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PubMed1981

Hybridization of nuclear matrix attached deoxyribonucleic acid fragments.

Annealing studies were performed on DNA fragments associated with rat and mouse liver interphase nuclear matrix and the metaphase scaffold of Chinese hamster DON cells. Matrix and scaffold bound DNA fragments, reassociated with an excess of total genomic DNA, displayed kinetics virtually identical with total nuclear DNA probes. Moreover, both the extent and kinetics of these hybridizations were independent of the matrix DNA fragment size (less than 350--5000 base pairs) and the method of nuclease digestion used in their preparation (DNase I, micrococcal nuclease or endogenous digestion). The repetitive DNA component of the matrix DNA was examined by reacting discrete sizes of matrix DNA fragments (less than 350--5000 base pairs) from mouse liver with a library of cloned repetitive sequence DNA fragments which included mouse major satellite sequences. Our results demonstrate that short DNA fragments anchored to the nuclear matrix contain these cloned sequences is similar proportion of total nuclear DNA and, when viewed in light of the annealing results, indicate that matrix DNA is not enriched in either repetitive or unique sequences. Furthermore, the matrix DNA fragments appear to contain the entire sequence complexity of the genome. Finally, we hybridized both matrix and total nuclear DNA fragments with cDNA to total nuclear polyadenylated RNA. The kinetics and extent of hybridization indicate that most, if not all, of the actively transcribed DNA sequences are present in similar concentrations. We conclude that in the overall organization of eukaryotic DNA within the nucleus, the repeating domains or loops which have been demonstrated by a number of investigators are not anchored at specific attachment sequences in interphase cells or during mitosis. These findings are discussed with regard to current concepts of eukaryotic DNA loop organization.

Animals↗

PubMed2005

Phosphorylation of AML1/RUNX1 regulates its degradation and nuclear matrix association.

The acute myeloid leukemia 1 (AML1) transcription factors are key regulators of hematopoietic differentiation. Cellular AML1c protein is found in the nucleus and can be separated into two fractions, one soluble in buffers containing salt and nonionic detergent and the other insoluble and tightly bound to the nuclear matrix. We find that the AML1c protein is modified by both phosphorylation and ubiquitination. Our studies show that the majority of the ubiquitinated AML1c is associated with the insoluble nuclear matrix. Treatment of cells with the proteasome inhibitor PS341 (Velcade, Bortezomib) increases the levels of ubiquitinated AML1c. Mutation of the four phosphorylation sites necessary for transcriptional regulation (serine 276, serine 293, serine 303, and threonine 300) mimics the effects of the proteasome inhibitor, increasing the levels of ubiquitinated, matrix-bound AML1c. We find that the soluble and insoluble forms of AML1c are degraded at a similar rate. However, mutation of these four serine/threonine residues statistically increases the half-life of the matrix-associated AML1c. Thus, phosphorylation of AML1c on specific serine/threonine residues controls both transcriptional activity and rate of degradation.

Animals↗

PubMed1995

Behavior of nuclear matrix proteins during camptothecin-induced apoptosis in HL-60 human leukemia cells.

In this study we focused our attention on the behavior of four nuclear matrix proteins during the various stages of apoptosis in the HL-60 cell line exposed to the DNA topoisomerase I inhibitor, camptothecin. We have examined the following antigens by immunocytochemical techniques: (i) the 180-kDa nucleolar isoform of DNA topoisomerase II; (ii) a 126-kDa polypeptide of nuclear bodies; (iii) a 125-kDa protein; and (iv) a 160-kDa polypeptide which are known to be components of the matrix inner network. Indirect immunofluorescence experiments were performed to follow these nuclear matrix antigens during apoptosis. Moreover, the ultrastructural localization of both 125- and 160-kDa proteins was investigated by electron microscope immunocytochemistry with gold-conjugated secondary antibodies. While the antibody to the nucleolar isoform of DNA topoisomerase II gave a fluorescent pattern that was well-maintained until the late phases of apoptosis, the other three nuclear antigens showed marked modifications in their distribution. A common feature, particularly evident for 125- and 160-kDa proteins, was their absence from cap-shaped chromatin marginations, whereas they were present in the areas of remaining decondensed chromatin. The 126-kDa polypeptide concentrated progressively in an irregular mass at the opposite side of the crescentic caps and then broke up in fine spots. The 125- and 160-kDa proteins localized in the nucleolus and precisely within certain granules which are known to appear in the nucleolar area after camptothecin administration. These results show that, in addition to the well-known chromatin changes, nuclear organization undergoes other rearrangements during the apoptotic process.

