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PubMed2001

Comparative study and prediction of DNA fragments associated with various elements of the nuclear matrix.

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.

Animals↗
PubMed1991

Nuclear matrix localization and specific matrix DNA binding by receptor binding factor 1 of the avian oviduct progesterone receptor.

A chromatin acceptor protein for the avian oviduct progesterone receptor (PR), termed receptor binding factor 1 (RBF-1), has recently been shown to (1) be a component of the nuclear binding sites (acceptor sites) for PR and (2) generate high-affinity binding sites (termed the RBF-1 class of sites) on avian genomic DNA [Schuchard et al. (1991) Biochemistry 30, 4535-4542]. A second class of sites and its associated protein (termed RBF-2) were also identified. This paper demonstrates that RBF-1 and also the PR nuclear binding sites are localized in the oviduct nuclear matrix. RBF-1 is found in abundance in the nuclear matrix of liver but only in traces in the nuclear matrix of spleen. Extraction of the nuclear matrix with 4.0 M Gdn-HCl results in the complete removal of RBF-1 as occurs with whole chromatin. Interestingly, a second class of specific PR binding, termed RBF-2, remains on the nuclear matrix after the removal of all RBF-1. Southern blot analysis indicates that the nuclear matrix DNA contains sequences homologous with the 5'-flanking domains of the rapidly steroid regulated c-myc and c-jun protooncogenes and the beta-actin gene, but not genomic sequences of the late sex steroid regulated gene, ovalbumin, or the alpha-actin gene. A specific, small region in the 5'-flanking domain of the c-myc gene appears to be associated with the nuclear matrix. Southwestern blot analysis using partially purified RBF-1 shows a marked affinity and specificity of the RBF-1 for the nuclear matrix DNA.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1998

Characteristic immunolocalization of Ku protein as nuclear matrix.

Two hybridoma clones, NMB1 and NML90, were established using nuclear matrix proteins from normal human thymi or malignant lymphoma as immunogens. They reacted with human Ku70 and Ku80, respectively, by immunoblotting. When HeLa cell nuclear proteins were fractionated and applied to immunoblotting, both Ku70 and Ku80 were detected in the nuclear matrix as well as the soluble nuclear protein fractions. By confocal scanning microscopy, the immunoreactivity of Ku70 and Ku80 was localized to distinct nucleoplasmic fibrillar network and fine granules in the interphase cell nuclei. When HeLa cells were fractionated in situ using DNase I and buffers containing 0.25 M (NH4)2SO4 and 2 M NaCl, the nucleoplasmic reticular structure was largely preserved, but granules disappeared. The nucleoplasmic distribution of Ku in the tissue and in cultured cells was distinct from each other. In the adult tissue, it consisted mostly of either distinct curvilinear lines along the nuclear periphery or of tangled, beaded lines throughout the nuclei. When xenotransplants of HeLa cell in Scid mice were examined, the "tissue type" immunolocalization pattern was reproduced consistently. In most fetal tissues, "tissue type" and "cell type" patterns were admixed. Monoclonal antibodies described here are useful tools for studying the structure and function of the nuclear matrix.

Animals↗
PubMed1992

Crosslinking of nuclear proteins to DNA by cis-diamminedichloroplatinum in intact cells. Involvement of nuclear matrix proteins.

In order to detect the nuclear matrix proteins involved in DNA binding, avoiding possible artifacts derived from the disruption of nuclei, proteins were crosslinked to DNA by the action of cis-diamminedichloroplatinum on intact chicken liver cells and analyzed by two-dimensional gel electrophoresis. At least eleven species of crosslinked proteins were found to derive from the nuclear matrix prepared from the same cell type, and five of these were found also among the proteins crosslinked to DNA in intact liver cells from ox and pig. This subset of common proteins, conserved in different animal species, is likely to have a fundamental role for the anchorage of DNA to the nuclear matrix.

