Nuclear Matrix Structure Research Articles

Textural analysis of nuclear mitotic apparatus antigen (NuMA) spatial distribution in interphase nuclei from human drug-resistant CEM lymphoblasts.

In tumour cell lines, the resistance of cancer cells to a variety of structurally unrelated chemotherapeutic drugs is termed multidrug‐resistance or MDR. We reported previously that MDR leukemic cells displayed nuclear texture changes, as assessed by image cytometry. The nature of these changes remained uncertain but they could be associated with alterations of the nuclear matrix which could serve an important role in DNA organization and chromatin structure. Therefore, we have compared the textural features observed in G0/G1 nuclei from human leukemic CEM cells and their MDR variant CEM‐VLB, after staining of either DNA by Feulgen method or nuclear matrix by immunodetection of NuMA antigen on DNase treated samples. Chromatin or NuMA distributions within the nucleus were evaluated by image cytometry. Changes in textural parameters indicate that modifications of NuMA distribution observed in MDR cells are parallel to those observed at the whole chromatin level (i.e., a more decondensed and coarse texture with increase of Energy and Long‐run sections and decrease of Contrast and Short‐run sections). Moreover, Optical Densities measurements indicate that MDR cells seem to contain less NuMA, a datum confirmed by immunoblotting of nuclear proteins. In conclusion, chromatin changes observed by image cytometry in drug‐resistant human leukemic CEM cells appear associated with modifications of the nuclear matrix structure.

Chromatin, nuclear matrix and the cytoskeleton: role of cell structure in neoplastic transformation (review).

Aberrant nuclear and cellular structures are hallmarks of malignant transformation. Thus it is not surprising that the three-dimensional structure of the cell both affects and is affected by changes in gene expression. Here we review the role of the cytoskeleton, nuclear matrix, and chromatin structure in the genesis of cancer. The shape of a cell is governed by a dynamic tissue matrix, which includes extracellular matrix, cytoskeleton and nuclear matrix. Mechanical and chemical signals are transmitted to the nucleus, resulting in alterations in the three-dimensional chromatin organization of genes. The signal transduction pathways affect histone modifications, such as acetylation and phosphorylation, resulting in a relaxed chromatin structure observed in oncogene-transformed cells.

Nuclear Association of Cyclin D1 in Human Fibroblasts: Tight Binding to Nuclear Structures and Modulation by Protein Kinase Inhibitors

The association of cyclin D1 with nuclear structures was investigated in normal human fibroblasts by using hypotonic detergent extraction procedures, immunofluorescence quantitation with flow cytometry, and Western blot analysis. About 20% of the total cellular levels of cyclin D1 was found to be tightly bound to nuclear structures, being the complex formation resistant to DNase I treatment and to high salt extraction. Maximal levels of the insoluble form of the protein were found in the middle to late G1 phase of the cell cycle. Cell fractionation and immunoprecipitation techniques after in vivo 32P-labeling showed that both soluble and nuclear-bound forms of cyclin D1 were phosphorylated. Both fractions were reactive to an anti-phosphotyrosine antibody, while only the latter was detectable with an anti-phosphoserine antibody. Treatment with the protein kinase inhibitor staurosporine, which induces a cell cycle arrest in early G1 phase, strongly reduced cyclin D1 phosphorylation. Concomitantly, the ratio of nuclear-bound/total cyclin D1 levels was reduced by about 60%, compared with the control value. The protein kinase A specific inhibitor isoquinoline-sulfonamide (H-89) induced a similar reduction in the ratio, with no significant modification in the total amount of protein. In contrast, both calphostin C and bisindolylmaleimide, specific inhibitors of protein kinase C, consistently increased by 30–50% the ratio of nuclear-bound/total amount of the cyclin protein. These results suggest that, during the G1 phase, formation of an insoluble complex of cyclin D1 occurs at nuclear matrix structures and that this association is mediated by a protein kinase A-dependent pathway.

