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PubMed1997

Mathematical model to predict regions of chromatin attachment to the nuclear matrix.

The potentiation and subsequent initiation of transcription are complex biological phenomena. The region of attachment of the chromatin fiber to the nuclear matrix, known as the matrix attachment region or scaffold attachment region (MAR or SAR), are thought to be requisite for the transcriptional regulation of the eukaryotic genome. As expressed sequences should be contained in these regions, it becomes significant to answer the following question: can these regions be identified from the primary sequence data alone and subsequently used as markers for expressed sequences? This paper represents an effort toward achieving this goal and describes a mathematical model for the detection of MARs. The location of matrix associated regions has been linked to a variety of sequence patterns. Consequently, a list of these patterns is compiled and represented as a set of decision rules using an AND-OR formulation. The DNA sequence was then searched for the presence of these patterns and a statistical significance was associated with the frequency of occurrence of the various patterns. Subsequently, a mathematical potential value,MAR-Potential, was assigned to a sequence region as the inverse proportion to the probability that the observed pattern population occurred at random. Such a MAR detection process was applied to the analysis of a variety of known MAR containing sequences. Regions of matrix association predicted by the software essentially correspond to those determined experimentally. The human T-cell receptor and the DNA sequence from the Drosophila bithorax region were also analyzed. This demonstrates the usefulness of the approach described as a means to direct experimental resources.

Base Sequence↗
PubMed1992

A monoclonal antibody recognizing nuclear matrix-associated nuclear bodies.

We have isolated a monoclonal antibody, 5E10, that labels discrete spots in the interphase nucleus. By immunoblotting mAb 5E10 recognized predominantly a 126 kDa polypeptide with an isoelectric point of 5.5. Indirect immunofluorescence showed that mAb 5E10 labeled spots in many cell lines and tissues from rat or human origin, but not in cells from mouse, chicken, African green monkey, or the lower eukaryotes Saccharomyces and Dictyostelium. In the human bladder carcinoma cell line T24 the number of nuclear spots were found to be 21 +/- 10 (n = 132). In many cells spots were found also in the cytoplasm. In a small fraction of T24 cells the mAb revealed thread-like structures in addition to spots. Throughout mitosis the antigen was found to be clustered in the cytoplasm, not associated with metaphase chromosomes. The spherical structures that contain the antigen were tightly bound to the nuclear matrix. Immunogold labeling with mAb 5E10 showed that the antigen is localized in 0.3 microns diameter spherical, electron-dense structures, reminiscent of nuclear bodies. Double-labeling experiments showed that these spots do not colocalize with U1 snRNPs and centromeres. The spots did colocalize with nuclear speckles recognized by a primary biliary cirrhosis autoimmune serum, which is thought to recognize nuclear bodies. On the basis of these observations we conclude that mAb 5E10 recognizes discrete nuclear substructures, most likely nuclear bodies.

Animals↗
PubMed2003

Interaction of EBV latent origin of replication with the nuclear matrix: identification of S/MAR sequences and protein components.

During latency, Epstein Barr virus (EBV) genome, as an episome, is attached to the nuclear matrix (NM) via the latent origin of replication ori P. Within this element, we have found that a region, 580 bp long, encompassing the replicator DS element, shows the strongest affinity for the NM. In addition, by cross-linking with cis-diamminedichloroplatinum, we have identified two NM proteins with an apparent molecular weight of 85 and 60 kDa that, with high affinity and specificity, bind ori P. These proteins are not induced by EBV infection, but their interaction with ori P is lost upon induction of EBV lytic cycle. These data strongly suggest that the binding of ori P to specific components of the NM is required for EBV latent replication.

Binding Sites↗
PubMed1986

[Differences in the DNA nucleotide sequences of the nuclear matrix of the myxomycete Physarum polycephalum in the G2- and S-phases of the cell cycle].

