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Different patterns of DNA fragmentation and degradation of nuclear matrix proteins during apoptosis induced by radiation, hyperthermia or etoposide.

Several nuclear matrix proteins are substrates for proteolytic cleavage during apoptosis. Using Western blotting, the temporal patterns of cleavage of three nuclear matrix proteins (lamin B, NUMA and the nucleoporin TPR) were compared in HL60 cells induced to undergo apoptosis after irradiation, heat shock or treatment with etoposide. Flow cytometry was used to compare the kinetics of post-cleavage degradation of lamin B, NUMA and TPR after irradiation, and to correlate DNA fragmentation with protein degradation in cells induced to undergo apoptosis with different agents. During radiation-induced apoptosis, cleavage and subsequent degradation of lamin B, NUMA and TPR occurred with different kinetics. Low-molecular-weight DNA fragmentation occurred subsequent to the initiation of NUMA cleavage, coincided with lamin B cleavage, but occurred before more extensive degradation of lamin B and NUMA. A similar sequence was observed for cells treated with etoposide. However, during heat-induced apoptosis, cleavage of lamin B and NUMA occurred much sooner compared to other agents, with NUMA cleaved into multiple fragments within 15 min after heating. We conclude that the hierarchical sequence and kinetics of degradative events contributing to nuclear disassembly during apoptosis are highly dependent on the inducing agent. Furthermore, the nuclear pore complex, like the nuclear lamina and internal nuclear matrix, is a target for proteolytic cleavage.

Antigens, Nuclear↗

Ultrastructural organization of the sperm nuclear matrix.

The organization of DNA-protamine complexes and their association with the nuclear matrix have been analyzed in sperm nuclei by in situ Nick Translation at the electron microscope. The data obtained indicate that the chromatin organization in sperm nuclei is maintained during the sperm condensation by means of interaction with the nuclear matrix at fixed sites. The fine structure of the sperm nucleus and sperm nuclear matrix, investigated by sectioning and replica of freeze-fractured specimens, suggests that the lamellar array observed by freeze-fracturing in the sperm nuclei, could depend on the inner matrix which presents a regular organization of globular structures involved in the maintenance of chromatin domains.

Animals↗

Distribution of the 70K U1 RNA-associated protein during interphase and mitosis. Correlation with other U RNP particles and proteins of the nuclear matrix.

Earlier studies suggested that the 70K (70 X 10(3) Mr) polypeptide is a nuclear matrix (associated) protein since it is the only U1 RNP-associated antigen that is not released from the nucleus after treatment of the cell with, successively, detergents, DNase I and/or RNase A and high salt. The possibility that the 70K protein functions in the binding of U1 RNP to the nuclear matrix is now further substantiated by the finding that U1 RNP particles that did or did not contain the 70K protein could be isolated, depending on the method of isolation. When U1 RNP particles were obtained by means of sonic disruption of the nucleus they contained the 70K polypeptide, whereas particles that were isolated by extraction at room temperature and a slightly alkaline pH lacked the 70K protein but contained the intact U1 RNA and the other U1 RNA-associated proteins. During interphase the localization of the 70K protein is restricted to the nucleus, giving a dot-like distribution pattern with exclusion of the nucleoli. During prophase to late anaphase the protein is dispersed throughout the entire cytoplasm with the exception of the chromatin regions. Immunofluorescence studies, using a monoclonal anti-70K antibody in combination with human autoimmune sera that react with U1 RNA-associated proteins, demonstrate that the 70K protein is localized in those areas of the cell where other U RNP proteins occur, also during mitosis. Topoisomerase I and nuclear lamins, typical nuclear matrix proteins, show completely different distribution patterns in all phases of the cell cycle. Assembly of the nuclear envelope is attended by the re-formation of the clustered appearance of the 70K antigen. These results suggest that, although associated with the nuclear matrix fraction in interphase cells, the 70K protein remains associated with the U1 RNP particles during cell division.

Animals↗

The terminal regions of adenovirus and minute virus of mice DNAs are preferentially associated with the nuclear matrix in infected cells.

