The relationship of the nuclear matrix to cellular structure and function

Communication of genome regulatory elements in a folded chromosome

The most popular model of gene activation by remote enhancers postulates that the enhancers interact directly with target promoters via the looping of intervening DNA fragments. This interaction is thought to be necessary for the stabilization of the Pol II pre-initiation complex and/or for the transfer of transcription factors and Pol II, which are initially accumulated at the enhancer, to the promoter. The direct interaction of enhancer(s) and promoter(s) is only possible when these elements are located in close proximity within the nuclear space. Here, we discuss the molecular mechanisms for maintaining the close proximity of the remote regulatory elements of the eukaryotic genome. The models of an active chromatin hub (ACH) and an active nuclear compartment are considered, focusing on the role of chromatin folding in juxtaposing remote DNA sequences. The interconnection between the functionally dependent architecture of the interphase chromosome and nuclear compartmentalization is also discussed.

On the history of nuclear matrix manifestation

The nonchromatin proteinous residue of the cell nucleus was revealed in our laboratory as early as in 1948 and then identified by light and electron microscopy as residual nucleoli, intranuclear network and nuclear envelope before 1960. This structure termed afterwards as "nuclear residue", "nuclear skeleton", "nuclear cage", "nuclear carcass" etc., was much later (in 1974) isolated, studied and entitled as "nuclear matrix" by Berezney and Coffey, to whom the discovery of this residual structure is often wrongly ascribed. The real history of nuclear matrix manifestation is reported in this paper.

Differential nuclear matrix protein expression in prostate cancers: correlation with pathologic stage

PURPOSE

Nuclear Matrix Proteins (NMP) have been shown to be tissue and cell-type specific. Several unique NMPs have been investigated in various cancerous tissues, including prostate, bladder and kidney, and some are presently utilized as tumor markers. This study was aimed at characterizing the differential NMP expression in the pathologically more aggressive prostate cancers.

METHODS

High resolution two-dimensional gel electrophoresis and silver staining was used to elucidate the NMP distribution of fresh prostate cancer nuclei, obtained from 39 radical prostatectomy specimens, surgically removed from men with clinically localized prostate cancer. Based on the final pathological grading, specimens were grouped according to predicted prognosis: poor--with seminal vesicle (SV) or lymph node (LN) involvement or established capsular penetration (ECP) with gleason score >7; intermediate--organ confined (OC) or focal capsular penetration (FCP) with gleason score 7 or ECP with gleason score 6; and good--with OC or FCP and gleason score <7.

RESULTS

A specific charged protein (YL-1) of molecular weight 76 kD and isoelectric range 6.0-6.6 was found to be consistently present in 19 of 19 aggressive cancers. It was present only in 1 of 10 in the group with good prognosis and weakly positive in 9 of 10 in the intermediate group.

CONCLUSIONS

Within this preliminary study, the expression of YL-1 appears to be related to aggressive prostate cancer, suggesting a potential marker of poor prognosis for clinically localized prostate cancer. Further characterization of the identity and function of this NMP is needed to fully ascertain its clinical potential.

DNA supercoiling changes and nuclear matrix-associated proteins: possible role in oncogene-mediated radioresistance

PURPOSE

Transfection with either H-ras or H-ras and c-myc has been shown to confer radioresistance in rat embryonal cells (REC). REC primary, transfected with either c-myc, H-ras or cotransfected with c-myc and H-ras (in ascending order of radioresistance and tumorigenicity), were used as an in vitro model system to determine if nuclear matrix-mediated higher order DNA organization contributes to oncogene-mediated radioresistance.

METHODS AND MATERIALS

DNA damage induction and repair were measured by the alkaline and neutral filter elution assays. Analysis of the ability of DNA loop domains to undergo supercoiling changes in the presence of radiation-induced damage was determined by the fluorescent halo assay (FHA). Because DNA loops are organized by the nuclear matrix (NM), a study of NM-associated proteins by high resolution two-dimensional gel electrophoresis was performed.

RESULTS

Induction and repair rates of DNA single- and double-strand breaks were similar for the relatively radiosensitive c-myc transfected and the radioresistant c-myc + H-ras transfected cells. However, the degree of inhibition of DNA supercoil rewinding in the presence of radiation-induced damage was less in the radioresistant cells and was inversely correlated with survival. A progressive loss of NM-associated proteins was observed, which correlated with increasing radioresistance and tumorigenicity in these cell lines. In addition, some protein changes were consistent with the possibility that these changes could be involved in DNA anchoring.

CONCLUSIONS

Increased radioresistance associated with increasing tumorigencity in these oncogene-transfected cell lines could be due to changes in NM-mediated DNA organization, possibly via differences in NM protein composition that occur following oncogenic transfection.

