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PubMed2007

Transcription factor Runx1 recruits the polyomavirus replication origin to replication factories.

Eukaryotic DNA replication takes place in the replication factories, where replication proteins are properly assembled to form replication forks. Thus, recruitment of DNA replication origins to the replication factories must be the key step for the regulation of DNA replication. The transcription factor Runx1 associates with the nuclear matrix, the putative substructure of DNA replication factories. An earlier report from our laboratory showed that Runx1 activates polyomavirus DNA replication, and that this requires its nuclear matrix-binding activity. Here, we show that Runx1 activates polyomavirus DNA replication by stimulating the binding of the viral-encoded replication initiator/helicase, large T antigen, to its replication origin. We found that newly replicated polyomavirus DNA is associated with the nuclear matrix and that large T antigen is targeted to replication factories, suggesting that polyomavirus is replicated in replication factories on the nuclear matrix. Although Runx1 did not co-localize with large T antigen-containing foci by itself, it co-localized with large T antigen-containing replication factories during Runx1-dependent polyomavirus DNA replication. These observations together suggest that Runx1 recruits the polyomavirus replication origin to the replication factory on the nuclear matrix, and that this requires the nuclear matrix-binding activity of Runx1.

Animals↗
PubMedDate not supplied

[Association of DNA with the nuclear skeleton].

A significant functional role is ascribed to DNA association with the nuclear skeleton. Specific proteins tightly bound to DNA have been discovered. According to one point of view these proteins perform constant attachment of DNA to the nuclear matrix, however, according to other authors this complex exists in transcribed genes only. In proliferating cell DNA is anchored by DNA-topoisomerase II and DNA-polymerase alpha. Except for proteins this function is performed by glycoproteins, neutral and phospholipids, RNA. Three types of specific DNA sequences have been elucidated: 1. AT-rich enhancers (SAR); 2. GC-rich origins of replication; 3. centromere and satellite DNA. In places of binding to the nuclear matrix DNA bears the numerous defects of secondary structure. Based on different criteria several types of DNA complexes with nuclear matrix proteins are distinguished: 1. resistant (lamina) and sensitive (intramolecular fibrils) to chelating agents; 2. formed by transcriptional complexes (transitory) and origins of replication (constant); 3. tight (resistant to salt-urea solutions, formed by replicative complex proteins) and weak (sensitive).

Animals↗
PubMed1995

Contributions of nuclear architecture to transcriptional control.

Three parameters of nuclear structure contribute to transcriptional control. The linear representation of promoter elements provides competency for physiological responsiveness within the contexts of development as well as cycle- and phenotype-dependent regulation. Chromatin structure and nucleosome organization reduce distances between independent regulatory elements providing a basis for integrating components of transcriptional control. The nuclear matrix supports gene expression by imposing physical constraints on chromatin related to three-dimensional genomic organization. In addition, the nuclear matrix facilitates gene localization as well as the concentration and targeting of transcription factors. Several lines of evidence are presented that are consistent with involvement of multiple levels of nuclear architecture in cell growth and tissue-specific gene expression during differentiation. Growth factor and steroid hormone responsive modifications in chromatin structure, nucleosome organization, and the nuclear matrix that influence transcription of the cell cycle-regulated histone gene and the bone tissue-specific osteocalcin gene during progressive expression of the osteoblast phenotype are considered.

Animals↗
PubMed1985

Localization of nuclear antigens during preparation of nuclear matrices in situ.

Nuclear matrix structure closely resembles the organization of nonchromatin components of nuclei in situ. However, reports on the extent to which nuclear components are reorganized during matrix isolation have produced conflicting results, and the reality of an in situ nuclear matrix is still in question. We have prepared nuclear matrices by processing cells still attached to the growth substrate through the extraction steps, thus avoiding mechanical disruption due to homogenization and centrifugation. Furthermore, the extensive residual cytoskeleton seems to keep the residual nuclei "stretched out" so that they retain many features of intact nuclei. Indirect immunofluorescence staining was used to compare the distribution of nuclear antigens in intact nuclei with their organization in nuclear matrices, as well as at each stage of nuclear matrix preparation. We have applied monoclonal antibodies P1, I1, PI1, and PI2, which had been generated against isolated matrices, as well as autoimmune sera detecting lamins, perichromin, and centromere antigens. Chromatin and RNA extraction was monitored with Hoechst 33258, ethidium bromide, and antihistone. The lamins, PI1, and, to a great extent, PI2 and centromere antigens were little affected by the extraction. The data suggest furthermore that PI1 is a fundamental nuclear matrix component and may serve in integrating peripheral and internal nuclear functions. P1 and perichromin were extensively redistributed after chromatin extraction, supporting a role for these antigens in spatial ordering of chromatin. I1 was progressively extracted at each stage of nuclear matrix preparation and was artifactually associated with matrices which had not been digested with RNase. This study demonstrates unequivocally that the organization of many nuclear matrix components in final preparations reflects their organization in situ. It does indicate, however, that some components retained in matrices are extensively redistributed during nuclear matrix preparation and that their role in nuclear organization must be evaluated in consequence.