Herpes simplex virus type 1 prereplicative sites are a heterogeneous population: only a subset are likely to be precursors to replication compartments.

When herpes simplex virus type 1 (HSV-1) DNA replication is blocked by viral polymerase inhibitors, such as phosphonoacetic acid (PAA) or acyclovir (ACV), UL29 (ICP8) localizes to numerous punctate nuclear foci which are called prereplicative sites. Since this pattern can form in cells infected with mutants which are defective in UL5, UL8, UL9, or UL52 in the presence of polymerase inhibitors (C. J. Lukonis and S. K. Weller, J. Virol. 70:1751-1758, 1996; L. M. Liptak, S. L. Uprichard, and D. M. Knipe, J. Virol. 70:1759-1767, 1996), we previously proposed that it is unlikely that these numerous UL29 foci actually represent a functional subassembly of viral replication proteins that could lead to the formation of replication compartments (C. J. Lukonis and S. K. Weller, J. Virol. 70:1751-1758, 1996). In this paper, we have investigated the requirement for formation of the prereplicative site pattern by using double mutants of HSV. From the analysis of mutants lacking both UL5 and UL9, we conclude that neither viral helicase is required for the prereplicative site pattern to form as long as a polymerase inhibitor is present. From the analysis of mutants defective in both UL30 and UL5, we suggest that the prereplicative site pattern can form under conditions in which viral and/or cellular polymerases are inhibited. Furthermore, reexamination of the UL29 staining pattern in cells infected with wild-type virus in the presence of PAA reveals that at least two different UL29 staining patterns can be detected in these cells. One population of cells contains numerous (greater than 20) punctate UL29 foci which are sites of cellular DNA synthesis. In another population of cells, fewer punctate foci (less than 15) are detected, and these structures do not colocalize with sites of cellular DNA synthesis. Instead, they colocalize with PML, a component of nuclear matrix structures known as ND10. We propose that ND10-associated UL29 sites represent domains at which replication compartments form.

Shift of DNA Polymerase α Nuclear Distribution and Activity in Apoptotic Human Leukaemia Cells

The changes in the distribution of DNA polymerase alpha in nuclei from HL-60 cells treated with Methotrexate (MTX) for up to 15 hr. were checked by means of both confocal analysis and electron microscopy analysis. The results provided evidence that, relative to controls, in the MTX treated cells the enzyme undergoes a topographical rearrangement throughout the nucleus, showing a pattern of distribution which calls to mind the nuclear matrix structure. The "in vitro" analysis of DNA polymerases alpha, beta, and gamma activities revealed that, in nuclei from control cells, DNA polymerase alpha was the principal DNA polymerase driving this "in vitro" system, while after 15 hr. of MTX treatment its activity was largely decreased and replaced by DNA polymerase beta, which is believed to be associated with DNA repair. Taken together, these results suggest that among the intracellular processes elicited by MTX-induced apoptosis in HL60 cells, the redistribution of DNA polymerase alpha and the stimulation of DNA polymerase beta activity might represent an extreme attempt of the cell to preserve the replicative machinery during fragmentation and chromatin margination.

Human myeloid cell nuclear differentiation antigen binds specifically to nucleolin.

The human myeloid cell nuclear differentiation antigen (MNDA) is a nuclear protein expressed specifically in cells of the myelomonocytic lineage and regulated by interferon alpha in a cell-specific fashion. MNDA is also a member of a family of interferon-regulated genes of unknown function. In an effort to elucidate the function of MNDA, three techniques (affinity purification, coimmunoprecipitation, and protein blot assay) were used to characterize its specific protein binding activities. Microsequence analysis showed that MNDA bound the 100 kDa nucleolin protein. The identification of nucleolin was confirmed by immunoreaction with specific antibodies. MNDA contains motifs which could account for specific binding to nucleolin. Nucleolin binds other macromolecules and exhibits features consistent with roles in signal transduction, production of ribosomes, nuclear matrix structure, and regulation of transcription. The present results indicate that the function of MNDA is most likely related to interactions with other proteins. Through these associations, MNDA could contribute cell/lineage- and differentiation-specific limits to the function of ubiquitous proteins such as nucleolin. Further analysis of MNDA protein binding could be critical to elucidating the function of MNDA and could contribute to understanding the function of the products of other members of this interferon-inducible family of genes.

