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Synthesis of 2',5'-oligoadenylate by rat liver nuclear matrix protein.

Nuclear matrix was prepared from unstimulated rat liver by treatment of nuclei with DNAse and 0.4 M NaCl and was further extracted with 2.0 M NaCl. Proteins were bound to poly(rI):(rC)-agarose, incubated with (alpha-32P) adenosine 5'-triphosphate and 2',5'-linked oligoadenylate was isolated from the supernatant. The substance inhibited amino acid incorporation in a reticulocyte translation system and was identified after enzymatic treatment followed by thin-layer chromatography on PEI-cellulose. The possible function of 2',5'-oligo(A) synthetase in the maturation of pre-mRNA associated with nuclear matrix is discussed.

Adenine Nucleotides↗

[Binding of triiodothyronine to the nuclear matrix of the rat liver. The effect of thyroid hormones on the phosphorylation of nuclear matrix proteins].

The interaction of thyroid hormones with rat liver nuclear matrix proteins was studied. It was shown that the nuclear matrix contains the sites which bind triiodothyronine with a high affinity (Ka = 1.07 X 10(9) M-1) and limited capacity (maximal binding capacity--28.5 fmol triiodothyronine/100 micrograms protein). Electrophoretic analysis of triiodothyronine-binding matrix proteins revealed that the molecular mass of the major triiodothyronine-binding fraction is 50 000-52 000 Da. Injections of triiodothyronine to thyroidectomized animals stimulated the phosphorylation of all protein fractions of the nuclear matrix.

Animals↗

Osteocalcin gene promoter-binding factors are tissue-specific nuclear matrix components.

The nuclear matrix appears to play an important role in developmental gene expression during osteoblast differentiation. To better understand this role, we examined nuclear matrix DNA-binding proteins that are sequence-specific and interact with the osteocalcin gene promoter. Multiple protein-DNA interactions involving two distinct nuclear matrix proteins occur within the 5' regulatory sequences (nt -640 to -430). One of these proteins, NMP-1, is a ubiquitous, cell growth-regulated protein that is related to the transcription factor ATF and resides in both the nuclear matrix and the nonmatrix nuclear compartment. The other protein, NMP-2, is a cell type-specific, 38-kDa promoter factor that recognizes binding sites resembling the consensus site for the CCAAT/enhancer-binding protein C/EBP and is localized exclusively on the nuclear matrix. NMP-1 and NMP-2 each interact with two nuclear matrix protein-binding elements. These elements are present near key regulatory sites of the osteocalcin gene promoter, such as the principal steroid hormone (vitamin D)-responsive sequences. Binding in this region of the osteocalcin gene promoter suggests transient associations with the nuclear matrix that are distinct from the stable interactions of matrix attachment regions. Our results are consistent with involvement of the nuclear matrix in concentrating and/or localizing transcription factors that mediate the basal and steroid hormone responsiveness of osteocalcin gene transcription.

Animals↗

Actin, myosin, cytokeratins and spectrin are components of the guinea pig sperm nuclear matrix.

The nuclear matrix (NM) of somatic cells is an internal nuclear framework structure, with a structural function and participation in DNA replication and transcription. The NM has been described in mouse, hamster and human spermatozoa. In this study, an NM structural component of the guinea pig sperm nucleus was obtained by removing nuclear proteins and DNA from DTT-CTAB nuclei. Removal was achieved with high ionic strength salt and microccocal nuclease treatments including a heparin treatment to cause a slight swelling of the nucleus and facilitate material extraction. Actin, myosin, cytokeratins and spectrin were detected associated to NM by indirect immunofluorescence, immunogold staining and Western blotting analysis using specific antibodies. The presence of NM in guinea pig sperm nucleus is shown for the first time and some of its components are identified. This is also the first report on cytokeratins and myosin presence in guinea pig sperm. A retarding effect of nuclear decondensation caused by heparin is induced after phalloidin and/or diacetyl-monoxime (a myosin ATPase activity inhibitor) treatment, suggesting a role for F-actin and myosin in the maintenance of nuclear stability in sperm. The actin role was supported by the decondensing effect that citochalasin D and gelsolin had on sperm nuclei.

Actins↗

Granules 25-30 nm in diameter: basic constituent of the nuclear matrix, chromosome scaffold, and nuclear envelope.