Animals↗
PubMed2000

Use of matrix attachment regions (MARs) to minimize transgene silencing.

Matrix attachment regions (MARs) are operationally defined as DNA elements that bind specifically to the nuclear matrix in vitro. It is possible, although unproven, that they also mediate binding of chromatin to the nuclear matrix in vivo and alter the topology of the genome in interphase nuclei. When MARs are positioned on either side of a transgene their presence usually results in higher and more stable expression in transgenic plants or cell lines, most likely by minimizing gene silencing. Our review explores current data and presents several plausible models to explain MAR effects on transgene expression.

Animals↗
PubMed2007

Activation of the S phase DNA damage checkpoint by mitomycin C.

We have studied the rate of DNA synthesis, cell cycle distribution, formation of gamma-H2AX, and Rad51 nuclear foci and association of Rad51 with the nuclear matrix after treatment of HeLa cells with the interstrand crosslinking agent mitomycin C (MMC) in the presence of the kinase inhibitors caffeine and wortmannin. The results showed that MMC treatment arrested the cells in S-phase and induced the appearance of gamma-H2AX and Rad51 nuclear foci, accompanied with a sequestering of Rad51 to the nuclear matrix. These effects were abrogated by caffeine, which inhibits the Ataxia-telangiectasia mutated (ATM) and ATM- and Rad3-related (ATR) kinases. However, wortmannin at a concentration that inhibits ATM, but not ATR did not affect cell cycle progression, damage-induced phosphorylation of H2AX and Rad51 foci formation, and association with the nuclear matrix, suggesting that the S-phase arrest induced by MMC is ATR-dependent. These findings were confirmed by experiments with ATR-deficient and AT cells. They indicate that the DNA damage ATR-dependent S-phase checkpoint pathway may regulate the spatiotemporal organization of the process of repair of interstrand crosslinks.

Androstadienes↗
PubMed2001

Identification and characterization of a silkgland-related matrix association region in Bombyx mori.

From DNA fragments in vivo attached to the nuclear matrix in silkglands of Bombyx mori 5th instar larvae, we have screened a matrix association region (MAR), termed BmMAR1, by means of in vitro binding assay. BmMAR1 was identified to be specifically in vivo attached to the nuclear matrix only in the silkglands, neither in other tissues nor in the silkworm cell line Bm5, indicating its silkgland-relatedness. This 1983-bp DNA fragment contains a 1.1-kb core necessary for the effective in vitro binding although it is of relatively lower A/T composition (61%) compared to the 5' and 3' flanking regions (73 and 69%, respectively). Two degenerate sequences derived from Bm1 and L1Bm repetitive elements are located in the core region. BmMAR1 shares the widely considered typical MAR's features, DNA unwinding motif, A-box, T-box, H-box, replication origin, MAR recognition signature (MRS), the 90%AT box and Drosophila topoisomerase II consensus sequence. Furthermore we compared the occurrences of these patterns in BmMAR1 and some MARs from other organisms.

Animals↗
PubMed1996

Agonist-induced desensitization and down-regulation of delta opioid receptors alter the levels of their 125I-beta-endorphin cross-linked products in subcellular fractions from NG108-15 cells.