The interaction of viral genomes with the cellular nuclear matrix was studied by using adenovirus-infected HeLa cells and minute virus of mice (MVM)-infected A-9 cells. Adenovirus DNA was associated with the nuclear matrix both early and late in infection, the tightest interaction being with DNA fragments that contain the covalently bound 5'-terminal protein. Replicative forms of MVM DNA were also found to be exclusively matrix associated during the first 16 to 20 h of infection; at later times viral DNA species accumulated in the soluble nuclear fraction at different rates, suggesting a saturation of nuclear matrix-binding sites. MVM DNA fragments enriched in the matrix fraction were also derived from the terminal regions of the viral genome. However, only the subset of fragments which possess a covalently bound 5'-terminal protein (i.e., DNA fragments in which the 5' palindromic DNA sequences are in the extended duplex rather than the hairpin conformation) were matrix associated. These observations suggest that the DNA-matrix interactions are, at least in part, mediated by the viral terminal proteins. Since these proteins have previously been shown to be intimately involved in viral DNA replication, our results further indicate that an association with the nuclear matrix may be important for viral genome replication and possibly also for efficient gene transcription.

Adenoviruses, Human↗

Tropomyosin is localized in the nuclear matrix and chromosome scaffold of Physarum polycephalum.

The nuclei and chromosomes were isolated from plasmodia of Physarum polycephalum. The nuclear matrix and chromosome scaffold were obtained after the DNA and most of the proteins were extracted with DNase I and 2 M NaCl. SDS-PAGE analyses revealed that the nuclear matrix and chromosome scaffold contained a 37 kD polypeptide which is equivalent to tropomyosin in molecular weight. Immunofluorescence observations upon slide preparations labeled with anti-tropomyosin antibody showed that the nuclear matrix and chromosome scaffold emanated bright fluorescence, suggesting the presence of the antigen in them. Immunodotting results confirmed the presence of tropomyosin in the nuclear matrix and chromosome scaffold. Immunoelectron microscopic observations further demonstrated that tropomyosin was dispersively distributed in the interphase nuclei and metaphase chromosomes.

Animals↗

Significance of anti-nuclear matrix antibodies in patients with in vivo speckled antinuclear antibody staining.

OBJECTIVE: Evidence suggests that patients with in vivo speckled antinuclear antibody (ANA) patterns have high titers of circulating ANA, specifically anti-U1 RNP antibody. A small percentage of patients with high titers of anti-U1 RNP antibody have anti-nuclear matrix antibodies, and some also demonstrate in vivo ANA. This study was designed to screen for the presence of anti-nuclear matrix antibodies in patients with in vivo ANA. METHODS: Anti-nuclear matrix antibodies were detected by indirect immunofluorescence on HCI-extracted HEp-2 cell substrate, by enzyme-linked immunosorbent assay, and by immunoblot analysis. RESULTS: All 10 patients with in vivo ANA were found to have anti-nuclear matrix antibody demonstrated using HCI-extracted HEp-2 cell substrate, and all exhibited antibody activity to a 36-kd protein from nuclear matrix antigen. CONCLUSION: These results suggest that anti-nuclear matrix antibodies are a major factor in the development of in vivo ANA.

Antibodies, Antinuclear↗

Preferential formation and repair of chromium-induced DNA adducts and DNA--protein crosslinks in nuclear matrix DNA.