Rapid and transient phosphorylation of nuclear matrix proteins upon interferon-alpha treatment in Daudi lymphoma cells.

Evidence for a rapid and transient hyperphosphorylation of a 45 kD protein in isolated nuclei from interferon-alpha-treated Daudi lymphoma cells is presented. Extraction of nuclear matrices from these nuclei has provided further evidence for the association of such a protein in the nuclear matrix structure. Because phosphorylation assays performed directly on nuclear matrices from interferon-treated cells have revealed rapid and transient increase of gamma 32P-ATP incorporation into this 45 kD band, an early involvement of the nuclear matrix in the response of the nucleus to the interferon antiproliferative message is suggested.

The channels model of nuclear matrix structure

The specificity of eukaryotic DNA organization into loops fixed to the nuclear matrix/chromosomal scaffold has been studied for more than fifteen years. The results and conclusions of different authors remain, however, controversial. Recently, we have elaborated a new approach to the study of chromosomal DNA loops. Instead of characterizing loop basements (nuclear matrix DNA), we have concentrated our efforts on the characterization of individual loops after their excision by DNA topoisomerase II-mediated DNA cleavage at matrix attachment sites. In this review the results of applying this mapping approach are compared with the results and conclusions from studies of nuclear matrix DNA. An attempt is also made to reconsider all data about the specificity of DNA interactions with the nuclear matrix and to suggest a model of spatial organization of the eukaryotic genome which resolves apparent contradictions between these data.

Nuclear matrix involvement in sperm head structural organization

In the sperm nuclei the DNA is packaged into a highly condensed form and is not organized into nucleosome and solenoid but is bound and stabilized mainly by the protamines that arrange the DNA in an almost crystalline state. As demonstrated for somatic cells, the sperm DNA has been reported to be organized in loop domains attached to the nuclear matrix structures. However, the possible role of the sperm head matrix in maintaining the loop organization in absence of a typical nucleosomal structures has not been fully elucidated. By using in situ nick translation at confocal and electron microscope level, we analyzed the organization of the DNAprotamine complex and its association with the sperm nuclear matrix. The data obtained indicate that the chromatin organization in sperm nuclei is maintained during the sperm condensation by means of interactions with the nuclear matrix at fixed sites. The fine stucture of sperm nucleus and of sperm nuclear matrix, investigated on sections and replicas 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 possibly involved in the maintenance of chromatin domains in highly condensed sperm nuclei also.

Biochemical and morphological characterization of the nuclear matrix during the synchronous cell cycle of Physarum polycephalum.

We have investigated biochemical and ultrastructural aspects of the nuclear matrix during the naturally synchronous cell cycle of Physarum polycephalum. The morphology of the in situ nuclear matrix exhibited significant cell cycle changes as revealed by electron microscopic examination, especially during the progression of nuclei through mitosis and S-phase. In mitosis the interchromatin matrix was found to be retracted to the nuclear periphery; during S-phase this interchromatin matrix gradually resembled, concomitant with the reconstruction of a nucleolar remnant structure. During the G2-period no significant changes in matrix morphology were observed. The pattern of nuclear matrix proteins was invariant during the cell cycle; no cycle phase-specific proteins could be detected. In vivo labelling of plasmodia with [35S]methionine/cysteine showed that only a few proteins are synthesized and assembled into nuclear matrix structures in a cell cycle-dependent way; the majority of proteins were synthesized almost continuously. This was also shown for nuclear lamins homologues. In contrast to bulk nuclear histones, those histones that remain tightly bound to the nuclear matrix were synthesized and assembled into nuclear structures in the very first hour of S-phase; assembly was terminated in mid-S-phase, indicating that nuclear matrix-bound chromatin is replicated early in S-phase. Comparison of the acetylation pattern of matrix-bound histone H4 with bulk nuclear H4 revealed a largely elevated acetate content of matrix H4. The percentage of acetylated subspecies was entirely different from that in bulk nuclear H4, indicating that matrix-associated histones represent a subpopulation of nuclear histones with distinct properties, reflecting specific structural requirements of matrix-attached chromatin.