The extent of homology of the nuclear matrix DNA isolated from the macroplasmodium of Physarum polycephalum at G2- and S-phases of the cell cycle was studied using the molecular reassociation method. The results obtained point to the incomplete homology of DNA samples prepared at G2- phases as compared to those obtained at S-phase. Bearing this in mind it seems reasonable to suppose that the DNA template may transfer through the nuclear matrix-attached replicative complex under the replication.

Cell Nucleus↗
PubMed1996

Translocation of diacylglycerol kinase alpha to the nuclear matrix of rat thymocytes and peripheral T-lymphocytes.

The cytosolic alpha-diacylglycerol kinase (DGK) was translocated to and tightly associated with the nuclear matrix when rat thymocytes and peripheral T-lymphocytes were stimulated with concanavalin A or anti-T-cell receptor antibody. This translocation occurred rather slowly and was completed in 3-4 h after cell stimulation. We also detected significant accumulation of nuclear phosphatidic acid interpreted as being formed by the translocated enzyme. The enzyme translocation is not directly linked to phosphoinositide turnover and protein phosphorylation, since phorbol myristate acetate and calcium ionophore did not affect the cellular DGK alpha and since we detected no covalent modification of the enzyme molecule. Although the mechanisms underlying the enzyme translocation remain unknown, our results indicate that DGK alpha participates in nuclear phospholipid metabolism occurring at the intermediate stage of lymphocyte activation.

Animals↗
PubMed1993

Modulation of DNA synthesis by microtubule-associated protein 2 in the nuclear matrix isolated from Physarum polycephalum.

The mechanism of stimulation of DNA synthesis by microtubule-associated protein 2 (MAP2) was examined in the nuclear matrix isolated from Physarum polycephalum. Porcine brain MAP2 stimulated DNA synthesis by the matrix with exogenous templates, but not with endogenous templates. Kinetic analyses showed that MAP2 decreases the Km of the matrix for deoxyribonucleoside triphosphates. Comparison of the Km values of active- and latent-type DNA replication machineries of Physarum suggested a possible role for MAPs or MAP-like proteins in DNA replication.

Animals↗
PubMed1991

Heat-induced stabilization of the nuclear matrix: a morphological and biochemical analysis in murine erythroleukemia cells.

Using mouse erythroleukemia cells we performed a comprehensive morphological and biochemical study of the nuclear matrix obtained after exposure of isolated nuclei to 37 degrees C or from cells heat shocked in vivo at 43 or 45 degrees C. At the ultrastructural level it was possible to see that in the absence of a 37 degrees C incubation of purified nuclei, the final matrix lacked well-defined nucleolar remnants but a peripheral lamina was clearly visible, as well as a sparse fibrogranular network which was located at the periphery of the structures. On the contrary, after a 37 degrees C nuclear incubation, very electron-dense nucleolar remnants were observed along with an abundant meshwork dispersed throughout the interior of the structures. When intact cells were heat shocked in vivo, electron-dense residual nucleoli were present only when isolated nuclei had been exposed to 37 degrees C in vitro, whereas without such an incubation, they were not as easily distinguishable and appeared less electron-dense. In the latter case the inner network was more evenly distributed. After purified nuclei were incubated at 37 degrees C for 45 min, the high salt and DNase I resistant fraction retained about 18% of the nuclear protein whereas if the heating was omitted protein recovery dropped to 6%. An increase in the recovery of intact structures in the matrix fraction was the main reason for the higher protein recovery. Heating nuclei in vitro further increased the amount of nuclear protein present in the matrix fraction even if intact cells had been heat shocked in vivo. No major qualitative differences were seen when the polypeptide pattern of the various types of nuclear matrices was analyzed on one-dimensional polyacrylamide gels and this finding was further supported by Western blot analysis with a monoclonal antibody to lamins A and C. These results show that heating mainly stabilizes the nucleolar remnants of the matrix and to a lesser extent the inner network, but the morphology of the final structures is different depending on whether the stabilization is performed in vivo or in vitro.

