange activity in rat liver plasma membranes. Evidence for regulation by G-protein and P2y-purinergic receptor. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(18)42617-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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