The nuclear matrix: a structural milieu for genomic function

While significant progress has been made in elucidating molecular properties of specific genes and their regulation, our understanding of how the whole genome is coordinated has lagged behind. To understand how the genome functions as a coordinated whole, we must understand how the nucleus is put together and functions as a whole. An important step in that direction occurred with the isolation and characterization of the nuclear matrix. Aside from the plethora of functional properties associated with these isolated nuclear structures, they have enabled the first direct examination and molecular cloning of specific nuclear matrix proteins. The isolated nuclear matrix can be used for providing an in vitro model for understanding nuclear matrix organization in whole cells. Recent development of high-resolution and three-dimensional approaches for visualizing domains of genomic organization and function in situ has provided corroborative evidence for the nuclear matrix as the site of organization for replication, transcription, and post-transcriptional processing. As more is learned about these in situ functional sites, appropriate experiments could be designed to test molecular mechanisms with the in vitro nuclear matrix systems. This is illustrated in this chapter by the studies of nuclear matrix-associated DNA replication which have evolved from biochemical studies of in vitro nuclear matrix systems toward three-dimensional computer image analysis of replication sites for individual genes.

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.

Nuclear matrins: identification of the major nuclear matrix proteins

A preparative two-dimensional polyacrylamide gel system was used to separate and purify the major Coomassie blue-stained proteins from the isolated rat liver nuclear matrix. Approximately 12 major proteins were consistently found. Of these, 5 proteins represented identified proteins, including nuclear lamins A, B, and C, the nucleolar protein B-23, and residual components of core heterogeneous nuclear ribonucleoproteins. The remaining eight major proteins termed the nuclear matrins consisted of matrin 3 (125 kDa, slightly acidic), matrin 4 (105 kDa, basic), matrins D-G (60-75 kDa, basic), and matrins 12 and 13 (42-48 kDa, acidic). Peptide mapping and two-dimensional immunoblot studies indicate that matrins D-G compose two pairs of related proteins (matrins D/E and F/G) and that none of the matrins resemble the nuclear lamins or any of the other major proteins detected on our two-dimensional gels. Subfractionation immunoblot experiments demonstrated the nearly exclusive localization of matrins F/G and other matrins to the nuclear matrix fraction of the cell. These results were further supported by indirect immunofluorescence microscopy that showed a strictly interior nuclear localization of the matrins in intact cells in contrast to the peripherally located nuclear lamins. We conclude that the nuclear matrins are a major class of proteins of the nuclear matrix interior and are distinct from the nuclear lamins.

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.

Electrophoretic analysis of nuclear matrix proteins and the potential clinical applications

Nuclear matrix proteins form the skeleton of the nucleus and participate in the various cellular functions of the nucleus. These proteins have been demonstrated to be tissue-type specific and can potentially reflect changes in the state of differentiation of the cell. Elucidating nuclear matrix protein changes necessitates the use of high-resolution two-dimensional polyacrylamide gel electrophoresis. Separation of this complex mixture into its component parts resolves protein changes when comparing the normal state to a diseased state of a cell. Evidence has been reviewed which shows the potential use of nuclear matrix proteins and antibodies to nuclear matrix proteins as diagnostic tools for various cancers, autoimmune diseases, adenoviral infection, and other diseases. Consequently, the central functions of the nuclear matrix in the cell allow it to have significant potential as a diagnostic agent.

Cellular harmonic information transfer through a tissue tensegrity-matrix system

Cells and intracellular elements are capable of vibrating in a dynamic manner with complex harmonics, the frequency of which can now be measured and analyzed in a quantitative manner by Fourier analysis. Cellular events such as changes in shape, membrane ruffling, motility, and signal transduction occur within spatial and temporal harmonics that have potential regulatory importance. These vibrations can be altered by growth factors and the process of carcinogenesis. It is important to understand the mechanism by which this vibrational information is transferred directly throughout the cell. From these observations we propose that vibrational information is transferred through a tissue tensegrity-matrix which acts as a coupled harmonic oscillator operating as a signal transucing system from the cell periphery to the nucleus and ultimately to the DNA. The vibrational interactions occur through a tissue matrix system consisting of the nuclear matrix, the cytoskeleton, and the extracellular matrix that is poised to couple the biologic oscillations of the cell from the peripheral membrane to the DNA through a tensegrity-matrix structure. Tensegrity has been defined as a structural system composed of discontinuous compression elements connected by continuous tension cables, which interact in a dynamic fashion. A tensegrity tissue matrix system allows for specific transfer of information through the cell by direct transmission of vibrational chemomechanical energy through harmonic wave motion.

Flow cytometric studies of the nuclear matrix

We have devised a method to measure the protein and nucleic acid content of the nuclear matrix using flow cytometry. Nuclear matrices were prepared from nuclei by DNase I digestion followed by 3 M NaCl extraction. The resulting particles were stained with fluorescein isothiocyanate (FITC) for protein and propidium iodide (PI) for double-stranded nucleic acids, and fluorescence as well as forward angle light scatter was detected. The matrices were also subjected to additional chemical or enzymatic perturbations, and changes in the above parameters were measured. Results showed that matrices from heat-shocked cells not only retained the majority of heat-induced excess nuclear protein, but also exhibited higher PI signals than controls after RNase A digestion. This observation did not hold if RNase A digestion preceded high-salt extraction, suggesting that a salt-extractable moiety had been replaced or altered by heat so that double-stranded RNA was protected from the nucleolytic attack. The residual PI fluorescence in matrices from heated cells bore a linear relationship to the increased protein content in those matrices, indicating that the excess protein sequesters matrix-associated RNA. Polyacrylamide gel electrophoresis of matrix polypeptides revealed increased amounts of many proteins as a result of heat as well as the appearance of several new proteins, one of which comigrates with the HSP72/73 heat-shock proteins. The results of these studies show that flow cytometry can be used to study the nuclear matrix and is capable of detecting changes that result from alterations in its protein composition.

