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PubMed2003

Type III intermediate filament proteins interact with four-way junction DNA and facilitate its cleavage by the junction-resolving enzyme T7 endonuclease I.

The isolation from proliferating mouse and human embryo fibroblasts of SDS-stable crosslinkage products of vimentin with DNA fragments containing inverted repeats capable of cruciform formation under superhelical stress and the competitive effect of a synthetic Holliday junction on the binding of cytoplasmic intermediate filament (cIF) proteins to supercoiled DNA prompted a detailed investigation of the proteins' capacity to associate with four-way junction DNA and to influence its processing by junction-resolving endonucleases. Electrophoretic mobility shift analysis of reaction products obtained from vimentin and Holliday junctions under varying ionic conditions revealed efficient complex formation of the filament protein not only with the unstacked, square-planar configuration of the junctions but also with their coaxially stacked X-conformation. Glial fibrillary acidic protein (GFAP) was less efficient and desmin virtually inactive in complex formation. Electron microscopy showed binding of vimentin tetramers or octamers almost exclusively to the branchpoint of the Holliday junctions under physiological ionic conditions. Even at several hundredfold molar excess, sequence-related single- and double-stranded DNAs were unable to chase Holliday junctions from their complexes with vimentin. Vimentin also stimulated bacteriophage T7 endonuclease I in introducing single-strand cuts diametrically across the branchpoint and thus in the resolution of the Holliday junctions. This effect is very likely due to vimentin-induced structural distortion of the branchpoint, as suggested by the results of hydroxyl radical footprinting of Holliday junctions in the absence and the presence of vimentin. Moreover, vimentin, and to a lesser extent GFAP and desmin, interacted with the cruciform structures of inverted repeats inserted into a supercoiled vector plasmid, thereby changing their configuration via branch migration and sensibilizing them to processing by T7 endonuclease I. This refers to both plasmid relaxation caused by unilateral scission and, particularly, linearization via bilateral scission at primary and cIF protein-induced secondary cruciform branchpoints that were identified by T7 endonuclease I footprinting. cIF proteins share these activities with a variety of other architectural proteins interacting with and structurally modulating four-way DNA junctions. In view of the known and hypothetical functions of four-way DNA junctions and associated protein factors in DNA metabolism, cIF proteins as complementary nuclear matrix proteins may play important roles in such nuclear matrix-associated processes as DNA replication, recombination, repair, and transcription, with special emphasis on both the preservation and evolution of the genome.

Bacteriophage T7↗
PubMed1994

Ultrastructural distribution of calcium in the rat testis.

Despite the important role of calcium in the growth and differentiation of a variety of cell types, its exact location and function in the somatic and germ cells of the testis remain to be determined. In the present study, we examined the subcellular distribution of calcium in the immature and adult rat testis. Calcium was localized at the electron microscopic level by ion-capture cytochemistry using combined oxalate and pyroantimonate procedures. Calcium-containing precipitates localized primarily within the nuclei, mitochondria, and cytosol of somatic and germ cells. Differences in the size and quantity of the calcium precipitates were observed among the various cellular compartments. In the somatic cells (Sertoli, Leydig, and myoid), the nuclei exhibited large round-shaped calcium-containing precipitates, whereas the mitochondria in these cell types contained numerous smaller precipitates. The cytoplasmic vesicles possessed single precipitates. These vesicles could be calciosomes, which have been described in other non-muscle cell types. Among germ cells, round spermatids exhibited a large number of vesicular, calsiosome-like structures in the cytoplasm containing single precipitates. The elongating spermatids from adult testis showed calcium localization within the nuclear matrix unassociated with the nuclear envelope, or in a peripheral alignment of precipitates along the nuclear envelope. Calciosome-like structures were also seen in round spermatids. Spermatogonia and spermatocytes exhibited calcium in nuclei, mitochondria, and cytoplasmic vesicles. These results demonstrate a differential distribution of calcium within the various cell types of the testis. The presence of calcium in the nucleus may suggest a role in cell growth and differentiation; calsiosome-like structures may represent the active exchangeable pool of calcium, and the differential type of distribution of calcium in elongating spermatids suggests a role for calcium in spermatid differentiation.

Animals↗
PubMed2003

Pathogenetic mechanisms of nuclear pleomorphism of tumour cells based on the mutator phenotype theory of carcinogenesis.

