[Position of 19 regions of DNA binding to nuclear matrix (MAR) on human chromosome 19].
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Is the nuclear matrix the site of DNA replication in eukaryotic cells?
Four types of experiment were carried out to test the recently proposed model of matrix-bound replication in eukaryotic cells. In experiments with pulse-labelling we found preferential association of newly replicated DNA with the matrix only when the procedure for isolation includes first high-salt treatment of isolated nuclei and then digestion with nucleases, or when prior to digestion the nuclei have been stored for a prolonged time. In both cases, however, evidence was found that this preferential association is due to a secondary, artifactual binding of the newly replicated chromatin region to the matrix elements. Pulse-chase experiments and experiments with continuous labelling were carried out to answer the question whether during replication the DNA is reeled through the replication complexes, i.e., whether newly replicated DNA is temporarily or permanently associated with the matrix. The results showed that at that time the matrix DNA does not move from its site of attachment. Since, according to the model of matrix-bound replication, the forks are assumed to be firmly anchored to high-salt resistant proteinaceous matrix structures, the chromatin fragments isolated with endonuclease not recognizing newly replicated DNA and purified by sucrose gradient centrifugation should be free of replication intermediates. The electronmicroscopic analysis of such fragments revealed the existence of intact replication micro-bubbles. Moreover, the fragments with replication configurations appeared as smooth chromatin fibres not attached to elements characteristic for the matrix. All these experiments suggest that the nuclear skeleton is not a native site of DNA replication in eukaryotic cells.
Animals↗
Mitotic stability of an episomal vector containing a human scaffold/matrix-attached region is provided by association with nuclear matrix.
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Animals↗
Nuclear matrix condensation and c-myc and c-fos expression are specifically altered in culture rat hepatocytes after exposure to cyproterone acetate and phenobarbital.
Regenerative or hyperplastic growth promotes carcinogenesis and can be induced by many nongenotoxic carcinogens. The mitogenic potential of the rodent liver tumor promoters, cyproterone acetate and phenobarbital was investigated in primary rat hepatocyte cultures. Two premitotic markers were analyzed, the expression of two immediate-early genes (c-fos and c-myc) and the decrease in the nuclear quinacrine dihydrochloride fluorescence indicative for a G0-G1 cell cycle shift. C-fos expression and decrease in nuclear fluorescence could be induced by both chemicals, phenobarbital being the lesser potent, whereas c-myc expression was only inducible by cyproterone acetate. In situ hybridization with c-myc revealed that both chemicals enhanced c-myc mRNA levels in individual cells, however the number of responding hepatocytes was increased by cyproterone acetate only. The chemical-induced premitotic changes in hepatocytes were highly specific in terms of affected genes and ploidy levels of responding hepatocytes.
Animals↗
Nuclear matrix attachment regions confer long-range function upon the immunoglobulin mu enhancer.
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Animals↗
Nuclear matrix localization and SUMO-1 modification of adenovirus type 5 E1b 55K protein are controlled by E4 Orf6 protein.
Human adenovirus serotype 5 encodes three proteins, E1b 55K, E4 Orf3 and E4 Orf6, which interact with each other and with components of the nucleus to regulate mRNA processing and export, viral DNA replication and p53-dependent apoptosis. Previous studies have shown that, during wild-type infection, 55K associates initially with structures termed ND10, which are sites of localization of the promyelocytic leukaemia protein, and then moves, dependent upon its interaction with Orf6, to the establishing virus replication centres. Absence of either Orf3 or Orf6 affects the localization of 55K and so may affect its function. In this study, the influence of Orf3 and Orf6 expression on the association of 55K with the insoluble matrix fraction of the nucleus and with ND10 particularly was examined. Overexpression of Orf6 was sufficient to block the association of 55K with this fraction, irrespective of the presence of Orf3. This effect depended upon the two proteins being able to interact. However, the association of 55K with ND10, which persists throughout infection in the absence of Orf6, required Orf3 to be present, thus distinguishing two subsets of matrix-associated 55K. A modified form of 55K, formation of which was blocked by mutating the known site of SUMO-1 attachment, was more abundant in the absence of Orf6 but unaffected by the absence of Orf3. Thus, this modification is favoured when 55K remains associated with the matrix but does not correlate with its stable association with ND10, many components of which are modified by SUMO-1.