Subnuclear localization of the trans-activating protein of human T-cell leukemia virus type I

Human T-cell leukemia virus type I is associated with human lymphoid malignancies. The p40xI protein encoded by the x gene of this virus is believed to play some role in virally mediated transformation. This gene is known to encode a transcriptional trans activator which previous studies have shown to be a nuclear protein. Further characterization of the intracellular kinetics of this protein showed that it migrated into the nucleus very soon after synthesis. Within the nucleus, p40xI was distributed almost equally between the nucleoplasm and the nuclear matrix. Given the proposed role of the nuclear matrix in RNA transcription, the association of p40xI with the matrix places it in an appropriate cellular compartment to exercise an effect on transcription.

Changes in transcriptional activity and matrix association of alpha 2u-globulin gene family in the rat liver during maturation and aging

Hepatic synthesis of alpha 2u-globulin in the male rat begins at puberty (about 40 days), reaches a peak level at about 80 days, and ceases at about 750-800 days of age. The age-dependent changes in alpha 2u-globulin synthesis are correlated with both the steady-state level of the hepatic mRNA for this protein and the rate of transcription of the alpha 2u-globulin gene family. Transcriptional activation of the alpha 2u-globulin gene family at puberty and cessation of transcription at senescence correlate with the association and dissociation of this gene domain with the nuclear matrix. Unlike the alpha 2u-globulin gene, the albumin gene in the liver shows preferential association with the nuclear matrix throughout the life. From these results we conclude that the age-dependent changes in alpha 2u-globulin synthesis are due to the alteration in the rate of transcription of the alpha 2u-globulin gene, and that the association of this gene domain to the nuclear matrix is a prerequisite to its transcriptional activation.

Ribosomal DNA sequences attached to the nuclear matrix

The organization of rat liver ribosomal DNA (rDNA) as matrix-attached DNA loops was examined using a protocol which fractionates chromatin from discrete regions of DNA loops. Southern blot analysis of matrix-attached and solubilized chromatin DNA fragments demonstrated that rDNA is associated with the matrix via its 5' and 3' nontranscribed spacer sequences (NTS). Although the 45 S rRNA coding sequences were approximately threefold enriched in matrix preparations, the recovery of this DNA (unlike the NTS) was dependent on the extent of nuclease digest and proportional to the length of the matrix-attached DNA fragments. The data suggest that rDNA is organized as matrix-attached DNA loops and only the NTS are directly involved in matrix binding. Further, we demonstrated that while the kinetics and extent of nuclease digestion were similar in all regions of the DNA loops, the nuclease digestion pattern of bulk nuclear and matrix DNA showed a typical nucleosome organization, but the rDNA fragments retained with the nuclear matrix did not.

Protein disulfide crosslinking stabilizes a polyoma large T antigen-host protein complex on the nuclear matrix

We have investigated the effects of intermolecular disulfide crosslinking and temperature-dependent insolubilization of nuclear proteins in vitro on the association of the polyoma large T antigen with the nuclear matrix in polyomavirus-infected mouse 3T6 cells. Nuclear matrices, prepared from polyomavirus-infected 3T6 cells by sequential extraction of isolated nuclei with 1% Triton X-100 (Triton wash), DNase I, and 2 M NaCl (high salt extract) at 4 degrees C, represented 18% of total nuclear protein. Incubation of nuclei with 1 mM sodium tetrathionate (NaTT) to induce disulfide crosslinks or at 37 degrees C to induce temperature-dependent insolubilization prior to extraction, transferred an additional 9-18% of the nuclear protein from the high salt extract to the nuclear matrix. This additional protein represented primarily an increased recovery of the same nuclear protein subset present in nuclear matrices prepared from untreated nuclei. Major constituents of chromatin including histones, hnRNP core proteins, and 98% of nuclear DNA were removed in the high salt extract following either incubation. Polyoma large T antigen was quantified in subcellular fractions by immunoblotting with rat anti-T ascites. Approximately 60-70% of the T antigen was retained in nuclei isolated in isotonic sucrose buffer at pH 7.2. Most (greater than 95%) of the T antigen retained in untreated nuclei was extracted by DNase-high salt treatment. Incubation at 37 degrees C or with NaTT transferred most (greater than 95%) of the T antigen to the nuclear matrix. T antigen solubilized from NaTT-treated matrices with 1% SDS sedimented on sucrose gradients as a large (50-S) complex. These complexes, isolated by immunoprecipitation with anti-T sera, were dissociated by reduction with 2-mercaptoethanol, and SDS-PAGE analysis revealed that T antigen was crosslinked in stoichiometric amounts to several host proteins: 150, 129, 72, and 70 kDa. These host proteins were not present in anti-T immunoprecipitates of solubilized nuclear matrices prepared from iodoacetamide-treated cells. Our results suggest that the majority of polyomavirus large T antigen in infected cells is localized to a specific subnuclear domain which is distinct from the bulk chromatin and is closely associated with the nuclear matrix.