Animals↗
PubMed1999

The plant nucleoskeleton: ultrastructural organization and identification of NuMA homologues in the nuclear matrix and mitotic spindle of plant cells.

In the present work we investigate the structural organization of the nucleoskeleton of Allium cepa meristematic root cells. Resinless sections reveal for the first time a residual filamentous network in plant nuclei. This network is composed of branched knobbed filaments with associated globular structures, connected to the lamina and to the dense aggregates of different sizes. Results of immunoblotting show that many components of this network are homologues of intermediate filament-type proteins. NuMA, a coiled-coil protein related to intermediate filaments, found in animal cells, can also be detected in this plant nuclear matrix system. Immunofluorescence reveals a diffuse distribution of the animal NuMA homologues in plant nuclear core filaments in interphase. Resinless immunoelectron microscopy further reveals a distribution along the extended filaments and the dense aggregates. During mitosis, in contrast to the accumulation at the poles in animal cells, NuMA homologues in plant onion cells show a diffuse pattern, which may correspond to the spindle matrix. Our data are the first report of the conservation in plants of NuMA proteins, which may be involved in both nuclear and mitotic spindle organizations.

Animals↗
PubMed2005

Specific radial positions of centromeres of human chromosomes X, 1, and 19 remain unchanged in chromatin-depleted nuclei of primary human fibroblasts: evidence for the organizing role of the nuclear matrix.

Radial positions of centromeres of human chromosomes X, 1, and 19 were determined in the nuclei of primary fibroblasts before and after removal of 60%-80% of chromatin. It has been demonstrated that the specific radial positions of these centromeres (more central for the chromosome 19 centromere and more peripheral for the centromeres of chromosomes 1 and X) remain unchanged in chromatin-depleted nuclei. Additional digestion of nuclear RNA did not influence this specific distribution. These results strongly suggest that the characteristic organization of interphase chromosomes is supported by the proteinous nuclear matrix and is not maintained by simple repulsing of negatively charged chromosomes.

Cell Nucleus↗
PubMed1984

Protein patterns of the nuclear matrix in differently proliferating and malignant cells.

SDS-polyacrylamide gel electrophoresis of the nuclear matrix proteins showed a predominance of high molecular weight and low molecular weight polypeptides in the nuclear matrices of hepatomas and cultured Chinese hamster fibroblasts as compared to quiescent and regenerating rat liver. These features were more prominent in solid hepatoma 27 than in Zajdela ascites hepatoma or in cultured cells. In proliferating cells (tumors, regenerating liver, log phase cell culture) a polypeptide band of 150 kD and lamin B were conspicuous at the expense of lamins A and C.

Animals↗
PubMed1995

A human autoantibody recognizing nuclear matrix-associated nuclear protein localized in dot structures.

A human autoimmune serum is used to characterize a protein which is located within a dot-like structure of the interphase nucleus. The dots are located in the nucleoplasma outside the nucleoli. The dot-like structure could be observed on a variety of human substrates (HEp-2, HepG2, HeLa, Molt-4, WI-38 cell lines, peripheral blood lymphocytes), mouse cell lines and tissues (3T3, L929, spleen sections), rat sections, marsupial PtK2 cells and hamster cell lines. The range of the number of dots and their size differed between cells and cell lines and varied between 1 and 24. The antigen could be identified as a 53 kDa protein with a pI of 8.7 and was named NDP53. Digestion experiments suggested that the protein is not associated with DNA or RNA, but is associated with the nuclear matrix. Immunelectron microscopy using ultra-thin sections revealed filamentous structures with a diameter of 0.1 to 0.6 microns. The antigen colocalizes with Sp100, PML and NDP55, which are part of a multiprotein complex known as PML oncogenic domain (POD), nuclear bodies, Kr bodies or ND10.

Animals↗
PubMed2003

Threonine 308 phosphorylated form of Akt translocates to the nucleus of PC12 cells under nerve growth factor stimulation and associates with the nuclear matrix protein nucleolin.