Adenovirus E1B Proteins↗
Association of multiple GTP-binding proteins with the plant cytoskeleton and nuclear matrix.
Several types of GTP-binding proteins exist in plant cells. These include the ras-related low-molecular-weight monomeric GTP-binding proteins and the multi-subunit group which more closely resembles members of the mammalian heterotrimeric G-protein family. Proteins belonging to both of these families are known to be involved in cell signalling events and have until recently been assumed to be associated predominantly with membranes. We have investigated the possibility that GTP-binding proteins in plants also can be associated with membrane-free carrot (Daucus carota L.) cytoskeletons and nuclear matrices. Our results demonstrate that several low-molecular-weight GTP-binding proteins, and at least one G-protein alpha-subunit homologue, are associated with these cellular compartments.
Blotting, Western↗
The amino terminus targets the mixed lineage leukemia (MLL) protein to the nucleolus, nuclear matrix and mitotic chromosomal scaffolds.
The mixed-lineage leukemia gene (MLL) is associated with more than 25 chromosomal translocations involving band 11q23 in diverse subtypes of human acute leukemia. Conditional expression of a 50 kDa amino terminal fragment spanning the AT hook motifs of MLL (MLL3AT) causes cell cycle arrest, upregulation of p21Cip1 and p27KiP1 and partial monocytic differentiation of the monoblastic U937 cell line, suggesting a major role for MLL3AT in MLL-AF9-induced myelomonocytic differentiation. In this study, we analyzed the subcellular localization of conditionally expressed MLL3AT in both U937 and HeLa cell lines. Immunofluorescence staining, confocal laser scanning microscopy and immunoelectron microscopy indicated that MLL3AT, like endogenous MLL, localized in the nucleoplasm in a punctate pattern of distribution, including regions attached to the nuclear envelope and the periphery of the nucleolus. We found that MLL3AT and endogenous MLL were present in interphase nuclear matrices and colocalized with topoisomerase II to mitotic chromosomal scaffolds. Nucleoplasm and nucleolar localization was observed even for MLL-AF9 and MLL-AF4 conditionally expressed chimeric proteins, suggesting a common target conferred by the amino terminus of MLL to many if not all the chimeric MLL proteins. The nuclear matrix/scaffold association suggests a role for the amino terminus of MLL in the modulation of chromatin structure, leading to epigenetic effects on the maintenance of gene expression.
Active Transport, Cell Nucleus↗
The elusive nuclear matrix.
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.
Animals↗
A serine/arginine-rich nuclear matrix cyclophilin interacts with the C-terminal domain of RNA polymerase II.
The largest subunit of RNA polymerase II shows a striking difference in the degree of phosphorylation, depending on its functional state: initiating and elongating polymerases are unphosphorylated and highly phosphorylated respectively. Phosphorylation mostly occurs at the C-terminal domain (CTD), which consists of a repetitive heptapeptide structure. Using the yeast two-hybrid system, we have selected for mammalian proteins that interact with the phosphorylated CTD of mammalian RNA polymerase II. A prominent isolate, designated SRcyp/CASP10, specifically interacts with the CTD not only in vivo but also in vitro . It contains a serine/arginine-rich (SR) domain, similar to that found in the SR protein family of pre-mRNA splicing factors, which is required for interaction with the CTD. Most remarkably, the N-terminal region of SRcyp includes a peptidyl-prolyl cis - trans isomerase domain characteristic of immunophilins/cyclophilins (Cyp), a protein family implicated in protein folding, assembly and transport. SRcyp is a nuclear protein with a characteristic distribution in large irregularly shaped nuclear speckles and co-localizes perfectly with the SR domain-containing splicing factor SC35. Recent independent investigations have provided complementary data, such as an association of the phosphorylated form of RNA polymerase II with the nuclear speckles, impaired splicing in a CTD deletion background and inhibition of in vitro splicing by CTD peptides. Taken together, these data indicate that factors directly or indirectly involved in splicing are associated with the elongating RNA polymerases, from where they might translocate to the nascent transcripts to ensure efficient splicing, concomitant with transcription.
Amino Acid Isomerases↗
The nuclear matrix of duck erythroblasts is associated with globin mRNA coding sequences but not with the major proteins of 40S nuclear RNP.
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Animals↗
The relationships between erythroblast denucleation and the nuclear matrix--intermediate filaments.
