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PubMed1999

Degradation of the nuclear matrix is a common element during radiation-induced apoptosis and necrosis.

Human promyelocytic leukemia (HL60) cells were irradiated with 10 or 50 Gy of X rays and studied for up to 72 h postirradiation to determine the mode of death and assess changes in the nuclear matrix. After 50 Gy irradiation, cells were found to die early, primarily by apoptosis, while cells irradiated with 10 Gy died predominantly by necrosis. Disassembly of the nuclear lamina and degradation of the nuclear matrix protein lamin B occurred in cells undergoing radiation-induced apoptosis or necrosis. However, using Western blotting and a recently developed flow cytometry assay to detect changes in nuclear matrix protein content, we found that the kinetics and mechanisms of disassembly of the nuclear lamina are different for each mode of cell death. During radiation-induced apoptosis, cleavage and degradation of lamin B to a approximately 28-kDa fragment was detected in most cells within 4-12 h after irradiation. Measurements of dual-labeled apoptotic cells revealed that nonrandom DNA fragmentation was evident prior to or concomitant with breakdown of the nuclear lamina. Disassembly of the nuclear lamina during radiation-induced necrosis occurred much later (between 30-60 h after irradiation), and a different cleavage pattern of lamin B was observed. Degradation of the nuclear lamina was also inhibited in apoptosis-resistant BCL2-overexpressing HL60 cells exposed to 50 Gy until approximately 48 h after irradiation. These data indicate that breakdown of the nuclear matrix may be a common element in radiation-induced apoptosis and necrosis, but that the mechanisms and temporal patterns of breakdown of the nuclear lamina during apoptosis are distinct from those of necrosis.

Apoptosis↗

PubMed1982

DNA polymerase alpha from the nuclear matrix of cells infected with simian virus 40.

The nuclear matrix prepared from normal, simian virus 40 (SV40)-infected, and SV40-transformed cells contained DNA polymerase activities. Approximately 12% of the total DNA polymerase activities in isolated nuclei remained with the nuclear matrix. alpha-polymerase was the major matrix DNA polymerase activity as judged by sensitivity to various inhibitors: aphidicolin, dideoxy-TTP, and N-ethylmaleimide. Approximately 2-4 fold higher DNA polymerase activity was detected in matrices obtained from lytically infected and virus-transformed cells than that found in normal cells. In lytically infected cells, 30-50% of the matrix-bound DNA polymerase activity solubilized by sonication co-sedimented with majority of the matrix T-antigen, and was co-precipitated with anti-T sera. The results suggest that alpha-polymerase and viral T-antigen may form a functional complex in the matrix.

Animals↗

PubMed1995

Interaction of the Pisum sativum nuclear matrix proteins with SAR DNA.

We have isolated the nuclear matrices from Pisum sativum cell nuclei using three methods: i. standard procedure involving extraction of cell nuclei with 2 M NaCl and 1% Triton X-100; ii. the same with pretreatment of cell nuclei with 0.5 mM CuSO4 (stabilisation step); and iii. method including lithium diiodosalicylate extraction. We compared the polypeptide pattern and residual DNA content of the nuclear matrices isolated. The nuclear matrices displayed a specific endonuclease activity which was due to the presence of a 32 kDa protein. The isolated nuclear matrices bound specifically the scaffold-attached (SAR) DNA derived from human beta interferon gene, in the exogenous SAR binding assay. Using the DNA-protein binding blot assay we demonstrated the presence of two nuclear matrix proteins of 66 kDa and 62 kDa which bound specifically SAR DNA.

Antigens, Nuclear↗

PubMedDate not supplied

[DNA and nucleotide triphosphate-activated proteinase from rat liver nuclear matrix specific for H1 histone].