The distributions of chromium-DNA adducts and DNA-protein crosslinks induced by treatment of intact CHO cells with carcinogenic chromium were examined in distinct chromatin subfractions: a chromatin subfraction released by digestion of isolated nuclei with micrococcal nuclease (1SF, 14% of total nuclear DNA), bulk chromatin (74% of total DNA) and a nuclear matrix fraction (12% of total DNA). The identity of the matrix fraction was confirmed by hybridization of DNA from each subfraction with a cDNA probe prepared from total mRNA isolated from CHO cells, which showed that the 1SF and nuclear matrix fractions were 2.3- and 3.8-fold enriched in actively transcribed genes respectively, compared to total unfractionated DNA. Immediately following treatment of cells with 150 microM sodium chromate for 2 h the binding of chromium to each chromatin fraction was found to be non-uniform. Compared with total unfractionated nuclei, the nuclear matrix fractions were enriched in chromatin-bound chromium (3.4-fold), whereas the bulk chromatin fraction was relatively depleted (0.5-fold). Approximately 13% of nuclear chromium was associated with the detergent-soluble lipid component of nuclei. A similar distribution of chromatin-bound chromium was also apparent 24 h after the chromate treatment. Immediately after the 2 h chromate treatment, chromium-DNA adducts were detected in all the chromatin subfractions. Total nuclear and bulk chromatin DNA contained similar levels of this type of damage. The 1SF fraction was depleted approximately 3-fold in this type of damage compared with total nuclear DNA. In contrast, the nuclear matrix was markedly enriched in chromium-DNA adducts (approximately 4-fold compared with total nuclear DNA) at this time. As previously demonstrated, chromium-DNA adducts in total nuclear DNA decreased within the first 24 h, but thereafter persisted at a similar level. Chromium-DNA adducts in nuclear matrix DNA also reached maximum levels at the end of the 2 h treatment and decreased to 68% and 39% of this level by 24 and 48 h after treatment respectively. In contrast, the adduct levels in the 1SF and bulk chromatin fractions did not change up to 48 h after treatment. Chromium-induced DNA-protein crosslinks, which were stable to 8 M urea and 2% SDS, occurred almost exclusively in the nuclear matrix fraction. The crosslinks in this fraction reached a maximum level at the end of the 2 h treatment, but returned to control levels 24 h later.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗

The application of flow cytometry to the study of nuclear matrix. A multiparametric analysis.

The nuclear matrix, which in situ corresponds essentially to the interchromatin ribonucleoprotein particles, once isolated appears constituted by a peripheral lamina connected to the nucleolar remnant by a fibrous network. The features of the matrix components depend on the procedure employed during its purification, a multistep method commonly involving nuclease digestion, low and high salt extractions and treatment with a non ionic detergent. Here is reported the application of flow cytometry to the analysis of matrix purification. The experimental data indicate that, despite deep changes of the nuclear content due to the selective extraction of almost all nucleohistone and membrane components, the scatter pattern of the matrix, which is drastically lowered as the nucleic acid content decreases, closely resembles that of the starting nuclei. This behaviour permits one to follow the different matrix populations deriving from diploid and polyploid parenchymal liver nuclei throughout the isolation procedure and confirms the feasibility of flow cytometry for both analysis and sorting of nuclei and nuclear matrices. In addition, an ultrastructural analysis on thin sections and a morphometric study by means of semiautomated image analysis of phase contrast micrographs have been performed. The image analysis showed a decrease in particle dimension to about 50% of the nuclear value, which could partially explain the reduction of forward light scatter.

Animals↗

[Trithorax protein, a global factor for maintenance of tissue specific gene activation in Drosophila melanogaster, is associated with the nuclear matrix].

Immunlfluorescence staining and Western blotting of proteins from the nuclear extract fractions showed for the first time that protein TRITHORAX, one of the most important proteins maintaining the tissue-specific transcriptionally active state of many Drosophila melanogaster genes, is associated with the nuclear matrix. TRITHORAX displayed similar staining at different stages of nuclear extraction and on the polytene chromosomes of the intact nuclei, as well as after partial or complete disruption of the nuclear envelope and chromosome release. This suggests that TRITHORAX bound to certain regulatory chromosome regions interacts with the adjacent elements of the nuclear scaffold, i.e., links the regions of actively transcribed genes with the nuclear matrix.

Animals↗

Nuclear matrix attachment regions of human papillomavirus type 16 point toward conservation of these genomic elements in all genital papillomaviruses.