We present a novel approach for making cybrids. By introducing neo gene expression plasmids into rabbit reticulocytes, fusing the gene transferred reticulocytes with K562 cells and selecting in G418 selection medium, a cybrid strain K-RRneo was established. Whole mount TEM study demonstrated that after cybridization, there was a reorganization of the intermediate filaments which showed a tendency to differentiate towards reticulocytes. SDS-PAGE and western blot analysis verified the above observation, in which the vimentin blot pattern of the cybrids was similar to that of reticulocytes, but totally different from that of K562 cells. Using this model, we reaffirmed the hypothesis that the erythroid differentiation factor (EDF) might be responsible for erythroid differentiation as well as the initiation of denucleation.
Animals↗
Extension of chromatin accessibility by nuclear matrix attachment regions.
Transcription of the variable region of the rearranged immunoglobulin mu gene is dependent on an enhancer sequence situated within one of the introns of the gene. Experiments with transgenic mice have shown that activation of the promoter controlling this transcription also requires the matrix-attachment regions (MARs) that flank the intronic enhancer. As this mu gene enhancer can establish local areas of accessible chromatin, we investigated whether the MARs can extend accessibility to more distal positions. We eliminated interactions between enhancer- and promoter-bound factors by linking mu enhancer/MAR fragments to the binding sites for bacteriophage RNA polymerases that were either close to or one kilobase distal to the enhancer. The mu enhancer alone mediated chromatin accessibility at the proximal site but required a flanking MAR to confer accessibility upon the distal promoter. This long-range accessibility correlates with extended demethylation of the gene construct but not with whether it is being actively transcribed. MARs thus collaborate with the mu enhancer to generate an extended domain of accessible chromatin.
Animals↗
Mapping of replication initiation sites in mammalian genomes by two-dimensional gel analysis: stabilization and enrichment of replication intermediates by isolation on the nuclear matrix.
Two complementary two-dimensional gel electrophoretic techniques have recently been developed that allow initiation sites to be mapped with relative precision in eukaryotic genomes at least as complex as those of yeast and Drosophila melanogaster. We reported the first application of these mapping methods to a mammalian genome in a study on the amplified dihydrofolate reductase (DHFR) domain of the methotrexate-resistant CHO cell line CHOC 400 (J.P. Vaughn, P.A. Dijkwel, and J.L. Hamlin, Cell 61:1075-1087, 1990). Our results suggested that in this 240-kb domain, initiation of nascent DNA strands occurs at many sites within a 30- to 35-kb zone mapping immediately downstream from the DHFR gene. In the course of these studies, it was necessary to develop methods to stabilize replication intermediates against branch migration and shear. This report describes these stabilization methods in detail and presents a new enrichment protocol that extends the neutral/neutral two-dimensional gel mapping method to single-copy loci in mammalian cells. Preliminary analysis of replication intermediates purified from CHO cells by this method suggests that DNA synthesis may initiate at many sites within a broad zone in the single-copy DHFR locus as well.
Animals↗
Effect of nuclear matrix attachment regions on transgene expression in tobacco plants.
Matrix attachment regions (MARs) are thought to participate in the organization and segregation of independent chromosomal loop domains. Although there are several reports on the action of natural MARs in the context of heterologous genes in transgenic plants, in our study we tested a synthetic MAR (sMAR) with the special property of unpairing when under superhelical strain, for its effect on reporter gene expression in tobacco plants. The synthetic MAR was a multimer of a short sequence from the MAR 3' end of the immunoglobulin heavy chain (IgH) enhancer. This sMAR sequence was used to flank the beta-glucuronidase (GUS) reporter gene within the T-DNA of the binary vector pBI121. Vectors with or without the sMARs were then used to transform tobacco plants by Agrobacterium tumefaciens. Transgenic plants containing the sMAR sequences flanking the GUS gene exhibited higher levels of transgene expression compared with transgenic plants which lacked the sMARs. This effect was observed independently of the position of the sMAR at the 5' side of the reporter gene. However, variation of the detected transgene expression was significant in all transformed plant populations, irrespective of the construct used.
Agrobacterium tumefaciens↗
Impaired nuclear translocation, nuclear matrix targeting, and intranuclear mobility of mutant androgen receptors carrying amino acid substitutions in the deoxyribonucleic acid-binding domain derived from androgen insensitivity syndrome patients.