The 70-kD Rat Liver Nucleoplasmic Protein-Binding Hormone-Responsive Element of Rat Haptoglobin Gene Shares Size, Charge and Epitopes with Lamin A

The 70 kD rat liver nucleoplasmic protein was shown previously to display binding affinity for hormone responsive element of rat haptoglobin gene which markedly increased during the acute-phase reaction. In this work the possibility of its structural homology to lamin-type intermediate filament proteins is assessed. The results of two-dimensional Southwestern and Western analyses pinpointed to size, charge and epitope homology between the 70 kD rat liver nucleoplasmic protein binding the hormone responsive element and the lamin A constituent of nuclear matrix structure.

Glycolytic enzymes as DNA binding proteins

1. 1. Numerous studies have demonstrated the presence of at least four glycolytic enzymes in the nuclear compartment of several cell systems. 2. 2. These include, lactate dehydrogenase, phosphoglycerate kinase, aldolase and glyceraldehyde-3-phosphate dehydrogenase. 3. 3. In some cases the glycolytic enzymes found in the nuclei were a modified form from that found in the cytoplasmic counterpart. 4. 4. In all four eases, the nuclear form of these glycolytic enzymes has been reported to bind DNA. 5. 5. Although none of these enzymes interact with a specific target DNA sequence, their association with DNA may play a role in transcription and replication of DNA through general stabilization of the nuclear matrix or chromatin structure. 6. 6. The present review aims to summarize the current understanding of this phenomenon and to examine the role of the DNA-binding activities of the glycolytic enzymes in cell growth and differentiation.

The stability of maize nuclei to restriction enzyme digestion differs with transcriptional activity

SUMMARYThe stability to restriction of nuclei obtained from plant cells of different transcriptional activity (dry embryo, root tip meristem and epicotyl protoplasts) has been studied. The morphological data obtained following fluorescent staining of nucleoid DNA with acridine orange indicate that the dry embryo structures are less stable than those actively involved in transcription, probably reflecting the lack of internal nuclear matrix structures in the dry embryo. The data support the suggestion for the key role these structures play in the functioning of the genome.

Intranuclear compartmentalization of transcribed and nontranscribed c-myc sequences in Namalva-S cells.

This investigation is centered on the intranuclear localization of transcribed and nontranscribed c-myc sequences in human Namalva-S cells bearing t(8;14) translocation. Southern hybridization showed that the breakpoint in the truncated allele of c-myc lies outside the characteristic 12.8-kbp EcoRI fragment: as Northern analysis indicated, this reorganization induces a high level of c-myc transcription. Following high-salt treatment, EcoRI digestion and centrifugation, isolated nuclei from the same cells are separated into two residual fractions: a heavier P fraction including nuclear matrix structures and a light S fraction representing dehistonized chromatin fibres. Comparative hybridization experiments revealed that the above procedure separates the c-myc sequences between the two fractions. To locate the site of intranuclear c-myc transcription, we performed run-on experiments with two fractions, topologically analogous to the residual P and S fractions but maintaining the original chromatin organization. These experiments indicated that chromatin P fraction harbours actively transcribed c-myc sequences while chromatin S harbours nontranscribed ones. Further experiments have clarified that the transcribed c-myc sequences are firmly bound to the matrix by multiple attachment sites, arranged throughout the entire gene locus. It was found, moreover, that at the site of attachment the interaction between DNA and the matrix components is realized via proteins. Controls with the beta-globin gene, which is constitutively nonexpressed in Namalva-S cells but upon induction is highly expressed in murine erythroleukemia cells, completely confirmed the conclusion we had made for the intranuclear localization of c-myc. Thus the experiments presented here support the more common idea that the transcribed and nontranscribed sequences are precisely compartmentalized.