Animals↗
PubMed1994

MspI8, the repetitive sequence specifically interacting with nuclear matrix of rat testis cells.

The nuclear matrix bound DNA fraction of rat testis showed enrichment in repetitive sequences found in the 450 bp band after gel electrophoresis of the MspI digested rat DNA. DNA fragments isolated from this band were cloned. DNA of the clone pMspI8 showed homology to some representatives of rat LINE sequence family, and complexed in vitro more efficiently with testes nuclear matrix proteins than with yeast ARS1 sequence containing the matrix association region (MAR) or DNA from an other clone, MspI19. Western blot analysis showed that MspI8 sequence interacts with testes matrix protein of about 120 kDa.

Animals↗
PubMed2006

Activation of phosphoinositide 3-kinase C2 beta in the nuclear matrix during compensatory liver growth.

In the nuclear matrix harvested 20 h after partial hepatectomy, an increase in immunoprecipitable PI3K-C2beta activity is observed, which is sensitive to wortmannin (10 Mm) and shows strong preference for PtdIns over PtdIns(4)P as a substrate. On western blots PI3K-C2beta revealed a single immunoreactive band of 180 kD, whereas 20 h after partial hepatectomy gel shift of 18kDa was noticed in the nuclear matrix, suggesting that observed activation of enzyme is achieved by proteolysis. As it is know that PI3K-C2alpha is associated with nuclear speckles [Didichenko SA, Thelen M. Phosphatidylinositol 3-kinase C2alpha contains a nuclear localization sequence and associates with nuclear speckles. J Biol Chem 2001;276:48135-42.], the data presented in this report show that in the nuclear matrix PI3K-C2beta is activated during the compensatory liver growth, which clearly demonstrates that different class II PI3K enzymes have different subnuclear localization and therefore might have different intranuclear functions.

Animals↗
PubMedDate not supplied

Nuclear matrix composition and in vitro cellular senescence.

The synthesis of nuclear matrix components from human diploid fibroblasts of different in vitro ages was analyzed. Radiolabeled nuclear matrices were prepared from human diploid fibroblasts at various stages of the cell cycle, and their components were separated by two dimensional electrophoresis. The same general electrophoretic pattern was observed at all cell cycle points analyzed, regardless of in vitro age. However, several of the more than 150 peptides that were observed exhibited some cell cycle or age-related variation in radiolabeling. Ten of these were chosen for further analysis. One peptide, with an approximate molecular weight of 47 kDa and pI of 6.8 exhibited the most significant cell cycle and age-related alterations. In matrices from younger cells, incorporation into this peptide was very low in GO but increased as these cells moved through the cell cycle, with maximum incorporation occurring in S phase. As cells neared the end of their in vitro lifespan, labeling of this peptide was elevated at all stages of the cell cycle. Since many of the functional alterations observed in senescent human diploid fibroblasts are nuclear-matrix-associated activities, these results suggest that the inappropriate expression of nuclear matrix components contribute to the functional changes which characterize in vitro senescence.

Antigens, Nuclear↗
PubMed1996

Nuclear matrix interactions within the sperm genome.

Analysis of the haploid-expressed human PRM1 --> PRM2 --> TNP2 genic domain has revealed two regions of attachment to the sperm nuclear matrix. These sperm nuclear matrix attachment regions delimit the DNase I-sensitive domain of this haploid-expressed locus. The domain is intermediately associated with but not attached to the nuclear matrix. DNase I-sensitive genes within the mature sperm nucleus, such as protamine 1, protamine 2, transition protein 2, alpha-globin, and beta-actin, display this intermediate affinity for the sperm nuclear matrix. This may denote their role in templating the male genome prior to fertilization, thus ensuring the formation of a viable male pronucleus during early embryonic development.

Base Sequence↗
PubMed1998

Alteration of nuclear matrix protein composition during apoptosis in rat embryo cells.