We have examined the issue of whether or not in PC12 cells it may be observed a nerve growth factor (NGF) nuclear translocation of an active (phosphorylated) Akt. Western blot analysis with antibodies to either total or phosphorylated Akt showed a maximal nuclear translocation after 15 min of NGF stimulation. NGF increased rapidly and transiently the enzymatic activity of immunoprecipitable nuclear Akt and after 45 min the values returned to a level close to the basal one. Enzyme translocation was blocked by the selective phosphoinositide 3-kinase inhibitor, LY294002. Confocal microscopy of samples stained with antibody to Akt showed an evident increase in immunostaining intensity in the nuclear interior after NGF treatment. Treatment of cells with inhibitors of protein phosphatase PP2A, calyculin A, or okadaic acid, maintained the phosphorylation levels of nuclear Akt. Immunoprecipitation experiments revealed an association between Akt and PP2A that was maximal when nuclear Akt activity was decreased. Both total and active Akt associated with the nuclear matrix and, in particular, with the protein nucleolin, with which Akt co-immunoprecipitated. These findings strongly suggest that the intranuclear translocation of active Akt is an important step in the signaling pathways elicited by the neurotrophin NGF and that the intranuclear control of Akt is achieved through the action of PP2A.

Animals↗
PubMed1983

Nuclear ribonucleoprotein release and nucleoside triphosphatase activity are inhibited by antibodies directed against one nuclear matrix glycoprotein.

Circumstantial evidence suggests that nucleocytoplasmic exchange or transport is an active process involving the nuclear pore complex of the nuclear envelope. To test this hypothesis, antibodies were generated against nuclear envelope components from a highly enriched pore complex fraction from Spisula solidissima oocytes. Some of these antibodies inhibited ATP-dependent ribonucleoprotein release from prelabeled, isolated rat nuclei and inhibited nucleoside triphosphatase activity essential in nucleocytoplasmic transport. Inhibition of both functions by lectins indicated that the antigen was a glycoprotein. It was identified as lamin B, a major component of the nuclear envelope and nuclear matrix. This glycoprotein may not only be a structural nuclear protein but also may have nucleoside triphosphatase activity. We speculate that lamin B represents the solid support for ribonucleoprotein transport. This protein is expected to be highly conserved if active transport in and out of the nucleus is essential in the eukaryotic system.

Adenosine Triphosphate↗
PubMed1994

Dependence of enhancer-mediated transcription of the immunoglobulin mu gene on nuclear matrix attachment regions.

Transcription of the immunoglobulin mu heavy chain locus is regulated by an intronic enhancer that is flanked on both sides by nuclear matrix attachment regions (MARs). These MARs have now been shown to be essential for transcription of a rearranged mu gene in transgenic B lymphocytes, but they were not required in stably transfected tissue culture cells. Normal rates of transcriptional initiation at a variable region promoter and the formation of an extended deoxyribonuclease I (DNase I)--sensitive chromatin domain were dependent on MARs, although DNase I hypersensitivity at the enhancer was detected in the absence of MARs. Thus, transcriptional activation of the mu gene during normal lymphoid development requires a synergistic collaboration between the enhancer and flanking MARs.

Animals↗
PubMed1993

Alterations in nuclear matrix ultrastructure of G1 mammalian cells following heat shock: resinless section electron microscopy, biochemical, and immunofluorescence studies.

Heat shock is known to inhibit vital nuclear functions associated with DNA and RNA metabolism. It has been proposed that the reported heat-induced excess protein accumulation in the nuclear matrix (NM) fraction may alter NM sites crucial for DNA and RNA processing. To test this hypothesis, we examined the fine structure of the NM in synchronous populations of G1 Chinese hamster ovary cells before and after heating by using the technique of resinless section electron microscopy. Heat did induce morphological alterations in the NM. The NM of control cells contained a honeycomb-like arrangement of fibers after chromatin removal. Following heat shock, NMs appeared as more highly anastomosing networks of polymorphic fibers and an overall increase in electron density was observed. Residual nucleoli from heated NMs underwent alterations in distributions of electron density both internally and at their peripheries. The increase in electron density observed in heated NMs was accompanied by an increase in protein mass and a relatively smaller increase in RNA mass as indicated by parallel sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS PAGE) and isotopic labeling (protein/DNA and RNA) studies. Some excess protein accumulation could also be directly localized onto NM fibers by use of antibodies to heterogeneous ribonucleoprotein complex antigens. It is concluded that alterations of NM fine structure can reflect the heat-stressed state of the cell, may account for the heat-induced inhibition of nucleic acid metabolism, and may be useful as an indicator of physiological or pathological stress in general.