Localization of nuclear matrix core filament proteins at interphase and mitosis

The gentle removal of chromatin uncovers a nuclear matrix consisting of two parts: a nuclear lamina connected to the intermediate filaments of the cytoskeleton and an internal matrix of thick, polymorphic fibers connecting the lamina to masses in the nuclear interior. This internal nuclear matrix can be further fractionated to uncover a highly branched network of 9 nm and 13 nm core filaments retaining some enmeshed bodies. The core filament network retains most of the nuclear RNA, as well as the fA12 RNP antigen, and may be the most basic or core element of internal nuclear structure. One high molecular weight protein component of the core filament network, the H1B2 antigen, is normally masked in the interphase nucleus and is uncovered as the chromatin condenses at mitosis. This protein is associated with a fibrogranular network surrounding and connected to the chromosomes. The core filament- associated fA12 antigen also becomes associated with this perichromosomal network. We propose that the core filament nuclear matrix structure may not completely disassemble at mitosis but, rather, that parts remain as a structural network connected to chromosomes and other mitotic structures. These mitotic networks may, in turn, serve as the core structures on which the nuclear matrices of daughter cells are built.

Dramatic increase in poly(A) synthesis after infection of Molt-3 cells with HIV

Infection of Molt-3 cells with human immunodeficiency virus-1 (HIV-1) was found to cause a rapid increase in extractable poly(A) polymerase activity, while the activity of poly(A) degrading endoribonuclease IV strongly decreased at the same time. The increase in poly(A) polymerase activity seems not to be due to a change in the actual number of enzyme molecules, but rather to posttranslational enzyme modification, most likely caused by phosphorylation by nuclear protein kinase NI or protein kinase C. Both kinases were found to be able to phosphorylate poly(A) polymerase in vitro [homogeneous enzyme as well as poly(A) polymerase in intact nuclei]. Phosphoamino acid analysis revealed an incorporation of phosphate into serine and, to a lower extent, into threonine residues of the enzyme protein; no phosphotyrosine could be detected. In the nucleus, the poly(A) polymerase and the endoribonuclease IV are bound to the nuclear matrix. The phosphorylation related enhancement of nuclear poly(A) polymerase activity could be abolished by addition of the zinc and copper chelator o-phenanthroline, which inhibited zinc-containing purified poly(A) polymerase and destroyed the poly(A) polymerase containing nuclear matrix structure, resulting in a solubilization of the enzyme.

Association of Tat protein and viral mRNA with nuclear matrix from HIV-1-infected H9 cells

The transactivating protein from human immunodeficiency virus type 1 (HIV-1), Tat, was found to bind to the nuclear matrix from uninfected and HIV-1-infected H9 cells. Addition of the Zn 2+, Cd 2+ and Cu 2+ chelator o-phenanthroline destroyed the matrix fibrils and the binding affinity of Tat to the matrix. A sequential treatment of the matrix, first with o-phenanthroline and then with ZnCl 2, partially restored the fibrillar-like matrix structure. Infection of H9 cells with HIV-1 resulted in a displacement of cellular mRNA by viral mRNA from the nuclear matrix. Both the matrix-bound host cell and HIV-1 mRNA were found to dissociate from the matrix in the presence of o-phenanthroline. This could be prevented by coincubation with Zn 2+ or Cu 2+ (but not Mg 2+), which stabilize the mRNA containing nuclear matrix structure.