Rat liver nuclear matrix and similar structures derived from isolated Chironomus polytene chromosomes, nuclear envelopes, and intranuclear bodies of frog late oocytes (the karyospheres) were studied by electron microscopy with platinum shadowing and negative staining. We have shown that the treatment of whole nuclei, nuclear envelopes, polytene chromosomes, or karyospheres with nonionic detergent, high salt, and RNase and DNase followed by dilute alkali or hyaluronidase digestion reveals numerous rather uniform granules 25-30 nm in diameter. With omission of the nucleases the granules appear to be associated with DNA strands mostly organized in loops. Many granules form clusters and are arranged in linear or arch-like aggregates or cycles resembling the pore complexes. We suppose that these spherical bodies constitute a basic component of the nuclear matrix, chromosome scaffold, and nuclear envelope and are bound together by hyaluronic acid or some similar glycosaminoglycan.

Animals↗

Human cervical cancer-associated nuclear matrix proteins.

The nuclear matrix is the nonchromatin protein structural component of the nucleus that governs nuclear shape and also exerts regulatory control over higher order gene organization. Recent studies have documented the presence of tumor-associated nuclear matrix proteins in several human cancers. We used high-resolution two-dimensional gel electrophoresis to compare nuclear matrix protein patterns in cervical carcinomas with those from normal cervical tissue. Tumors obtained from 20 patients undergoing hysterectomy for clinically localized cervical cancer were compared with normal cervical tissue. We have identified five polypeptides (CvC-1: Mr = 69,408 Da, pI = 5. 78; CvC-2: Mr = 53,752 Da, pI = 5.54; CvC-3: Mr = 47,887 Da, pI = 5. 60; CvC-4: Mr = 46,006 Da, pI = 5.07; and CvC-5: Mr = 44,864 Da, pI = 6.61) in the nuclear matrix from cervical carcinomas that were present in 20 of 20 cervical tumors but 0 of 10 normal tissues. These data extend similar findings of cancer-associated nuclear matrix proteins in other human cancers and suggest that nuclear matrix proteins may represent a new class of cancer markers that could aid the diagnosis or management of some types of cancer.

Antigens, Nuclear↗

Recent advances in nuclear matrix function.

The nuclear matrix in eukaryotes is a non-histone proteinaceous nucleoskeleton structure having attachment sites for DNA loops during DNA replication. The nuclear matrix has been implicated in transcription, regulation of gene expression, primary transcription processing and provides a mooring for certain hormone receptors. Moreover, the nuclear matrix protein has linkages to intermediate filaments of the cytoskeleton. This review presents recent advances concerning the involvement of the nuclear matrix in DNA replication, relaxation of the superhelical strain in DNA, processing of hnRNA and snRNP, and RNA transport.

Animals↗

Small nuclear RNA-protein complex anchors on the actin filaments in bovine lymphocyte nuclear matrix.

When the nuclear matrix from bovine lymphocytes was digested by RNase-depleted trypsin, the bulk of the matrix proteins, except actin, were hydrolyzed. The digestion left rapidly sedimented spherical structures (trypsin-treated nuclear matrix), which mainly were composed of actin (Nakayasu, H. and K. Ueda. Exp. Cell Res. 143, 55-62, 1983). Almost all the small nuclear RNAs of the original nuclear matrix remained associated with these actin spheres after trypsin digestion. By sonication, the small nuclear RNPs (snRNPs) in both untreated and trypsin-treated nuclear matrices were solubilized in association with proteinous filaments of various size. The sedimentation pattern of these snRNP complexes was not changed by the digestion of the bulk of the proteins. The snRNP complex was adsorbed on rabbit muscle myosin-Sepharose then eluted by the addition of 5 mM ATP. We concluded that snRNPs are associated with actin filaments in the nuclear matrix of bovine lymphocytes.

Actins↗

Association of actin with the nuclear matrix from bovine lymphocytes.