Steroid hormone receptor localization in the nuclear matrix: interaction with acceptor sites

The nuclear matrix is a conceptually attractive candidate for the site in the nucleus where steroid hormone-receptor complexes might interact to modulate DNA structure and function. We have demonstrated that in sex steroid target tissues a major proportion (50-100%) of the high affinity and steroid-specific receptors that become associated with the nucleus following hormonal stimulation are localized in the nuclear matrix. Direct cell-free binding assays confirm that this localization is due to the presence of specific acceptor sites in the matrix to which steroid-receptor complexes bind with high affinity and tissue specificity, and is not the result of spurious binding. The nuclear matrix appears to be a major site of hormone receptor binding in the nucleus, and this situation is consistent with the known ability of steroid hormones to stimulate gene transcription, a process which also appears to occur in association with the nuclear matrix.

Nuclear compartmentalization of the v-myb oncogene product

Nuclei obtained from chicken leukemic myeloblasts transformed by avian myeloblastosis virus were fractionated into various subnuclear compartments, which were then analyzed by specific immunoprecipitation for the presence of the leukemogenic product, p48v-myb, of the viral oncogene. In cells labeled for 30 or 60 min with L-[35S]methionine and in unlabeled exponentially dividing leukemic cells analyzed by Western blotting, p48v-myb was detected within the nucleoplasm (29 +/- 9% [standard deviation] of the total), chromatin (7 +/- 4%), and lamina-nuclear matrix (64 +/- 9%). Also, in myeloblasts analyzed by immunofluorescence during mitosis, p48v-myb appeared to be dispersed through the cell like the lamina-nuclear matrix complex. Strong attachment to the nuclear matrix-lamina complex suggests that p48v-myb may be involved in DNA replication or transcription or both.

The association of acute phase protein genes with the nuclear matrix of rat liver during experimental inflammation

The association of acute phase protein genes with the nuclear matrix in livers from healthy rats and rats suffering from inflammation was studied. alpha 1-Acid glycoprotein and transthyretin are synthesized at low levels in normal liver and no matrix association of their genes was observed. Albumin, transferrin and the beta-chain of fibrinogen are synthesized at much higher levels in normal liver and their genes were found to be associated with the nuclear matrix. An inflammation induced increase in synthesis of alpha 1-acid glycoprotein and the beta-chain of fibrinogen resulted in stronger matrix association of their genes. However, inflammation induced decrease in the synthesis of albumin did not influence matrix association of its gene.

The relationship between chromosomal origins of replication and the nuclear matrix during the cell cycle

A cytological investigation into the dynamic behaviour of the origins of replication with respect to the nuclear matrix has been carried out on Xenopus laevis cultured cells. In order to preferentially label origins or 'non-origin' regions along DNA fibres, 5-fluoro-2'-deoxyuridine (FUdR)-treated cells were pulsed with [3H]deoxyadenosine in early or late S phase. Samples were then allowed to proceed through the cell cycle for increasing times. The DNA loops were induced in situ to completely uncoil around the nuclear matrix. The autoradiographic analysis shows that, under the experimental conditions used, 'non-origin' regions behave as expected from previous studies, i.e., they associate with the nuclear matrix only when they become part of a replication fork, whereas active origins of replication remain associated with the matrix throughout the cell cycle.

Is the nuclear matrix the site of DNA replication in eukaryotic cells?

Four types of experiment were carried out to test the recently proposed model of matrix-bound replication in eukaryotic cells. In experiments with pulse-labelling we found preferential association of newly replicated DNA with the matrix only when the procedure for isolation includes first high-salt treatment of isolated nuclei and then digestion with nucleases, or when prior to digestion the nuclei have been stored for a prolonged time. In both cases, however, evidence was found that this preferential association is due to a secondary, artifactual binding of the newly replicated chromatin region to the matrix elements. Pulse-chase experiments and experiments with continuous labelling were carried out to answer the question whether during replication the DNA is reeled through the replication complexes, i.e., whether newly replicated DNA is temporarily or permanently associated with the matrix. The results showed that at that time the matrix DNA does not move from its site of attachment. Since, according to the model of matrix-bound replication, the forks are assumed to be firmly anchored to high-salt resistant proteinaceous matrix structures, the chromatin fragments isolated with endonuclease not recognizing newly replicated DNA and purified by sucrose gradient centrifugation should be free of replication intermediates. The electronmicroscopic analysis of such fragments revealed the existence of intact replication micro-bubbles. Moreover, the fragments with replication configurations appeared as smooth chromatin fibres not attached to elements characteristic for the matrix. All these experiments suggest that the nuclear skeleton is not a native site of DNA replication in eukaryotic cells.