The nuclei of the cells of most solid tumours in histopathologic preparations vary in size, shape and chromatin pattern, both from normal nuclei and from each other. These features have not been explained in terms of conventional concepts of nuclear structure and theories of carcinogenesis. In recent years, the unfolded chromosomes have been shown to occupy "domains" in the nucleus during interphase, providing a relatively uniform density of fine chromatin fibres throughout the nucleus in the living state. This is in contrast to the appearances of interphase chromatin existing as coarse clumps and fibres (heterochromatin and euchromatin respectively) as are seen in histologic preparations. Additionally, the binding of chromatin to nuclear membrane, the possible existence of a nuclear matrix, the functions of nuclear pores, and the attachments of cytoskeletal structures to the outer nuclear membrane are now recognised. Studies of genetic instability of cancer cells (many random mutations are present in the genome, which vary from nucleus-to-nucleus in individual tumours) have shown that this phenomenon occurs early in tumour formation, can be present in morphologically-normal cells adjacent to tumours, and can result in thousands of genomic events per tumour cell. These observations form the basis for the mutator phenotype/clonal selection theory of carcinogenesis, which proposes that genetic instability is an essential early part of carcinogenesis. Genetic instability has been used to explain significant cell-to-cell variability of behaviour (tumour cell heterogeneity) among cells of individual tumours. This paper proposes that a high incidence of nucleus-to-nucleus-variable mutation of the genes for factors controlling nuclear morphology in tumours can explain nucleus-to-nucleus variations of histopathologic appearance of these nuclei when some additional effects of histological processing are taken into account.

Animals↗
PubMed2004

MAR/SAR elements flank the rat hst70 gene transcription unit.

The rat hst70 gene is specifically expressed in spermatocytes and spermatids. This tissue-specific expression of the gene is primarily mediated through cis-acting elements located within the 0.4 kb segment upstream of the coding region, including two transcription initiation sites. Here, we study the 5' and 3' distal elements flanking the hst70 gene and find that they possess structural motifs characteristic of MAR/SAR elements, and exhibit enhanced affinities for nuclear matrix binding in vitro. Such elements bind efficiently to matrices from either the testis or the liver, i.e. tissues where the gene is either fully active or repressed, although one subfragment in the 5' region was identified as exhibiting testis-specific interactions. Surprisingly, the activity of the CAT reporter gene was repressed in testis-transient transfection assays when the hst70 promoter sequences were extended into the 5' MAR/SAR.

Animals↗
PubMed1995

[The formation of the karyosphere in the oogenesis of insects and amphibians].

This review deals with the authors' own and literary data on the ultrastructural and cytochemical organization of insect and amphibian oocyte nuclei, with special attention being paid to the karyosphere and its capsule. The evidence provided is supplemented with data on isolated karyospheres in Rana temporaria oocytes. A conclusion is made that the karyosphere is a complex structure which contains all chromosomes in the limited space of the oocyte nucleus, and that these chromosomes are, as a rule, in the process of inactivation. It is inferred that the karyosphere capsule commonly appears in gigantic oocyte nuclei (more than 100 micron in diameter) containing extrachromosomal DNA. The analogy of capsule organization in different invertebrate and vertebrate species is discussed, in addition to the involvement of presumably homologous nuclear structures (e.g. derivatives of synaptonemal complexes and nuclear envelope) in capsule formation. It is assumed that the karyosphere capsule is a specially organized part of the nuclear matrix. The capsule provides nuclear compartmentalization and chromosome localization in the germinal vesicle. Studies of this sort open up new possibilities to further investigation of intranuclear morphogenesis.

Amphibians↗
PubMed2000

Two nuclear localization signals in the HIV-1 matrix protein regulate nuclear import of the HIV-1 pre-integration complex.