The delta opioid binding sites in subcellular fractions from NG108-15 cells were characterized with respect to their relative molecular size and levels under conditions of receptor adaptation. 125I-beta-Endorphin was cross-linked to preparations enriched in plasma membranes (P20), nuclear membranes or nuclear matrices. Five cross-linked bands appear in all subcellular fractions. The largest molecular size reaction product in nuclear matrix preparations (approximately 72 kDa) differed from that in the other two fractions-(approximately 83 kDa). Immunoblot analyses with an antibody to the delta opioid receptor gave a P20 band pattern similar to that for the corresponding cross-linked products. To determine which cross-linked products in P20 are glycoproteins, labeled membranes were solubilized and purified by wheat germ agglutinin chromatography. The absence of a approximately 36 kDa band after purification suggests that this product is not a glycoprotein. The remaining four bands were present in N-acetyl-D-glucosamine eluates, although their % distribution changes in favor of the largest molecular size band (approximately 83 kDa). Immunoblotting of the eluate gave a single diffuse band at approximately 73 kDa, suggesting the native glycoprotein has a molecular size in the 70-80 kDa range. Etorphine-induced desensitization of cell surface receptors increased the amount of some cross-linked products associated with nuclear membranes. The same treatment did not affect the relative density of the four larger molecular size bands in P20, but increased the density of the approximately 26 kDa product two fold. Etorphine-induced down-regulation evoked an elevation of cross-linked products in nuclear matrix preparations, while all band densities of P20 were diminished. These results suggest that nuclear matrix associated opioid binding sites represent internalized, truncated forms of the glycosylated delta opioid receptor found in P20.

Cell Line↗
PubMed1993

Structural requirements for simian virus 40 replication and virion maturation.

The nuclear matrix plays an important role in simian virus 40 (SV40) DNA replication in vivo, since functional replication complexes containing large T and replicating SV40 minichromosomes are anchored to this structure (R. Schirmbeck and W. Deppert, J. Virol. 65:2578-2588, 1991). In the present study, we have analyzed the course of events leading from nuclear matrix-associated replicating SV40 minichromosomes to fully replicated minichromosomes and, further, to their encapsidation into mature SV40 virions. Pulse-chase experiments revealed that newly replicated SV40 minichromosomes accumulated at the nuclear matrix and were directly encapsidated into DNase-resistant SV40 virions at this nuclear structure. Alternatively, a small fraction of newly replicated minichromosomes left the nuclear matrix to associate with the cellular chromatin. During the course of infection, progeny virions continuously were released from the nuclear matrix to the cellular chromatin and into the cytoplasm-nucleoplasm. The bulk of SV40 progeny virions, however, remained at the nuclear matrix until virus-induced cell lysis.

Cell Compartmentation↗
PubMed1996

Dynamic remodeling of nuclear architecture during the cell cycle.

The nuclear matrix is an integral part of nuclear structure which undergoes a profound reorganization during the cell cycle reflecting major changes in functional requirements. This includes the processes of DNA replication and gene expression at interphase and partitioning of the nuclear contents during mitosis. Using a monoclonal antibody (mAb2A) which specifically stains a novel nuclear meshwork which reorganizes during the cell cycle in Drosophila, we have initiated a study to: 1) more closely analyze this structural reorganization; 2) clone and characterize the antigens recognized by this antibody; and 3) isolate other interacting proteins in order to gain insight into the regulation of this process. The mAb2A-labeled structure changes from what appears as a diffuse meshwork at interphase to a distinct spindle-like scaffold at prophase. Since at metaphase the microtubules of the mitotic apparatus co-localize with the mAb2A spindle structure, a model is considered whereby the nuclear mAb2A-labeled scaffolding reorganizes during the cell cycle to provide a guide for the establishment of the mitotic apparatus. The mAb2A has identified two separate antigens, each of which shows similar distribution patterns. One of these antigens has been partially cloned and contains an unusual tandem ser-thr kinase domain. The association of this kinase homologue with a nuclear scaffold which reorganizes during the cell cycle suggests that it may be involved in regulating changes in nuclear architecture during the cell cycle and/or in mediating the downstream consequences of such changes.

Animals↗
PubMed1990

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.

Cell Line↗
PubMed2000

Regulation of the processing of glucose-6-phosphate dehydrogenase mRNA by nutritional status.

Expression of glucose-6-phosphate dehydrogenase (G6PD) gene during starvation and refeeding is regulated by a posttranscriptional mechanism occurring in the nucleus. The amount of G6PD mRNA at different stages of processing was measured in RNA isolated from the nuclear matrix fraction of mouse liver. This nuclear fraction contains nascent transcripts and RNA undergoing processing. Using a ribonuclease protection assay with probes that cross an exon-intron boundary in the G6PD transcript, the abundance of mRNAs that contain the intron (unspliced) and without the intron (spliced) was measured. Refeeding resulted in 6- and 8-fold increases in abundance of G6PD unspliced and spliced RNA, respectively, in the nuclear matrix fraction. However, the amount of G6PD unspliced RNA was at most 15% of the amount of spliced RNA. During refeeding, G6PD spliced RNA accumulated at a rate significantly greater than unspliced RNA. Further, the amount of partially spliced RNA exceeded the amount of unspliced RNA indicating that the enhanced accumulation occurs early in processing. Starvation and refeeding did not regulate either the rate of polyadenylation or the length of the poly(A) tail. Thus, the G6PD gene is regulated during refeeding by enhanced efficiency of splicing of its RNA, and this processing protects the mRNA from decay, a novel mechanism for nutritional regulation of gene expression.