Nuclear matrix prepared from bovine lymphocytes contained a significant amount of actin. Both nuclear matrix actin and rabbit muscle actin showed the same electrophoretic mobility on SDS-gel. The matrix-associated actin could be separated into three isoproteins which may correspond to alpha-, beta- and gamma-actin. The most acidic spot of these isoproteins co-migrated with rabbit muscle actin (alpha-actin) on two-dimensional electrophoresis. The amino-acid composition of the nuclear matrix actin was closely related to that of rabbit muscle and to that of porcine brain actin. Moreover, the actin filaments, treated with 0.75 M guanidine hydrochloride, changed from the polymerized form of the nuclear matrix actin into a monomeric form (G-actin), which had strong inhibitor activity against pancreatic DNase I. From this inhibition, the actin content of the nuclear matrix was estimated to be about 12% of total matrix protein. When the nuclear matrix was digested with trypsin, the bulk of matrix protein was hydrolyzed, but about 80% of the actin remained associated with sphere structures (trypsin-treated nuclear matrix) precipitable by low speed centrifugation. SDS-gel analysis revealed that actin was one of the major components of the trypsin-treated nuclear matrix, which had a similar size and structure as the untreated nuclear matrix. The fibrogranular structure and residual nucleoli of the original nuclear matrix were well preserved against trypsin digestion; however, the peripheral lamina was removed. These results indicate that the matrix-associated actin is localized predominantly in the matrix interior, where it presumably interacts closely with the fibrogranular structure and/or the residual nucleoli.

Actins↗

NMPdb: Database of Nuclear Matrix Proteins.

The nuclear matrix (NM) is a structure resulting from the aggregation of proteins and RNA in the nucleus of eukaryotic cells; it is the 'sticky bit' that remains after aggressive DNAse digestion and salt extraction protocols. Owing to the important role of the NM in DNA replication, DNA transcription and RNA splicing, the expression pattern of NM proteins has become an important early indicator for numerous cancers/tumors. Recent descriptions of the NM structure distinguish between a network-like 'internal nuclear matrix' (INM) and a 'nuclear shell' that connects the INM to the inner and outer nuclear membranes. A cautious NM preparation protocol reveals a coat of proteins on top of the INM; these proteins are usually referred to as the 'nuclear matrix-associated proteins'. Here, we describe a new database (NMPdb at http://www.rostlab.org/db/NMPdb/) that currently contains details of 398 NM proteins. We collected these data through a semi-automated analysis of over 3000 scientific articles in PubMed. We could match these 398 proteins to 302 protein sequences in UniProt or GenBank. Our NMPdb repository annotates these links along with the following annotations: organism, cell type, PubMed identifier, sequence-based predictions of structural and functional features and for some entries the explicit sequence segment that is responsible for localization (nuclear matrix targeting signal).

Amino Acid Sequence↗

Experimental observations of a nuclear matrix.

Nuclei are intricately structured, and nuclear metabolism has an elaborate spatial organization. The architecture of the nucleus includes two overlapping and nucleic-acid-containing structures - chromatin and a nuclear matrix. The nuclear matrix is observed by microscopy in live, fixed and extracted cells. Its ultrastructure and composition show it to be, in large part, the ribonucleoprotein (RNP) network first seen in unfractionated cells more than 30 years ago. At that time, the discovery of this RNP structure explained surprising observations that RNA, packaged in proteins, is attached to an intranuclear, non-chromatin structure. Periodic and specific attachments of chromatin fibers to the nuclear matrix create the chromatin loop domains that can be directly observed by microscopy or inferred from biochemical experiments. The ultrastructure of the nuclear matrix is well characterized and consists of a nuclear lamina and an internal nuclear network of subassemblies linked together by highly structured fibers. These complex fibers are built on an underlying scaffolding of branched 10-nm filaments that connect to the nuclear lamina. The structural proteins of the nuclear lamina have been well characterized, but the structural biochemistry of the internal nuclear matrix has received less attention. Many internal matrix proteins have been identified, but far less is known about how these proteins assemble to make the fibers, filaments and other assemblies of the internal nuclear matrix. Correcting this imbalance will require the combined application of biochemistry and electron microscopy. The central problem in trying to define nuclear matrix structure is to identify the proteins that assemble into the 10-nm filaments upon which the interior architecture of the nucleus is constructed. Only by achieving a biochemical characterization of the nuclear matrix will we advance beyond simple microscopic observations of structure to a better understanding of nuclear matrix function, regulation and post-mitotic assembly.

Animals↗

The nuclear matrix as a site of anticancer drug action.

Many nuclear functions, including the organization of the chromatin within the nucleus, depend upon the presence of a nuclear matrix. Nuclear matrix proteins are involved in the formation of chromatin loops, control of DNA supercoiling, and regulation and coordination of transcriptional and replicational activities within individual loops. Various structural and functional components of the nuclear matrix represent potential targets for anticancer agents. Alkylating agents and ionizing radiation interact preferentially with nuclear matrix proteins and matrix-associated DNA. Other chemotherapeutic agents, such as fludarabine phosphate and topoisomerase II-active drugs, interact specifically with matrix-associated enzymes, such as DNA primase and the DNA topoisomerase II alpha isozyme. The interactions of these agents at the level of the nuclear matrix may compromise multiple nuclear functions and be relevant to their antitumor activities.