The action of DNA and nucleotide phosphate on histone hydrolysis by nuclear matrix preparations from rat liver has been studied. It is shown that proteinase specific for H1 histone is associated with the nuclear matrix. This proteinase is activated by denatured DNA and by DNA treatment with DNase I or gamma-irradiation, but it is not activated by UV-irradiated DNA. In the presence of nucleotide triphosphates, particularly GTP and ATP, proteolysis of H1 histone is markedly increased. The nuclear matrix proteinase specific for H1 histone and activated by DNA or GTP and ATP appears inhibited by antipain, leupeptin, phenylmethylsulfonyl fluoride (the inhibitors of serine proteinases) as well as by dithiotreitol.

Adenosine Triphosphate↗

PubMed2001

Fanconi anemia proteins localize to chromatin and the nuclear matrix in a DNA damage- and cell cycle-regulated manner.

Fanconi anemia (FA) is a genetic disease characterized by congenital defects, bone marrow failure, and cancer susceptibility. Cells from patients with FA exhibit genomic instability and hypersensitivity to DNA cross linking agents such as mitomycin C. Despite the identification of seven complementation groups and the cloning of six genes, the function of the encoded gene products remains elusive. The FancA (Fanconi anemia complementation group A), FancC, and FancG proteins have been detected within a nuclear complex, but no change in level, binding, or localization has been reported as a result of drug treatment or cell cycle. We show that in immunofluorescence studies, FancA appears as a non-nucleolar nuclear protein that is excluded from condensed, mitotic chromosomes. Biochemical fractionation reveals that the FA proteins are found in nuclear matrix and chromatin and that treatment with mitomycin C results in increase of the FA proteins in nuclear matrix and chromatin fractions. This induction occurs in wild-type cells and mutant FA-D (Fanconi complementation group D) cells but not in mutant FA-A cells. Immunoprecipitation of FancA protein in chromatin demonstrates the coprecipitation of FancA, FancC, and FancG, showing that the FA proteins move together as a complex. Also, fractionation of mitotic cells confirms the lack of FA proteins in chromatin or the nuclear matrix. Furthermore, phosphorylation of FancG was found to be temporally correlated with exit of the FA complex from chromosomes at mitosis. Taken together, these findings suggest a role for FA proteins in chromatin and nuclear matrix.

Cell Cycle↗

PubMed1987

Alterations in nuclear matrix structure after adenovirus infection.

Infection of HeLa cells with adenovirus serotype 2 causes rearrangements in nuclear matrix morphology which can best be seen by gentle cell extraction and embedment-free section electron microscopy. We used these techniques to examine the nuclear matrices and cytoskeletons of cells at 6, 13, 28, and 44 h after infection. As infection progressed, chromatin condensed onto the nucleoli and the nuclear lamina. Virus-related inclusions appeared in the nucleus, where they partitioned with the nuclear matrix. These virus centers consisted of at least three distinguishable areas: amorphously dense regions, granular regions whose granulations appeared to be viral capsids, and filaments connecting these regions to each other and to the nuclear lamina. The filaments became decorated with viral capsids of two different densities, which may be empty capsid shells and capsids with DNA-protein cores. The interaction of some capsids with the filaments persisted even after lysis of the cell. We propose that granulated virus-related structures are sites of capsid assembly and storage and that the filaments may be involved in the transport of capsids and capsid intermediates. The nuclear lamina became increasingly crenated after infection, with some extensions appearing to bud off and form blebs of nuclear material in the cytoplasm. The perinuclear cytoskeleton became rearranged after infection, forming a corona of decreased filament number around the nucleus. In summary, we propose that adenovirus rearranges the nuclear matrix and cytoskeleton to support its own replication.

Adenoviruses, Human↗

PubMed2002

Cleared extrachromosomal domain (CED): a nuclear domain enriched in nuclear matrix filaments is a common structure in sturgeon podocytes.