The gene functions, transcriptional regulation, and genome replication of human papillomaviruses (HPVs) have been extensively studied. Thus far, however, there has been little research on the organization of HPV genomes in the nuclei of infected cells. As a first step to understand how chromatin and suprachromatin structures may modulate the life cycles of these viruses, we have identified and mapped interactions of HPV DNAs with the nuclear matrix. The endogenous genomes of HPV type 16 (HPV-16) which are present in SiHa, HPKI, and HPKII cells, adhere in vivo to the nuclear matrixes of these cell lines. A tight association with the nuclear matrix in vivo may be common to all genital HPV types, as the genomes of HPV-11, HPV-16, HPV-18, and HPV-33 showed high affinity in vitro to preparations of the nuclear matrix of C33A cells, as did the well-known nuclear matrix attachment region (MAR) of the cellular beta interferon gene. Affinity to the nuclear matrix is not evenly spread over the HPV-16 genome. Five genomic segments have strong MAR properties, while the other parts of the genome have low or no affinity. Some of the five MARs correlate with known cis-responsive elements: a strong MAR lies in the 5' segment of the long control region (LCR), and another one lies in the E6 gene, flanking the HPV enhancer, the replication origin, and the E6 promoter. The strongest MAR coincides with the E5 gene and the early-late intergenic region. Weak MAR activity is present in the E1 and E2 genes and in the 3' part of L2. The in vitro map of MAR activity appears to reflect MAR properties in vivo, as we found for two selected fragments with and without MAR activity. As is typical for many MARs, the two segments with highest affinity, namely, the 5' LCR and the early-late intergenic region, have an extraordinarily high A-T content (up to 85%). It is likely that these MARs have specific functions in the viral life cycle, as MARs predicted by nucleotide sequence analysis, patterns of A-T content, transcription factor YY1 binding sites, and likely topoisomerase II cleavage sites are conserved in similar positions throughout all genital HPVs.

Adenine↗

Identification of a nuclear matrix targeting signal in the leukemia and bone-related AML/CBF-alpha transcription factors.

Transcription factors of the AML (core binding factor-alpha/polyoma enhancer binding protein 2) class are key transactivators of tissue-specific genes of the hematopoietic and bone lineages. Alternative splicing of the AML-1 gene results in two major AML variants, AML-1 and AML-1B. We show here that the transcriptionally active AML-1B binds to the nuclear matrix, and the inactive AML-1 does not. The association of AML-1B with the nuclear matrix is independent of DNA binding and requires a nuclear matrix targeting signal (NMTS), a 31 amino acid segment near the C terminus that is distinct from nuclear localization signals. A similar NMTS is present in AML-2 and the bone-related AML-3 transcription factors. Fusion of the AML-1B NMTS to the heterologous GAL4-(1-147) protein directs GAL4 to the nuclear matrix. Thus, the NMTS is necessary and sufficient to target the transcriptionally active AML-1B to the nuclear matrix. The loss of the C-terminal domain of AML-1B is a frequent consequence of the leukemia-related t(8;21) and t(3;21) translocations. Our results suggest this loss may be functionally linked to the modified interrelationships between nuclear structure and gene expression characteristic of cancer cells.

Amino Acid Sequence↗

Recruitment of damaged DNA to the nuclear matrix in hamster cells following ultraviolet irradiation.

We examined the relationship between the nuclear matrix and DNA in the dihydrofolate reductase domain following irradiation of Chinese hamster cells with UV light. The fraction of matrix-bound DNA increased in transcribed and non-transcribed regions during a 3 h period after irradiation. However, no increase was observed with excision repair-deficient cells mutant for the ERCC1 gene. The major UV-induced lesion, the cyclobutane pyrimidine dimer, increased in frequency in the matrix-bound DNA 1 h after irradiation, in both transcribed and non-transcribed regions, but decreased subsequently. This phenomenon was also lacking in excision repair-deficient cells. These data demonstrate that recruitment of lesion-containing DNA to the nuclear matrix occurs following UV irradiation and suggest that this recruitment is dependent upon nucleotide excision repair. This is consistent with the concept of a 'repair factory' residing on the nuclear matrix at which excision repair occurs.

Animals↗

Spatial distribution of DNA loop attachment and replicational sites in the nuclear matrix.