Replication of HIV-1 in non-dividing and slowly proliferating cell populations depends on active import of the viral pre-integration complex (PIC) into the cell nucleus. While it is commonly accepted that this process is mediated by an interaction between the HIV-1 PIC and the cellular nuclear import machinery, controversial results have been reported concerning the mechanisms of this interaction. Here, we demonstrate that a recently identified nuclear localization signal within the HIV-1 matrix protein (MA), MA NLS-2, together with previously described MA NLS-1, mediates nuclear import of the HIV-1 PIC. Inactivation of both MA NLSs precluded nuclear translocation of MA and rendered the virus defective in nuclear import and replication in non-dividing macrophage cultures, even when functional Vpr and integrase (IN), two more viral proteins implicated in HIV-1 nuclear import, were present. Taken together, these results indicate that Vpr does not function as an independent nuclear import factor and demonstrate that HIV-1 MA, by virtue of its two nuclear localization signals, regulates HIV-1 nuclear import.

Amino Acid Sequence↗
PubMed1995

Nucleolin is a matrix attachment region DNA-binding protein that specifically recognizes a region with high base-unpairing potential.

A DNA affinity column containing a synthetic double-stranded nuclear matrix attachment region (MAR) was used to purify a 100-kDa protein from human erythroleukemia K562 cells. This protein was identified as nucleolin, the key nucleolar protein of dividing cells, which is thought to control rRNA gene transcription and ribosome assembly. Nucleolin is known to bind RNA and single-stranded DNA. We report here that nucleolin is also a MAR-binding protein. It binds double-stranded MARs from different species with high affinity. Nucleolin effectively distinguishes between a double-stranded wild-type synthetic MAR sequence with a high base-unpairing potential and its mutated version that has lost the unpairing capability but is still A+T rich. Thus, nucleolin is not merely an A+T-rich sequence-binding protein but specifically binds the base-unpairing region of MARs. This binding specificity is similar to that of the previously cloned tissue-specific MAR-binding protein SATB1. Unlike SATB1, which binds only double-stranded MARs, nucleolin binds the single-stranded T-rich strand of the synthetic MAR probe approximately 45-fold more efficiently than its complementary A-rich strand, which has an affinity comparable to that of the double-stranded form of the MAR. In contrast to the high selectivity of binding to double-stranded MARs, nucleolin shows only a small but distinct sequence preference for the T-rich strand of the wild-type synthetic MAR over the T-rich strand of its mutated version. The affinity to the T-rich synthetic MAR is severalfold higher than to its corresponding RNA and human telomere DNA. Quantitative cellular fractionation and extraction experiments indicate that nucleolin is present both as a soluble protein and tightly bound to the matrix, similar to other known MAR-binding proteins.

Base Sequence↗
PubMed1984

Lamin B from rat liver nuclei exists both as a lamina protein and as an intrinsic membrane protein.

Rat liver nuclear matrix structures were isolated while preserving the integrity of the nuclear envelope, i.e. in the absence of any detergent extraction. In order to determine the relationships between the nuclear membranes and peripheral lamina, nuclear matrix-envelope preparations were submitted to sodium carbonate extraction (0.1 M, pH 11.5), a solvent which solubilizes both peripheral membrane proteins and membrane-enclosed contents. One-dimensional and two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of material insoluble in sodium carbonate confirmed that intrinsic membrane proteins were indeed retained in the membrane structures. Approximately 50 to 60% of the lamin B present in matrix-envelope preparations was found in these insoluble membranes while a smaller amount of lamin A and even less of lamin C resisted complete extraction. The identity of the lamins was confirmed by their migration on two-dimensional gels and by comparison of one-dimensional peptide maps. The same results were obtained using nuclear membranes prepared by a milder heparin procedure. The location of lamin B as an intrinsic membrane protein was also established by photoaffinity labeling with the membrane-penetrating reagent azidopyrene. A small but reproducible amount of labeling occurred as well on lamin A polypeptides. These results support the hypothesis that the peripheral lamina is attached to the nuclear envelope and anchored there via the presence of lamin B molecules within the bilayer of the inner nuclear membrane.

Animals↗
PubMed2000

Bone tissue specific transcriptional control: options for targeting gene therapy to the skeleton.