Antigens, Nuclear↗

PubMed2004

Heat induced 'masking' of redox sensitive component(s) of the DNA-nuclear matrix anchoring complex.

The 'masking effect' is the observation that heat shock reduces or masks the apparent expression of ionizing radiation (IR) damage to DNA. The mechanism of this effect is thought to involve the aggregation of proteins to the nuclear matrix or chromatin, thereby stabilizing these structures and masking actual DNA damage from assays and presumably from DNA repair complexes. Previously, using the 'halo assay', it has been shown that nucleoids treated with 1 mM dithiothreitol (DTT) and/or inhibited the rewinding of DNA supercoils and that this effect was masked in nucloids isolated from heated cells. Here it is reported that treatment of living cells with reducing agents diminishes the interaction between DNA and Protein Disulphide Isomerase (PDI) and that hyperthermia restored the PDI-DNA interaction, indicating that the masking effect occurred in vivo. PDI is a nuclear matrix protein which binds MAR DNA sequences and may be involved in regulating the degree of DNA supercoiling. It is hypothesized that heat-induced stabilization of PDI-DNA interaction will mask changes in supercoiling observed with reducing reagents and also IR. This stabilization may be affected through either the heat-induced association or enhancement of the binding of proteins to MAR DNA at the NM. Several proteins, including B23 and Hsp60, have been identified whose interaction with DNA increased following heat shock. Further work will be needed to determine if these proteins do, in fact, play a role in the masking effect.

Cross-Linking Reagents↗

PubMed1984

Caffeine-induced reorganization of DNA replicating system occurs on or near nuclear matrix in HeLa cells.

Since caffeine reorganizes the DNA replicating system, with several consequences, we studied the effect of caffeine on the DNA replication which normally occurs on or near the nuclear matrix in a variety of eukaryotic cells. When HeLa cells, treated with or without the DNA-damaging agent, neocarzinostatin, were postincubated in the presence or absence of caffeine and then pulse-labeled with [3H]thymidine, the DNA remaining tightly associated with the matrix was enriched in the newly synthesized DNA at the same level as that seen in untreated cells. The nuclear matrix-bound DNA polymerase alpha activity was also the same in these cells. Therefore, in the presence of caffeine, DNA replication, with or without DNA damage, also occurs on or near the nuclear matrix, as is the case in normal DNA replication.

Caffeine↗

PubMed2006

Altered expression and localization of creatine kinase B, heterogeneous nuclear ribonucleoprotein F, and high mobility group box 1 protein in the nuclear matrix associated with colon cancer.

Identification of biomarkers could lead to the development of effective screening tests for colorectal cancer. A previous study from our laboratory showed specific alterations of nuclear structure in colon cancer. In an effort to characterize these biomarkers, protein spots were selected from separations made by two-dimensional gel electrophoresis, which were analyzed by mass spectrometry. The sequences obtained from the isolated spots revealed that they have close similarity to creatine kinase B (CKB) isoforms, heterogeneous nuclear ribonucleoprotein F (hnRNP F) and high mobility group box 1 protein (HMGB1) isoforms. To determine the expression of these proteins in colon cancer, expression was studied in 9 tumor and matched adjacent normal pairs, 5 donor colons, 16 polyps, 4 metastatic liver lesions and matched adjacent normal pairs, and 3 liver donors. CKB and hnRNP F were expressed in 78% and 89% of colon tumors, respectively. hnRNP F had a higher frequency of expression than CKB in premalignant polyps. With the establishment of differential expression of the proteins in colon cancer, their subcellular localization was analyzed. The subcellular fractions studied both showed high protein levels of hnRNP F in colon tumors compared with normal colon tissues. Surprisingly, subcellular levels of CKB were decreased in colon tumors, suggesting that the observed high CKB levels in nuclear matrix extracts are caused by the enhanced localization of CKB to the nuclear matrix during colon tumorigenesis. These results suggest an involvement of hnRNP F and CKB in colorectal cancer. Additionally, they suggest that hnRNP F is a potential marker for colorectal cancer progression.

Adenocarcinoma↗

PubMed1996

A hyperphosphorylated form of the large subunit of RNA polymerase II is associated with splicing complexes and the nuclear matrix.