Alterations of Neuronal Nuclear Matrix and Chromatin Structure after Irradiation under Aerobic and Anoxic Conditions

This study was undertaken to determine if structural alterations of the bulk chromatin and the amount of protein associated with the nuclear matrix in cerebellar neurons depend on radiation dose and a cell's state of oxygenation. After irradiation with 2.5 to 25.0 Gy under both aerobic and anoxic conditions, the sensitivity of the neuronal chromatin to m. nuclease digestion increase linearly with dose up to about 5 Gy, beyond which there was no further increase. The same increase in accessibility of chromatin to micrococcal nuclease digestion was observed when neuronal nuclei were irradiated at 4 degrees C. Neuronal nuclei were stained with propidium iodide (PI) for DNA and with fluorescein isothiocyanate (FITC) for protein, both before and after complete digestion with DNase I, and analyzed by flow cytometry. There was no change in either the PI (P greater than 0.4) or the FITC (P greater than 0.9) fluorescence of undigested nuclei after irradiation. For the DNase I digested nuclei, the PI fluorescence was unchanged after irradiation (P greater than 0.4), but the FITC fluorescence increased significantly (P less than 0.02). This increase in the FITC fluorescence was linear with dose up to about 5 Gy, beyond which there was no further increase. The flow cytometry results from DNase I digested nuclei were identical for neurons irradiated under aerobic or anoxic conditions, indicating that this phenomenon is oxygen independent. This increase in FITC fluorescence after irradiation was inhibited at ice-cold temperatures and probably reflects an increase in protein content at the nuclear matrix that requires metabolism. This may explain our previously observed resistance of nuclear matrix-associated DNA to digestion by DNase I. This protein increase at the nuclear matrix appears to follow "saturation" kinetics identical to that previously reported for repair of DNA strand breaks in cerebellar neurons. However, the exact molecular nature of this process and its role in DNA repair or cell survival remains to be determined.

Regulation of the synthesis of DNA polymerase-alpha in regenerating liver by calcium and 1,25-dihydroxyvitamin D3.

Digestion of nuclei from normal or partially hepatectomised rat livers with endogenous nucleases liberated a pool of cryptic DNA polymerase-alpha activity which had previously gone unrecognised. Most of this activity is released into the supernatant as free enzyme molecules (11S), but a small fraction of it is released as a complex of 16S (probably with DNA primase). About 40% of the enzyme remains in the pellet, which contains undigested chromatin and components of the residual nuclear matrix and nucleoskeletal structures. Virtually all of this remaining activity is extracted by 2.0 M salt. The activity of DNA polymerase-alpha increases equally in all nuclear fractions during the period of DNA replication in regenerating rat liver. Lowering of the serum calcium level by thyroparathyroidectomy does not affect basal DNA polymerase-alpha activity, but prevents induction of the enzyme during the later stages of prereplicative development. However, an injection of 1 alpha,25-dihydroxy vitamin D3 into the rat during the first 6 h after parital hepatectomy restores the ability of the hepatocytes to induce DNA polymerase-alpha activity and initiate DNA synthesis. These results are discussed in terms of the role of calcium ions in the regulation of the critical stage of prereplicative development which commits the cells to DNA replication.

Mapping replicational sites in the eucaryotic cell nucleus.

We have used fluorescent microscopy to map DNA replication sites in the interphase cell nucleus after incorporation of biotinylated dUTP into permeabilized PtK-1 kangaroo kidney or 3T3 mouse fibroblast cells. Discrete replication granules were found distributed throughout the nuclear interior and along the periphery. Three distinct patterns of replication sites in relationship to chromatin domains in the cell nucleus and the period of S phase were detected and termed type I (early to mid S), type II (mid to late S) and type III (late S). Similar patterns were seen with in vivo replicated DNA using antibodies to 5-bromodeoxyuridine. Extraction of the permeabilized cells with DNase I and 0.2 M ammonium sulfate revealed a striking maintenance of these replication granules and their distinct intranuclear arrangements with the remaining nuclear matrix structures despite the removal of greater than 90% of the total nuclear DNA. The in situ prepared nuclear matrix structures also incorporated biotinylated dUTP into replication granules that were indistinguishable from those detected within the intact nucleus.