BACKGROUND: The transplantation of multipotential bone marrow cells containing bone tissue specific promoter-controlled transgenes provides an efficacious approach to deliver therapeutic gene expression to osteoblasts for the treatment of patients with bone disorders or tumor metastasis to the skeleton. The specificity of tissue-restricted gene therapy can be refined by utilization of a 31-amino-acid segment of the hematopoietic and osteogenic AML/CBF transcription factors that direct the regulatory proteins to subnuclear sites that support gene expression. METHODS: Unfractionated adherent bone marrow cells from transgenic mice constructed with the proximal 1.7 kb of the osteocalcin gene promoter fused to a CAT reporter were transplanted by intravenous infusion. Engraftment and expression at the single-cell level within the context of tissue organization was established by immunohistochemistry using an anti-CAT antibody. Sequences that support the intranuclear trafficking of AML/CBF transcription factors to subnuclear sites that support transcription were determined by the expression and visualization of mutated and epitope tagged AML/CBF proteins. RESULTS: Immunohistochemical staining of an extensive series of tissue sections from mice posttransplantation using an anti-CAT antibody indicated that CAT-positive osteoblasts and osteocytes were present in bone sections. These findings indicate that donor bone marrow-derived cells engraft in bone tissue in an environment that supports maturation to the developmental stage at which a bone specific osteocalcin promoter is transcriptionally active. Characterization of functional domains in AML/CBF transcription factors has established that there are at least two regulated events that are required for targeting the factors to transcriptionally active nuclear domains: A nuclear localization signal in the amino terminal region controls nuclear import and retention, and a nuclear matrix targeting signal in the carboxyl region controls association with nuclear matrix-linked sites where transcription occurs. CONCLUSIONS: The specificity of hematopoietic and bone phenotypic promoters, together with the additional level of specificity inherent in the AML/CBF family of hematopoietic and osteogenic intranuclear targeting signals, offers viable options for constructing gene therapy regimens that are targeted to the skeleton for the control of metastatic disease. It is realistic to anticipate that, as additional parameters of gene regulatory mechanisms are defined, particularly components of transcriptional control that are operative within a three-dimensional context of nuclear architecture, opportunities for enhancing the effectiveness of treating patients with tumors that metastasize to bone will be extended.

Animals↗
PubMed2004

Chromatin organization during spermiogenesis in Octopus vulgaris. I: Morphological structures.

In the process of the chromatin remodeling that occurs during spermiogenesis in some animal species, it is possible to distinguish between two separate aspects: the chromatin condensation pattern itself (granular, fibrillar, or lamellar), and the architecture of this pattern, that is to say, its arrangement within the nucleus. In the cephalopod Octopus vulgaris these two aspects are clearly differentiated. The condensation pattern develops from 25 nm fibers to fibers with a tubular aspect and with a progressively increasing diameter (40-60 nm and then to 80 nm), to end finally in the form of very thin fibers (3-5 nm) product of the coalescence and dissolution of the major fibers. The main directive force that governs this process lies in the global change that occurs in the proteins that interact with all (or the major part) of the genomic DNA. The condensation pattern by itself in this species does not present a fixed order: most of the fibers appear without any predominant spatial direction in the spermiogenic nuclei. However, as the nuclei elongate, the chromatin fibers arrange in parallel following the elongation axis. This parallel disposition of the chromatin fibers appears to be mediated by two specific areas, each of which we call a "polar nuclear matrix" (PNM). These matrices differentiate in the basal and apical nuclear poles adjacent to the centriolar implantation fosse and the acrosome, respectively. The areas that constitute the PNM have the following characteristics: (a) they are the only areas where DNA is found anchored to the nuclear membrane; (b) they are the zones from which the chromatin condensation pattern (fibers/tubules) begins; and (c) they are most probably the points through which the mechanical forces originating from nuclear elongation are transmitted to chromatin, causing the chromatin fibers/tubules to adopt an almost perfectly parallel disposition. Finally, we discuss the importance of the architecture of the chromatin condensation pattern, as it is one of the determining factors of the spatial organization of the mature sperm genome and chromosome positioning.

Animals↗
PubMed2003

From DNA structure to gene expression: mediators of nuclear compartmentalization and dynamics.

Eukaryotic genomes are functionally compartmentalized into chromatin domains by their attachment to a supporting structure that has traditionally been termed the nuclear matrix. Present evidence indicates the dynamics of this entity, which requires particular properties of the elements that mediate this kind of interaction. Above all, this is enabled by the so-called 'mass binding phenomenon' by which scaffold/matrix-attachment regions (S/MARs) reversibly associate with ubiquitous factors. Recent investigations and novel techniques have shown that these contacts can be altered by modulators as well as by specific interactions with the components of enhancers and locus control regions.