A hyperphosphorylated form of the largest subunit of RNA polymerase II (pol IIo) is associated with the pre-mRNA splicing process. Pol IIo was detected in association with a subset of small nuclear ribonucleoprotein particle and Ser-Arg protein splicing factors and also with pre-mRNA splicing complexes assembled in vitro. A subpopulation of pol IIo was localized to nuclear "speckle" domains enriched in splicing factors, indicating that it may also be associated with RNA processing in vivo. Moreover, pol IIo was retained in a similar pattern following in situ extraction of cells and was quantitatively recovered in the nuclear matrix fraction. The results implicate nuclear matrix-associated hyperphosphorylated pol IIo as a possible link in the coordination of transcription and splicing processes.

Animals↗

PubMed2006

Sea urchin arylsulfatase insulator exerts its anti-silencing effect without interacting with the nuclear matrix.

Chromatin insulators have been shown to stabilize transgene expression. Although insulators have been suggested to regulate the subcellular localization of chromosomes, it is still unclear whether this property is important for their anti-silencing activity. To investigate the underlying mechanisms governing the anti-silencing function of insulators, we studied the association of sea urchin arylsulfatase insulator (ArsI) with the nuclear matrix, which is a key component of the subnuclear localization of the genome. ArsI did not potentiate the nuclear matrix association with the transgene, even though it showed strong anti-silencing activity. This observation was in clear contrast to the results of the experiment using a human interferon-beta scaffold attachment region, in which the anti-silencing effect coincided with the enhanced matrix association. Chromatin immunoprecipitation analyses suggested that the absence of the matrix binding by ArsI was due to a lack of its binding to CCCTC-binding factor (CTCF), a protein known to be associated with matrix binding by chicken beta-globin insulator. Furthermore, ArsI maintained the nucleosome occupancy within the transgene at a constant level during long-term culture, although ArsI itself was not a nucleosome-excluding sequence. Taken together, these results suggest that this insulator exerts its anti-silencing activity by counteracting silencing-associated factors to maintain local chromatin environment, rather than by remodeling the subnuclear localization of the transgene locus.

Animals↗

PubMedDate not supplied

[Effects of gamma irradiation on biosynthesis of nuclear matrix proteins of the liver in pregnant rats and their embryos].

A study was made of the incorporation of 35S-methionine into nuclear matrix proteins of hepatic cells of pregnant rats and their embryos subjected to single gamma-irradiation (60Co, 1 and 2 Gy, 0.0233 Gy/s) on days 3, 13 and 17 of pregnancy and embryogenesis. On day 21 of pregnancy and embryogenesis a decrease in the rate of incorporation of 35S-methionine into nuclear matrix proteins was shown to be a function of radiation dose and time of pregnancy and embryogenesis on the moment of exposure.

Animals↗

PubMed1984

Androgen receptor binding to nuclear matrix in vitro and its inhibition by 8S androgen receptor promoting factor.

The partially purified 4.5S [3H]dihydrotestosterone receptor binds to nuclear matrix isolated from rat Dunning prostate tumor with properties similar to those reported for androgen receptor binding in intact nuclei [Colvard, D.S., & Wilson, E.M. (1984) Biochemistry (preceding paper in this issue)] in that it requires Zn2+ and mercaptoethanol, is saturable, and is temperature dependent and of high affinity (Ka approximately 10(13) M-1). On a milligrams of DNA equivalent basis, the extent of matrix binding of androgen receptor (700 fmol of receptor bound/mg of matrix protein) is similar to that of intact nuclei, corresponding to approximately 1400 sites/nucleus. Association rate constants (ka) for 4.5S androgen receptor binding to matrix at 0, 15, and 25 degrees C are 2.7 X 10(5), 1.2 X 10(6), and 2.4 X 10(6) M-1 min-1, respectively, indicating an energy of activation of 15 kcal/mol. Up to 50% of matrix-bound receptor is extractable in buffer containing 3 mM ethylenediaminetetraacetic acid plus either 0.4 M KCl or 5 mM pyridoxal 5'-phosphate. A protein fraction designated 8S androgen receptor promoting factor that promotes conversion of the 4.5S androgen receptor to 8 S [Colvard, D. S., & Wilson, E. M. (1981) Endocrinology (Baltimore) 109, 496-504] has been further purified and found to inhibit the binding of the 4.5S androgen receptor to isolated nuclei and nuclear matrix in a concentration-dependent manner. The results support the hypothesis that the 8S steroid receptor is a complex of the activated 4.5S androgen receptor with a non-steroid binding protein that renders the receptor incapable of binding in nuclei.