Animals↗
PubMedDate not supplied

The normal association between newly replicated DNA and the nuclear matrix is abolished in cells infected by herpes simplex virus type 1.

In cells infected by herpes simplex virus type 1 (HSV1), a series of nuclear changes can be observed in a temporal sequence. Such changes are related to important modifications in the higher-order structure of host cell chromatin, such as loss of DNA loop supercoiling and wholesale DNA loop disorganization. It is known that the topological relationship between DNA and the nuclear substructure is a critical factor for proper nuclear physiology. Here we report that the usual association between newly replicated DNA and the nuclear substructure, commonly known as nuclear matrix, is abrogated in cells infected by HSV1, thus establishing a correlation between the virus-induced modifications in chromatin higher-order structure and a major biochemical change within the infected cell nucleus.

Animals↗
PubMed2000

hNMP 200: a novel human common nuclear matrix protein combining structural and regulatory functions.

Previously we have reported about human nuclear matrix proteins (hNMPs) with increased reassembling and potential filament-forming capability [C. Gerner et al., 1999, J. Cell. Biochem. 74, 145-151]. Here, we cloned the cDNA of one of these proteins, hNMP 200, following partial amino acid sequencing of the novel 56-kDa nuclear protein. Sequence alignments show hNMP 200-related proteins in metazoans, plants, and yeast, the homologous Saccharomyces cerevisiae protein prp19 being an accessory, but essential, factor for pre-mRNA processing. Evidence for any enzymatic activity was not detected. However, the hNMP 200 primary sequence contained five consensus WD-repeat sequences, indicative of participation and regulatory function in larger protein assemblies. Northern blot analysis and 2D protein electrophoresis showed ubiquitous expression of hNMP 200 in a variety of cell types. (35)S labeling studies indicated a high metabolic stability of the protein. The hNMP 200 gene was assigned to chromosomal region 11q12.2. Confocal laser scanning microscopy revealed that the intracellular localization conformed with that reported for other structural nuclear proteins. In interphase cells, green fluorescent protein-tagged hNMP 200 was predominantly nucleoplasmic. Structures with speckled appearance extended through several sections of in situ-isolated nuclear matrices. During cell division hNMP 200 became irregularly distributed in prophase, sparing regions of condensing chromatin. In anaphase it was concentrated in the spindle midzone. The putative dual function of the novel NMP is discussed. Being a component of the nuclear framework, it may provide structural support for components of the RNA-processing machinery, thereby also modulating splicing activities.

Amino Acid Sequence↗
PubMedDate not supplied

[Electrophoretic pattern of the nuclear matrix proteins from rat hepatoma-27, and the effect of various proteinase inhibitors].

Nuclear matrix preparations of rat hepatoma 27 differed from those of rat liver tissue in predominance of polypeptides with molecular weights of about 220, 160, 100, 45 and 31 kilodaltons. An inhibitor of serine proteinases phenylmethylsulfonyl fluoride did not alter practically the yield or protein pattern of rat liver or hepatoma 27 nuclear matrices. At the same time, thiol reagents mersalyl and 5,5-dithio-bis(2-nitro-benzoic acid) increased 2-3-fold the yield of both rat liver and hepatoma 27 nuclear matrices elevating mainly the content of polypeptides of 34-45 kilodaltons molecular weights.

Animals↗