The cell nucleus is divided into chromosome territories and the extrachromosomal domain. The latter includes several structural and functional compartments involved in RNA processing and transport. Morphological and cytochemical analyses of the cell nucleus in sturgeon podocytes revealed the existence of a previously uncharacterised nuclear compartment. It appears as a cleared nucleoplasmic area of variable size within the extrachromosomal domain. Conventional light and electron microscopy revealed that this compartment, here referred to as cleared extrachromosomal domain (CED), appears free of chromatin and RNA-containing organelles and is closely surrounded by heterochromatin masses. Cytochemical and immunogold electron microscope studies indicated that CEDs lack DNA, RNA and glycoconjugates. The ultrastructural examination of Lowicryl-embedded sections showed that CEDs are formed by a fibrillar network. In resinless preparations, this network appears as a dense mesh of crosslinked nuclear matrix filaments. The density of nuclear matrix filaments within the CED is remarkably higher than that observed in the rest of the nucleus. Our results indicate that the CED is a single, distinct extrachromosomal domain of the nuclear matrix of sturgeon podocytes. The absence in the CED of detectable DNA and RNA, as well as the lack of chromatin and RNA-containing structures, suggests that transcription and RNA processing do not occur in this novel nuclear compartment. The volume occupied by the CED may preserve the volume-to-cytoplasm ratio in the podocyte and contribute to modulate the spatial organisation and the volume occupied by the chromosomal territories.

Aging↗

PubMed2000

Detection of bladder cancer using a novel nuclear matrix protein, BLCA-4.

We have identified previously six nuclear matrix proteins (NMPs) that are bladder cancer specific. In this study, we analyzed the expression of one of these proteins, BLCA-4, in bladder tumors and normal bladder tissue. We also examined the appearance of BLCA-4 in the urine as a biomarker for bladder cancer. BLCA-4 was isolated from nuclear matrix preparations of bladder tumors, and its peptide sequence was determined. The antibodies generated against the resulting BLCA-4 peptides were then used to detect its presence in immunoblots and in urine samples by immunoassay. We analyzed tissue samples of bladder tumor and normal donor bladders and urine obtained from 51 normal individuals and 54 patients with pathologically confirmed bladder cancer. The BLCA-4 peptide sequences do not resemble any known human protein sequences. On immunoblot analysis, BLCA-4 expression was detectable in tumor and normal tissues from patients with bladder cancer but not in any of the normal bladder tissue obtained from organ donors. Using a prospectively determined cutoff level of 13 A (absorbance) units/microg protein, all 51 normal individuals tested were negative for BLCA-4 expression, whereas 53 of 55 samples from patients with bladder cancer were positive. These results suggest that BLCA-4 is present throughout the bladder in both the tumor and morphologically normal areas in bladder cancer patients. BLCA-4 is a very sensitive (96.4%) and specific (100%) marker for bladder cancer. BLCA-4 is a bladder cancer-specific marker that can be detected using a urine-based assay and can be used in the diagnosis of bladder cancer.

Adult↗

PubMed1991

The nuclear matrix: a heuristic model for investigating genomic organization and function in the cell nucleus.

Despite significant advances in deciphering the molecular events underlying genomic function, our understanding of these integrated processes inside the functioning cell nucleus has, until recently, met with only very limited success. A major conundrum has been the "layers of complexity" characteristic of all cell structure and function. To understand how the cell nucleus functions, we must also understand how the cell nucleus is put together and functions as a whole. The value of this neo-holistic approach is demonstrated by the enormous progress made in recent years in identifying a wide variety of nuclear functions associated with the nuclear matrix. In this article we summarize basic properties of in situ nuclear structure, isolated nuclear matrix systems, nuclear matrix-associated functions, and DNA replication in particular. Emphasis is placed on identifying current problems and directions of research in this field and illustrating the intrinsic heuristic value of this global approach to genomic organization and function.

Amino Acid Sequence↗

PubMed1983

Proteins tightly bound to HeLa cell DNA at nuclear matrix attachment sites.