Animals↗
PubMed2000

Active remodeling of somatic nuclei in egg cytoplasm by the nucleosomal ATPase ISWI.

Cloning by the transplantation of somatic nuclei into unfertilized eggs requires a dramatic remodeling of chromosomal architecture. Many proteins are specifically lost from nuclei, and others are taken up from the egg cytoplasm. Recreating this exchange in vitro, we identified the chromatin-remodeling nucleosomal adenosine triphosphatase (ATPase) ISWI as a key molecule in this process. ISWI actively erases the TATA binding protein from association with the nuclear matrix. Defining the biochemistry of global nuclear remodeling may facilitate the efficiency of cloning and other dedifferentiation events that establish new stem cell lineages.

Adenosine Triphosphatases↗
PubMed2006

Functional studies of BCL11A: characterization of the conserved BCL11A-XL splice variant and its interaction with BCL6 in nuclear paraspeckles of germinal center B cells.

BACKGROUND: Chromosomal aberrations of BCL11A at 2p16.1 have been reported in a variety of B-cell malignancies and its deficiency in mice leads to a profound block in B-cell development. RESULTS: Alternative pre-mRNA splicing of BCL11A produces multiple isoforms sharing a common N-terminus. The most abundant isoform we have identified in human lymphoid samples is BCL11A-XL, the longest transcript produced at this locus, and here we report the conservation of this major isoform and its functional characterization. We show that BCL11A-XL is a DNA-sequence-specific transcriptional repressor that associates with itself and with other BCL11A isoforms, as well as with the BCL6 proto-oncogene. Western blot data for BCL11A-XL expression coupled with data previously published for BCL6 indicates that these genes are expressed abundantly in germinal-center-derived B cells but that expression is extinguished upon terminal differentiation to the plasma cell stage. Although BCL11A-XL/BCL6 interaction can modulate BCL6 DNA binding in vitro, their heteromeric association does not alter the homomeric transcriptional properties of either on model reporter activity. BCL11A-XL partitions into the nuclear matrix and colocalizes with BCL6 in nuclear paraspeckles. CONCLUSION: We propose that the conserved N-terminus of BCL11A defines a superfamily of C2HC zinc-finger transcription factors involved in hematopoietic malignancies.

Alternative Splicing↗
PubMed2002

Chromatin (dis)organization and cancer: BUR-binding proteins as biomarkers for cancer.

Malignant transformation of cells is associated with changes in gene expression. Gross alterations in chromatin organization may be involved in such gene dysregulation, as well as the involvement of specific transcription factors. Specialized genomic DNA segments that exhibit high affinity to the nuclear matrix in vitro have been designated as matrix/scaffold attachment regions (MARs/SARs). MARs are postulated to anchor chromatin onto the nuclear matrix, thereby organizing genomic DNA into topologically distinct loop domains that are important in replication and transcription. In support of this notion, MARs often colocalize or exist in close proximity to regulatory sequences including enhancers. Base unpairing regions (BURs) are typically 100-150 bp regions within MARs, possess an intrinsic propensity to unwind under negative superhelical strain, and are considered to be hallmark of MARs. To investigate a potential mechanism that could lead to significant alterations in gene expression in cancer cells, this review focuses on a group of chromatin-associated proteins that specifically recognize double stranded BURs. Several important proteins have been identified from cancer cells as BUR-binding proteins, including poly (ADP-ribose) polymerase (PARP-1), Ku autoantigen, SAF-A, HMG-I(Y), nucleolin and p53. Many of these proteins are dramatically upregulated in malignancy of the breast. Increase in the amount of these BUR-binding proteins, some of which are known to interact with each other, may not only provide an architectural core but also recruit functional multi-molecular complexes at the base of chromatin loops to affect multiple distant genes. Experimental strategies by which these proteins can be exploited as carcinoma-specific diagnostic markers and as targets for antineoplastic therapy are discussed.

Animals↗
PubMed1999

The SRm160/300 splicing coactivator is required for exon-enhancer function.