Biochemical fractionation was combined with high resolution electron microscopic autoradiography to study the localization in rat liver nuclear matrix of attached DNA fragments, in vivo replicated DNA, and in vitro synthesized DNA. In particular, we determined the distribution of these DNA components with the peripheral nuclear lamina versus more internally localized structural elements of isolated nuclear matrix. Autoradiography demonstrated that the bulk of in vivo newly replicated DNA associated with the nuclear matrix (71%) was found within internal matrix regions. A similar interior localization was observed in isolated nuclei and in situ in whole liver tissue. Likewise, isolated nuclear lamina contained only a small amount (12%) of the total matrix-bound, newly replicated DNA. The structural localization of matrix-bound DNA fragments was examined following long-term in vivo labeling of the DNA. The radioactive DNA fragments were found predominantly within interior regions of the matrix structure (77%), and isolated nuclear lamina contained less than 15% of the total nuclear matrix-associated DNA. Most of the endogenous DNA template sites for the replicative enzyme DNA polymerase alpha (approximately 70%) were also sequestered within interior regions of the matrix. In contrast, a majority of the endogenous DNA template sites for DNA polymerase beta (a presumptive repair enzyme) were closely associated with the peripheral nuclear lamina. A similar spatial distribution for both polymerase activities was measured in isolated nuclei before matrix fractionation. Furthermore, isolated nuclear lamina contained only a small proportion of total matrix-bound DNA polymerase alpha endogenous and exogenous template activities (3-12%), but a considerable amount of the corresponding beta polymerase activities (47-52%). Our results support the hypothesis that DNA loops are both anchored and replicated at nuclear matrix-bound sites that are predominantly but not exclusively associated with interior components of the matrix structure. Our results also suggest that the sites of nuclear DNA polymerase beta-driven DNA synthesis are uniquely sequestered within the characteristic peripheral heterochromatin shell and associated nuclear envelope structure, where they may potentially participate in DNA repair and/or replicative functions.

Animals↗

Interactions of Epstein-Barr virus origins of replication with nuclear matrix in the latent and in the lytic phases of viral infection.

Eukaryotic DNA is organized into domains or loops generated by the attachment of chromatin fibers to the nuclear matrix via specific regions called scaffold or matrix attachment regions. The role of these regions in DNA replication is currently under investigation since they have been found in close association with origins of replication. Also, viral DNA sequences, containing the origins of replication, have been found attached to the nuclear matrix. To investigate the functional role of this binding we have studied, in Raji cells, the interaction between Epstein-Barr virus (EBV) origins of replication and the nuclear matrix in relation to the viral cycle of infection. We report here that both the latent (ori P) and the lytic (ori Lyt) EBV origins of replication are attached to the nuclear matrix, the first during the latent cycle of infection and the second after induction of the lytic cycle. These findings suggest that the binding of the origins of replication with the nuclear matrix modulates viral replication and expression in the two different phases of infection.

Chromosome Mapping↗

Nuclear matrix of the lower eukaryote Physarum polycephalum and the mammalian epithelial LLC-PK1 cell line. A comprehensive investigation of different preparation procedures.

Agarose-encapsulated nuclear matrix preparations of the lower eukaryote Physarum polycephalum and the mammalian renal epithelial LLC-PK1 cell line were analyzed after various experimental protocols with respect to the protein composition. The effect of the mode of deproteinization (2 M NaCl, 0.25 M ammonium sulfate or 25 mM lithium diiodosalicylate), presence of 2-mercaptoethanol, Ca2+, Cu2+, chelating agents, the sequence of protein extraction and nuclease digestion, the use of RNase, the temperature at which the experimental manipulations were performed and the use of hypotonic or isotonic conditions was investigated. No significant differences in the final nuclear matrix composition could be observed, regardless of the experimental procedure applied. In Physarum, the major nuclear matrix proteins range over 12-70 kDa with prominent bands at 24, 31, 37 and 45 kDa; the proteins of the matrix in LLC-PK1 cells extend predominantly over 40-80 kDa. Furthermore, no essential differences in the protein composition could be observed when type I and type II nuclear matrices from the highly differentiated LLC-PK1 cell line were compared. The same was found for analogous matrix preparations of Physarum. Therefore, in both systems a distinction between type I/II matrix is questionable. Immunoblotting of the matrix preparations with a variety of antibodies against intermediate filament proteins and with antinuclear autoantibodies revealed the presence of intermediate filament proteins as components of the nuclear matrix. We conclude that the nuclear matrix represents a much more stable and reproducible structure than has been proposed so far, largely independent of changes in the preparation protocol.