CONTEXT: Recent imaging studies revealed that androgen receptor (AR) is ligand-dependently translocated from the cytoplasm into the nucleus and forms intranuclear fine foci. In this study, we examined whether intracellular dynamics of mutant ARs detected in two androgen insensitivity syndrome (AIS) patients was impaired. OBJECTIVE: ARs with mutations in the DNA-binding domain were functionally characterized and compared with the wild-type AR. PATIENTS: In a complete AIS patient (subject 1), cysteine residue 579 in the first zinc finger motif of AR was substituted for phenylalanine (AR-C579F). Another mutation (AR-F582Y) was found in a partial AIS patient (subject 2). RESULTS: AR-F582Y retained less than 10% of the transactivation activity of the wild-type AR, whereas no ligand-dependent transactivation was detected for AR-C579F. Image analyses of the receptors fused to green fluorescent protein showed that the wild-type AR was ligand-dependently translocated into the nucleus in which it formed fine subnuclear foci. Surprisingly, after the addition of dihydrotestosterone, the two mutant ARs initially formed large cytoplasmic dots, many of which were found to be close to mitochondria by electron microscopy. Subsequently, a part of the ligand-bound mutant ARs gradually entered the nucleus to form a smaller number of larger dots, compared with the wild-type AR. Fluorescence recovery after photobleaching analysis revealed that the intranuclear mobility of the mutant ARs decreased, compared with that of the wild-type AR. CONCLUSIONS: These results suggest that the abnormal translocation, localization, and mobility of the mutant ARs may be the cause of AIS in these subjects.
Active Transport, Cell Nucleus↗
Evaluation of the function of the human apolipoprotein B gene nuclear matrix association regions in transgenic mice.
The human apolipoprotein B (apoB) gene resides in a 47.5 kb DNasel-sensitive chromosomal domain in hepatic and intestinal cells, flanked by the 5' distal matrix association region (MAR) and the 3' proximal MAR. A third MAR, the 5' proximal MAR, is found only in transcriptionally active hepatic (HepG2) cells. Hepatic expression of the apoB gene requires a tissue-specific promoter (-898 to +121) and an enhancer from the second intron of the gene (+360 to +1064). A vector containing this portion of the gene linked to the beta-galactosidase reporter is sufficient for low level expression in the livers of transgenic mice. Expression in transgenic mice was increased when the promoter-enhancer beta-gal vector was flanked by MARs. The results were similar whether the 5' distal, the 5' proximal or the 3' proximal MARs were placed at both ends of the construct, or whether the construct was flanked by the 5' distal and the 3' MAR, suggesting that the apoB MARs play a role in gene expression in vivo. When the MAR-containing constructs were transiently transfected into HepG2 cells, the resulting beta-gal activities were similar to that of the construct lacking MARs, thus demonstrating that the MARs do not exhibit any enhancer activity. Recent experiments (Kalos, M., and R. E. K. Fournier. 1995. Mol. Cell. Biol. 15: 198-207) examining stable integration of some of our constructs into human and rat hepatoma transfectants suggest that in single and double copy transfectants, the apoB MARs behave as boundary "insulators", protecting the integrated transgenes against position effects regardless of their site of integration. However, multicopy transfectants are transcriptionally inactive and when the MARs are absent, expression of the transgenes drops to background levels. Our results to date with single and low-copy number transgenes do not support an insulator function for the apoB MARs, although they appear to be required to increase the levels of expression.
Animals↗
Ultrastructural study on the development of the rat [correction of mouse] spermatocyte nuclear matrix during epididymal maturation.
The rat sperm nucleus, after sequential extraction with detergents, nuclease and ammonium sulfate, consists of a skeletal structure that resembles the original nuclear shape. This chromatin-depleted skeleton is formed by thick and thin fibers as well as globular structures of different sizes. These fibers form anastomosis. The sperm nuclei obtained from testis and caput epididymis exhibits a loose fibrous network with thin fibers at the center. The entire nucleus of the sperm in the caudal epididymis is formed by a dense network of thick and thin fibers. These highly branched matrix fibers had diameters of 35 and 12 nm. It is concluded that the increase in density of the matrix fibers is related to the condensation of the chromatin in the maturation of the spermatozoa.
Animals↗