Animals↗

PubMed2005

AIRE recruits multiple transcriptional components to specific genomic regions through tethering to nuclear matrix.

Thymic selection requires that diverse self antigens be presented to developing thymocytes by stromal cells. Consistent with this function, medullary thymic epithelial cells have been shown to express a large number of genes, many of which are tissue restricted. Autoimmune regulator (AIRE) is a nuclear protein, which has recently been identified as a regulator of this process, however, the mechanism by which AIRE functions is not well understood. Here we use a transrepression assay to demonstrate that AIRE interacts with multiple components of the transcription complex including a novel interaction with the UBA domain protein, GBDR1. When AIRE is expressed in cultured human thymic epithelial cells, it tightly associates with nuclear matrix, suggesting that AIRE responsive genes may be localized to specific regions. Using a mathematical approach we have re-analyzed an Affymetrix dataset identifying AIRE responsive genes and show that they tend to localize to specific regions of the genome. Together, these data suggest that AIRE regulates gene expression by recruiting components of the transcription complex to specific regions of the genome via interactions with nuclear matrix.

Animals↗

PubMed2000

Identification of the goldfish 20S proteasome beta6 subunit bound to nuclear matrix.

Proteasomes are large, multisubunit particles that act as the proteolytic machinery for most of the regulated intracellular protein breakdown in eukaryotic cells. Proteasomes are present in both the nucleus and cytoplasm. When we analyzed the molecular composition of protein constituents of the nuclear matrix preparation of goldfish oocytes by two-dimensional polyacrylamide gel electrophoresis followed by sequence analysis, we found a 26 kDa spot identical in amino acid sequence to the beta6 subunits of the 20S proteasome. No spot of other subunits of 20S proteasome was detected. Here we describe the cloning, sequencing and expression analysis of Carassius auratus, beta6_ca, which encodes one of the proteasome beta subunits from goldfish ovary. From the screening of an ovarian cDNA library, two types of cDNA were obtained, one 941 bp and the other 884 bp long. The deduced amino acid sequences comprise 239 and 238 residues, respectively. These deduced amino acid sequences are highly homologous to those of beta6 subunits of other vertebrates. Immunoblot analysis of nuclear matrix using anti-proteasome antibodies showed only a spot of beta6_ca. These results suggest that the beta6 subunit of the goldfish 20S proteasome, beta6_ca, is responsible for anchoring proteasomes in the nucleus.

Amino Acid Sequence↗

PubMed1996

A soluble transcription factor, Oct-1, is also found in the insoluble nuclear matrix and possesses silencing activity in its alanine-rich domain.

Expression of the human thyrotropin beta (hTSHbeta) gene is restricted to thyrotrophs, at least in part, by silencing. Using transient-transfection assays, we have localized a silencer element to a region between -128 and -480 bp upstream of the transcription initiation site. The silencing activity was overcome in a thyrotroph-specific manner by an unknown enhancer located in the sequences at -approximately 10000 to -1200 bp. The ubiquitous POU homeodomain protein Oct-1 recognized the A/T-rich silencer element at multiple sites in gel mobility shift assays and in vitro footprinting analyses. The silencing activity of Oct-1 was localized in its C-terminal alanine-rich domain, suggesting that Oct-1 plays a role in silencing of the hTSHbeta promoter. Further, a significant fraction of Oct-1 was shown to be associated with the nuclear matrix, and the hTSHbeta silencer region was tethered to a nuclear matrix of human cells in vivo, suggesting a possible role of the Oct-1-hTSHbeta silencer region interaction in chromatin organization.

Animals↗

PubMed1997

Cleavage of the nuclear matrix protein NuMA during apoptosis.

NuMA is a component of the nuclear matrix which may play a structural role in the architecture of the interphase nucleus. During apoptosis NuMA is redistributed within the nucleus and is proteolysed from a 238-kDa form to a 180- to 200-kDa form. Here we show that the cleavage site leading to the stable fragment occurs between residues 1701 and 1725. Both the changes in morphology associated with apoptosis and the cleavage of NuMA were retarded by treatment with TPCK but not by treatment by other protease inhibitors including ICE inhibitor II.

Animals↗

PubMed1993

Absence of high levels of DNA polymerase alpha activity in the nuclear matrix prepared from mouse erythroleukemia cells.