DNA-protein complexes have been isolated from HeLa cell nuclei and nuclear matrix preparations. Two proteins, 55 and 66 kilodaltons in size, remain bound to HeLa DNA after treatment at 80 degrees C in 2% sodium dodecyl sulfate and purification by exclusion chromatography on Sepharose 2B-CL in the presence of 0.3% sodium dodecyl sulfate. These proteins appear to be tightly bound but not covalently linked to the DNA, and they are distributed over the DNA with an average spacing of 40 kilobase pairs. This spacing distribution remains essentially constant throughout the cell cycle. The proteins are bound to the residual 2% of HeLa cell DNA which remains attached to the nuclear matrix after extensive nuclease digestion, a condition which reduces the average size of the DNA to approximately 150 base pairs. Our results suggest that these tightly bound proteins are involved in anchoring cellular DNA to the nuclear matrix. These tightly bound proteins are identical by partial peptide mapping to proteins found tightly bound to the DNA of mammalian, plant, and bacterial cells (D. Werner and C. Petzelt, J. Mol. Biol. 150:297-302, 1981), implying that these proteins are involved in the organization of chromosomal domains and are highly conserved in both procaryotic and eucaryotic cells.

Binding Sites↗

PubMed1986

Synthesis and stability of nuclear matrix proteins in resting and serum-stimulated Swiss 3T3 cells.

The major [35S]methionine-radiolabeled nuclear matrix proteins of mouse 3T3 cells were isolated, and most of these were found to be similar in molecular weight, charge, and protease fingerprint to the nuclear matrix proteins of African green monkey kidney cells, which are found tightly bound to simian virus 40 chromosomes. These nuclear matrix proteins were found to be synthesized in quiescent and serum-stimulated cells and to be turned over slowly during pulse-chase experiments. In contrast, a 70-Kd (kilodalton) neutral protein identified as lamin a was found to be turned over rapidly, producing a 68-Kd protein with a similar isoelectric point. In addition, we observed a decrease in the amounts of two chromatin-bound matrix proteins and a relative increase in lamin a following labeling in the presence of 2 micrograms/ml actinomycin D. However, these effects do not appear to be a result of inhibition of transcription, since they were not observed with other inhibitors (alpha-amanitin and 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole).

Amanitins↗

PubMed1983

[Peculiarities of protein composition of nuclear matrix in some tumors and cultures of embryonic fibroblasts of the Chinese hamster].

The polypeptide pattern of the nuclear matrix of hepatomas differs significantly from that of intact liver. On the contrary, the polypeptide pattern of the nuclear matrix of Chinese hamster fibroblast culture is similar to that of tumour cells. In our studies the nuclear matrix was characterized by an increased content of polypeptides with Mr = 120,000-135,000 and 150,000-200,000 and a protein group with Mr of about 13,000 and lower. In metabolically active hepatomas and fibroblasts of Chinese hamster the content of high and low molecular weight components of the protein band triplet (Mr = = 65,000-70,000) in the logarithmic phase is decreased, while in hepatomas the content of the middle component of the triplet is increased. It is assumed that these peculiarities are due to the inhibition of differentiation and to an increased metabolic activity of the cells.

Animals↗

PubMed1983

Status of the nuclear matrix in mature and embryonic chick erythrocyte nuclei.

The adult chicken erythrocyte nucleus was found to lack an internal nuclear matrix: even milder extraction procedures resulted in the production of empty shells of pore complex-lamina together with loose aggregates of core histone. In contrast, rat liver nuclei showed a typical intranuclear salt-resistant skeleton. These results show that an internal matrix is not an obligatory nuclear component, and is not required for the spatial organization of chromatin. 5-day-old embryonic erythrocytes did, however, contain an interchromatinic nuclear matrix, suggesting a correlation between the presence of matrix structures, and nuclear 'activity'.

Animals↗

PubMed2001

Dynamics of association of origins of DNA replication with the nuclear matrix during the cell cycle.

DNA of replication foci attached to the nuclear matrix was isolated from Chinese hamster ovary cells and human HeLa cells synchronized at different stages of the G(1) and S phases of the cell cycle. The abundance of sequences from dihydrofolate reductase ori-beta and the beta-globin replicator was determined in matrix-attached DNA. The results show that matrix-attached DNA isolated from cells in late G(1) phase was enriched in origin sequences in comparison with matrix-attached DNA from early G(1) phase cells. The concentration of the early firing ori-beta in DNA attached to the matrix decreased in early S phase, while the late firing beta-globin origin remained attached until late S phase. We conclude that replication origins associate with the nuclear matrix in late G(1) phase and dissociate after initiation of DNA replication in S phase.