Morphometric analysis and topological organization of nuclear matrix in freeze-fractured electron microscopy

The ultrastructural organization of nuclear matrix, purified from intact or membrane-denuded rat liver nuclei, has been analysed by means of freeze-fracturing technique. This method avoids dehydration and embedding which, in conventional thin sectioning, partly distort or mask the matrix ultrastructure. The various matrix components, and mainly the peripheral lamina and the inner network revealed complex arrangements undetectable with conventional techniques. Morphometric analyses performed with a Texture Analysis System (TAS) Leitz, allowed to obtain precise information on the matrix constituents, based on the histograms of their size distribution. These textural characteristics have been utilized in order to identify, by means of a particular computer programme, the putative matrix localization within intact freeze-fractured nuclei.

Association states of androgen receptors in nuclei of human benign hypertrophic prostate

Androgen receptors (AR) were quantified in nuclei purified from unfractionated benign hypertrophic prostate (bph) tissue and from separated epithelium and stroma from bph specimens. Both epithelial and stromal cell nuclei contained AR, although concentrations in epithelial cell nuclei were higher and more variable. Variations in AR levels in epithelial cell nuclei reflected variations in unfractionated-tissue nuclei. Nuclear AR were further characterized regarding extractability with or resistance to 0.6 mol/lKCl and micrococcal nuclease. Nuclei from unfractionated tissue, epithelium, and stroma contained populations of AR susceptible and refractory to solubilization with KC1 and nuclease. Nuclease- and salt-sensitive populations of AR were similar numerically. The observed variability in epithelial cell nuclear AR was attributable to a wide range of solubilizable AR. Nuclease-digestion profiles and sedimentation analyses revealed that this wide range was not due to AR associated with soluble chromatin oligomers but to AR not detectably associated with other nuclear components. In contrast, AR in stromal cell nuclei was predominantly resistant to KC1 and nuclease, and variability in total nuclear AR concentration was due to variation in the nonextractable population.

Nuclear compartmentalization of the v-myb oncogene product

Nuclei obtained from chicken leukemic myeloblasts transformed by avian myeloblastosis virus were fractionated into various subnuclear compartments, which were then analyzed by specific immunoprecipitation for the presence of the leukemogenic product, p48v-myb, of the viral oncogene. In cells labeled for 30 or 60 min with L-[35S]methionine and in unlabeled exponentially dividing leukemic cells analyzed by Western blotting, p48v-myb was detected within the nucleoplasm (29 +/- 9% [standard deviation] of the total), chromatin (7 +/- 4%), and lamina-nuclear matrix (64 +/- 9%). Also, in myeloblasts analyzed by immunofluorescence during mitosis, p48v-myb appeared to be dispersed through the cell like the lamina-nuclear matrix complex. Strong attachment to the nuclear matrix-lamina complex suggests that p48v-myb may be involved in DNA replication or transcription or both.

A constitutively transcribed actin gene is associated with the nuclear matrix in a Drosophila cell line

The relationship between transcriptional activity and gene association with the nuclear matrix has been investigated in Drosophila melanogaster. The nuclear matrix of Schneider cell line 2 of Drosophila was isolated and observed to conform to expected dimensions in phase contrast and scanning electron microscopic preparations. This structure contains proteins that appear similar to the intact nucleus. High salt extracted nuclei digested with DNase I released 98% of the DNA, whereas digestion with Eco RI released a maximum of 80%. These and other nuclease digestions indicate that satellite DNA as well as some unique sequence DNA are bound to the nuclear matrix. A constitutively transcribed actin gene was enriched in the nuclear matrix bound DNA. Two other nontranscribed genes, a muscle-specific actin gene and the myosin heavy chain gene, showed no enrichment in nuclear matrix DNA.

The nuclear matrix continues DNA synthesis at in vivo replicational forks

Alkaline cesium chloride gradient analysis of in vivo [3H]bromodeoxyuridine-labeled and in vitro [alpha-32P]dCTP-labeled DNA was used to determine whether in vitro DNA synthesis in regenerating rat liver nuclei and nuclear matrices continued from sites of replication initiated in vivo. At least 70 and 50% of the products of total nuclear and matrix-bound in vitro DNA synthesis, respectively, were continuations of in vivo initiated replicational forks. The relationship of the in vitro DNA synthetic sites in total nuclei versus the nuclear matrix was examined by using [3H]bromodeoxyuridine triphosphate to density label in vitro synthesized DNA in isolated nuclei and [alpha-32P]dCTP to label DNA synthesized in isolated nuclear matrix. A minimum of about 40% of matrix-bound DNA synthesis continued from sites being used in vitro by isolated nuclei. Furthermore, nuclear matrices prepared from in vitro labeled nuclei were 5-fold enriched in DNA synthesized by the nuclei and were several-fold enriched, compared to total nuclear DNA, in a particularly high density labeled population of DNA molecules.