Alteration of the nuclear matrix protein composition during active cell death was investigated by high resolution 2-dimensional gel electrophoresis and computer-assisted image analysis. Nuclear matrices were isolated from purified nuclei of a rat embryo cell line showing an immediate apoptotic response to serum reduction. While cell shrinkage and cytoplasmic compaction, characteristic features of apoptosis, were induced, the nuclear matrix protein pattern was not altered 1 h after induction of apoptosis. However, two sets of novel nuclear matrix protein spots appeared with differing kinetics within the following 5 h of apoptosis. They consisted of five and six protein spots, respectively. In addition, the intensity of five nuclear matrix protein spots that had already been present in the uninduced cells increased continuously within an observation period of 12 h. These coincidences point to a potential involvement of the described nuclear matrix proteins in the apoptotic process.

Animals↗
PubMed2001

Altered profiles in nuclear matrix proteins associated with DNA in situ during progression of breast cancer cells.

Nuclear matrix proteins (NMPs) show promise as informative biomarkers in following the pathogenesis of breast cancer. The nuclear matrix is a dynamic RNA-protein network involved in the organization and expression of chromatin. Cisplatin, which preferentially cross-links nuclear matrix proteins to DNA in situ, may be used to identify NMPs that organize and/or regulate the processing of DNA. In this study, we analyzed the nuclear matrix proteins from an estrogen receptor-positive breast cancer cell line panel consisting of MCF-7, MIII, LCC1, and LCC2 cell lines. This cell line panel reflects the stages of malignant progression in breast cancer. Proteins isolated from nuclear matrices and proteins cross-linked to nuclear DNA in situ with cisplatin were analyzed by two-dimensional gel electrophoresis. Specific changes in nuclear matrix proteins bound to nuclear DNA were identified. In concordance with estrogen independence and antiestrogen insensitivity, a loss in cisplatin cross-linking of specific NMPs to nuclear DNA was observed. Our results suggest that progression of breast cancer is accompanied by a reorganization of chromosomal domains, which may lead to alterations in gene expression.

Antigens, Nuclear↗
PubMed2000

Differential nuclear localization and nuclear matrix association of the splicing factors PSF and PTB.

A monoclonal antibody raised against nuclear matrix proteins detected a protein of basic pI in human nuclear matrix protein samples of various cellular origin. The ubiquitously occurring (common) nuclear matrix protein was identified as splicing factor PSF (PTB associated splicing factor). The interaction between the splicing factors PSF and PTB/hnRNP I was confirmed by co-immunoprecipitation from nuclear salt extracts. However, the nuclear localization of PSF and PTB and their distribution in subnuclear fractions differed markedly. Isolated nuclear matrices contained the bulk of PSF, but only minor amounts of PTB. In confocal microscopy both proteins appeared in speckles, the majority of which did not co-localize. Removing a large fraction of the soluble PTB structures by salt extraction revealed some colocalization of the more stable PTB fraction with PSF. These PTB/PSF complexes as well as the observed PSF-PTB interaction may reflect the previously reported presence of PTB and PSF in spliceosomal complexes during RNA processing. The present data, however, point to different cellular distribution and nuclear matrix association of the majority of PSF and PTB.

Antibodies, Monoclonal↗
PubMed1999

Spatial distribution of lamin A and B1 in the K562 cell nuclear matrix stabilized with metal ions.