Animals↗

Binding of the androgen receptor to the nuclear matrix of human foreskin.

The nuclear matrix (NM) is a salt and nuclease-resistant nuclear substructure. It is associated with active DNA transcription and has been shown to contain acceptor sites for steroid receptors in a number of specific target tissues. We have investigated the presence of acceptor sites for the androgen receptor (AR) in the NM of human newborn foreskin. The NM was prepared from the 800 g pellet by successive treatments with detergent, DNase and high salt extraction. It contained 13 +/- 7% of total proteins and 10 +/- 6% of total DNA. After extensive washing, the NM spheres were incubated in the presence of cytosol and [3H]methyltrienolone +/- 200-fold excess of unlabeled steroid. Maximal binding of the AR to NM was reached in 30 min and decreased slightly thereafter to reach an equilibrium which was maintained for 18 h. Binding was saturable. In the absence of AR, the steroid did not bind to NM. When Scatchard analysis was performed on cytosol previously incubated with NM, cytosolic binding capacity significantly decreased relative to preincubation values (3.6 +/- 1.9 to 1.3 +/- 1.2 fmol/mg protein, P less than 0.05, n = 6). In contrast, apparent binding affinity was not changed. 0.8 mg of NM protein could bind AR from 2.4 mg of cytosol protein. In conclusion, NM from human foreskin binds the AR with high affinity. This binding is rapid and is maintained for at least 18 h. This is consistent with a potential role of NM in the mechanism of action of androgens in their target tissues.

Cell Nucleus↗

Tissue-specific association of the human tyrosine hydroxylase gene with the nuclear matrix.

Association of the human tyrosine hydroxylase (TH) gene with the nuclear matrix was studied using bovine matrices from tissues differing in expression of the gene. An in vitro binding assay was performed with fragments encompassing the -2300/+2300 region of the human TH gene. All fragments bound to the nuclear matrix from the adrenal medulla but none bound to that from the liver. A computer search of the sequenced part of the studied region revealed putative matrix attachment regions (S/MAR) - one in the promoter and two in the first intron. The (TCAT)(n) microsatellite repeat included in one of the intronic S/MARs seems to influence the binding potential of the human TH gene to the nuclear matrices.

Animals↗

Marking characteristics of anti-nuclear matrix protein NM200.4 in human breast carcinomas and normal human tissues.

Nuclear matrix proteins are a group of recently described proteins that are thought to be cell-type specific. Using a monoclonal antibody (NM 200.4; Matritech, Cambridge, MA) generated against nuclear matrix proteins isolated from a human breast carcinoma cell line, we examined frozen tissue sections from 30 breast carcinomas, and a variety of normal tissues to determine the antibody specificity, and to assess the relationship with the staining pattern and tumor type and hormone receptor status. Most breast carcinomas marked with the antibody, but stromal and vascular endothelial cells in the tissues surrounding these lesions also marked focally. Marking of vascular endothelium in a variety of benign tissues, renal tubular epithelium, and occasionally uterine smooth muscle cells was also observed. Normal breast tissue from 4 patients without breast cancer did not react. Studies on breast tumors revealed that 15/20 invasive ductal, 3/4 in situ ductal, 3/3 medullary, 2/2 invasive lobular, and 1/1 colloid carcinomas marked with this antibody. Image analysis revealed that the staining intensity of medullary carcinoma was twice that found in invasive ductal carcinoma (avg pixel density 76.6 vs. 30.1; P < 0.05). Invasive lobular and in situ ductal carcinoma also expressed higher staining intensities than invasive ductal carcinoma, but these differences were not significant. Invasive ductal carcinomas had heterogeneity in staining intensity (avg. pixel intensity range: 0-94 units). Tumors with multiple aneuploid populations had significantly higher stain intensity values than either diploid lesions or lesions containing a single aneuploid population (P < 0.05).(ABSTRACT TRUNCATED AT 250 WORDS)

Antibodies, Antinuclear↗