V-myc- and c-myc-encoded proteins are associated with the nuclear matrix

A series of extraction procedures were applied to avian nuclei which allowed us to define three types of association of v-myc- and c-myc-encoded proteins with nuclei: (i) a major fraction (60 to 90%) which is retained in DNA- and RNA-depleted nuclei after low- and high-salt extraction, (ii) a small fraction (1%) released during nuclease digestion of DNA in intact nuclei in the presence of low-salt buffer, and (iii) a fraction of myc protein (less than 10%) extractable with salt or detergents and found to have affinity for both single- and double-stranded DNA. Immunofluorescence analysis with anti-myc peptide sera on cells extracted sequentially with nucleases and salts confirmed the idea that myc proteins were associated with a complex residual nuclear structure (matrix-lamin fraction) which also contained avian nuclear lamin protein. Dispersal of myc proteins into the cytoplasm was found to occur during mitosis. Both c-myc and v-myc proteins were associated with the matrix-lamin, suggesting that the function of myc may relate to nuclear structural organization.

Lateral diffusion in nuclear membranes

Chemical modification of rat liver nuclei with citraconic anhydride selectively removed outer nuclear membrane. This conclusion was based on (a) transmission electron microscopy, (b) lipid analysis, (c) lamin B as an inner membrane-associated marker, and (d) the demonstration of phospholipid lateral mobility on outer membrane-depleted nuclei as a criteria for inner membrane integrity. Addition of urea or N-ethylmaleimide resulted in the additional disruption of inner membrane. Fluorescence photobleaching was used to determine the long range (greater than 4 microns) lateral transport of lectin receptors and a phospholipid analog in both membranes. The diffusion coefficient for wheat germ agglutinin on whole nuclei was 3.9 X 10(-10) cm2/s whereas the diffusion coefficient for wheat germ agglutinin in outer membrane-depleted nuclei was less than or equal to 10(-12) cm2/s. Phospholipid mobilities were the same in whole and outer membrane-depleted nuclei (3.8 X 10(-9) cm2/s). The protein diffusion differences observed between whole and outer membrane-depleted nuclei may be interpreted in the context of two functionally different membrane systems that compose the double bilayer of the nucleus.

V-myc- and c-myc-encoded proteins are associated with the nuclear matrix

A series of extraction procedures were applied to avian nuclei which allowed us to define three types of association of v-myc- and c-myc-encoded proteins with nuclei: (i) a major fraction (60 to 90%) which is retained in DNA- and RNA-depleted nuclei after low- and high-salt extraction, (ii) a small fraction (1%) released during nuclease digestion of DNA in intact nuclei in the presence of low-salt buffer, and (iii) a fraction of myc protein (less than 10%) extractable with salt or detergents and found to have affinity for both single- and double-stranded DNA. Immunofluorescence analysis with anti-myc peptide sera on cells extracted sequentially with nucleases and salts confirmed the idea that myc proteins were associated with a complex residual nuclear structure (matrix-lamin fraction) which also contained avian nuclear lamin protein. Dispersal of myc proteins into the cytoplasm was found to occur during mitosis. Both c-myc and v-myc proteins were associated with the matrix-lamin, suggesting that the function of myc may relate to nuclear structural organization.

Attenuation may regulate gene expression in animal viruses and cells

In eukaryotes, an abundant population of promoter-proximal RNA chains have been observed and studied, mainly in whole nuclear RNA, in denovirus type 2, and in SV40. On the basis of these results it has been suggested that a premature termination process resembling attenuation in prokaryotes occurs in eukaryotes. Moreover, these studies have shown that the adenosine analog 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB) enhances premature termination, but its mode of action is not understood. The determination of the nucleotide sequences of SV40 and other viruses and cellular genes provide means for elucidating the nucleotide sequences involved in the attenuation mechanism. A model has recently been described in which attenuation and mRNA modulation in a feedback control system quantitatively regulate SV40 gene expression. The suggested mechanism described in this model opens up approaches to the investigation of attenuation and mRNA modulation as a possible mechanism whereby eukaryotes may regulate transcription in a variety of different circumstances.

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.

Thermal down-regulation of exportable rRNA in nuclei

The export of rRNP particles from nuclei isolated from Tetrahymena was investigated after preincubating the nuclei at different temperatures under nonpermissive export-conditions. We observed a new phenomenon: Temperature elevation from the sublethal cells' growth temperature, 8 degrees C, to the optimal temperature, 28 degrees C, lead to a gradual down-regulation in the maximal proportion of rRNP particles subsequently exported from nuclei at 28 degrees C. This thermal down-regulation is apparently not due to qualitative changes in the exported rRNP particles, a derangement in the gross nuclear organization, a degradation and/or nicking of the nuclear rRNA, a gross decomposition of the major nuclear proteins, a random cross-linking of nuclear components by disulfide bonds, or an elution of nuclear factors possibly required for rRNP export. Moreover, there is a corresponding thermal down-regulation in nuclear envelope-free nuclei. Our data indicate that nuclei possess a mechanism that regulates the number of potentially exportable rRNP particles at a level preceding the rRNP passage through the nuclear envelope.

Ca2+/calmodulin-dependent protein kinases from the neuronal nuclear matrix and post-synaptic density are structurally related

A major Ca2+/calmodulin-dependent protein kinase has been isolated in association with the neuronal nuclear matrix. Nuclear matrix preparations contain highly phosphorylated polypeptides with Mr values of 50,000 and 60,000. These polypeptides were further characterized by peptide and phospho peptide mapping, two-dimensional isoelectrofocusing/NaDodSO4/PAGE, and 125I-labeled calmodulin binding. The results indicate that the Mr 50,000 and 60,000 polypeptides of the nuclear matrix closely resemble the alpha and beta subunits, respectively, of the Ca2+/calmodulin-dependent protein kinase of the post-synaptic density. These findings indicate that similar protein kinases mediate the neuronal effects of Ca2+ at the cytosolic, synaptosomal, and nuclear levels.