Animals↗

PubMed1992

RFP is a DNA binding protein associated with the nuclear matrix.

We reported that the RFP gene encodes a protein with putative zinc finger domains and was involved in the activation of the ret proto-oncogene. To further characterize the RFP protein, we developed a polyclonal antibody against the product synthesized from a fragment of the RFP cDNA expressed in Escherichia coli. Western blot analysis showed that RFP was identified as a 58 kDa protein in cell lysates from four human and rodent cell lines and from mouse testis. In addition, a unique 68 kDa protein was detected in the testis. Using AH7974 (rat ascites hepatoma) and Raji (human Burkitt lymphoma) cells, we demonstrated strong association of RFP with the nuclear matrix. Furthermore, RFP solubilized from the nuclear matrix had DNA-binding activity although it appears to bind more preferentially to double-stranded DNA than to single-stranded DNA. These results thus suggest that RFP may play a role in molecular processes which occur in the nuclear matrix.

Amino Acid Sequence↗

PubMed1989

The protein composition of the nuclear matrix of murine P19 embryonal carcinoma cells is differentiation-stage dependent.

The protein composition of the nuclear matrix of murine P19 embryonal carcinoma (EC) cells was compared with that of clonal derivatives of P19 EC differentiated in vitro, and with that of P19 EC cells induced to differentiate with retinoic acid (RA). Several major differences in nuclear matrix protein composition were found between the cell lines tested. Some polypeptides were found to occur only in EC cells, whereas others proved to be restricted to one or more of the differentiated derivatives. During RA treatment of EC cells a transient expression of some matrix proteins was observed. Several new proteins appeared, and others disappeared. Our data indicate that the protein composition of the nuclear matrix is a sensitive gauge for the differentiation state of cells.

Animals↗

PubMed2001

[The murine nuclear matrix protein specificcaly binds to centromeric satellite DNA].

The nuclear matrix (NM) of mouse contains a protein (miSat BP) that can specifically bind to mouse centromeric minor satellite DNA as shown by gel shift assay. The ion-exchange chromatography on DEAE-Sepharose was used as the first miSat BP purification. MiSat BT was eluted by 0.2 M NaCl. Antibodies against p70, a human NM protein of 70 kDa described earlier as a protein recognizing human alphoid DNA, produce hypershift effect when added to the retardation incubation mix. Immunoblotting of NM and an active NM fraction (0.2 M NaCl) with these antibodies revealed a protein with 70 kDa in both preparations. This antigen retained in NM in situ being associated with residual DNA as shown by indirect immunofluorescent staining. In the untreated interphase nucleus most of miSat BP granules were shown to be colocalized with prekinetochores. We suggest that miSat BP is capable of recognizing the minor satellite DNA due to its structural features, but it does not belong to a group of constitutive centromeric proteins.

Animals↗

PubMed1986

Permanent attachment of replication origins to the nuclear matrix in BHK-cells.

The position of replication origins and replication forks relative to the nuclear matrix was analysed by autoradiography. Analysis of 2M NaCl-extracted extracted BHK-nuclei, prepared on coverslips, showed that after brief pulses grains were exclusively found over the central core of the residual nuclei, which corresponds to positions in the nuclear matrix. In asynchronous cells these grains were found to migrate into the DNA-halo surrounding the matrix during a subsequent chase. When the pulse had been administered to synchronous cells at the onset of S-phase, it was observed, however, that in the majority of the structures no such migration had occurred. From this, and from the fact that label incorporated later in S-phase could be chased into the halo, we conclude that, contrary to DNA in replication forks, DNA containing replication origins is permanently attached to the nuclear matrix.

Animals↗