We have examined the association of DNA polymerase alpha activity with the nuclear matrix prepared by different techniques from mouse erythroleukemia cells. At variance with the data obtained using other cell types we have found that only a small amount (less than 2%) of nuclear DNA polymerase alpha activity resisted extraction with high-ionic strength buffers, even if nuclei were heat-stabilized by incubation at 37 degrees C for 45 min prior to subfractionation. The recovery of DNA polymerase alpha activity bound to the matrix was unaffected by the type of extracting agent used (NaCl or (NH4)2 SO4), by the extraction sequence or by the method employed for obtaining nuclei. These results could indicate that in some types of cells the nuclear matrix is not involved in DNA replication.

Animals↗

PubMed1993

The product of the UL31 gene of herpes simplex virus 1 is a nuclear phosphoprotein which partitions with the nuclear matrix.

The nucleotide sequence of the UL31 open reading frame is predicted to encode a basic protein with a hydrophilic amino terminus and a nuclear localization signal. To identify its gene product, we constructed a viral genome in which the thymidine kinase gene was inserted between the UL31 and UL32 open reading frames. The thymidine kinase gene was then deleted, and in the process, the 5' terminus of the UL31 open reading frame was replaced with a 64-bp sequence in frame with the complete, authentic sequence of the UL31 open reading frame. The inserted sequence encoded a hydrophilic epitope derived from glycoprotein B of human cytomegalovirus and for which a monoclonal antibody is available. We report that in infected cells, the tagged protein localized in and was dispersed throughout the nucleus. Nuclear fractionation studies revealed that the UL31 protein partitions with the nuclear matrix. The protein is phosphorylated in infected cells maintained in medium containing 32Pi.

Base Sequence↗

PubMed1986

Nuclear matrix generation during reactivation of avian erythrocyte nuclei: an analysis of the protein traffic in cybrids.

It has previously been shown that an internal nuclear matrix is generated during the reactivation of the chick erythrocyte nucleus in mouse L-cell cytoplasts. This experimental system has now been used to identify the major polypeptides that migrate into the nucleus during the reactivation process. Mouse L-cells were prelabelled with [35S]methionine, enucleated using cytochalasin B, and fused with 14- to 17-day embryonic chick erythrocytes. Sixteen hours post-fusion, the redistribution of the labelled proteins was examined by electron microscopic autoradiography, and two-dimensional polyacrylamide gel fluorography of the isolated nuclei was used to identify the major imported species. After allowing for cytoplasmic contamination, 15 nucleus-associated polypeptides were identified, two of which also matched with counterparts in the L-cell nuclear preparation. Five of the nucleus-associated polypeptides were tentatively identified (on the basis of one-dimensional gel matches) as nuclear matrix proteins; these five included the two that had counterparts in L-cell nuclei. The autoradiographic results showed that 16 h post-fusion, the specific activity (silver grains/unit area) of the reactivated nucleus was about half that of the cytoplasm, with no evidence for an accumulation of labelled protein at the nuclear periphery. When well-reactivated nuclei were distinguished from poorly reactivated nuclei on the basis of the extent of chromatin decondensation, it was found that their specific activities were quite similar, but because of the difference in size, the well-reactivated nuclei contained about twice as much labelled protein. Estimates of the protein traffic based upon the autoradiographic data indicated that the nuclei had increased in mass by 10-20% during the 16 h reactivation period.

Animals↗

PubMed1996

Changes in chromatin structure and nuclear matrix association of the rat cytochrome P450 2B1/2 (CYP2B1/2) gene following induction with phenobarbital.

Treatment of rats with phenobarbital has been shown to result in an enormous increase in CYP2B1/2 mRNA levels in the liver. This study was performed in order to relate this effect of phenobarbital treatment to changes in the chromatin structure of the CYP2B1/2 gene. Phenobarbital treatment was shown to be associated with a twofold increase in DNase I sensitivity of the CYP2B1/2 gene in the liver. In addition, induction of the CYP2B1/2 gene transcription by phenobarbital resulted in a marked enrichment in the liver of CYP2B1/2 sequences in the nuclear matrix as compared to the matrix-free fraction. Control studies with the CYP1A2 gene, of which the transcriptional activity is not influenced by phenobarbital, did not show any changes in both DNase I sensitivity and matrix association upon phenobarbital treatment. Furthermore, after phenobarbital treatment, no changes in DNasel sensitivity or nuclear matrix association of the CYP2B1/2 gene were observed in the kidney. These data indicate a direct, positive correlation between the structure of the rat CYP2B1/2 gene and its activity.

Analysis of Variance↗