Thermal diminution and augmentation of the retention of transportable rRNA in nuclear envelope-free nuclei

We have examined the effect of temperature on the rRNA transport from nuclei isolated from Tetrahymena after removal of both nuclear membranes and pore complexes by 1% Triton X-100. These nuclei export rRNA as precursor ribosomal ribonucleoprotein particles at both 28 degrees C and 8 degrees C which are qualitatively the same in terms of rRNA pattern, sedimentation coefficients and buoyant densities. At 8 degrees C, however, significantly fewer ribosomal ribonucleoprotein particles can be maximally exported than at 28 degrees C, though nuclei contain enough potentially transportable particles. These are increasingly released with increasing temperatures. Under conditions non-permissive for export, temperature elevation decreases the number of the potentially transportable ribosomal ribonucleoprotein particles in nuclei. Our data show: transportable ribosomal ribonucleoprotein particles inside nuclei are not 'free', but rather are subject to a complex temperature-sensitive retention: this retention is gradually diminished under export conditions and augmented under non-permissive export conditions with increasing temperatures. These retention mechanisms operate at an intranuclear level preceding the ribosomal ribonucleoprotein passage through the nuclear envelope pore complexes, i.e., the nuclear envelope regulates neither the number of potentially transportable ribosomal ribonucleoprotein particles in nuclei nor the number of those particles which can be maximally exported from nuclei at a given temperature. We suggest that these retention mechanisms involve temperature-sensitive domains of the nuclear matrix.

Control of late simian virus 40 transcription by the attenuation mechanism and transcriptionally active ternary complexes are associated with the nuclear matrix

Isolated nuclei derived from simian virus 40 (SV40)-infected cells and incubated with [alpha-32P]UTP can elongate the in vivo preinitiated SV40 late RNA, synthesizing a viral RNA species 94 nucleotides long (attenuator RNA) as well as longer RNA molecules. In contrast to newly synthesized SV40 RNA, the attenuator RNA is not associated with the nuclear matrix. Pretreating the cells with 5,6-dichloro-1-beta-ribofuranosylbenzimidazole before the incubation of isolated nuclei in vitro, enhances the accumulation of the attenuator RNA, but again it is removed from nuclei by DNase and high salt. In contrast, pretreating the cells with proflavine, an intercalating drug that interferes with RNA secondary structure, prevents the accumulation of the attenuator RNA and increases the amount of the long RNA molecules. These RNA molecules become associated with the nuclear matrix. Isolated nuclear matrices from SV40-infected cells are highly enriched in transcriptionally active ternary complexes. Thus, isolated nuclear matrices that contain from 2 to 6% of SV40 DNA are capable of synthesizing at least 35% of the viral RNA synthesized in isolated nuclei after 2 to 15 minutes incubation with [alpha-32P]UTP. The RNA synthesized in vitro on purified nuclear matrices and isolated nuclei is derived from the same regions of the viral genome, suggesting that there is an association between transcribed DNA sequences and the nuclear matrix. The results suggest a major role for the nuclear matrix in controlling SV40 gene expression.

Protein patterns of the nuclear matrix in differently proliferating and malignant cells

SDS-polyacrylamide gel electrophoresis of the nuclear matrix proteins showed a predominance of high molecular weight and low molecular weight polypeptides in the nuclear matrices of hepatomas and cultured Chinese hamster fibroblasts as compared to quiescent and regenerating rat liver. These features were more prominent in solid hepatoma 27 than in Zajdela ascites hepatoma or in cultured cells. In proliferating cells (tumors, regenerating liver, log phase cell culture) a polypeptide band of 150 kD and lamin B were conspicuous at the expense of lamins A and C.

Analysis of the distribution of DNA repair patches in the DNA-nuclear matrix complex from human cells

The distribution of ultraviolet-induced repair patches along DNA loops attached to the nuclear matrix, was investigated by digestion with DNA-degrading enzymes and neutral sucrose gradient centrifugation. When DNA was gradually removed by DNAase 1, pulse label incorporated by ultraviolet-irradiated cells during 10 min in the presence of hydroxyurea or hydroxyurea/arabinosylcytosine showed similar degradation kinetics as prelabelled DNA. No preferential association of pulse label with the nuclear matrix was observed, neither within 30 min nor 13 h after irradiation. When the pulse label was incorporated by replicative synthesis under the same conditions, a preferential association of newly-synthesized DNA with the nuclear matrix was observed. Single-strand specific digestion with nuclease S1 of nuclear lysates from ultraviolet-irradiated cells, pulse labelled in the presence of hydroxyurea/arabinosylcytosine, caused a release of about 70% of the prelabelled DNA and 90% of the pulse-labelled DNA from the rapidly sedimenting material in sucrose gradients. The results suggest no specific involvement of the nuclear matrix in repair synthesis, a random distribution of repair patches along the DNA loops, and simultaneously multiple incision events per DNA loop.