Chromatin↗
PubMedDate not supplied

Specificity of SAF-A and lamin B binding in vitro correlates with the satellite DNA bending state.

There is evidence that Matrix Attachment Region (MAR)-binding proteins also bind satellite DNA (satDNA). The aim of the current work was to determine whether the major nuclear matrix (NM) MAR-binding proteins are able to recognize satDNAs of different locations and what DNA structural features are important for the recognition. In nuclei and NM, a number of the same polypeptides were recognized on a southwestern blot when MAR of immunoglobulin kappa gene (Ig kappa MAR) and pericentromeric (periCEN) satDNA fragments were used. However, the binding decreased dramatically when human and mouse CEN satDNA were used for the probes. After an NM extract was subjected to ion exchange chromatography, the main DNA-binding proteins were identified as SAF-A (scaffold attachment factor A) and lamin B. It was not possible to test the binding of lamin B by gel mobility shift assay (GMSA), but SAF-A showed an ability to distinguish CEN and periCEN satDNA fragments in GMSA. While periCEN fragments have an abnormally slow mobility on electrophoresis, which is a hallmark of bent DNA, CEN satDNA fragments have a normal mobility. A computer analysis was done using the wedge model (Ulanovsky and Trifonov [1987] Nature 326:720-722), which describes how the curved state depends on particular nucleotide sequences. The curved states of the fragments predicted by the model are in good agreement with their ability to be recognized by NM proteins. Thus SAF-A and lamin B are able to recognize conserved structural features of satDNA in the same way that MAR-binding proteins recognize MARs in spite of a lack of a consensus sequence. CEN and periCEN satDNAs are distinguished by proteins in correlation with the helical curvature of these fragments.

Animals↗
PubMed2004

Nuclear diacylglycerol kinase-theta is activated in response to nerve growth factor stimulation of PC12 cells.

Previous evidence from independent laboratories has shown that the nucleus contains diacylglycerol kinase (DGK) isoforms, i.e., the enzymes, which yield phosphatidic acid from diacylglycerol, thus terminating protein kinase C-mediated signaling events. A DGK isoform, which resides in the nucleus of PC12 cells, is DGK-theta. Here, we show that nerve growth factor (NGF) treatment of serum-starved PC12 cells results in the stimulation of both a cytoplasmic and a nuclear DGK activity. However, time course analysis shows that cytoplasmic DGK activity peaked earlier than its nuclear counterpart. While nuclear DGK activity was dramatically down-regulated by a monoclonal antibody known for selectively inhibiting DGK-theta, cytoplasmic DGK activity was not. Moreover, nuclear DGK activity was stimulated by phosphatidylserine, an anionic phospholipid that had no effect on cytoplasmic DGK activity. Upon NGF stimulation, the amount and the activity of DGK-theta, which was bound to the insoluble nuclear matrix fraction, substantially increased. Epidermal growth factor up-regulated a nuclear DGK activity insensitive to anti-DGK-theta monoclonal antibody. Overall, our findings identify nuclear DGK-theta as a down-stream target of NGF signaling in PC12 cells.

Animals↗
PubMed1994

Drosophila ribosomal protein S3 contains an activity that cleaves DNA at apurinic/apyrimidinic sites.

A rat cDNA-encoding ribosomal protein S3 was used to clone the S3 homolog in Drosophila melanogaster. The Drosophila gene was in turn used to construct fusions between S3 and glutathione S-transferase that were overexpressed in Escherichia coli, purified on affinity columns, and subsequently used for antibody production and biochemical analysis. Antibody specific for S3 was originally tested to determine the subcellular location of S3 by Western (immunoblot) analysis. As expected, the S3 antigen was found associated with purified preparations of ribosomes, but notably the protein was also observed in the nucleus where it was found to be tightly associated with the nuclear matrix. This result, combined with the fact that S3 contains a nuclear localization signal and that the protein shares some homology to a yeast nuclease gene, suggested that S3 might possibly have a role in DNA metabolism. Tests were initially performed to see if S3 contained DNase activity, where it was subsequently determined that the protein specifically cleaved DNA containing an apurinic/apyrimidinic site via a beta-elimination reaction. The DNase activity was inactivated by antibody to S3, indicating that the apurinic/apyrimidinic lyase activity was associated with the Drosophila S3 protein. Taken together, these results suggest that S3 is among a growing class of multifunctional proteins with roles in transcription/translation and DNA repair.