Exonic splicing enhancer (ESE) sequences are important for the recognition of splice sites in pre-mRNA. These sequences are bound by specific serine-arginine (SR) repeat proteins that promote the assembly of splicing complexes at adjacent splice sites. We have recently identified a splicing "coactivator," SRm160/300, which contains SRm160 (the SR nuclear matrix protein of 160 kDa) and a 300-kDa nuclear matrix antigen. In the present study, we show that SRm160/300 is required for a purine-rich ESE to promote the splicing of a pre-mRNA derived from the Drosophila doublesex gene. The association of SRm160/300 and U2 small nuclear ribonucleoprotein particle (snRNP) with this pre-mRNA requires both U1 snRNP and factors bound to the ESE. Independently of pre-mRNA, SRm160/300 specifically interacts with U2 snRNP and with a human homolog of the Drosophila alternative splicing regulator Transformer 2, which binds to purine-rich ESEs. The results suggest a model for ESE function in which the SRm160/300 splicing coactivator promotes critical interactions between ESE-bound "activators" and the snRNP machinery of the spliceosome.

Animals↗
PubMed2005

Chromatin supraorganization and extensibility in mouse hepatocytes following starvation and refeeding.

BACKGROUND: The effect of 48 h of starvation and of 48 h of refeeding subsequent to starvation on chromatin supraorganization and extensibility was studied in hepatocytes from adult mice. METHODS: Methods used involved topochemical assays, image analysis, gravity action, and polarization microscopy. RESULTS: Starvation increased the chromatin packing states, especially in areas of noncondensed chromatin, and induced drastic decreases in concanavalin A reactivity due to nuclear matrix glycoproteins and the frequency of nuclei with chromatin extensibility under gravity. Changes in chromatin packing state were accompanied by shifts of nuclear areas of part of the nuclear population to smaller values but did not affect the respective Feulgen-DNA amounts except for a few nuclei. The extent of chromatin unpackaging, but not of frequency of nuclei with formation of extended chromatin fibers, in starved mice that were refed was greater than in well-fed controls. Refeeding induced increase in Feulgen-DNA amounts and regain and redistribution of concanavalin A-reactive nuclear glycoproteins. However, the duration of refeeding used was probably insufficient to reestablish the stereo arrangement of the chromatin-nuclear matrix and to restore chromatin fluidity to the level seen in well-fed mice. CONCLUSIONS: The changes in the liver cell nuclei associated with starvation and refeeding of adult mice involved chromatin supraorganization, hepatocyte proliferation (refeeding), and the loss, regain, and redistribution of nuclear proteins, especially nuclear matrix components, related to chromatin organization and extensibility. These changes are suggested as favoring the silencing and reactivation of transcriptional activities, depending on the organism's nutritional state.

Animals↗
PubMed2001

The matrix attachment regions (MARs) associated with the Heat Shock Cognate 80 gene ( HSC80) of tomato represent specific regulatory elements.

Matrix Attachment Regions (MARs) flank certain plant genes and appear in certain cases to be necessary for their proper regulation. For example, we previously demonstrated that the MARs and introns from the Heat Shock Cognate 80 gene of tomato (HSC80) are necessary for efficient expression of HSC80-based transgenes. MARs may exert their effect by anchoring the ends of a chromatin loop to the nuclear matrix, thereby establishing an independent chromatin domain. Alternatively, MARs may facilitate interactions between activating complexes and DNA. In the first case, MARs should enhance the expression of most genes, while in the latter case, their action might be gene-specific. We addressed this problem by testing whether the HSC80 MARs affected the regulation of an unrelated transgene. We constructed a chimeric transgene composed of the Arabidopsis ADENINE PHOSPHORIBOSYLTRANSFERASE (APT) promoter fused to the maize gene Lc, which encodes a regulator of anthocyanin synthesis, and compared the expression of Lc in Arabidopsis transparent testa glabra (ttg) mutants (which lack anthocyanin pigments) transformed with transgene constructs incorporating the MARs or control DNA fragments that do not bind to the nuclear matrix. Quantitative RT-PCR analysis was used to compare Lc expression in the different transgenic lines. Whether the APT-Lc transgene was flanked by the HSC80 MARs or a control fragment had no effect on expression, while the use of a different MAR, the ARS1 MAR from yeast, significantly decreased expression (P=0.03). Comparison of single-copy and multicopy T-DNA insertions indicated that neither the HSC80 MARs nor the ARS1 MAR could protect the APT-Lc transgene from the negative effect of the integration of multiple copies. In conclusion, this work supports a model in which different regulatory elements within the HSC80 locus interact with the nuclear matrix to induce transcriptional competence.

Adenine Phosphoribosyltransferase↗