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'.

Generation of an internal matrix in mature avian erythrocyte nuclei during reactivation in cytoplasts

When fused with mouse L-cell cytoplasts, chick erythrocyte nuclei enlarge, take up proteins from the host cytoplasm, and recommence RNA synthesis. We found that during this transition the erythrocyte nuclei gain an internal nuclear matrix, thus providing a novel approach to questions concerning the nature of the salt-resistant intranuclear skeleton. A new method for preparation and examination of the nuclear matrix in situ is also described.

Synaptonemal complexes are integral components of the isolated mouse spermatocyte nuclear matrix

Synaptonemal complexes (SCs) have been isolated as integral components of the nuclear matrix from purified mouse pachytene spermatocytes. These nuclear synaptonemal complex-matrices are prepared by extracting Triton X-100-treated nuclei with low (0.2 M) and high (1.0 or 2.0 M) NaCl, DNase I, and RNase A to remove 85% of the nuclear proteins, 97% of the RNA, and 99% of the DNA. Studies with the light and electron microscopes indicate that these matrices, while lacking a distinct lamina, contain nuclear pores interconnected by a fiber network, residual nucleoli, and interchromatin fibers. In addition, the pachytene spermatocyte matrices contain residual XY heterochromatin and the principal components of the SCs, including two lateral elements, a central element, a presumptive centromere, and attachment plaques. These SCs are preserved within the matrix and retain their structural association with the pore-fiber complex, even when subjected to strong dissociating conditions. Nuclear matrices from pachytene spermatocytes and spermatids (steps 1-8), when analyzed by SDS PAGE, contain an array of polypeptides distinct from those of mouse liver nuclear matrices. Proteins of spermatogenic matrices range in Mr from 8,000 to approximately 150,000. The prominent lamina proteins (Mr approximately 60,000-70,000) of somatic nuclear matrices are either absent or represent only a minor part of the spermatogenic matrix. The polypeptide composition of the pachytene spermatocyte and spermatid matrices are similar, although minor quantitative and qualitative differences are evident. These observations suggest that the SC constituents may consist of a heterogeneous group of proteins present in low proportion relative to total matrix proteins, or they may be retained, but in a different form, within the spermatid matrix.

Changes in structure and composition of lymphocyte nuclei during mitogenic stimulation

Nuclei of lymphocytes stimulated in vitro with concanavalin A (Con A) were classified into three morphotypes: I--unstimulated; II--partially stimulated; III--fully stimulated, lymphoblastic nuclei. During the Con A-induced change from morphotype I to III nuclear volume increased up to sixfold, due to a near 10-fold increase in the interchromatinic region. At the same time, condensed chromatin rose in volume by only about 1.5-fold and became disaggregated in to small clumps. Regressive EDTA-uranyl staining demonstrated a large increase in interchromatinic fibrillar material in morphotypes II and III. Nuclear matrices isolated from stimulated murine lymphocytes showed structures comparable to the interchromatinic region of the morphotypes. The Con A-stimulated change in nuclear structure preceded onset of DNA replication and was unaffected by hydroxyurea or cytosine arabinoside. Cycloheximide blocked the structural change, even when given 20 hr after Con A. Autoradiography after [3H]leucine showed incorporation of label in the interchromatinic region of morphotype II and III nuclei, much of which remained stable during a 48-hr chase period. Nuclear structural activation was inhibited by alpha-amanitin but a significant stable nuclear RNA fraction was not detected. We conclude that an important event in lymphocyte activation is extensive synthesis of stable proteinaceous interchromatinic matrix which may be involved in chromatin remodeling and DNA replication and/or transcription.

Proteins of de-membraned protamine-depleted mouse sperm. Homology with proteins of somatic cell nuclear envelope/matrix

Following treatment with Triton X/1 M NaCl/2-mercaptoethanol, mouse sperm heads are divested of protamines and other basic proteins; the residual structure is one in which the general morphological organization of the decondensed chromatin and the nuclear boundaries are conserved [1]. In this study, the protein complement of that residual structure has been characterized and subdivided into two sets: 1. Those that are sperm-unique, including constituents of the sperm head that may be intrinsically nuclear (or extra-nuclear, but exceedingly adherent to the nuclear envelope). 2. Those that display corresponding electrophoretic properties and immunologic cross-reactivity with proteins of similarly treated mouse somatic cell nuclei. Among the latter are proteins of molecular weight 52, 63 and 69 kD, two of which (63 and 69 kD) appear to be homologous to polypeptides of somatic nuclear envelope/pore complex lamina. Absence from sperm nuclei of the third of the characteristic predominant triplet of somatic nuclear lamina polypeptides of mammalian cells, here designated 67 kD, indicates cell-type variation in these structures. On the other hand, the identification of homologous polypeptides in the sperm and somatic complements suggests that those are specific instances of conservation and may represent the paternal contribution to the pool of polypeptides for assembly of the envelopes of the pronuclei of the one-cell embryo.