Animals↗
PubMed2000

Conservation of matrix attachment region-binding filament-like protein 1 among higher plants.

The interaction of chromatin with the nuclear matrix via matrix attachment regions (MARs) on the DNA is considered to be of fundamental importance for higher-order chromatin organization and the regulation of gene expression. We have previously isolated a novel nuclear matrix-localized protein (MFP1) from tomato (Lycopersicon esculentum) that preferentially binds to MAR DNA. Tomato MFP1 has a predicted filament-protein-like structure and is associated with the nuclear envelope via an N-terminal targeting domain. Based on the antigenic relationship, we report here that MFP1 is conserved in a large number of dicot and monocot species. Several cDNAs were cloned from tobacco (Nicotiana tabacum) and shown to correspond to two tobacco MFP1 genes. Comparison of the primary and predicted secondary structures of MFP1 from tomato, tobacco, and Arabidopsis indicates a high degree of conservation of the N-terminal targeting domain, the overall putative coiled-coil structure of the protein, and the C-terminal DNA-binding domain. In addition, we show that tobacco MFP1 is regulated in an organ-specific and developmental fashion, and that this regulation occurs at the level of transcription or RNA stability.

Amino Acid Sequence↗
PubMed2002

Identification of a candidate regulatory region in the human CD8 gene complex by colocalization of DNase I hypersensitive sites and matrix attachment regions which bind SATB1 and GATA-3.

To locate elements regulating the human CD8 gene complex, we mapped nuclear matrix attachment regions (MARs) and DNase I hypersensitive (HS) sites over a 100-kb region that included the CD8B gene, the intergenic region, and the CD8A gene. MARs facilitate long-range chromatin remodeling required for enhancer activity and have been found closely linked to several lymphoid enhancers. Within the human CD8 gene complex, we identified six DNase HS clusters, four strong MARs, and several weaker MARs. Three of the strong MARs were closely linked to two tissue-specific DNase HS clusters (III and IV) at the 3' end of the CD8B gene. To further establish the importance of this region, we obtained 19 kb of sequence and screened for potential binding sites for the MAR-binding protein, SATB1, and for GATA-3, both of which are critical for T cell development. By gel shift analysis we identified two strong SATB1 binding sites, located 4.5 kb apart, in strong MARs. We also detected strong GATA-3 binding to an oligonucleotide containing two GATA-3 motifs located at an HS site in cluster IV. This clustering of DNase HS sites and MARs capable of binding SATB1 and GATA-3 at the 3' end of the CD8B gene suggests that this region is an epigenetic regulator of CD8 expression.

Base Sequence↗
PubMed1998

Phosphorothioate antisense oligonucleotides induce the formation of nuclear bodies.

Antisense oligonucleotides are powerful tools for the in vivo regulation of gene expression. We have characterized the intracellular distribution of fluorescently tagged phosphorothioate oligodeoxynucleotides (PS-ONs) at high resolution under conditions in which PS-ONs have the potential to display antisense activity. Under these conditions PS-ONs predominantly localized to the cell nucleus where they accumulated in 20-30 bright spherical foci designated phosphorothioate bodies (PS bodies), which were set against a diffuse nucleoplasmic population excluding nucleoli. PS bodies are nuclear structures that formed in cells after PS-ON delivery by transfection agents or microinjection but were observed irrespectively of antisense activity or sequence. Ultrastructurally, PS bodies corresponded to electron-dense structures of 150-300 nm diameter and resembled nuclear bodies that were found with lower frequency in cells lacking PS-ONs. The environment of a living cell was required for the de novo formation of PS bodies, which occurred within minutes after the introduction of PS-ONs. PS bodies were stable entities that underwent noticeable reorganization only during mitosis. Upon exit from mitosis, PS bodies were assembled de novo from diffuse PS-ON pools in the daughter nuclei. In situ fractionation demonstrated an association of PS-ONs with the nuclear matrix. Taken together, our data provide evidence for the formation of a nuclear body in cells after introduction of phosphorothioate oligodeoxynucleotides.

Antigens↗