When the nucleus is stripped of most DNA, RNA, and soluble proteins, a structure remains that has been referred to as the nuclear matrix, which acts as a framework to determine the higher order of chromatin organization. However, there is always uncertainty as to whether or not the nuclear matrix, isolated in vitro, could really represent a skeleton of the nucleus in vivo. In fact, the only nuclear framework of which the existence is universally accepted is the nuclear lamina, a continuous thin layer that underlies the inner nuclear membrane and is mainly composed of three related proteins: lamins A, B, and C. Nevertheless, a number of recent investigations performed on different cell types have suggested that nuclear lamins are also present within the nucleoplasm and could be important constituents of the nuclear matrix. In most cell types investigated, the nuclear matrix does not spontaneously resist the extraction steps, but must rather be stabilized before the application of extracting agents. In this investigation, by immunochemical and morphological analysis, we studied the effect of stabilization with different divalent cations (Zn(2+), Cu(2+), Cd(2+)) on the distribution of lamin A and B1 in the nuclear matrix obtained from K562 human erythroleukemia cells. In intact cells, antibodies to both lamin A and B1 mainly stained the nuclear periphery, although some immunoreactivity was detected in the nuclear interior. The fluorescent lamin A pattern detected in Cu(2+)- and Cd(2+)-stabilized nuclei was markedly modified, whereas Zn(2+)-incubated nuclei showed an unaltered pattern of lamin A distribution. By contrast, the distribution of lamin B1 in isolated nuclei was not modified by the stabilizing cations. When chromatin was removed by nuclease digestion and extraction with solutions of high ionic strength, a previously masked immunoreactivity for lamin A, but not for lamin B1, became evident in the internal part of the residual structures representing the nuclear matrix. Our results indicate that when metal ions are used as stabilizing agents for the recovery of the nuclear matrix, the distribution of both lamin A and lamin B1 in the final structures, corresponds to the pattern we have very recently reported using different extraction procedures. This observation strengthen the concept that intranuclear lamins may act as structural components of the nuclear matrix.

Cadmium↗
PubMed2001

Changes in the ultrastructure of cytoskeleton and nuclear matrix during HaCaT keratinocyte differentiation.

The cellular scaffold that comprises nuclear matrix and cytoskeleton provides mechanical support for the cell and plays a crucial role in motility, cellular signaling, regulation of gene transcription and DNA replication. In this study we examined the structure of cytoskeleton and nuclear matrix in the keratinocyte cell line HaCaT using a recently developed technique, embedment-free electron microscopy. With this method the three-dimensional structure of cellular scaffold is visualized in the cells extracted from soluble proteins and the chromatin. In actively proliferating cells the cytoskeleton appeared to consist of a continuous meshwork of 10--15 nm filaments with a smaller amount of thin (5 nm) and ultrathin (1--2 nm) filaments. In contrast to what could be expected from earlier immunofluorescence and electron microscopy studies, the cytoskeleton in HaCaT keratinocytes did not consist of superposed autonomous networks of different filaments but was a highly integrated, continuous structure filling whole cytoplasmic territory. Moreover, cytoskeletons of adjacent cells were in a direct physical contact. Nuclear matrix consisted of globular ribonucleoprotein aggregates attached to the meshwork of 20--40 nm filaments. Nuclear envelope was firmly fastened to the cytoskeleton. In keratinocytes induced to differentiation by calcium switch both the cytoskeleton and nuclear matrix were drastically rearranged and comprised a monomorphic, dense and regular meshwork of 10--15 nm filaments. Our data underscore the fact that in HaCaT keratinocyte monolayer in vitro, and probably also in the epidermis in vivo, the nuclear matrices and the cytoskeletons of adjacent cells seemed to form a continuous, highly ordered structure which is rapidly rearranged during cell differentiation. This feature may be crucial for the understanding of how the signal initiated by, e.g. mechanical forces generated through the cell--cell and cell--matrix interaction is transmitted to the nucleus producing ultimately changes in the pattern of gene expression.

Calcium↗
PubMedDate not supplied

Electron microscopic analysis of the relationship between nuclear matrix stability and cell differentiation.

Two cell lines, the less differentiated CC2/CUHK2 and the more differentiated CC3/CUHKE3, were used to study the difference in nuclear matrix stability against DNase 1 digestion. The nuclear matrix was almost totally extracted when the CC3/CUHK3 cells were digested with 100 micrograms/ml DNase 1, while that of the CC2/CUHK2 cells was still present even when 200 micrograms/ml DNase 1 was used. It is suggested that more differentiated cells have a less stable nuclear matrix while the less differentiated ones have a more stable nuclear matrix. The same phenomenon was also observed in normal human and rat cervical epithelia. The nuclear matrix of the poorly differentiated basal cells was more stable than that of the more differentiated superficial cells. This cell differentiation stage dependent stability of the nuclear matrix is probably related to the nuclear activity and gene expression.