Animals↗

Immunologically-related nucleic acid-binding proteins associated with the nuclear matrix of Physarum polycephalum.

The nuclear matrix of Physarum polycephalum is composed of two abundant polypeptides of 27 and 38 kDa as well as numerous minor polypeptides of various molecular weight. By contrast, the nuclear matrix of vertebrates consists of three major (the lamins) and many minor polypeptides mainly in the 60-70 kDa molecular weight range. In order to better characterize the major nuclear matrix proteins of P. polycephalum and, perhaps, define their relationship with the major nuclear matrix proteins of vertebrates, we have purified the abundant nuclear matrix proteins of P. polycephalum. In Western blot analyses, polyclonal antibodies raised against the purified 27 kDa polypeptide recognised polypeptides of 50 kDa, 45 kDa and several low molecular weight species (14-21 kDa) in the P. polycephalum nuclear matrix. The polyclonal antibodies did not react with the other abundant nuclear matrix protein of 38 kDa from P. polycephalum nor with polypeptides of the mouse nuclear matrix. Two-dimensional gel electrophoresis showed that the major nuclear matrix proteins of P. polycephalum were more basic than the major nuclear matrix proteins of vertebrates, the lamins. Moreover, both the 27 and 38 kDa polypeptides are post-translationally modified by either D-mannosyl or D-glycosyl moieties, and not by phosphorylation as has been demonstrated for the vertebrate lamins. DNA-binding assays further revealed that the immunologically related polypeptides of 50 kDa, 45 kDa, 27 kDa and low molecular weight species of 14-21 kDa preferentially bound single-stranded DNA, but the 38 kDa polypeptide of Physarum matrix did not. Based on these findings, we conclude that the abundant nuclear matrix protein of 27 kDa belongs to a group of immunologically-related nucleic acid-binding proteins, and is immunologically and functionally distinct from the other major nuclear matrix protein of 38 kDa from P. polycephalum and the vertebrate lamins.

Autoradiography↗

Developmental changes in transcription factors associated with the nuclear matrix of chicken erythrocytes.

The nuclear matrix has roles in organizing nuclear DNA and in controlling transcription. Transcription factors are associated with the nuclear matrix, with the spectra of transcription factors differing from one cell type to another. In this study we identified the transcription factors and enzymes functioning in the regulation of gene expression that were associated with nuclear matrix and nonmatrix nuclear fractions in erythrocytes isolated from chick embryos at different stages of development, anemic and normal adult birds. We found that the primitive erythroid nuclear matrix had the greatest histone deacetylase activity and highest levels of several transcription factors, including GATA-1, CACCC-binding proteins, and NF1. These transcription factors have key roles in erythroid-specific gene expression. The levels of these transcription factors were lower in the nonmatrix and matrix fractions isolated from definitive erythrocytes. For primitive and definitive erythrocytes, the level of CACCC-binding proteins in the nuclear matrix fraction was greater than that of Sp1. The relative levels of these transcription factors were reversed in the nonmatrix fraction. Casein kinase II was not found in erythroid nuclear matrices. The observed erythroid lineage specific alterations in erythroid nuclear matrix transcription factor composition and abundance may be involved in erythroid-specific gene expression.

Animals↗

Isolation and characterization of a proteinaceous subnuclear fraction composed of nuclear matrix, peripheral lamina, and nuclear pore complexes from embryos of Drosophila melanogaster.

Morphologically intact nuclei have been prepared from embryos of Drosophila melanogaster by a simple and rapid procedure. These nuclei have been further treated with high concentrations of DNase I and RNase A followed by sequential extraction with 2% Triton X-100 and 1 M NaCl to produce a structurally and biochemically distinct preparation designated Drosophila subnuclear fraction I (DSNF-I). As seen by phase-contrast microscopy, DSNF-I is composed of material which closely resembles unfractionated nuclei; residual internal nuclear structures including nucleolar remnants are clearly visible. By transmission electron microscopy, nuclear lamina, pore complexes, and a nuclear matrix are similarly identified. Biochemically, DSNF-I is composed almost entirely of protein (greater than 93%). SDS PAGE analysis reveals several major polypeptides; species at 174,000, 74,000, and 42,000 predominate. A polypeptide coincident with the Coomassie Blue-stainable 174-kdalton band has been shown by a novel technique of lectin affinity labeling to be a glycoprotein; a glycoprotein of similar or identical molecular weight has been found to be a component of nuclear envelope fractions isolated from the livers of rats, guinea pigs, opossums, and chickens. Antisera against several of the polypeptides in DSNF-I have been obtained from rabbits, and all of them show only little or no cross-reactivity with Drosophila cytoplasmic fractions. Initial results of immunocytochemical studies, while failing to positively localize either the 174- or 16-kdalton polypeptides, demonstrate a nuclear localization of the 74-kdalton antigen in all of several interphase cell types obtained from both Drosophila embryos and third-instar larvae.