Animals↗
PubMed1991

Expression of nuclear matrix proteins in rat liver tissue.

We have studied the synthesis of nuclear matrix proteins as it occurs in the rat liver. To investigate their kinetics in tissue, nuclear matrix proteins were prepared from liver of rats injected with radioactive methionine. Synthesis of lamins was not observed in quiescent hepatocytes although they were the principal proteins of this subcellular fraction, suggesting that lamins are very stable in the liver. When hepatocytes were stimulated to divide by partial hepatectomy, only synthesis of lamin B was initiated. Many proteins not visible on Coomassie blue-stained gels were detectable by autoradiography. In the nuclear matrix extracts of quiescent hepatocytes, one of the most prominently labeled ones was a protein of 70 kDa. After hepatectomy, an additional protein of 62 kDa was detectable. These proteins were visible 1 h after the injection of radioactivity, but were no longer observed in nuclear matrices prepared 24 h after injection. These experiments indicate that in addition to lamins, two nuclear matrix proteins are present in the rat liver that were not detected previously, perhaps because of their rapid turnover.

Animals↗
PubMed1980

The isolation and characterisation of the nuclear matrix from sea urchin embryos.

The minimal residual nuclear structure, which is referred to as the nuclear matrix, was isolated from whole sea urchin embryos of the species Paracentrotus lividus. Electron microscopy of the blastula and pluteus nuclear matrices revealed structures which preserved the spherical shape of intact nuclei. When compared with the pluteus nuclear matrix, the blastula matrix was found to retain significantly more nuclear material. Evidence is presented for a stage-specific composition of the nuclear matrices of sea urchin embryos along with preliminary results pointing to an involvement of some of the nuclear matrix proteins in the formation of the chromatin complex.

Animals↗
PubMed1998

Comparison of nuclear matrix protein composition in colon cancer and dysplasia.

BACKGROUND: Abnormal nuclear morphology associated with cancer may reflect changes in the proteins of the nuclear matrix. METHODS: Nuclear matrix (NM) proteins were isolated from colonic tissue and analyzed by two-dimensional gel electrophoresis. RESULTS: Several matrix proteins that were found in ulcerative colitis (UC) dysplasia (n = 5) and/or UC cancer (n = 4) were not identified in normal colonic tissue. UC dysplasia tissue showed three specific NM proteins with molecular masses of 49.2 kDa, 20.0 kDa, and 19.0 kDa, whereas 29.0-kDa and 32.0-kDa proteins were specific to UC cancer. Three proteins with 59.5-kDa (pI 6.3 and 6.6) and 33.75-kDa (pI 7.5) masses were common to both dysplasia and cancer tissue. CONCLUSIONS: These data suggest that NM proteins may have a role in the transition of tissue towards the malignant phenotype.

Antigens, Nuclear↗
PubMed1998

Peripheral nuclear matrix actin forms perinuclear shells.

Perinuclear actin shells have been reported in a variety of organisms. The shells have been identified by staining perinuclear material with fluorescently-labelled phalloidin, but have not been localized to a specific subcellular compartment at the ultrastructural level. We show here that the shells of 3T3 cells lie in the peripheral nuclear matrix. Nuclear shells and matrix actin in other parts of the nucleus are not usually detected by immunohistochemical staining because they are inaccessible to antibodies or to phalloidin. Immunohistochemical detection of nuclear actin is only possible during its deposition at the end of mitosis, or in interphase nuclei that have been extracted with detergent, digested with nucleases and washed with high salt buffers.

3T3 Cells↗