Animals↗

Effect of organ site on nuclear matrix protein composition.

The nuclear matrix has been linked to several important cellular functions within cells, such as DNA organization and replication, as well as regulation of gene expression. It has been reported that the nuclear matrix protein composition is altered in cells grown on different extracellular matrices in vitro. This study examined the nuclear matrix protein composition of tumors produced by MAT-LyLu (MLL) rat prostate tumor cells implanted at different organ sites within the rat. When high resolution two-dimensional gels were utilized to compare nuclear matrix protein composition to the prostate orthotopic tumor, it was found that there were distinct protein differences depending upon where the tumor grew. In particular, there were 14 proteins found in the lung, six proteins found in intramuscular, 17 proteins is the heart, and five proteins in the tail vein tumor tissue that were not present in the prostate orthotopic tumor tissue. Therefore, this study adds evidence to support that the nuclear matrix composition of a cell is dependent, at least in part, by the extracellular matrix and/or different cellular environments and may have a role in site-specific differences in tumor properties.

Animals↗

Association of nuclear matrix proteins with granular and threaded nuclear bodies in cell lines undergoing apoptosis.

The granules which appear in the nucleolar area in apoptotic HL-60 cells after camptothecin administration (Zweyer et al., Exp. Cell Res. 221,27-40, 1995) were detected also in several other cell lines induced to undergo apoptosis by different stimuli, such as MOLT-4 treated with staurosporine, K-562 incubated with actinomycin D, P-815 exposed to temperature causing heat shock, Jurkat cells treated with EGTA, U-937 growing in the presence of cycloheximide and tumor necrosis factor-alpha, and HeLa cells treated with etoposide. Using immunoelectron microscopy techniques, we demonstrate that, besides the already described nuclear matrix proteins p125 and p160, these granules contain other nucleoskeletal polypeptides such as proliferating cell nuclear antigen, a component of ribonucleoprotein particles, a 105-kDa constituent of nuclear spliceosomes, and the 240-kDa nuclear mitotic apparatus-associated protein referred to as NuMA. Moreover, we also found in the granules SAF-A/hn-RNP-U and SATB1 proteins, two polypeptides that have been reported to bind scaffold-associated regions DNA sequences in vitro, thus mediating the formation of looped DNA structures in vivo. Fibrillarin and coilin are not present in these granules or the PML protein. Thus, the granules seen during the apoptotic process apparently are different from coiled bodies or other types of nuclear bodies. Furthermore, these granules do not contain chromatin components such as histones and DNA. Last, Western blotting analysis revealed that nuclear matrix proteins present in the granules are not proteolytically degraded except for the NuMA polypeptide. We propose that these granules might represent aggregates of nuclear matrix proteins forming during the apoptotic process. Moreover, since the granules are present in several cell lines undergoing apoptosis, they could be considered a previously unrecognized morphological hallmark of the apoptotic process.

Antigens, Nuclear↗

In-silico prediction and observations of nuclear matrix attachment.

The nuclear matrix is a functionally adaptive structural framework interior to the nuclear envelope. The nature and function of this nuclear organizer remains the subject of widespread discussion in the epigenetic literature. To draw this discussion together with a view to suggest a way forward we summarize the biochemical evidence for the modalities of DNA-matrix binding alongside the in-silico predictions. Concordance is exhibited at various, but not all levels. On the one hand, both the reiteration and sequence similarity of some elements of Matrix Attachment Regions suggest conservation. On the other hand, in-silico predictions suggest additional unique components. In bringing together biological and sequence evidence we conclude that binding may be hierarchical in nature, reflective of a biological role in replicating, transcribing and potentiating chromatin. Nuclear matrix binding may well be more complex than the widely accepted simple loop model.

Algorithms↗